Biochem Lek Endterm Notes

FEBRUARY 2022
INTRODUCTION
TO
BIOCHEMISTRY
BIOCHEMISTRY
INTRODUCTION
A Brief History of Earth and Life
• Earth was formed about 5 billion

years ago, when our solar system
(formed 15 billion years ago) took
shape around the sun.
INTRODUCTION
• The origin of life is still a mystery, but there are some theories that
speculate how inorganic matter was transformed into the organic
matter that created life.
• In 1992, it was proposed that bubbles in the sea were the key to
helping create complex organic matter that eventually became life.
INTRODUCTION
• The first cells are thought to have arisen from aggregations of

molecules that were more stable and, therefore, persisted longer.
• It has been suggested that RNA may have arisen before cells and
subsequently became packaged within a membrane (RNA world).
• Bacteria were the only life-forms on earth for about 1 billion years.
INTRODUCTION

• Oxygen levels rise about 2.5 billion years ago, which is thought to
have been created by photosynthesis by cyanobacteria living in the
sea.
• The oxygen-rich ozone layer was also established, shielding the

Earth's surface from harmful solar radiation.
• This further provided our planet for appearance and inhabitation

by other organisms including us.
INTRODUCTION

• Fossils indicate our own species, Homo sapiens, arose in eastern
Africa some 190,000 years ago.
• First venturing beyond Africa about 70,000 years ago.
• The first eukaryotes can be seen in the fossil record about 1.5
billion years ago. All organisms other than bacteria are their
descendants.
INTRODUCTION
A Brief History of Biochemistry
• In 1780’s, Antoine Lavoisier proposed that the combustion of a

candle is similar to the respiration of animals, as both need O2.
• For the first time a physiological process was explained with

reference to a nonliving mechanism.
INTRODUCTION

• Until the early 1800s “vitalism” was a common belief: the
compounds found in living organisms (i.e., organic molecules) can
only be produced by living organisms and could not be produced in
the laboratory.
• Now an obsolete scientific doctrine, vitalists argued that it was the

presence of a “vital force” (life force or spirit) that distinguished the
living organic world from the inanimate inorganic world.
INTRODUCTION
• Friedrich Wöhler disproved this belief (i.e., vitalism) in 1828 by

synthesizing urea, an organic molecule and a waste product of
animal metabolism, from ammonium cyanate, an inorganic
molecule obtained from mineral (i.e., nonliving) sources.
• Many science historians said that in vitro synthesis of urea by

Wöhler is the starting point of Biochemistry.
INTRODUCTION

• However, many consider Eduard Buchner's first demonstration of
alcoholic fermentation in 1893 in cell-free yeast extracts as the
starting point for the birth of biochemistry.
• This was another blow to the vitalistic thinking, showing that the
presence of living yeast cells were not needed for fermentation.
Previously, scientists believed that only living cells could catalyze
such complex biological reactions.
INTRODUCTION

• Experiments recreating the atmosphere of primitive earth, with the
energy sources and temperatures have led to the spontaneous
formation of amino acids and other biologically significant
molecules.
• The Miller-Urey experiment showed that a variety of organic

molecules, including the amino acids could form in an early,
reducing atmosphere.
INTRODUCTION

• In 1810s-1830s, a major substance from animals and plants was
identified, composed of C, H, O, and N. The term “protein”,
meaning the most important thing, was first used in 1838.
• In 1850s-1890s, carbohydrates, lipids, and nucleic acids were

recognized.
• The term “biochemistry” was coined by German chemist Carl

Alexander Neuberg in the 1903.
Pioneer Discovery/Work Pioneer Discovery/Work
Jon Jakob Berzelius Enzymes Catalysis Watson and Crick Double Stranded
DNA
Eduard Buchner Enzyme Extraction
Karl Landsteiner Protein Structure
Louis Pasteur Fermentation Peter Mitchell Oxidative
Process Phosphorylation
Karl Lohmann Role of Creatine Marshall Warren Genetic Code on
PO4 in muscles Nirenberg mRNA
Hans Adolf Krebs TCA Cycle Paul Berg Recombinant DNA
Banting & Macleod Insulin Technology
Kary Mullis Polymerase Chain
Fiske & Subbarow Role of ATPs Reaction
Har Gobind Khorana Synthesized Gene
INTRODUCTION
What is BIOCHEMISTRY?
INTRODUCTION
• The word ‘BIOCHEMISTRY’ means Chemistry of Living beings or
Chemical Basis of Life.
Life in Biochemistry Point of View:
• Hundreds of biochemical reactions and biochemical processes

occurring in subcellular organelles of a cell in an organized
manner.
INTRODUCTION
• The study of the chemical substances found in living organisms
and the chemical interactions of these substances with each other.
• The main focus of biochemistry is to understand how biological

molecules give rise to the processes that occur within living cells
and whole organisms.
INTRODUCTION
Biochemical Substance
A chemical substance found in living organisms.
Water
Bioinorganic Substances
Inorganic salts
Biochemical Substances
Proteins
Lipids
Bioorganic Substances
Carbohydrates
Nucleic acids
FEBRUARY 2022
CYTOLOGY
Cell Structure and Functions
BIOCHEMISTRY
CYTOLOGY
NUCLEUS ❑Nuclear Envelope

-outer ribosomes
-inner lamins
❑Nuclear pores
-transport
❑Nucleolus
-rRNA synthesis
-Combine proteins Ribosomes
❑Chromatin (DNA + histones)
tRNA
RNA
DNA mRNA
DNA rRNA
CYTOLOGY
ENDOPLASMIC RETICULUM
ROUGH ENDOPLASMIC RETICULUM (RER)
❑ Ribosomes
❑ Protein synthesis
- lysosome
-membrane
-excreted
SMOOTH ENDOPLASMIC RETICULUM (SER)
❑ NO Ribosomes
❑ Lipid synthesis
- fatty acids ❑ Sarcoplasmic reticulum
-phospholipids -stores calcium
-cholesterol
CYTOLOGY
GOLGI BODIES
❑ Receiving vessel from RER and SER
❑ Packages molecules
-lysosomes
-membrane
-excreted
CYTOLOGY
CELL MEMBRANE
❑ Barrier
entrance
-semipermeable
exit
CYTOLOGY
LYSOSOME
❑ Breakdown macromolecules
▪ Hydrolytic enzymes
▪ Proteases
▪ Nucleases
▪ Lipases
▪ Glucosidases
❑ Autophagy of organelles
❑ Autolysis of damaged cells
CYTOLOGY
MITOCHONDRIA
❑ ATP synthesis
❑ Metabolic reactions
▪ Kreb’s cycle
CYTOLOGY
RIBOSOMES
❑ rRNA + Proteins
❑ Site of protein synthesis
❑ Types
▪ Bound
▪ Free
CYTOLOGY
VACUOLES
❑ FOOD VACUOLE- contain food
undergoing digestion by
enzymes
❑ CONTRACTILE VACUOLE-
remove excess water and
wastes.
❑ SAP VACUOLE- store salts and
nutrients
CYTOLOGY
CYTOSKELETON
❑ Microfilaments
▪ Cytokinesis of mitosis
❑ Intermediate filament
▪ Anchors
▪ Cell to cell
▪ Cell to organelles
▪ Cell to ECM
❑ Microtubules
▪ Intracellular transport
CYTOLOGY
CENTROSOME
❑ Formation of spindle fibers during cell
division
❑ Creation and expansion of microtubules
that constitute the cytoskeleton
CENTRIOLES
❑ Formation of spindle fibers during cell
division
❑ Determines the position of the nucleus
and other organelles
❑ Cellular extension
▪ Cilla
▪ Flagella
BIOCHEMISTRY
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CELL STRUCTURE AND FUNCTIONS
Organisms are composed of cells, and these cells have specific structures within them that allow them to
carry out their functions. The principal structures or parts of a cell are (1) the cell membrane, (2) the protoplasm
and its organelles, and (3) the nucleus (in some types of cells).
THE CELL MEMBRANE
The cell membrane also known as plasma membrane is a thin layer surrounding and protecting the cell and
its protoplasmic contents, and controlling the entry and exit of certain substances. When examined under an electron
microscope, the plasma membrane appears to be a
double layer of phospholipid molecules. Each
phospholipid is composed of a lipid, a phosphate
group, and a small amount of carbohydrate
(oligosaccharide). Protein molecules are also found
embedded in phospholipids. Thus, the membrane is
composed of both protein and phospholipid
molecules.
The cell membrane is often pictured as a
fluid mosaic model. This is because its molecules
look like pieces of tile in a mosaic that are constantly moving. The phospholipid molecules move sideways within the
membrane. Since the plasma membrane is fluid, it can seal itself if it is damaged or broken. Because of the structure
of the cell membrane, it is semipermeable or
selectively permeable. It allows only chosen
substances to enter and leave the cell.
The plasma membrane also serves as a boundary
between the environment and the inside of a cell.
Furthermore, the membrane gives form and shape
to cells. The plasma membrane also plays the role
of connecting one cell to two or more adjacent
cells. At times it can serve as an organ for
locomotion like that of an Amoeba, a protozoan
which utilizes its membrane as pseudopodia or
“false feet” for movement.
THE PROTOPLASM AND ITS ORGANELLES

The plasma membrane encloses a mass of jellylike material called protoplasm. The protoplasm is a colorless
or somewhat grayish, translucent, viscous substance that can flow. It is a colloid so that it can change its state from
a semisolid gel to a semiliquid solution.
The protoplasm of one cell differs from the protoplasm of the other cells of the same organism and of the
same kind of cell of different organisms. For example, the
protoplasmic substance of a red blood cell differs from
that of a bone cell, a brain cells, or a liver cell.
Various organized organelles, also called little
organs, are also present in the protoplasm. Some of them
are visible under the light microscope; others are not.
Each of these minute living substructures is associated
with a specific process of the cell’s activity. A cell function
may be classified according to the number and kinds of
organelles present.
PROTOPLASM
Cytoplasm and Karyoplasm or Nucleoplasm
If a nucleus is present in a cell, the protoplasm is
differentiated into two: (1) cytoplasm, the protoplasm lying
outside the nucleus; and (2) karyoplasm or nucleoplasm,
the protoplasm inside the nucleus.
Many types of organelles are suspended in the
gel-like cytoplasm. Among them are mitochondria,
ribosomes, endoplasmic reticulum, Golgi bodies, vacuoles, lysosomes, centrosomes and centrioles, and
cytoskeleton. Other organelles peculiar to plant cells are the cell wall and the plastids.
MITOCHONDRIA: POWERHOUSES OF THE CELL

The name mitochondrion (plural, mitochondria) means ‘thread granule’. This describes what the
mitochondrion looks like under the light microscope – a tiny, rod-like structure in the cytoplasm of almost all cells.
Mitochondria appear in electron micrographs as cylindrical organelles. Occasionally, they can exist in other shapes
such as rods or filaments. They vary in size but within the range of 0.5-1.5 μm wide and 3.0-10.0 μm long.
a. Each mitochondrion is bound by a double
unit membrane, the outer membrane being
a smooth continuous boundary.
b. The inner membrane is extensively
enfolded to form partitions called cristae
(singular, crista).
c. The intermembrane space between the
outer and inner membrane is narrow and
filled with fluid.
d. The cristae extend into and partially
partition the interior of mitochondria which
is filled with a fluid called the mitochondrial
matrix.
e. The matrix is a mixture of enzymes, mitochondrial DNA, RNA and ribosomes. The surface of cristae facing the
matrix is covered with stalked particles. The number of cristae is proportional to the energy requirement of the
cell.
Mitochondria provide the energy a cell needs for all its activities such as movement, cell division and
production of secretory products. They are centers of cellular respiration, a process in which the energy-rich
adenosine triphosphate or ATP, a high energy compound in cells that functions in energy storage and transfer, is
produced. Thus, mitochondria are termed the “powerhouse of the cell”.
RIBOSOME: PROTEIN FACTORIES OF THE CELL
Ribosomes are seen as a solid spherical granule
when observed through the electron microscope. They
are the most numerous of all cytoplasmic structures.
Each ribosome has a diameter of about 20-25nm. Each
ribosome is an assembly of two ribosomal subunits: the
large subunit and the small subunit. Ribosomal
subunits are synthesized in the nucleolus. These
subunits then pass through the nuclear pores into the
cytoplasm, where they can combine to form ribosomes.
Each ribosome consists of about 70 protein molecules
and several ribosomal RNA (rRNA) molecules.
Ribosomes are protein factories of the
cell. Ribosomes synthesize protein molecules from amino acid, using genetic information carried by mRNA molecules
from the DNA in the nucleus. The proteins synthesized on free ribosomes are released into the cytosol, where they
perform their functions as enzymes or as structural proteins for growth within the cell. The proteins synthesized by
ribosomes attached to rough ER pass into the cisternal space of the reticulum and are then transferred to the Golgi
body. They are ultimately secreted from the cell in the form of enzymes or hormones.
Ribosomes are found in two places in the cell.
a. Bound ribosomes- attached to the cytoplasmic
surface of rough ER and the nuclear envelope.
b. Free ribosomes- suspended freely in the cytosol.
Bound and free ribosomes are structurally identical and
can alternate between the two roles depending on the Bound
ribosome
metabolic needs of the cell.
ENDOPLASMIC RETICULUM: MANUFACTURES AND SHIPPERS OF THE CELL
Endoplasmic reticulum (ER) is an extensive membranous network that is denser in the interior region
(endoplasm) than in the exterior region of the cytoplasm (ectoplasm). This organelle is found penetrating the
cytoplasm of all nucleated cells (eukaryotic cells) and is especially well developed in growing cells.
The ER consist of a network of membranous
tubules and flattened sacs called cisternae (singular,
cisterna). The ER membrane separate the internal
compartment of the ER called cisternal space, from
the cytosol. The ER membrane which is a single-unit
membrane is continuous with the nuclear envelope.
Therefore, the space between two membranes of the
nuclear envelope is continuous with the cisternal
space of the ER.
Ribosomes are often attached to long strands
of membrane called the endoplasmic reticulum or ER,
which forms a network of tiny canals through the cell.
These canals are formed by two parallel membranes.
They connect the nuclear membrane and the plasma
membrane, thus serving as passageway for food
substances. The ER may either have a rough or
smooth appearance.
Rough Endoplasmic Reticulum (RER)

Rough endoplasmic reticulum is named as such because the cytoplasmic surface of its cisternae appears
rough due to the ribosomes that stud it. It collects proteins synthesized by ribosomes attached at its surface, packages
them in inert form, stores them temporarily and transports them to the cell surface for secretion. Cells of secretory
glands like pancreas, salivary glands, pituitary gland and mammary glands which actively synthesize and excrete
proteins (insulin, digestive enzymes, hormones, and milk proteins, respectively) are densely packed with rough ER.
The system of canals formed by the cisternal spaces of rough ER function as intracellular transport system
that facilitate the movement of substances from one part of the cell to another.
When an enzyme is synthesized by a ribosome bound to the surface of RER, the growing polypeptide chain
is threaded into the cisternal space through a pore formed by a protein
in the ER membrane. As it enters the cisternal space, the new protein
folds into its native conformation and is stored there temporarily.
In the RER, a short carbohydrate chain is added to the protein
converting it to a glycoprotein. The carbohydrate is attached to the
protein by specialized molecules built into the ER membrane.
a. Once the secretory proteins are formed, the molecules are ready for
export. The molecules then moved to a specialized region of the
RER called transitional ER. Here, they are packaged into tiny sacs
called transport vesicles.
b. The vesicles then bud off from the ER membrane like bubbles. The vesicles containing secretory proteins will
now travel to the Golgi body for further processing.
c. From there, transport vesicle containing the finished molecules will make their way to the plasma membrane and
release their contents form the cell.
d. Another function of the RER is to manufacture more membrane for the cell.
e. Some of the proteins made by the ER ribosomes are inserted into the ER membrane, as are membrane
phospholipids made by the ER enzymes.
f. As a result, the ER membrane enlarges, and some of it can be transferred to other organelles as well as the
plasma membrane through the transport vesicles.
Smooth Endoplasmic Reticulum (SER)
The cytoplasmic surface of smooth ER lacks ribosomes. The cisternae of smooth ER are the form of
interconnected tubes and not flatted sacs. The smooth ER of various cells functions in diverse metabolic processes,
including synthesis and transport of lipids, metabolism of carbohydrates and detoxification of drugs and poisons.
Much of its activity results from enzymes embedded in its membrane.
a. Enzymes of smooth ER are important for the
synthesis of lipids, including oils, phospholipids and
steroids. Cells that are active in lipid metabolism
such as gut epithelium cells, adrenal gland cells and
cells I the testes and ovaries are rich in smooth ER.
b. In the gut epithelium cells, smooth ER synthesizes
lipids from fatty acids and glycerol. These are then
sent to the Golgi body to be exported out of the cell.
c. Cells in the testes and ovaries synthesize the steroid
sex hormones, testosterone and estrogen,
respectively.
d. Cells in the adrenal glands are involved in the
synthesis of some steroid hormones.
Our liver cells also have large amounts of smooth ER. Certain enzymes in the smooth ER of the liver help
regulate the amount of sugar released from the liver cells into the bloodstream. Other liver enzymes hep break down
drugs and other potentially harmful substances such as alcohol.
GOLGI BODIES OR GOLGI APPARATUS: PACKAGING COUNTERS OF THE CELL
In 1898, an Italian scientist, Camilo Golgi, observed a series of vesicles in the nerve cells of an owl. These
vesicles were named Golgi Apparatus, after the discoverer. The Golgi body consists of a stack of flattened
membranous sacs (cisternae). Each Golgi stack in a mammalian cell can consist of 5-6 cisternae whereas those in
plant cells can consist of 20 or more.
The Golgi body is found in all eukaryotic cells. it is clearly seen in active secretory cells such as nerve cells,
pancreatic cells and cells of root apex. Most cells have a single Golgi body located near the nucleus. Root apex cells
may have several or a few hundred Golgi bodies within the cytoplasm.
The Golgi body acts as a warehouse and packaging factory for macromolecules. It receives, stores, modifies,
finishes, sorts and packages secretory proteins arriving
from the RER prior to sending them to other destinations.
Products of ER are modified during their transit from the cis
pole to the trans pole of the Golgi body. For example,
various Golgi enzymes modify the oligosaccharide portions
of glycoproteins which were first added in the RER.
The Golgi remove some sugar monomers and substitute
others, producing a variety of oligosaccharides.in this way,
the secretory proteins are marked and then sorted into
various batches for different destinations. The molecules
move from cisternae to cisterna within the Golgi body
through transport vesicles. Finally, the Golgi body
dispatches its products by packaging them in small
secretory vesicles which bud from the trans face. The secretory vesicles will be delivered to and fused with other
organelles within the cell such as lysosome. In other cases, they are delivered to the plasma membrane where they
fuse with the membrane and their protein contents are released to the outside of the cell in a process called
exocytosis.
The secretory vesicles produced by the Golgi body play an important role in adding surface area to the cell
membrane. When releasing its contents to the exterior through the process of exocytosis, the membrane of the
ruptured vesicles may remain as a permanent addition to the plasma membrane.
VACUOLES: STORAGE TANKS OF THE CELLS
A vacuole is a fluid-filled sac bounded by a single membrane. It is clearly seen within the cytoplasm of the
plant cells. Most mature plant cells have one large central vacuole.
a. As the cell grows, the size of one vacuole increases due to the merging of various small vacuoles to form a large
central vacuole that occupies 90% of the volume in a plant cell. (Figure beside)
b. To make way for the increasing
volume of a vacuole, cytoplasm is
pushed aside forming only a very thin
layer pressing against the inside of the
cell wall.
The single membrane that
surrounds the vacuole is called the
tonoplast. The fluid within the vacuole is called cell sap. Cell sap is a concentrated solution of mineral salts, sugars,
amino acids, wastes (such as tannins) and sometimes pigments such as anthocyanins.
Plants lack waste disposal systems and often utilize vacuoles as a storage place for waste materials. Such
waste products often aggregate and form small crystals inside the vacuole, usually in the form of calcium oxalate
crystals. The vacuole may also be a site of pigment deposition. Anthocyanins are a group of pigments that cause
brilliant red, dark red and blue colors of many vegetables, fruits, flowers, and leaves. Unlike most other plant pigments,
anthocyanins are readily soluble in water and are readily dissolved within the cell sap.
Vacuoles also play a role in plant defense. The vacuoles of some plants store tannin, a poisonous substance
used to protect the plant from animals.
c. Vacuoles play a very important role in improving the surface area to volume ratio of the plant cell. The surface
area to volume ratio is important to cells since it determines the number of metabolites that can move into the
cell efficiently through diffusion.
d. Animal cells can improve this ratio by changing their shapes or by the folding of plasma membrane; but plant
cells can do neither of these as they are limited by their cell walls.
e. However, plant cells overcome this problem by having a large central vacuole pushing the cytoplasm to the side,
thus forming a very thin layer pressing against the cell wall. This ensures that the cytoplasm and nucleus are only
short distance away from the cell surface where
diffusion is most efficient. vacuole
Some plant vacuoles contain hydrolytic
enzymes that work exactly like the enzymes in
lysosomes. The tonoplasts, just like other membranes,
will lose its semi-permeability after cell death and
release enzyme from the vacuole, causing autolysis of
the cell.
f. Large vacuoles are not found in animal cells.
Animal cells usually have small vacuoles which are sometimes referred to as vesicles. Example of vacuoles fond
in animal cells are phagocytic vesicles, pinocytic vesicles, autophagy vacuoles and excretory vacuoles.
g. Many single-celled protozoa have food vacuoles or digestive vacuoles that contain food undergoing digestion,
and many have contractile vacuoles, which remove excess water and some wastes from the cell.
LYSOSOME: SUICIDE BAGS OF THE CELLS
Lysosome are found in all animal cells and in some plant cells. Lyso means ‘dissolving power’ and some
means “body”. These organelles, discovered in 1952 are found to be rich in strong hydrolytic enzymes, that the cell
uses to digest macromolecules, which are kept intact by thick lysosomal membrane that is highly acidic.
When observed through an electron microscope, they appear as dark spherical bodies in the cytoplasm and
their diameters are generally smaller than that of mitochondria. The RER and Golgi body cooperate to make
lysosomes. First, the RER puts the enzymes and membrane together. Then the Golgi body chemically refine the
enzymes and releases mature lysosomes.
The membrane of the lysosome is very unique. This is a single membrane compared to the double membrane
of the mitochondrion. This membrane can prevent the leakage of the enzymes and is able to resist digestion. This is
important as excessive leakage of the enzymes from the number of lysosomes can lead to the autodigestion of the
cell. The lysosomal membrane encloses a compartment where digestive enzymes are stored and safely isolated from
the rest of the cytoplasm. Without lysosome, a cell cannot carry highly hydrolytic enzymes without digesting itself.
The main function of
lysosomes is intracellular
digestion, digesting the food
wastes of the cell. It also plays a
very important role in the defense
system. White blood cells ingest
bacteria into vacuoles and
lysosomal enzymes emptied into
these vacuoles rupture the
bacterial cell walls. Lysosome
serves as recycling centers for
redundant and damaged
organelles. Old and worn-out cell
organelles that no longer function
normally are enclosed in a
membrane and broken down by
lysosomes in a similar manner.
The whole process is called
autophagy. The resulting simple molecules are reused to construct new organelles. When a cell dies, its own
lysosomes releases enzymes that digest the remains of the cell in process called autolysis.
CENTROSOMES AND CENTRIOLES: HELPERS IN CELL DIVISION
A centrosome is a mass of dense protoplasm with structures
called centrioles at the center. Centrioles are hollow cylinders about 0.2
μm in diameter and 0.5 μm long. Each hollow cylinder is composed of nine
sets of triplet microtubules arranged in a ring. The centrioles as part of
the cytoplasm, duplicate and form at the center for spindle fiber formation
during cell division.
CYTOSKELETON: FRAMEWORK OF THE CELL
The most modern research has revealed that the cytoplasm
contains a cytoskeleton (cellular framework). Just as hollow blocks or
steel gives shape to
buildings, a cytoskeleton
supports the internal system and gives the cell its shape. It consists
of a network of at least three distinct structures such as microtubule,
intermediate filament, and microfilament.
Organelles Peculiar to Plant Cells
CELL WALL
The cells of plants, fungi, and some single-celled organisms are protected and supported by a rigid cell wall,
which lies outside the plasma membrane and is composed mainly of cellulose, except in the case of fungi and
bacteria.
The cell wall is consisted of several
distinct layers. The primary cell wall is the
outer layer. It expands as the cell grows. As
the plant reaches its full size, a secondary
cell wall develops inside the primary cell
wall. This new layer adds strength to the
wall. Two primary cell walls of adjacent
cells are separated by another layer, the
middle lamella, which is composed of a
jellylike polysaccharide called pectin.
Pectin is generally present in the form of
calcium pectate. When a fruit ripens, the
calcium pectate is partly converted into more soluble forms. This loosens the cells; then the fruit becomes softer.
Both primary and secondary walls are composed mainly of the polysaccharide cellulose. Soft plant structures,
such as leaf blades or flower petals, have thin primary walls. Aside from cellulose, the secondary walls usually contain
lignin, a complex organic compound that adds hardness and rigidity to cell walls. The cell wall remains intact even
after the rest of the cell has died. It is typical of the cork cells which compose the wood of trees, plant fibers, and nut
shells.
PLASTIDS – CHROMOPLASTS AND LEUCOPLASTS
Large membrane-bound organelles, called plastids, are found in the cytoplasm of most plant cells. There are
three categories of plastids: chloroplasts, chromoplasts, and leucoplasts.
Chloroplasts are green-colored plastids containing the
green pigment called chlorophyll. Chlorophyll is very essential
in the manufacture of food by green plants. Chromoplasts
contain various yellow or orange pigments called carotenoids.
These chromoplasts give many flowers, ripened fruits, and autumn leaves their characteristic yellow or orange color.
Chromoplasts in tomatoes contain red pigment, rheodoplast. This pigment makes tomatoes red.
Leucoplasts are colorless plastids that serve as food storehouses in many plant cells. They may contain oil,
starch grains, and proteins, as well as enzymes necessary to link glucose molecules together and form starch
molecules. Starch-laden leucoplasts are usually abundant in the cells of roots, stems, and storage areas of plants,
like the potato tuber.
THE NUCLEUS: CONTROL CENTER OF THE CELL
The nucleus (plural, nuclei) was the first organelle that
biologists observed in a cell. It is a spherical structure that is
usually located near the center of the cell. The nucleus is the
largest and most prominent organelle. There is one nucleus in
each living cell except mammalian red blood cells and mature
sieve tube cells (in plants) which are without nuclei. The
nucleus is usually spherical or oval in shape and averages
5micro meter in diameter. The nuclei of some cells such as
that of the white blood cells are multi-lobed.
The nucleus in enclosed by a nuclear envelope,
which consists of two membranes perforated by nuclear
pores. The diameter of a nuclear pore is about 20-50nm.
These pores control the exchange of materials between the nucleus and the cytoplasm. The space between the two
membranes of the nuclear envelope is called the perinuclear space and has a width of about 20nm.
The nucleus contain chromatin, the form that chromosomes take up when the cell is not dividing. Chromatin
contains DNA, the molecule of inheritance which controls the activities of the cell. Two forms of chromatin are visible.
a. Euchromatin- stains lightly and is thought to contain active DNA.
b. Heterochromatin- stains deeply and is thought to contain inactive DNA.
Nucleoplasm or karyoplasm is the semi-fluid substance in the nucleus. The nucleus also contains one or
more very prominent structures called nucleoli (singular, nucleolus). The nucleolus appears as dense mass of
granules and fibers when observed through the electron microscope. The nucleolus synthesizes ribosomal RNA
(rRNA). In addition, proteins imported from the cytoplasm are combined with the rRNA in the nucleolus to form large
and small ribosomal subunits. These ribosomal subunits then move pores to the cytoplasm. In the cytoplasm, the
large and small subunits are assembled into ribosomes which take up positions on the rough endoplasmic reticulum
where they play a vital role for protein synthesis.
The nucleus is the information center of the cell. Its functions include the following.
a. To carry the genetic material of a cell in the form of chromosomes.
b. To act as a control center that directs all the activities of a cell by regulating protein and enzyme synthesis.
c. To contain the nuclear DNA which carries the instructions for the synthesis of proteins.
d. To assist in the production of ribosomes and RNA and is essential for cell division.
References:
Alberts et al. (2017). Molecular biology of the cell. (2nd ed.) New York: Garland Publishing
Reece et al. (2011). Campbell Biology (4th ed.) Boston: Pearson
Rey & Ramos (2018). General Biology 1. Malaysia: Oxford Publishing
CYTOLOGY
PROKARYOTIC CELLS EUKARYOTIC CELLS
❑ From Greek word: ❑ From Greek word:

pro - before eu - good or true
karyon - kernel or nut karyon - kernel or nut
(nucleus) (nucleus)
❑Exist before eukaryotic ❑Have a well-defined
cells nucleus
CYTOLOGY
❑ No nucleus or nucleoli ❑ Have nucleus

❑ No membrane-bound ❑ Have membrane-bound
organelles organelles
▪ Golgi apparatus
▪ Lysosomes
▪ Mitochondria
▪ Endoplasmic reticulum
CYTOLOGY

❑ Unicellular ❑ Unicellular
▪ Bacteria ▪ Protist
▪ Archaea ❑ Multicellular
▪ Plant and animal
❑ Uni/multicellular
▪ Fungi
CYTOLOGY
❑ Cell divides by binary ❑ Cell divides by mitosis or

fission meiosis
CYTOLOGY
SIMILARITIES
❑Both cells are enclosed by cell membranes and
have cytoplasm and ribosomes.
❑Both have DNA as genetic material.
❑Both carry on all the necessary functions of life.
CYTOLOGY
Prokaryotic or Eukaryotic?
E.coli
Prokaryotic
CYTOLOGY
Paramecium
Eukaryotic
CYTOLOGY
Prokaryotic
CYTOLOGY
PLANT CELL VS ANIMAL CELL
Plant Cell Both Animal Cell

▪ Cell membrane
▪ Cell wall ▪ Endoplasmic reticulum ▪ Centrioles
▪ Golgi apparatus ▪ Centrosomes
▪ Chloroplasts
▪ Mitochondria ▪ Small vacuoles
▪ Large vacuoles
▪ Nucleus
▪ Cilia or Flagella
▪ Cytoplasm
▪ Ribosomes
FEBRUARY 2022
Water:
The Solvent for
Biochemical Reactions
BIOCHEMISTRY
WATER
Lesson Outline
• Water and Polarity

• Hydrogen Bonds
• Acids, Bases, and pH
• Titration Curves
• Buffers
WATER
The formation and function of molecules

depend on chemical bonding between atoms
• Atoms with incomplete valence shells can share or

transfer valence electrons with certain other atoms.
• These interactions usually result in atoms staying

close together, held by attractions called chemical
bonds.
WATER
Covalent Bonds
• A covalent bond is the
sharing of a pair of
valence electrons by
two atoms.
• In a covalent bond,
the shared electrons
count as part of each
atom’s valence shell.
WATER
Covalent Bonds
• A molecule is consist of two or

more atoms held together by
covalent bonds.
• A single covalent bond, or
single bond, is the sharing of
one pair of valence electrons.
• A double covalent bond, or
double bond, is the sharing of
two pairs of valence electrons.
WATER
Electronegativity
• Atoms in a molecule attract electrons to varying degrees.
• Electronegativity is an atom’s attraction for the electrons in a

covalent bond.
• The more electronegative an atom, the more strongly it pulls

shared electrons toward itself.
WATER
Electronegativity
• Oxygen and nitrogen, more

electronegative than carbon
and hydrogen.
• Fluorine is most
electronegative (4).
WATER
Covalent Bonds
• In a nonpolar covalent bond, the atoms share electron equally.
• In a polar covalent bond, one atom is more electronegative, and

the atoms do not share the electron equally.
• Unequal sharing of electrons causes a partial positive or

negative charge for each atom or molecule.
WATER
What makes water polar?
Polar bond
• Electrons are unequally
shared, more negative
charge found closer to one
atom due to difference in
electronegativity of atoms
involved in bond.
WATER
Polar Bonds and Molecules
• Molecules such as CO2 have

polar bonds but given their
geometry, are nonpolar
molecules; that is, they have
a zero dipole moments.
WATER
Polar bond
involved in bond.
WATER
Solvent Properties of Water

• Ionic Bonds: Held together by positive and negative ions.
• Salt Bridge: Attraction that occurs when oppositely charged
molecules are in close proximity.
• Ion-dipole Interactions: When ions in solution interact with
molecules with dipoles, e.g., KCl dissolved in H2O.
• Van der Waals Forces: Bonds that do not involve electrostatic
interactions.
• Dipole-dipole Interactions: Forces that occur between molecules
with dipoles, one positive and one negative.
• Dipole induced-dipole Interactions: Weak and generally do not
lead to solubility in water.
WATER
Ionic Bonds
• Atoms sometimes strip electrons from their bonding partners.

• An example is the transfer of an electron from sodium to chlorine.
• After the transfer of an electron, both atoms have charges.
• A charged atom (molecule) is called an ion.
• A cation is a positively charged ion.
• An anion is a negatively charged ion.
• An ionic bond is an attraction between an anion and a cation.
Sodium: Chlorine:
11 protons 17 protons
11 electrons
10 electrons 17
18 electrons
E- E-
E-
E- E-
E- E- E-
E- E- P+
N
P+
E- P+ P+ N
E- P+ P+ N
P+ N P+ E-
P+
N
N P+
P+
E- N
N
NN
N
P
P+
N N
N
N
N
P+
N
P+
P
E- P+ N
N N
P+ P+
P+ P+
+ E-
N N N + N
P+ P+ N P+ N
N N P+
P+ P+ N
P+ N E-
E-
E- E- E-
E- E- E- E-
E-
unstable unstable
E- E-
Cation Anion
WATER
Hydration Shells Surrounding Ions in Water

WATER
Ion-dipole and Dipole-Dipole Interactions
• Ion-dipole and dipole-dipole interactions help ionic and polar

compounds dissolve in water.
WATER
Induced Dipole-Induced Dipole Interactions or

London dispersion Forces
Two nonpolar atoms or molecules Momentary attractions and Correlation of the electron motions
repulsions between nuclei and between the two atoms or molecules
electrons in neighboring molecules (which are polar) leads to a lower
lead to induced dipoles. energy and stabilizes the system.
• Upon cooling, both Cl2 and Br2 forms solids.

• London dispersion forces are responsible for the formation of the
solids. As the elements are cooled, the KE of the Cl2 and Br2
molecules decreases and the London dispersion forces are strong
enough to overcome the KE and hold the molecules in solid.
WATER
Biochemically-Relevant Bond Energies

WATER

• Hydrophilic: water-loving
• Tend to dissolve in water
• Hydrophobic: water-fearing
• Tend to not dissolve in water
WATER
Amphipathic Molecules
• Amphipathic: has
characteristics of both
properties
• Molecules that contain
one or more
hydrophobic and one or
more hydrophilic
regions, e.g., sodium
palmitate
WATER
Micelle Formation by Amphipathic Molecules
• Micelle: a spherical arrangement of organic

in water solution clustered so that
▪ their hydrophobic parts are buried inside
the sphere
▪ their hydrophilic parts are on the surface
of the sphere and in contact with water
environment
WATER
Hydrogen Bonds
• Hydrogen bond: the attractive interaction between dipoles when:
• positive end of one dipole is a hydrogen atom bonded to an
atom of high electronegativity, most commonly O or N, and
• The negative end of the other dipole is an atom with a lone
pair of electrons, most commonly O or N
• Hydrogen bond is non-covalent.
WATER
Hydrogen Bonding Sites

WATER
Hydrogen Bonding Between Polar Groups and Water

WATER
Other Biologically Important Hydrogen Bonds

• Hydrogen bonding is important in stabilization of 3-D structures
of biological molecules such as: DNA, RNA, and proteins
WATER

WATER
Acids, Bases and pH
• Acid: a molecule that behaves as a proton donor.
• Base: a molecule that behaves as a proton acceptor.

WATER
Acid Strength
• One can derive the numerical value for the strength of an acid
(amount of hydrogen ions released when a given amount of acid
is dissolved in water).
• Described by Ka:
• Written correctly,
WATER
Ionization of Water and pH

• Let’s quantitatively examine the dissociation of water:
• Molar concentration of water (55M)

• KW is called the ion product constant for water.
• Must define a quantity to express hydrogen ion concentrations…pH

WATER
Henderson-Hasselbalch Equation
• Equation to connect Ka to pH solution containing both acid and
base.
• We can calculate the ratio of the weak acid, HA, to its conjugate
base, A-, in the following way.
WATER
• Henderson-Hasselbalch equation
𝐶𝑜𝑛𝑗𝑢𝑔𝑎𝑡𝑒 𝑏𝑎𝑠𝑒
• pH = pka + log 𝑤𝑒𝑎𝑘 𝑎𝑐𝑖𝑑
• From this equation, we see that

• When the concentration of weak acid and its conjugate base are
equal, the pH of the solution equals the pKa of the weak acid
• When pH<pKa, the weak acid predominates
• When pH>pKa, the conjugate base predominates
BIOCHEMISTRY
THANK YOU!
CYTOLOGY
❑ From Greek word: ❑ From Greek word:

pro - before eu - good or true
karyon - kernel or nut karyon - kernel or nut
(nucleus) (nucleus)
❑Exist before eukaryotic ❑Have a well-defined
cells nucleus
CYTOLOGY
❑ No nucleus or nucleoli ❑ Have nucleus

❑ No membrane-bound ❑ Have membrane-bound
organelles organelles
▪ Golgi apparatus
▪ Lysosomes
▪ Mitochondria
▪ Endoplasmic reticulum
CYTOLOGY

❑ Unicellular ❑ Unicellular
▪ Bacteria ▪ Protist
▪ Archaea ❑ Multicellular
▪ Plant and animal
❑ Uni/multicellular
▪ Fungi
CYTOLOGY
❑ Cell divides by binary ❑ Cell divides by mitosis or

fission meiosis
CYTOLOGY
SIMILARITIES
❑Both cells are enclosed by cell membranes and
have cytoplasm and ribosomes.
❑Both have DNA as genetic material.
❑Both carry on all the necessary functions of life.
CYTOLOGY
E.coli
Prokaryotic
CYTOLOGY
Paramecium
Eukaryotic
CYTOLOGY
Prokaryotic
CYTOLOGY
PLANT CELL VS ANIMAL CELL
Plant Cell Both Animal Cell

▪ Cell membrane
▪ Cell wall ▪ Endoplasmic reticulum ▪ Centrioles
▪ Golgi apparatus ▪ Centrosomes
▪ Chloroplasts
▪ Mitochondria ▪ Small vacuoles
▪ Large vacuoles
▪ Nucleus
▪ Cilia or Flagella
▪ Cytoplasm
▪ Ribosomes
FEBRUARY 2022
Water:
The Solvent for
Biochemical Reactions
BIOCHEMISTRY
WATER
Lesson Outline
• Water and Polarity

• Hydrogen Bonds
• Acids, Bases, and pH
• Titration Curves
• Buffers
WATER
The formation and function of molecules

depend on chemical bonding between atoms
• Atoms with incomplete valence shells can share or

transfer valence electrons with certain other atoms.
• These interactions usually result in atoms staying

close together, held by attractions called chemical
bonds.
WATER
Covalent Bonds
• A covalent bond is the
sharing of a pair of
valence electrons by
two atoms.
• In a covalent bond,
the shared electrons
count as part of each
atom’s valence shell.
WATER
Covalent Bonds
• A molecule is consist of two or

more atoms held together by
covalent bonds.
• A single covalent bond, or
single bond, is the sharing of
one pair of valence electrons.
• A double covalent bond, or
double bond, is the sharing of
two pairs of valence electrons.
WATER
Electronegativity
• Atoms in a molecule attract electrons to varying degrees.
• Electronegativity is an atom’s attraction for the electrons in a

covalent bond.
• The more electronegative an atom, the more strongly it pulls

shared electrons toward itself.
WATER
Electronegativity
• Oxygen and nitrogen, more

electronegative than carbon
and hydrogen.
• Fluorine is most
electronegative (4).
WATER
Covalent Bonds
• In a nonpolar covalent bond, the atoms share electron equally.
• In a polar covalent bond, one atom is more electronegative, and

the atoms do not share the electron equally.
• Unequal sharing of electrons causes a partial positive or

negative charge for each atom or molecule.
WATER
Polar bond
involved in bond.
WATER
Polar Bonds and Molecules
• Molecules such as CO2 have

polar bonds but given their
geometry, are nonpolar
molecules; that is, they have
a zero dipole moments.
WATER
Polar bond
involved in bond.
WATER

• Ionic Bonds: Held together by positive and negative ions.
• Salt Bridge: Attraction that occurs when oppositely charged
molecules are in close proximity.
• Ion-dipole Interactions: When ions in solution interact with
molecules with dipoles, e.g., KCl dissolved in H2O.
• Van der Waals Forces: Bonds that do not involve electrostatic
interactions.
• Dipole-dipole Interactions: Forces that occur between molecules
with dipoles, one positive and one negative.
• Dipole induced-dipole Interactions: Weak and generally do not
lead to solubility in water.
WATER
Ionic Bonds
• Atoms sometimes strip electrons from their bonding partners.

• An example is the transfer of an electron from sodium to chlorine.
• After the transfer of an electron, both atoms have charges.
• A charged atom (molecule) is called an ion.
• A cation is a positively charged ion.
• An anion is a negatively charged ion.
• An ionic bond is an attraction between an anion and a cation.
Sodium: Chlorine:
11 protons 17 protons
11 electrons
10 electrons 17
18 electrons
E- E-
E-
E- E-
E- E- E-
E- E- P+
N
P+
E- P+ P+ N
E- P+ P+ N
P+ N P+ E-
P+
N
N P+
P+
E- N
N
NN
N
P
P+
N N
N
N
N
P+
N
P+
P
E- P+ N
N N
P+ P+
P+ P+
+ E-
N N N + N
P+ P+ N P+ N
N N P+
P+ P+ N
P+ N E-
E-
E- E- E-
E- E- E- E-
E-
unstable unstable
E- E-
Cation Anion
WATER
Hydration Shells Surrounding Ions in Water

WATER
Ion-dipole and Dipole-Dipole Interactions
• Ion-dipole and dipole-dipole interactions help ionic and polar

compounds dissolve in water.
WATER
Induced Dipole-Induced Dipole Interactions or

London dispersion Forces
Two nonpolar atoms or molecules Momentary attractions and Correlation of the electron motions
repulsions between nuclei and between the two atoms or molecules
electrons in neighboring molecules (which are polar) leads to a lower
lead to induced dipoles. energy and stabilizes the system.
• Upon cooling, both Cl2 and Br2 forms solids.

• London dispersion forces are responsible for the formation of the
solids. As the elements are cooled, the KE of the Cl2 and Br2
molecules decreases and the London dispersion forces are strong
enough to overcome the KE and hold the molecules in solid.
WATER
Biochemically-Relevant Bond Energies

WATER

• Hydrophilic: water-loving
• Tend to dissolve in water
• Hydrophobic: water-fearing
• Tend to not dissolve in water
WATER
Amphipathic Molecules
• Amphipathic: has
characteristics of both
properties
• Molecules that contain
one or more
hydrophobic and one or
more hydrophilic
regions, e.g., sodium
palmitate
WATER
Micelle Formation by Amphipathic Molecules
• Micelle: a spherical arrangement of organic

in water solution clustered so that
▪ their hydrophobic parts are buried inside
the sphere
▪ their hydrophilic parts are on the surface
of the sphere and in contact with water
environment
WATER
Hydrogen Bonds
• Hydrogen bond: the attractive interaction between dipoles when:
• positive end of one dipole is a hydrogen atom bonded to an
atom of high electronegativity, most commonly O or N, and
• The negative end of the other dipole is an atom with a lone
pair of electrons, most commonly O or N
• Hydrogen bond is non-covalent.
WATER
Hydrogen Bonding Sites

WATER
Hydrogen Bonding Between Polar Groups and Water

WATER

WATER

WATER
Acids, Bases and pH
• Acid: a molecule that behaves as a proton donor.
• Base: a molecule that behaves as a proton acceptor.

WATER
Acid Strength
• One can derive the numerical value for the strength of an acid
(amount of hydrogen ions released when a given amount of acid
is dissolved in water).
• Described by Ka:
• Written correctly,
WATER
Ionization of Water and pH

• Let’s quantitatively examine the dissociation of water:
• Molar concentration of water (55M)

• KW is called the ion product constant for water.
• Must define a quantity to express hydrogen ion concentrations…pH

WATER
• Equation to connect Ka to pH solution containing both acid and
base.
• We can calculate the ratio of the weak acid, HA, to its conjugate
base, A-, in the following way.
WATER
• Henderson-Hasselbalch equation
𝐶𝑜𝑛𝑗𝑢𝑔𝑎𝑡𝑒 𝑏𝑎𝑠𝑒
• pH = pka + log 𝑤𝑒𝑎𝑘 𝑎𝑐𝑖𝑑
• From this equation, we see that

• When the concentration of weak acid and its conjugate base are
equal, the pH of the solution equals the pKa of the weak acid
• When pH<pKa, the weak acid predominates
• When pH>pKa, the conjugate base predominates
BIOCHEMISTRY
THANK YOU!
CELL STRUCTURE AND FUNCTIONS
Organisms are composed of cells, and these cells have specific structures within them that allow them to
carry out their functions. The principal structures or parts of a cell are (1) the cell membrane, (2) the protoplasm
and its organelles, and (3) the nucleus (in some types of cells).
THE CELL MEMBRANE
The cell membrane also known as plasma membrane is a thin layer surrounding and protecting the cell and
its protoplasmic contents, and controlling the entry and exit of certain substances. When examined under an electron
microscope, the plasma membrane appears to be a
double layer of phospholipid molecules. Each
phospholipid is composed of a lipid, a phosphate
group, and a small amount of carbohydrate
(oligosaccharide). Protein molecules are also found
embedded in phospholipids. Thus, the membrane is
composed of both protein and phospholipid
molecules.
The cell membrane is often pictured as a
fluid mosaic model. This is because its molecules
look like pieces of tile in a mosaic that are constantly moving. The phospholipid molecules move sideways within the
membrane. Since the plasma membrane is fluid, it can seal itself if it is damaged or broken. Because of the structure
of the cell membrane, it is semipermeable or
selectively permeable. It allows only chosen
substances to enter and leave the cell.
The plasma membrane also serves as a boundary
between the environment and the inside of a cell.
Furthermore, the membrane gives form and shape
to cells. The plasma membrane also plays the role
of connecting one cell to two or more adjacent
cells. At times it can serve as an organ for
locomotion like that of an Amoeba, a protozoan
which utilizes its membrane as pseudopodia or
“false feet” for movement.
THE PROTOPLASM AND ITS ORGANELLES

The plasma membrane encloses a mass of jellylike material called protoplasm. The protoplasm is a colorless
or somewhat grayish, translucent, viscous substance that can flow. It is a colloid so that it can change its state from
a semisolid gel to a semiliquid solution.
The protoplasm of one cell differs from the protoplasm of the other cells of the same organism and of the
same kind of cell of different organisms. For example, the
protoplasmic substance of a red blood cell differs from
that of a bone cell, a brain cells, or a liver cell.
Various organized organelles, also called little
organs, are also present in the protoplasm. Some of them
are visible under the light microscope; others are not.
Each of these minute living substructures is associated
with a specific process of the cell’s activity. A cell function
may be classified according to the number and kinds of
organelles present.
PROTOPLASM
Cytoplasm and Karyoplasm or Nucleoplasm
If a nucleus is present in a cell, the protoplasm is
differentiated into two: (1) cytoplasm, the protoplasm lying
outside the nucleus; and (2) karyoplasm or nucleoplasm,
the protoplasm inside the nucleus.
Many types of organelles are suspended in the
gel-like cytoplasm. Among them are mitochondria,
ribosomes, endoplasmic reticulum, Golgi bodies, vacuoles, lysosomes, centrosomes and centrioles, and
cytoskeleton. Other organelles peculiar to plant cells are the cell wall and the plastids.
MITOCHONDRIA: POWERHOUSES OF THE CELL

The name mitochondrion (plural, mitochondria) means ‘thread granule’. This describes what the
mitochondrion looks like under the light microscope – a tiny, rod-like structure in the cytoplasm of almost all cells.
Mitochondria appear in electron micrographs as cylindrical organelles. Occasionally, they can exist in other shapes
such as rods or filaments. They vary in size but within the range of 0.5-1.5 μm wide and 3.0-10.0 μm long.
a. Each mitochondrion is bound by a double
unit membrane, the outer membrane being
a smooth continuous boundary.
b. The inner membrane is extensively
enfolded to form partitions called cristae
(singular, crista).
c. The intermembrane space between the
outer and inner membrane is narrow and
filled with fluid.
d. The cristae extend into and partially
partition the interior of mitochondria which
is filled with a fluid called the mitochondrial
matrix.
e. The matrix is a mixture of enzymes, mitochondrial DNA, RNA and ribosomes. The surface of cristae facing the
matrix is covered with stalked particles. The number of cristae is proportional to the energy requirement of the
cell.
Mitochondria provide the energy a cell needs for all its activities such as movement, cell division and
production of secretory products. They are centers of cellular respiration, a process in which the energy-rich
adenosine triphosphate or ATP, a high energy compound in cells that functions in energy storage and transfer, is
produced. Thus, mitochondria are termed the “powerhouse of the cell”.
RIBOSOME: PROTEIN FACTORIES OF THE CELL
Ribosomes are seen as a solid spherical granule
when observed through the electron microscope. They
are the most numerous of all cytoplasmic structures.
Each ribosome has a diameter of about 20-25nm. Each
ribosome is an assembly of two ribosomal subunits: the
large subunit and the small subunit. Ribosomal
subunits are synthesized in the nucleolus. These
subunits then pass through the nuclear pores into the
cytoplasm, where they can combine to form ribosomes.
Each ribosome consists of about 70 protein molecules
and several ribosomal RNA (rRNA) molecules.
Ribosomes are protein factories of the
cell. Ribosomes synthesize protein molecules from amino acid, using genetic information carried by mRNA molecules
from the DNA in the nucleus. The proteins synthesized on free ribosomes are released into the cytosol, where they
perform their functions as enzymes or as structural proteins for growth within the cell. The proteins synthesized by
ribosomes attached to rough ER pass into the cisternal space of the reticulum and are then transferred to the Golgi
body. They are ultimately secreted from the cell in the form of enzymes or hormones.
Ribosomes are found in two places in the cell.
a. Bound ribosomes- attached to the cytoplasmic
surface of rough ER and the nuclear envelope.
b. Free ribosomes- suspended freely in the cytosol.
Bound and free ribosomes are structurally identical and
can alternate between the two roles depending on the Bound
ribosome
metabolic needs of the cell.
ENDOPLASMIC RETICULUM: MANUFACTURES AND SHIPPERS OF THE CELL
Endoplasmic reticulum (ER) is an extensive membranous network that is denser in the interior region
(endoplasm) than in the exterior region of the cytoplasm (ectoplasm). This organelle is found penetrating the
cytoplasm of all nucleated cells (eukaryotic cells) and is especially well developed in growing cells.
The ER consist of a network of membranous
tubules and flattened sacs called cisternae (singular,
cisterna). The ER membrane separate the internal
compartment of the ER called cisternal space, from
the cytosol. The ER membrane which is a single-unit
membrane is continuous with the nuclear envelope.
Therefore, the space between two membranes of the
nuclear envelope is continuous with the cisternal
space of the ER.
Ribosomes are often attached to long strands
of membrane called the endoplasmic reticulum or ER,
which forms a network of tiny canals through the cell.
These canals are formed by two parallel membranes.
They connect the nuclear membrane and the plasma
membrane, thus serving as passageway for food
substances. The ER may either have a rough or
smooth appearance.
Rough Endoplasmic Reticulum (RER)

Rough endoplasmic reticulum is named as such because the cytoplasmic surface of its cisternae appears
rough due to the ribosomes that stud it. It collects proteins synthesized by ribosomes attached at its surface, packages
them in inert form, stores them temporarily and transports them to the cell surface for secretion. Cells of secretory
glands like pancreas, salivary glands, pituitary gland and mammary glands which actively synthesize and excrete
proteins (insulin, digestive enzymes, hormones, and milk proteins, respectively) are densely packed with rough ER.
The system of canals formed by the cisternal spaces of rough ER function as intracellular transport system
that facilitate the movement of substances from one part of the cell to another.
When an enzyme is synthesized by a ribosome bound to the surface of RER, the growing polypeptide chain
is threaded into the cisternal space through a pore formed by a protein
in the ER membrane. As it enters the cisternal space, the new protein
folds into its native conformation and is stored there temporarily.
In the RER, a short carbohydrate chain is added to the protein
converting it to a glycoprotein. The carbohydrate is attached to the
protein by specialized molecules built into the ER membrane.
a. Once the secretory proteins are formed, the molecules are ready for
export. The molecules then moved to a specialized region of the
RER called transitional ER. Here, they are packaged into tiny sacs
called transport vesicles.
b. The vesicles then bud off from the ER membrane like bubbles. The vesicles containing secretory proteins will
now travel to the Golgi body for further processing.
c. From there, transport vesicle containing the finished molecules will make their way to the plasma membrane and
release their contents form the cell.
d. Another function of the RER is to manufacture more membrane for the cell.
e. Some of the proteins made by the ER ribosomes are inserted into the ER membrane, as are membrane
phospholipids made by the ER enzymes.
f. As a result, the ER membrane enlarges, and some of it can be transferred to other organelles as well as the
plasma membrane through the transport vesicles.
Smooth Endoplasmic Reticulum (SER)
The cytoplasmic surface of smooth ER lacks ribosomes. The cisternae of smooth ER are the form of
interconnected tubes and not flatted sacs. The smooth ER of various cells functions in diverse metabolic processes,
including synthesis and transport of lipids, metabolism of carbohydrates and detoxification of drugs and poisons.
Much of its activity results from enzymes embedded in its membrane.
a. Enzymes of smooth ER are important for the
synthesis of lipids, including oils, phospholipids and
steroids. Cells that are active in lipid metabolism
such as gut epithelium cells, adrenal gland cells and
cells I the testes and ovaries are rich in smooth ER.
b. In the gut epithelium cells, smooth ER synthesizes
lipids from fatty acids and glycerol. These are then
sent to the Golgi body to be exported out of the cell.
c. Cells in the testes and ovaries synthesize the steroid
sex hormones, testosterone and estrogen,
respectively.
d. Cells in the adrenal glands are involved in the
synthesis of some steroid hormones.
Our liver cells also have large amounts of smooth ER. Certain enzymes in the smooth ER of the liver help
regulate the amount of sugar released from the liver cells into the bloodstream. Other liver enzymes hep break down
drugs and other potentially harmful substances such as alcohol.
GOLGI BODIES OR GOLGI APPARATUS: PACKAGING COUNTERS OF THE CELL
In 1898, an Italian scientist, Camilo Golgi, observed a series of vesicles in the nerve cells of an owl. These
vesicles were named Golgi Apparatus, after the discoverer. The Golgi body consists of a stack of flattened
membranous sacs (cisternae). Each Golgi stack in a mammalian cell can consist of 5-6 cisternae whereas those in
plant cells can consist of 20 or more.
The Golgi body is found in all eukaryotic cells. it is clearly seen in active secretory cells such as nerve cells,
pancreatic cells and cells of root apex. Most cells have a single Golgi body located near the nucleus. Root apex cells
may have several or a few hundred Golgi bodies within the cytoplasm.
The Golgi body acts as a warehouse and packaging factory for macromolecules. It receives, stores, modifies,
finishes, sorts and packages secretory proteins arriving
from the RER prior to sending them to other destinations.
Products of ER are modified during their transit from the cis
pole to the trans pole of the Golgi body. For example,
various Golgi enzymes modify the oligosaccharide portions
of glycoproteins which were first added in the RER.
The Golgi remove some sugar monomers and substitute
others, producing a variety of oligosaccharides.in this way,
the secretory proteins are marked and then sorted into
various batches for different destinations. The molecules
move from cisternae to cisterna within the Golgi body
through transport vesicles. Finally, the Golgi body
dispatches its products by packaging them in small
secretory vesicles which bud from the trans face. The secretory vesicles will be delivered to and fused with other
organelles within the cell such as lysosome. In other cases, they are delivered to the plasma membrane where they
fuse with the membrane and their protein contents are released to the outside of the cell in a process called
exocytosis.
The secretory vesicles produced by the Golgi body play an important role in adding surface area to the cell
membrane. When releasing its contents to the exterior through the process of exocytosis, the membrane of the
ruptured vesicles may remain as a permanent addition to the plasma membrane.
VACUOLES: STORAGE TANKS OF THE CELLS
A vacuole is a fluid-filled sac bounded by a single membrane. It is clearly seen within the cytoplasm of the
plant cells. Most mature plant cells have one large central vacuole.
a. As the cell grows, the size of one vacuole increases due to the merging of various small vacuoles to form a large
central vacuole that occupies 90% of the volume in a plant cell. (Figure beside)
b. To make way for the increasing
volume of a vacuole, cytoplasm is
pushed aside forming only a very thin
layer pressing against the inside of the
cell wall.
The single membrane that
surrounds the vacuole is called the
tonoplast. The fluid within the vacuole is called cell sap. Cell sap is a concentrated solution of mineral salts, sugars,
amino acids, wastes (such as tannins) and sometimes pigments such as anthocyanins.
Plants lack waste disposal systems and often utilize vacuoles as a storage place for waste materials. Such
waste products often aggregate and form small crystals inside the vacuole, usually in the form of calcium oxalate
crystals. The vacuole may also be a site of pigment deposition. Anthocyanins are a group of pigments that cause
brilliant red, dark red and blue colors of many vegetables, fruits, flowers, and leaves. Unlike most other plant pigments,
anthocyanins are readily soluble in water and are readily dissolved within the cell sap.
Vacuoles also play a role in plant defense. The vacuoles of some plants store tannin, a poisonous substance
used to protect the plant from animals.
c. Vacuoles play a very important role in improving the surface area to volume ratio of the plant cell. The surface
area to volume ratio is important to cells since it determines the number of metabolites that can move into the
cell efficiently through diffusion.
d. Animal cells can improve this ratio by changing their shapes or by the folding of plasma membrane; but plant
cells can do neither of these as they are limited by their cell walls.
e. However, plant cells overcome this problem by having a large central vacuole pushing the cytoplasm to the side,
thus forming a very thin layer pressing against the cell wall. This ensures that the cytoplasm and nucleus are only
short distance away from the cell surface where
diffusion is most efficient. vacuole
Some plant vacuoles contain hydrolytic
enzymes that work exactly like the enzymes in
lysosomes. The tonoplasts, just like other membranes,
will lose its semi-permeability after cell death and
release enzyme from the vacuole, causing autolysis of
the cell.
f. Large vacuoles are not found in animal cells.
Animal cells usually have small vacuoles which are sometimes referred to as vesicles. Example of vacuoles fond
in animal cells are phagocytic vesicles, pinocytic vesicles, autophagy vacuoles and excretory vacuoles.
g. Many single-celled protozoa have food vacuoles or digestive vacuoles that contain food undergoing digestion,
and many have contractile vacuoles, which remove excess water and some wastes from the cell.
LYSOSOME: SUICIDE BAGS OF THE CELLS
Lysosome are found in all animal cells and in some plant cells. Lyso means ‘dissolving power’ and some
means “body”. These organelles, discovered in 1952 are found to be rich in strong hydrolytic enzymes, that the cell
uses to digest macromolecules, which are kept intact by thick lysosomal membrane that is highly acidic.
When observed through an electron microscope, they appear as dark spherical bodies in the cytoplasm and
their diameters are generally smaller than that of mitochondria. The RER and Golgi body cooperate to make
lysosomes. First, the RER puts the enzymes and membrane together. Then the Golgi body chemically refine the
enzymes and releases mature lysosomes.
The membrane of the lysosome is very unique. This is a single membrane compared to the double membrane
of the mitochondrion. This membrane can prevent the leakage of the enzymes and is able to resist digestion. This is
important as excessive leakage of the enzymes from the number of lysosomes can lead to the autodigestion of the
cell. The lysosomal membrane encloses a compartment where digestive enzymes are stored and safely isolated from
the rest of the cytoplasm. Without lysosome, a cell cannot carry highly hydrolytic enzymes without digesting itself.
The main function of
lysosomes is intracellular
digestion, digesting the food
wastes of the cell. It also plays a
very important role in the defense
system. White blood cells ingest
bacteria into vacuoles and
lysosomal enzymes emptied into
these vacuoles rupture the
bacterial cell walls. Lysosome
serves as recycling centers for
redundant and damaged
organelles. Old and worn-out cell
organelles that no longer function
normally are enclosed in a
membrane and broken down by
lysosomes in a similar manner.
The whole process is called
autophagy. The resulting simple molecules are reused to construct new organelles. When a cell dies, its own
lysosomes releases enzymes that digest the remains of the cell in process called autolysis.
CENTROSOMES AND CENTRIOLES: HELPERS IN CELL DIVISION
A centrosome is a mass of dense protoplasm with structures
called centrioles at the center. Centrioles are hollow cylinders about 0.2
μm in diameter and 0.5 μm long. Each hollow cylinder is composed of nine
sets of triplet microtubules arranged in a ring. The centrioles as part of
the cytoplasm, duplicate and form at the center for spindle fiber formation
during cell division.
CYTOSKELETON: FRAMEWORK OF THE CELL
The most modern research has revealed that the cytoplasm
contains a cytoskeleton (cellular framework). Just as hollow blocks or
steel gives shape to
buildings, a cytoskeleton
supports the internal system and gives the cell its shape. It consists
of a network of at least three distinct structures such as microtubule,
intermediate filament, and microfilament.
Organelles Peculiar to Plant Cells
CELL WALL
The cells of plants, fungi, and some single-celled organisms are protected and supported by a rigid cell wall,
which lies outside the plasma membrane and is composed mainly of cellulose, except in the case of fungi and
bacteria.
The cell wall is consisted of several
distinct layers. The primary cell wall is the
outer layer. It expands as the cell grows. As
the plant reaches its full size, a secondary
cell wall develops inside the primary cell
wall. This new layer adds strength to the
wall. Two primary cell walls of adjacent
cells are separated by another layer, the
middle lamella, which is composed of a
jellylike polysaccharide called pectin.
Pectin is generally present in the form of
calcium pectate. When a fruit ripens, the
calcium pectate is partly converted into more soluble forms. This loosens the cells; then the fruit becomes softer.
Both primary and secondary walls are composed mainly of the polysaccharide cellulose. Soft plant structures,
such as leaf blades or flower petals, have thin primary walls. Aside from cellulose, the secondary walls usually contain
lignin, a complex organic compound that adds hardness and rigidity to cell walls. The cell wall remains intact even
after the rest of the cell has died. It is typical of the cork cells which compose the wood of trees, plant fibers, and nut
shells.
PLASTIDS – CHROMOPLASTS AND LEUCOPLASTS
Large membrane-bound organelles, called plastids, are found in the cytoplasm of most plant cells. There are
three categories of plastids: chloroplasts, chromoplasts, and leucoplasts.
Chloroplasts are green-colored plastids containing the
green pigment called chlorophyll. Chlorophyll is very essential
in the manufacture of food by green plants. Chromoplasts
contain various yellow or orange pigments called carotenoids.
These chromoplasts give many flowers, ripened fruits, and autumn leaves their characteristic yellow or orange color.
Chromoplasts in tomatoes contain red pigment, rheodoplast. This pigment makes tomatoes red.
Leucoplasts are colorless plastids that serve as food storehouses in many plant cells. They may contain oil,
starch grains, and proteins, as well as enzymes necessary to link glucose molecules together and form starch
molecules. Starch-laden leucoplasts are usually abundant in the cells of roots, stems, and storage areas of plants,
like the potato tuber.
THE NUCLEUS: CONTROL CENTER OF THE CELL
The nucleus (plural, nuclei) was the first organelle that
biologists observed in a cell. It is a spherical structure that is
usually located near the center of the cell. The nucleus is the
largest and most prominent organelle. There is one nucleus in
each living cell except mammalian red blood cells and mature
sieve tube cells (in plants) which are without nuclei. The
nucleus is usually spherical or oval in shape and averages
5micro meter in diameter. The nuclei of some cells such as
that of the white blood cells are multi-lobed.
The nucleus in enclosed by a nuclear envelope,
which consists of two membranes perforated by nuclear
pores. The diameter of a nuclear pore is about 20-50nm.
These pores control the exchange of materials between the nucleus and the cytoplasm. The space between the two
membranes of the nuclear envelope is called the perinuclear space and has a width of about 20nm.
The nucleus contain chromatin, the form that chromosomes take up when the cell is not dividing. Chromatin
contains DNA, the molecule of inheritance which controls the activities of the cell. Two forms of chromatin are visible.
a. Euchromatin- stains lightly and is thought to contain active DNA.
b. Heterochromatin- stains deeply and is thought to contain inactive DNA.
Nucleoplasm or karyoplasm is the semi-fluid substance in the nucleus. The nucleus also contains one or
more very prominent structures called nucleoli (singular, nucleolus). The nucleolus appears as dense mass of
granules and fibers when observed through the electron microscope. The nucleolus synthesizes ribosomal RNA
(rRNA). In addition, proteins imported from the cytoplasm are combined with the rRNA in the nucleolus to form large
and small ribosomal subunits. These ribosomal subunits then move pores to the cytoplasm. In the cytoplasm, the
large and small subunits are assembled into ribosomes which take up positions on the rough endoplasmic reticulum
where they play a vital role for protein synthesis.
The nucleus is the information center of the cell. Its functions include the following.
a. To carry the genetic material of a cell in the form of chromosomes.
b. To act as a control center that directs all the activities of a cell by regulating protein and enzyme synthesis.
c. To contain the nuclear DNA which carries the instructions for the synthesis of proteins.
d. To assist in the production of ribosomes and RNA and is essential for cell division.
References:
Alberts et al. (2017). Molecular biology of the cell. (2nd ed.) New York: Garland Publishing
Reece et al. (2011). Campbell Biology (4th ed.) Boston: Pearson
Rey & Ramos (2018). General Biology 1. Malaysia: Oxford Publishing
MARCH 2022
CARBOHYDRATES
Carbohydrates
BIOCHEMISTRY
CARBOHYDRATES
CARBOHYDRATES
Section 18.2
Occurrence and Functions of Carbohydrates
Carbohydrates
CARBOHYDRATES
CARBOHYDRATES
Section 18.2
Carbohydrates
• Most of the matter in plants, except water, is
carbohydrate material.
• Carbohydrates account for 75% of dry plant material
and are produced by photosynthesis.
– Cellulose: structural element.
– Starch/glycogen: energy reservoir.
- small amount in human body.
• Plant products are source of carbohydrates.
- Average human diet contains 2/3 of carbohydrates.
CARBOHYDRATES
Section 18.2
Photosynthesis
• A process in which plants produce carbohydrates using
carbon dioxide, water and solar energy.
Chlorophyll
CO2 + H2O + Solar Energy Carbohydrates + O2
Plant Enzymes
Copyright © Cengage Learning. All rights reserved 4

CARBOHYDRATES
Section 18.2
Functions of Carbohydrates in the Human Body

• Carbohydrate oxidation - provides energy
• Carbohydrate storage, in the form of glycogen, provides a
short-term energy reserve
• Carbohydrates supply carbon atoms for the synthesis of other
biochemical substances (proteins, lipids, and nucleic acids)
• Carbohydrates form part of the structural framework of DNA
and RNA molecules
• Carbohydrates linked to lipids are structural components of
cell membranes
• Carbohydrates linked to proteins function in a variety of cell–
cell and cell–molecule recognition processes

CARBOHYDRATES
Section 18.3
Classification of Carbohydrates
• Simpler Formula:
– CnH2nOn or Cn(H2O)n (hydrates of C).
– n= number of atoms.
• Carbohydrates are polyhydroxy aldehydes or ketones or
compounds that produce such substances upon
hydrolysis.

CARBOHYDRATES
Section 18.3
Monosaccharide
• Contain single polyhydroxy aldehyde or ketone unit
• They can’t be broken down into simpler substances by
hydrolysis (reaction with water) reactions
• Contains 3-7 C atoms
• 5 and 6 carbon species are more common
• Water soluble white crystalline solids

CARBOHYDRATES
Section 18.3
Oligosaccharides
• Contains 2-10 monosaccharide units - covalently bonded
to each other
• Free oligosaccharides are less common in nature
• Usually found associated with proteins and lipids in
complex molecules.
– Serve structural and regulatory functions

CARBOHYDRATES
Section 18.3
Disaccharides
• Contains 2 monosaccharide units covalently bonded to
each other.
• Disaccharides are crystalline and water soluble
substances
• Table sugar (sucrose) and milk sugar (lactose) are
common disaccharides
• Upon hydrolysis they produce monosaccharides

CARBOHYDRATES
Section 18.3
Polysaccharides
• Contains many monosaccharide units covalently bonded
• Polymers: May contain a few 100s to > million
monosaccharide units
• Examples:
• Cellulose: Paper, cotton, wood
• Starch: Bread, pasta, potatoes, rice, corn, beans,
peas, etc.

CARBOHYDRATES
Section 18.4
Chirality: Handedness in Molecules
Objects and handedness
• Most biological molecules,

including carbohydrates,
exhibit the property of
“handedness” (isomerism)
• Most monosaccharides exist
in two forms: a “left handed”
and “right handed” form -
same as two hands that are
“mirror images” of each other.

CARBOHYDRATES
Section 18.4
Mirror Images
• Mirror Image: the reflection of an
object in a mirror
• Two types of objects:
- Superimposable mirror images:
Images that coincide at all
points when the images are
laid upon each other -- Achiral
- Non-superimposable mirror
images: Images where not all
points coincide when the
images are laid upon each
other -- Chiral (handedness)

CARBOHYDRATES
Section 18.4
Chirality
• Chiral Center: C atom attached to 4 different groups
• A molecule with chiral center is a chiral molecule
– Best way to visualize - look at all C atoms and see if there are at
least two H atoms then that can’t be a chiral center
– C atoms with less than one H atoms are worth looking at for
their chirality.
• Be careful as a C atom may apparently look similar but may not
have four DIFFERENT groups.
– E. g. 3-bromopentane – has no chiral carbons, whereas
bromochloroiodomethane has a chiral carbon.
– A chiral C is usually denoted by *

CARBOHYDRATES
Section 18.4
Practice Exercise
Indicate whether the circled carbon atom in each of the
following molecules is a chiral center.
Answers:
a. Not a chiral center
b. Not a chiral center
c. Chiral center
d. Not a chiral center
CARBOHYDRATES
Section 18.4
Responses of Left and Right Handed Forms of a Molecule in a
Human Body
– Both may be active, one may be more active or one

may be active and other non-active
– Example: Right handed hormone epinephrine is 20
times more active than left handed form
– Almost all monosaccharides are right handed
– Amino acids are almost always left handed

CARBOHYDRATES
Section 18.5
Stereoisomerism: Enantiomers and Diasterioisomers
Stereoisomers
• Stereoisomers are isomers that have the same molecular and
structural formulas but differ in the orientation of atoms in space.
• Two types:
– Enantiomers: stereoisomers whose molecules are non-
superimposable mirror images of each other. Molecules with
chiral center.
– Diastereomers: stereoisomers whose molecules are not mirror
images of each other. Cis-Trans isomers

CARBOHYDRATES
Section 18.5

CARBOHYDRATES
Section 18.6
Designating Handedness Using Fischer Projection Formulas
Fischer Project Formulas

• Fischer projection formula: - A two-dimensional structural
notation for showing the spatial arrangement of groups
about chiral centers in molecules.
• In a Fischer projection formula a chiral center (Carbon) is
represented as the intersection of vertical and horizontal
lines
• Functional groups of high priority will be written at top
CHO CHO
H OH HO H
CH2OH CH2OH
D-Glyceroldehyde L-Glyceroldehyde
(-OH on right side) (-OH on left side)

CARBOHYDRATES
Section 18.6

• We now consider Fischer projection formulas for the
compound 2,3,4-trihydroxybutanal - a monosaccharide
with four carbons and two chiral centers
• There are four stereoisomers for this compound—two
pairs of enantiomers

CARBOHYDRATES
Section 18.6

• The D,L system used to designate the handedness of
glyceraldehyde enantiomers can be extended to other
monosaccharides with more than one chiral center
• The carbon chain is numbered starting at the carbonyl group end of
the molecule, and the highest-numbered chiral center is used to
determine D or L configuration
• Epimers: Diastereomers whose molecules differ only in the
configuration at one chiral center

CARBOHYDRATES
Section 18.7
Properties of Enantiomers
Constitutional Isomers and Diastereomers

• Constitutional isomers differ in most chemical and
physical properties -- they have different boiling points
and melting points.
• Diastereomers also differ in most chemical and physical
properties --They too have different boiling points and
freezing points.
• In contrast, nearly all the properties of a pair of
enantiomers have the same chemical and physical
properties
– Two differences:
1. Their interaction with plane polarized light
2. Their interaction with other chiral substances
CARBOHYDRATES
Section 18.7
Interaction of Enantiomers with

Plane-Polarized Light
• Properties of light
– Ordinary Light: Move in all directions
– Plane polarized light move only in
one direction (see Figure on right
side)
• Plane polarized light is rotated clockwise
(to right) or counterclockwise (to left)
when passed through enantiomers
• Direction and extent of rotation will
depend upon the enantiomer
• Same concentration of two enantiomers
rotate light to same extent but in opposite
direction

CARBOHYDRATES
Section 18.7
Interaction of Enantiomers with Plane-Polarized Light

CARBOHYDRATES
Section 18.7
Dextrorotary and Levorotatory Compounds

• Enantiomers are optically active: Compounds that rotate plane
polarized light
• Two Types:
– Dextrorotatory:
• Chiral compound that rotates light towards right (clockwise; +)
• (+)-glucose - dextrorotatory – to the right - clockwise
– Levorotatory:
• Chiral compound that rotates light towards left
(counterclockwise; -)
• (-)-glucose - levorotatory – to the left - counterclockwise
– There is no correlation between D, L and +, -
• In D and L system you need to look at the structure
• + and – can be determined using a polarimeter
CARBOHYDRATES
Section 18.7
Interactions Between Chiral Compounds

• Right and Left handed baseball players can’t use same
glove (chiral) but can use same hat (achiral)
– Two members of enantiomer pair (chiral) react
differently with other chiral molecules
• Enantiomeric pairs have same solubility in achiral
solvents like ethanol and have different solubility in chiral
solvent like D-2-butanol
• Enantiomers have same boiling points, melting points
and densities - all these are dependent upon
intermolecular forces and chirality doesn’t depend on
them

CARBOHYDRATES
Section 18.8
Classification of Monosaccharides
Monosaccharides
• Classification based on # of carbon atoms:
– Triose --- 3 carbon atoms
– Tetrose -- 4 carbon atoms
– Pentoses – 5 carbon atoms
– Hexoses -- 6 carbon atoms
• Classification based on functional groups:
– Aldoses: Monosaccharides with one aldehyde group
– Ketoses: Monosaccharides with one ketone group
• Combined # of C atoms and functional group:
– Example:
Aldohexose: Monosaccharide with aldehyde group and 6 C atoms
Ketopentose: Monosaccharide with ketone group and 5 C atoms

CARBOHYDRATES
Section 18.8
• Other Example:
– Aldohexose:
CHO CH2OH
Monosaccharide with
aldehyde group and 6 C H OH O
atoms – D-glucose HO H HO H
– Ketohexose: H OH H OH
Monosaccharide with
H OH H OH
aldehyde group and 6 C
atoms – D-fructose CH2OH CH2OH
D-Glucose D-Fructose
(aldohexose) (ketohexose)

CARBOHYDRATES
Section 18.8
Exercise
Classify each of the following monosaccharides according
to both the number of carbon atoms and the type of
carbonyl group present.
Answers:
a. Aldopentose;
b. Ketohexose;
c. Aldohexose;
d. Ketopentose

CARBOHYDRATES
Section 18.8
Aldoses

CARBOHYDRATES
Section 18.8
Ketoses

CARBOHYDRATES
Section 18.9
Biochemically Important Monosaccharides
Glucose and Fructose

CHO
H OH 1. Most abundant in nature

HO H 2. Nutritionally most important
H OH 3. Grape fruit good source of glucose (20 - 30%
H OH
by mass) -- also named grape sugar, dextrose
CH2OH
and blood sugar (70 - 100 mg/100 mL of blood)
D-Glucose 4. Six membered cyclic form
(aldohexose)
CH2OH
O
1. Ketohexose
HO H
2. Sweetest tasting of all sugars
H OH
3. Found in many fruits and in honey
H OH
4. Good dietary sugar-- due to higher sweetness
5. Five membered cyclic form
CH2OH
D-Fructose
(ketohexose)

CARBOHYDRATES
Section 18.9
Galactose and Ribose
1. Milk sugar
2. Synthesize in human
3. Also called brain sugar-- part of brain and
nerve tissue
4. Six membered cyclic form
1. Part of RNA
2. Part of ATP
3. Part of DNA

CARBOHYDRATES
Section 18.10
Cyclic Forms of Monosaccharides
Cyclic Hemiacetal
Forms of D-Glucose
• Dominant form of
monosaccharides
with 5 or more C
atoms is cyclic -
cyclic forms are in
equilibrium with
open chain form
• Cyclic forms are
formed by the
reaction of carbonyl
group (C=O) with
hydroxyl (-OH)
group on carbon 5

CARBOHYDRATES
Section 18.10
Cyclic Hemiacetal Forms of D-Glucose

• 2 forms of D-glucose:
– Alpha-form: -OH of C1 and CH2OH of C5 are on opposite sides
– Beta-form: -OH of C1 and CH2OH of C5 are on same sides
6 6
CH2 OH Anomeric CH 2OH
O Carbon O OH
5 5
4 1
OH 4 OH
1
2 OH 2
OH OH
3 3 Anomeric
OH OH Carbon
a-D-Glucose b-D-Glucose
– Anomers: Cyclic monosaccharides that differ only in the position

of the substituents on the anomeric carbon atom.

CARBOHYDRATES
Section 18.10
• Intramolecular cyclic hemiacetal formation and the

equilibrium between various forms are not restricted to
glucose.
• All aldoses with five or more carbon atoms establish
similar equilibria, but with different percentages of the
alpha, beta, and open-chain forms.
• Fructose and other ketoses with a sufficient number of
carbon atoms also cyclize.

CARBOHYDRATES
Section 18.10
Pyranose and Furanose

• A cyclic monosaccharide containing a six-atom ring is
called a pyranose, and one containing a five-atom ring is
called furanose because their ring structures resemble
the ring structures in the cyclic ethers pyran and furan
respectively.
Pyran Furan
O
O
CH2 OH
CH2OH CH2OH
OH CH2OH O
O
OH OH
OH
OH
a-D-Glucose OH
OH
OH OH
OH
a -D-Fructose a -D-Ribose
Pyranose Furanoses
CARBOHYDRATES
Section 18.11
Haworth Projection Formulas
• A Haworth projection formula is a two-dimensional

structural notation that specifies the three-dimensional
structure of a cyclic form of a monosaccharide.
CH2 OH
O CH2 OH
CH2 OH CH2 OH
O O
OH
OH
OH OH
OH
OH
OH OH
OH OH
a-D-Glucose a -D-Fructose a -D-Ribose

CARBOHYDRATES
Section 18.11
Alpha and Beta Configuration

• Alpha or Beta configuration is determined by the position of the —
OH group on C1 relative to the CH2OH group that determines D or L
series.
• In a Beta configuration, both of these groups point in the same
direction
• In an Alpha configuration, the two groups point in opposite
directions.

CARBOHYDRATES
Section 18.11
OH Group Position
• The specific identity of a monosaccharide is determined by the
positioning of the other —OH groups in the Haworth projection
formula.
• Any —OH group at a chiral center that is to the right in a Fischer
projection formula points down in the Haworth projection formula
and any —OH group to the left in a Fischer projection formula points
up in the Haworth projection formula.

CARBOHYDRATES
Section 18.11
Practice Exercise
• Which of the monosaccharides glucose, fructose, galactose, and

ribose has each of the following structural characteristics? (There
may be more than one correct answer for a given characteristic)
a. It is a pentose.
b. It is a ketose.
c. Its cyclic form has a 6-membered ring.
d. Its cyclic form has two carbon atoms outside the ring.
Answers:
a. Ribose
b. Fructose
c. Glucose, galactose
d. Fructose

CARBOHYDRATES
Section 18.11
Glycoside Formation
• Glycoside formation: Cyclic forms of monosaccharides
are hemiacetals, they react with alcohols to form acetals:
– Monosaccharide acetals are called glycosides
• A glycoside is an acetal formed from a cyclic
monosaccharide by replacement of the hemiacetal
carbon —OH group with an —OR group:
– A glycoside produced from glucose - glucoside
– A glycoside produced from galactose – galactoside

CARBOHYDRATES
Section 18.11
Glycoside Formation
– Glycosides exist in both Alpha and Beta forms

CARBOHYDRATES
Section 18.13
Disaccharides
• Two monosaccharides can react to form disaccharide

• One monosaccharide act as a hemiacetal and other as
alcohol and the resulting ether bond is a glycosidic
linkage.

CARBOHYDRATES
Section 18.13
Disaccharides
Cellobiose
• Cellobiose is produced as an intermediate in the
hydrolysis of the polysaccharide cellulose:
– Cellobiose contains two beta - D-glucose
monosaccharide units linked through a beta (1→4)
glycosidic linkage.

CARBOHYDRATES
Section 18.13
Disaccharides
Maltose
• Maltose also known as malt sugar
• Structurally maltose made of 2 alpha-D-glucose units linked via an
alpha 1→4 linkage.
• Maltose is digested easily by humans because we have enzymes
that can break alpha (1→4) linkages but not beta (1→4) linkages of
cellobiose. Therefore cellobiose cannot be digested by humans.
• Baby foods are rich in maltose.

CARBOHYDRATES
Section 18.13
Disaccharides
Lactose
• Lactose is made up of beta-D-galactose unit and a beta-D-glucose
unit joined by a beta (1→4) glycosidic linkage.
• Milk is rich in lactose disaccharide..
– Lactose intolerance: a condition in which people lack the
enzyme lactase needed to hydrolyze lactose to galactose and
glucose.
– Lactase hydrolyzes beta (1→4) glycosidic linkages.

CARBOHYDRATES
Section 18.13
Disaccharides
Sucrose
• Sucrose (table sugar): The most abundant of all disaccharides
and found in plants.
• It is produced commercially from the juice of sugar cane and
sugar beets.

CARBOHYDRATES
Section 18.13
Disaccharides
Practice Exercise
• Which of these disaccharides, i.e., maltose, cellobiose, lactose, and

sucrose, have the following structural or reaction characteristics?
(There may be more than one correct answer for a given
characteristic)
a. Two different monosaccharide units are present.
b. Hydrolysis produces only monosaccharides.
c. Its glycosidic linkage is a “head-to-head” linkage.
d. It is not a reducing sugar.
Answers:
a. Lactose, sucrose
b. Maltose, cellobiose, lactose, sucrose
c. Sucrose
d. Sucrose

CARBOHYDRATES
Section 18.14
Oligosaccharides
• Carbohydrates that contain 3-10 monosaccharide units

boded to each other via glycosidic linkages.
• Not as common as disaccharides in nature. Generally
present in association with other complex molecules.
• Examples:
• Raffinose: made of one each of galactose, glucose
and fructose.
• Stachyose: made of 2 galactose, 1 glucose and 1
fructose units.
• Commonly found in onions, cabbage, broccoli and
wheat.

CARBOHYDRATES
Section 18.15
General Characteristics of Polysaccharides
• Polymers of many
monosaccharide
units bonded with
glycosidic linkages
• Two types:
– Linear and
branched, homo-
and hetero-
polysaccharides

CARBOHYDRATES
Section 18.15
• Polysaccharides are not sweet

• Limited water solubility
• Examples:
– Cellulose, starch in plants
– Glycogen in animals
– Chitin in arthropods

CARBOHYDRATES
Section 18.16
Storage Polysaccharides
Starch
• A plant storage polysaccharide that is a storage form for
monosaccharides and is used as an energy source in
plant cells.
• Glucose is the monomeric unit

CARBOHYDRATES
Section 18.16
Starch
• Amylose: Straight chain polymer - 15 - 20% of the starch and has
alpha (1 → 4) glycosidic bonds
– Molecular Mass: up to 1000 glucose units)
• Amylopectin:
– Branched chain polymer - 80 - 85 % of the starch alpha (1→4)
glycosidic bond for straight chain and alpha (1→6) for branch
– Molecular Mass: up to 100,000 glucose units) - higher than
amylose
– Amylopectin is digested more readily by humans (can hydrolyze
alpha linkages but not beta linkages)

CARBOHYDRATES
Section 18.16
Starch

CARBOHYDRATES
Section 18.16
Glycogen
– Human and animal storage polysaccharide
– Contains only glucose units
– Branched chain polymer – alpha (1→4) glycosidic bonds in
straight chains and alpha (1→6) in branches
– Molecular Mass: up to 1,000,000 glucose units)
– Three times more highly branched than amylopectin in starch
– Excess glucose in blood stored in the form of glycogen

CARBOHYDRATES
Section 18.17
Structural Polysaccharides
Cellulose
• Linear homopolysaccharide with beta (1→4) glycosidic bond
• Up to 5000 glucose units with molecular mass of ~900,000 amu
– Humans don’t have enzymes that hydrolyze beta (1→4) linkages - so
they can not digest cellulose -- animals also lack these enzymes but
they can digest cellulose because they have bacteria in their guts to
hydrolyze cellulose
– Cotton ~95% cellulose and wood ~50% cellulose
HO
HO O O
OH
HO O O
OH b(1-4) OH
O O
HO
OH b (1-4)
O O OH
OH b(1-4)
O OH
OH

CARBOHYDRATES
Section 18.17
Chitin
– Similar to cellulose in both function and structure
– Linear polymer with all beta (1→4) glycosidic linkages - it has a
N-acetyl amino derivative of glucose
– Function is to give rigidity to the exoskeletons of crabs, lobsters,
shrimp, insects, and other arthropods
HO
HO O O
OH
HO O N-Acetyl
O
OH HN b-D-Glucoseamine
O O
HO
OH HN O
O O
O OH HN O
HN O

CARBOHYDRATES
Section 18.18
Acidic Polysaccharides
• Acidic polysaccharides - polysaccharides with a repeating

disaccharide unit containing an amino sugar and a sugar with a
negative charge due to a sulfate or a carboxyl group.
• Structural polysaccharide present in connective tissue associated
with joints, cartilage, synovial fluids in animals and humans
– Primary function is lubrication necessary for joint movement
– These are heteropolysaccharides - have more than one type of
monosaccharide monomers is present.
• Examples:
– Hyaluronic acid
– Heparin

CARBOHYDRATES
Section 18.18
Hyaluronic Acid and Heparin

• Hyaluronic acid:
– Alternating residues of N-
acetyl-beta-D-glucosamine
and D-glucuronic acid.
– Highly viscous - serve as
lubricants in the fluid of
joints and part of vitreous
humor of the eye.
• Heparin:
– An anticoagulant-prevents
blood clots.
– Polysaccharide with 15–90
disaccharide residues per
chain.
CARBOHYDRATES
Section 18.20
Glycolipids and Glycoproteins: Cell Recognition
• A glycolipid is a lipid molecule that has one or more
carbohydrate (or carbohydrate derivative) units
covalently bonded to it.
• A glycoprotein is a protein molecule that has one or
more carbohydrate (or carbohydrate derivative) units

MARCH 2022
Chapter 20
PROTEINS
Proteins
BIOCHEMISTRY
PROTEINS
Section 20.1
Characteristics of Proteins
• A protein is a naturally-occurring, unbranched polymer in

which the monomer units are amino acids
• Proteins are most abundant molecules in the cells after
water – account for about 15% of a cell’s overall mass
• Elemental composition - Contain Carbon (C), Hydrogen
(H), Nitrogen (N), Oxygen (O), and Sulfur (S)
• The average nitrogen content of proteins is 15.4% by
mass
• Also present are Iron (Fe), phosphorus (P) and some
other metals in some specialized proteins

PROTEINS
Section 20.2
Amino Acids: The Building Blocks for Proteins
• Amino acid - An organic compound that contains both an amino (-NH2) and
a carboxyl (-COOH) group attached to same carbon atom
– The position of carbon atom is Alpha (a)
– -NH2 group is attached at alpha (a) carbon atom.
– -COOH group is attached at alpha (a) carbon atom.
– R = side chain –vary in size, shape, charge, acidity, functional groups
present, hydrogen-bonding ability, and chemical reactivity.
– >700 amino acids are known
– Based on common “R” groups, there are 20 standard amino acids
Side Chain
R a -Carbon Atom
H2N C COOH
a-Carboxyl
a-Amino H Group
Group

PROTEINS
Section 20.2
• All amino acids differ from one another by their R-groups

– There are 20 common (standard) amino acids
• Standard amino acids are divided into four groups based
on the properties of R-groups
• Non-polar amino acids: R-groups are non-polar
– Such amino acids are hydrophobic-water fearing
(insoluble in water)
– 8 of the 20 standard amino acids are non polar
– When present in proteins, they are located in the
interior of protein where there is no polarity

PROTEINS
Section 20.2
• Polar amino acids: R-groups are polar

– Three types: Polar neutral; Polar acidic; and Polar
basic
• Polar-neutral: contains polar but neutral side chains
– Seven amino acids belong to this category
• Polar acidic: Contain carboxyl group as part of the side
chains
– Two amino acids belong to this category
• Polar basic: Contain amino group as part of the side
chain
PROTEINS
Section 20.2
Nomenclature
• Common names assigned to the amino acids are currently used.
• Three letter abbreviations - widely used for naming:
– First letter of amino acid name is compulsory and capitalized
followed by next two letters not capitalized except in the case of
Asparagine (Asn), Glutamine (Gln) and tryptophan (Trp).
• One-letter symbols - commonly used for comparing amino acid
sequences of proteins:
– Usually the first letter of the name
– When more than one amino acid has the same letter the most
abundant amino acid gets the 1st letter.
• Both types of abbreviations are given in the following slides

PROTEINS
Section 20.2
Non-Polar Amino Acids

PROTEINS
Section 20.2
Polar Neutral Amino Acids

PROTEINS
Section 20.2
Polar Acidic and Basic Amino Acids

PROTEINS
Section 20.2
Practice Exercise
• Classify the following amino acids based on the polarity of their R-groups

PROTEINS
Section 20.2
Practice Exercise
Non-polar
Non-polar
Polar Neutral
Polar Basic
Polar Acidic

PROTEINS
Section 20.3
Essential Amino Acids
• Essential Amino acid: A standard amino acid needed for

protein synthesis that must be obtained from dietary
sources – adequate amounts cannot be synthesized in
human body.
• Nine of the 20 standard amino acids are considered
essential
Lysine Methionine
Histidine Phenylalanine
Isoleucine Threonine
Leucine Tryptophan
*Required for growth in children
Valine and is not essential for adults.

PROTEINS
Section 20.4
Chirality and Amino Acids
• Four different groups are attached to the a-carbon atom

in all of the standard amino acids except glycine
– In glycine R-group is hydrogen
• Therefore 19 of the 20 standard amino acids contain a
chiral center
• Molecules with chiral centers exhibit enantiomerism (left-
and right-handed forms)

PROTEINS
Section 20.4
• The amino acids found in nature as well

as in proteins are L isomers.
– Bacteria do have some D-amino acids
– With monosaccharides nature favors
D-isomers
• The rules for drawing Fischer projection
formulas for amino acid structures
– The — COOH group is put at the top,
– The R group is place at the bottom
position of the carbon chain vertically
– The — NH2 group is placed in a
horizontal position.
– Positioning — NH2 on the left - L
isomer Designation of Mirror
– Positioning — NH2 on the right - D handedness in standard amino
acid structures
isomer.

PROTEINS
Section 20.4
Practice Exercise
• Name the following amino acids with correct designation for
the enantiomer (chiral carbon is indicated by *).
A B C
COOH COOH COOH
*C H2N *C H
H 2N H H *C NH2
CH CH3 CH2 CH2
CH2 SH
CH3
OH

PROTEINS
Section 20.4
Practice Exercise
A B C
COOH COOH COOH
*C H2N *C H
H 2N H H *C NH2
CH CH3 CH2 CH2
CH2 SH
CH3
OH
A = L-Isoleucine
B = D-Cysteine
C = L-Tyrosine
PROTEINS
Section 20.5
Acid–Base Properties of Amino Acids
• In pure form amino acids are white crystalline solids

• Most amino acids decompose before they melt
• Not very soluble in water
• Under physiological conditions exists as Zwitterions: An ion with +
(positive) and – (Negative) charges on the same molecule with a net
zero charge
– Carboxyl groups give-up a proton to get negative charge
– Amino groups accept a proton to become positive
Net charge = Zero Net charge = Zero
COO- COO-
NH 3+ H NH 3+ H
R CH 3
L-Amino acid L-Alanine

(general)
Zwitterions Carry Net Zero Charge

PROTEINS
Section 20.5
Isoelectric Point (pI)

• Amino acids in solution exist in three different species (zwitterions,
positive ion, and negative ion) - Equilibrium shifts with change in pH
• Isoelectric point (pI) – pH at which the concentration of Zwitterion is
maximum -- net charge is zero
– Different amino acids have different isoelectric points
– At isoelectric point - amino acids are not attracted towards an
applied electric field because they carry net zero charge.
COOH COO- COO-
+
+
H3N C H H3N C H H2N C H
CH3 CH3 CH3

Low pH High pH
Zwitter Ion (net - charge)
(net + charge) (net neutral charge)
Neutral pH

PROTEINS
Section 20.6
Cysteine: A Chemically Unique Amino Acid
• Cysteine: the only standard

amino acid with a sulfhydryl
group ( — SH group). NH 3 + NH3 +
• The sulfhydryl group imparts -OOC CH

H2
C SH HS
H2
C CH COO-
cysteine a chemical property Cysteine Cysteine
unique among the standard Oxidation

amino acids.
NH 3 + NH3 +
• Cysteine in the presence of -
OOC CH
H2
C S S
H2
C CH COO-
mild oxidizing agents dimerizes Cystine
to form a cystine molecule.
– Cystine - two cysteine
residues linked via a
covalent disulfide bond.

PROTEINS
Section 20.7
Peptides
Nature of Peptide Bond

• Under proper conditions, amino acids can bond together to produce
an unbranched chain of amino acids.
– The reactions is between amino group of one amino acid and
carboxyl group of another amino acid.
• The length of the amino acid chain can vary from a few amino acids
to hundreds of amino acids.
• Such a chain of covalently-linked amino acids is called a peptide.
• The covalent bonds between amino acids in a peptide are called
peptide bonds (amide).
Peptide
(amide)
H H H O bond H
+
NH 3+ COO- + NH 3 COO- NH 3+ C N COO-
R1 R2 R1 H R2

PROTEINS
Section 20.7
Peptides
• Dipeptide: bond between two amino acids

• Oligopeptide: bond between ~ 10 - 20 amino acids
• Polypeptide: bond between large number of amino acids
• Every peptide has an N-terminal end and a C-terminal end
+H N-aa-aa-aa-aa-aa-aa-aa-aa-aa-COO-
3
OH
N-terminal end
O O CH2 O
+
H H
H 3N CH C N CH C N CH C O-
CH3 CH2 C-terminal end
Alanine Phenylalanine Serine

PROTEINS
Section 20.7
Peptides
Peptide Nomenclature
• The C-terminal amino acid residue keeps its full amino
acid name.
• All of the other amino acid residues have names that end
in -yl. The -yl suffix replaces the -ine or -ic acid ending of
the amino acid name, except for tryptophan, for which -yl
is added to the name.
• The amino acid naming sequence begins at the N-
terminal amino acid residue.
• Example:
– Ala-leu-gly has the IUPAC name of
alanylleucylglycine

PROTEINS
Section 20.7
Peptides
Isomeric Peptides
• Peptides that contain the same amino acids but present
in different order are different molecules (constitutional
isomers) with different properties
– For example, two different dipeptides can be formed
between alanine and glycine
• The number of isomeric peptides possible increases
rapidly as the length of the peptide chain increases
O H O H
+
+
H3 N CH C N CH COO- H3 N CH C N CH COO-
CH 3 H H CH 3
Ala-Gly Gly-Ala

PROTEINS
Section 20.8
Biochemically Important Small Peptides
• Many relatively small peptides are biochemically active:
– Hormones
– Neurotransmitters
– Antioxidants
• Small Peptide Hormones:
– Best-known peptide hormones: oxytocin and vasopressin
– Produced by the pituitary gland
– Nonapeptide (nine amino acid residues) with six of the residues held in
the form of a loop by a disulfide bond formed between two cysteine
residues

PROTEINS
Section 20.8
Small Peptide Neurotransmitters

• Enkephalins are pentapeptide neurotransmitters
produced by the brain and bind receptors within the brain
• Help reduce pain
• Best-known enkephalins:
– Met-enkephalin: Tyr–Gly–Gly–Phe–Met
– Leu-enkephalin: Tyr–Gly–Gly–Phe–Leu

PROTEINS
Section 20.8
Small Peptide Antioxidants

• Glutathione (Glu–Cys–Gly) – a tripeptide – is present is in high levels in
most cells
• Regulator of oxidation–reduction reactions.
• Glutathione is an antioxidant and protects cellular contents from oxidizing
agents such as peroxides and superoxides
– Highly reactive forms of oxygen often generated within the cell in
response to bacterial invasion
• Unusual structural feature – Glu is bonded to Cys through the side-chain
carboxyl group.
O
H2 H2 H H
+
H 3N CH C C C N CH C N CH COO -
COO- O H2 C H
SH
Glu Cys Gly

PROTEINS
Section 20.9
General Structural Characteristics of Proteins
• General definition: A protein is a naturally-occurring, unbranched

polymer in which the monomer units are amino acids.
• Specific definition: A protein is a peptide in which at least 40 amino
acid residues are present:
– The terms polypeptide and protein are often used
interchangeably to describe a protein
– Several proteins with >10,000 amino acid residues are known
– Common proteins contain 400–500 amino acid residues
– Small proteins contain 40–100 amino acid residues
• More than one polypeptide chain may be present in a protein:
– Monomeric : Contains one polypeptide chain
– Multimeric: Contains 2 or polypeptide chains

PROTEINS
Section 20.9
Protein Classification Based on Chemical Composition

• Simple proteins: A protein in which only amino acid residues are
present:
– More than one protein subunit may be present but all subunits
contain only amino acids
• Conjugated (complex) proteins: A protein that has one or more non-
amino acid entities (prosthetic groups) present in its structure:
– One or more polypeptide chains may be present
– Non-amino acid components - may be organic or inorganic -
prosthetic groups
– Lipoproteins contain lipid prosthetic groups
– Glycoproteins contain carbohydrate groups,
– Metalloproteins contain a specific metal as prosthetic group

PROTEINS
Section 20.10
Primary Structure of Proteins
Four Types of Structures

– Primary Structure
– Secondary Structure
– Tertiary Structure
– Quaternary
• Primary Structure: Primary structure of protein refers to
the order in which amino acids are linked together in a
protein
• Every protein has its own unique amino acid sequence
– Frederick Sanger (1953) sequenced and determined
the primary structure for the first protein - Insulin

PROTEINS
Section 20.10
Primary Structure of a
Human Myoglobin

PROTEINS
Section 20.10
• Proteins of the same organism always same sequence.

• Same protein from different sources:, e.g., Insulin from pigs, cows,
sheep, humans, are similar but not identical.
• Some differences:
Species Chain A Chain B
AA #8 AA #9 AA #10 AA #30
Human Thr Ser Ile Thr
Pig (porcine) Thr Ser Ile Ala
Cow (bovin e) Ala Ser Val Ala
• Due to the differences, insulin may show some difference in response

over time.
• Now human insulin produced from genetically engineered bacteria

PROTEINS
Section 20.11
Secondary Structure of Proteins
• Arrangement of atoms of backbone in space.

• The two most common types : alpha-helix (a-helix) and the
beta-pleated sheet (b-pleated sheet).
• The peptide linkages are essentially planar thus allows only
two possible arrangements for the peptide backbone for the
following reasons:
– For two amino acids linked through a peptide bond six
atoms lie in the same plane
– The planar peptide linkage structure has considerable
rigidity, therefore rotation of groups about the C–N bond is
hindered
– Cis–trans isomerism is possible about C–N bond.
– The trans isomer is the preferred orientation

PROTEINS
Section 20.11
Alpha-helix (a-helix)
• A single protein chain
adopts a shape that
resembles a coiled spring
(helix):
– H-bonding between
amino acids with in
the same chain –
intramolecular H-
bonding
– Coiled helical spring
– R-groups stay outside
of the helix -- not
enough room for them
to stay inside

PROTEINS
Section 20.11
Beta-Pleated Sheets
• Completely extended amino acid chains
• H-bonding between two different chains – inter and/or
intramolecular
• Side chains below or above the axis

PROTEINS
Section 20.12
Tertiary Structure of Proteins
• The overall three-dimensional shape of a protein

• Results from the interactions between amino acid side
chains (R groups) that are widely separated from each
other.
• In general 4 types of interactions are observed.
– Disulfide bonding
– Electrostatic interactions
– H-Bonding
– Hydrophobic interactions

PROTEINS
Section 20.12
Four Types of Interactions

• Disulfide bond: covalent, strong, between two cysteine
groups
• Electrostatic interactions: Salt Bridge between charged
side chains of acidic and basic amino acids
– -OH, -NH2, -COOH, -CONH2
• H-Bonding between polar, acidic and/or basic R groups
– For H-bonding to occur, the H must be attached to O,
N or F
• Hydrophobic interactions: Between non-polar side chains

PROTEINS
Section 20.12

PROTEINS
Section 20.13
Quaternary Structure of Proteins
• Quaternary structure of protein refers to the organization

among the various polypeptide chains in a multimeric
protein:
• Highest level of protein organization
• Present only in proteins that have 2 or more
polypeptide chains (subunits)
• Subunits are generally independent of each other -
not covalently bonded
• Proteins with quaternary structure are often referred
to as oligomeric proteins
• Contain even number of subunits

PROTEINS
Section 20.14
Protein Hydrolysis
• Hydrolysis of proteins - reverse of peptide bond

formation:
– Results in the generation of an amine and a
carboxylic acid functional groups.
– Digestion of ingested protein is enzyme-catalyzed
hydrolysis
– Free amino acids produced are absorbed into the
bloodstream and transported to the liver for the
synthesis of new proteins.
– Hydrolysis of cellular proteins and their resynthesis is
a continuous process.

PROTEINS
Section 20.15
Protein Denaturation
• Partial or complete disorganization of protein’s tertiary structure

• Cooking food denatures the protein but does not change protein
nutritional value
• Coagulation: Precipitation (denaturation of proteins)
– Egg white - a concentrated solution of protein albumin - forms a
jelly when heated because the albumin is denatured
• Cooking:
– Denatures proteins – Makes it easy for enzymes in our body to
hydrolyze/digest protein
– Kills microorganisms by denaturation of proteins
– Fever: >104ºF – the critical enzymes of the body start getting
denatured

PROTEINS
Section 20.16
Protein Classification Based on Shape
• Three types of proteins: fibrous, globular, and membrane

• Fibrous proteins: protein molecules with elongated shape:
– Generally insoluble in water
– Single type of secondary structure
– Tend to have simple, regular, linear structures
– Tend to aggregate together to form macromolecular structures, e.g., hair, nails,
etc
• Globular proteins: protein molecules with peptide chains folded into
spherical or globular shapes:
– Generally water soluble – hydrophobic amino acid residues are in the protein
core
– Function as enzymes and intracellular signaling molecules
• Membrane proteins: associated with cell membranes
– Insoluble in water – hydrophobic amino acid residues on the surface
– Help in transport of molecules across the membrane

PROTEINS
Section 20.16
Fibrous Proteins: Alpha-Keratin

• Provide protective coating for organs
• Major protein constituent of hair, feather, nails, horns
and turtle shells
• Mainly made of hydrophobic amino acid residues
• Hardness of keratin depends upon -S-S- bonds
– More –S-S– bonds make nail and bones hard and
hair brittle

PROTEINS
Section 20.16
Fibrous Proteins: Collagen

• Most abundant proteins in humans (30% of total body
protein)
• Major structural material in tendons, ligaments, blood
vessels, and skin
• Organic component of bones and teeth
• Predominant structure - triple helix
• Rich in proline (up to 20%) – important to maintain
structure

PROTEINS
Section 20.16
Globular Proteins: Myoglobin

• Globular Proteins: Myoglobin:
– An oxygen storage molecule in muscles.
– Monomer - single peptide chain with one heme unit
– Binds one O2 molecule
– Has a higher affinity for oxygen than hemoglobin.
– Oxygen stored in myoglobin molecules serves as a
reserve oxygen source for working muscles

PROTEINS
Section 20.16
Globular Proteins: Hemoglobin

• An oxygen carrier molecule in blood
• Transports oxygen from lungs to tissues
• Tetramer (four polypeptide chains) - each subunit has a
heme group
• Can transport up to 4 oxygen molecules at time
• Iron atom in heme interacts with oxygen

PROTEINS
Section 20.17
Protein Classification Based on Function
• Proteins play crucial roles in most biochemical

processes.
• The diversity of functions exhibited by proteins far
exceeds the role of other biochemical molecules
• The functional versatility of proteins stems from:
– Ability to bind small molecules specifically and
strongly
– Ability to bind other proteins and form fiber-like
structures, and
– Ability integrated into cell membranes

PROTEINS
Section 20.17
Major Categories of Proteins Based on Function

• Catalytic proteins: Enzymes are best known for their catalytic role.
– Almost every chemical reaction in the body is driven by an
enzyme
• Defense proteins: Immunoglobulins or antibodies are central to
functioning of the body’s immune system.
• Transport proteins: Bind small biomolecules, e.g., oxygen and other
ligands, and transport them to other locations in the body and
release them on demand.
• Messenger proteins: transmit signals to coordinate biochemical
processes between different cells, tissues, and organs.
– Insulin and glucagon - regulate carbohydrate metabolism
– Human growth hormone – regulate body growth

PROTEINS
Section 20.17

• Contractile proteins: Necessary for all forms of movement.
– Muscles contain filament-like contractile proteins (actin and
myosin).
– Human reproduction depends on the movement of sperm –
possible because of contractile proteins.
• Structural proteins: Confer stiffness and rigidity
– Collagen is a component of cartilage a
– Keratin gives mechanical strength as well as protective covering
to hair, fingernails, feathers, hooves, etc.
• Transmembrane proteins: Span a cell membrane and help control
the movement of small molecules and ions.
– Have channels – help molecules to enter and exist the cell.
– Transport is very selective - allow passage of one type of
molecule or ion.
PROTEINS
Section 20.17

• Storage proteins: Bind (and store) small molecules.
– Ferritin - an iron-storage protein - saves iron for use in the
biosynthesis of new hemoglobin molecules.
– Myoglobin - an oxygen-storage protein present in muscle
• Regulatory proteins: Often found “embedded” in the exterior surface
of cell membranes - act as sites for receptor molecules
– Often the molecules that bind to enzymes (catalytic proteins),
thereby turning them “on” and “off,” and thus controlling
enzymatic action.
• Nutrient proteins: Particularly important in the early stages of life -
from embryo to infant.
– Casein (milk) and ovalalbumin (egg white) are nutrient proteins
– Milk also provide immunological protection for mammalian
young.
PROTEINS
Section 20.18
Glycoproteins
• Conjugated proteins with carbohydrates linked to them:

– Many of plasma membrane proteins are glycoproteins
– Blood group markers of the ABO system are also glycoproteins
– Collagen and immunoglobulins are glycoproteins
• Collagen -- glycoprotein
– Most abundant protein in human body (30% of total body
protein)
– Triple helix structure
– Rich in 4-hydroxyproline (5%) and 5-hydroxylysine (1%) —
derivatives
– Some hydroxylysines are linked to glucose, galactose, and their
disaccharides – help in aggregation of collagen fibrils.

PROTEINS
Section 20.18
Glycoproteins
Immunoglobulins
• Glycoproteins produced as a protective response to the
invasion of microorganisms or foreign molecules -
antibodies against antigens.
• Immunoglobulin bonding to an antigen via variable
region of an immunoglobulin occurs through hydrophobic
interactions, dipole – dipole interactions, and hydrogen
bonds.

PROTEINS
Section 20.19
Lipoproteins
• Lipoprotein: a conjugated protein that contains lipids in addition to

amino acids
• Major function - help suspend lipids and transport them through the
bloodstream
• Four major classes of plasma lipoproteins:
– Chylomicrons: Transport dietary triacylglycerols from intestine
to liver and to adipose tissue.
– Very-low-density lipoproteins (VLDL): Transport triacylglycerols
synthesized in the liver to adipose tissue.
– Low-density lipoproteins (LDL): Transport cholesterol
synthesized in the liver to cells throughout the body.
– High-density lipoproteins (HDL): Collect excess cholesterol from
body tissues and transport it back to the liver for degradation to
bile acids.

Cell membrane => controls the entry and exit of certain substances@
Cytoskeleton => gives the cell its shape ###
Lysosomes => serves as recycling centers for redundant and damaged organelles@
Nucleus => acts as a control center that directs all the activities of a cell @
Nucleolus => synthesizes ribosomal RNA@
Golgi Apparatus => receives, stores, modifies, and packages proteins and lipids arriving
from the RER and SER@
Rough Endoplasmic Reticulum => synthesizes protein
Smooth Endoplasmic Reticulum => synthesizes lipids
Mitochondria => provides energy a cell needs for all its activities
Vacuoles => removes excess water and some wastes from the cell
Question 2
Choose "True" if the statement is correct. If otherwise, change the underlined word/s to make the statement correct.
Vacuoles supply energy to the cell.
False, Mitochondria
Question 3
The presence of ribosome differentiates smooth from rough endoplasmic reticulum.
True
Question 4
Friedrich Wohler disproved the vitalism belief by synthesizing urea from ammonium cyanate.
True
Question 5
The term "biochemistry" was coined by Carl Alexander Neuberg in 1903.
True
Question 6
Karl Mullis discovered the double helix structure of DNA.
False, Francis Crick and James Watson SALA ******
Question 7
Which of the following is the main function of the Golgi Body?
Process and deliver proteins
Question 8
A cell with relatively few energy needs will probably have a relatively small number of
__________.
Mitochondria
Question 9
The organelle which acts as the centers of cellular respiration is called _________.
Mitochondria
Question 10
These scientists proved that organic molecules formed from inorganic molecules
present in the Earth’s early atmosphere when given energy from lightening.
Milley and Urey
Question 11
This bacteria formed 3.5 billion years ago and was photosynthetic and release oxygen
into the atmosphere.
Cyanobacteria
TEST 2
Question 1
Choose "YES" if the given organelle is present in a prokaryotic cell, and choose "NO" if
otherwise.
cell wall => YES
centrioles => NO
mitochondria => NO
nucleus => NO
ribosomes => YES
Question 2
Choose "YES" if the given organelle is present in a typical animal eukaryotic cell, and
choose "NO" if otherwise.
cell wall => No
centrioles => YES
mitochondria => YES
nucleus => YES
ribosomes => YES
Question 3
The more electronegative an atom, the more strongly it pulls shared electrons toward itself.
True
Question 4
Water is a linear molecule.
False, Bent
Question 5
Ionic compounds with full charges tend to dissolve in water.
True
Question 6
Carbon dioxide is a polar molecule.
False, Nonpolar
Question 7
Hydrogen bonding are responsible for the formation of solids.
False, London dispersion forces
Question 8
Which of the following structures would be found in a plant cell but not in a bacterial cell?
Mitichondria
Question 9
A hydrogen bond is a special case of what type of intermolecular force?
dipole-dipole interaction
Question 10
Why can water have no net charge but have slight charges in different parts of the
molecule?
The oxygen end is slightly negative and the hydrogen end is slightly positive.
Question 11
Potassium chloride dissolved in water is an example of what type of intermolecular
force?
ion-dipole interaction
Question 12
The Henderson-Hasselbalch equation:
relates the pH of a solution to the pKa and the concentrations of acid and conjugate
base.
Question 1
Match the organelles in COLUMN A to their functions in COLUMN B.
Response: Cell membrane => controls the entry and exit of certain
substances
Response: Cytoskeleton => gives the cell its shape
Response: Lysosomes => serves as recycling centers for redundant and

damaged organelles
Response: Nucleus => acts as a control center that directs all the activities of
a cell
Response: Nucleolus => synthesizes ribosomal RNA
Response: Golgi Apparatus => receives, stores, modifies, and packages

proteins and lipids arriving from the RER and SER
Response: Rough Endoplasmic Reticulum => synthesizes protein
Response: Smooth Endoplasmic Reticulum => synthesizes lipids
Response: Mitochondria => provides energy a cell needs for all its activities
Response: Vacuoles => removes excess water and some wastes from the cell
Score: 10 out of 10 Yes
Question 2
Response: False, Mitochondria
Question 3

Response: True
Question 4
Response: True
Question 5
Response: True
Question 6
Response: False, Watson and Crick
Question 7
Response: Process and deliver proteins
Question 8
A cell with relatively few energy needs will probably have a relatively small
number of __________.
Response: Mitochondria
Question 9
The organelle which acts as the centers of cellular respiration is called
_________.
Question 10
These scientists proved that organic molecules formed from inorganic
molecules present in the Earth’s early atmosphere when given energy from
lightening.
Response: Milley and Urey
Question 11
This bacteria formed 3.5 billion years ago and was photosynthetic and
release oxygen into the atmosphere.
Response: Cyanobacteria
Score: 1 out of 1
Question 1
Choose "YES" if the given organelle is present in a prokaryotic cell, and
Response: cell wall => YES
Response: centrioles => NO
Response: mitochondria => NO
Response: nucleus => NO

Response: ribosomes => YES
Question 2
Choose "YES" if the given organelle is present in a typical animal eukaryotic
cell, and choose "NO" if otherwise.
Response: cell wall => NO
Response: centrioles => YES
Response: mitochondria => YES
Response: nucleus => YES
Question 3
Response: True
Question 4
Response: False, Bent
Question 5
Response: True
Question 6
Response: False, Nonpolar
Question 7
Response: False, London dispersion forces
Question 8
Which of the following structures would be found in a plant cell but not in
a bacterial cell?
Question 9
Response: dipole-dipole interaction
Question 10
Why can water have no net charge but have slight charges in different
parts of the molecule?
Response: The oxygen end is slightly negative and the hydrogen end is
slightly positive.
Question 11
Potassium chloride dissolved in water is an example of what type of
intermolecular force?
Response: Ion-dipole interaction
Question 12
Response: relates the pH of a solution to the pKa and the concentrations of

acid and conjugate base.
Score: 1 out of 1
MARCH 2022
Chapter 20
PROTEINS
Proteins
BIOCHEMISTRY
PROTEINS
Section 20.1
Characteristics of Proteins
• A protein is a naturally-occurring, unbranched polymer in

which the monomer units are amino acids
• Proteins are most abundant molecules in the cells after
water – account for about 15% of a cell’s overall mass
• Elemental composition - Contain Carbon (C), Hydrogen
(H), Nitrogen (N), Oxygen (O), and Sulfur (S)
• The average nitrogen content of proteins is 15.4% by
mass
• Also present are Iron (Fe), phosphorus (P) and some
other metals in some specialized proteins

PROTEINS
Section 20.2
• Amino acid - An organic compound that contains both an amino (-NH2) and
a carboxyl (-COOH) group attached to same carbon atom
– The position of carbon atom is Alpha (a)
– -NH2 group is attached at alpha (a) carbon atom.
– -COOH group is attached at alpha (a) carbon atom.
– R = side chain –vary in size, shape, charge, acidity, functional groups
present, hydrogen-bonding ability, and chemical reactivity.
– >700 amino acids are known
– Based on common “R” groups, there are 20 standard amino acids
Side Chain
R a -Carbon Atom
H2N C COOH
a-Carboxyl
a-Amino H Group
Group

PROTEINS
Section 20.2
• All amino acids differ from one another by their R-groups

– There are 20 common (standard) amino acids
• Standard amino acids are divided into four groups based
on the properties of R-groups
• Non-polar amino acids: R-groups are non-polar
– Such amino acids are hydrophobic-water fearing
(insoluble in water)
– 8 of the 20 standard amino acids are non polar
– When present in proteins, they are located in the
interior of protein where there is no polarity

PROTEINS
Section 20.2
• Polar amino acids: R-groups are polar

– Three types: Polar neutral; Polar acidic; and Polar
basic
• Polar-neutral: contains polar but neutral side chains
– Seven amino acids belong to this category
• Polar acidic: Contain carboxyl group as part of the side
chains
• Polar basic: Contain amino group as part of the side
chain
PROTEINS
Section 20.2
Nomenclature
• Common names assigned to the amino acids are currently used.
• Three letter abbreviations - widely used for naming:
– First letter of amino acid name is compulsory and capitalized
followed by next two letters not capitalized except in the case of
Asparagine (Asn), Glutamine (Gln) and tryptophan (Trp).
• One-letter symbols - commonly used for comparing amino acid
sequences of proteins:
– Usually the first letter of the name
– When more than one amino acid has the same letter the most
abundant amino acid gets the 1st letter.
• Both types of abbreviations are given in the following slides

PROTEINS
Section 20.2
Non-Polar Amino Acids

PROTEINS
Section 20.2
Polar Neutral Amino Acids

PROTEINS
Section 20.2
Polar Acidic and Basic Amino Acids

PROTEINS
Section 20.2
Practice Exercise

PROTEINS
Section 20.2
Practice Exercise
Non-polar
Non-polar
Polar Neutral
Polar Basic
Polar Acidic

PROTEINS
Section 20.3
• Essential Amino acid: A standard amino acid needed for

protein synthesis that must be obtained from dietary
sources – adequate amounts cannot be synthesized in
human body.
• Nine of the 20 standard amino acids are considered
essential
Lysine Methionine
Histidine Phenylalanine
Isoleucine Threonine
Leucine Tryptophan
*Required for growth in children
Valine and is not essential for adults.

PROTEINS
Section 20.4
• Four different groups are attached to the a-carbon atom

in all of the standard amino acids except glycine
– In glycine R-group is hydrogen
• Therefore 19 of the 20 standard amino acids contain a
chiral center
• Molecules with chiral centers exhibit enantiomerism (left-
and right-handed forms)

PROTEINS
Section 20.4
• The amino acids found in nature as well

as in proteins are L isomers.
– Bacteria do have some D-amino acids
– With monosaccharides nature favors
D-isomers
• The rules for drawing Fischer projection
formulas for amino acid structures
– The — COOH group is put at the top,
– The R group is place at the bottom
position of the carbon chain vertically
– The — NH2 group is placed in a
horizontal position.
– Positioning — NH2 on the left - L
isomer Designation of Mirror
– Positioning — NH2 on the right - D handedness in standard amino
acid structures
isomer.

PROTEINS
Section 20.4
Practice Exercise
A B C
COOH COOH COOH
*C H2N *C H
H 2N H H *C NH2
CH CH3 CH2 CH2
CH2 SH
CH3
OH

PROTEINS
Section 20.4
Practice Exercise
A B C
COOH COOH COOH
*C H2N *C H
H 2N H H *C NH2
CH CH3 CH2 CH2
CH2 SH
CH3
OH
A = L-Isoleucine
B = D-Cysteine
C = L-Tyrosine
PROTEINS
Section 20.5
• In pure form amino acids are white crystalline solids

• Most amino acids decompose before they melt
• Not very soluble in water
• Under physiological conditions exists as Zwitterions: An ion with +
(positive) and – (Negative) charges on the same molecule with a net
zero charge
– Carboxyl groups give-up a proton to get negative charge
– Amino groups accept a proton to become positive
Net charge = Zero Net charge = Zero
COO- COO-
NH 3+ H NH 3+ H
R CH 3
L-Amino acid L-Alanine

(general)
Zwitterions Carry Net Zero Charge

PROTEINS
Section 20.5
Isoelectric Point (pI)

• Amino acids in solution exist in three different species (zwitterions,
positive ion, and negative ion) - Equilibrium shifts with change in pH
• Isoelectric point (pI) – pH at which the concentration of Zwitterion is
maximum -- net charge is zero
– Different amino acids have different isoelectric points
– At isoelectric point - amino acids are not attracted towards an
applied electric field because they carry net zero charge.
COOH COO- COO-
+
+
H3N C H H3N C H H2N C H
CH3 CH3 CH3

Low pH High pH
Zwitter Ion (net - charge)
(net + charge) (net neutral charge)
Neutral pH

PROTEINS
Section 20.6
Cysteine: A Chemically Unique Amino Acid
• Cysteine: the only standard

amino acid with a sulfhydryl
group ( — SH group). NH 3 + NH3 +
• The sulfhydryl group imparts -OOC CH

H2
C SH HS
H2
C CH COO-
cysteine a chemical property Cysteine Cysteine
unique among the standard Oxidation

amino acids.
NH 3 + NH3 +
• Cysteine in the presence of -
OOC CH
H2
C S S
H2
C CH COO-
mild oxidizing agents dimerizes Cystine
to form a cystine molecule.
– Cystine - two cysteine
residues linked via a
covalent disulfide bond.

PROTEINS
Section 20.7
Peptides
Nature of Peptide Bond

• Under proper conditions, amino acids can bond together to produce
an unbranched chain of amino acids.
– The reactions is between amino group of one amino acid and
carboxyl group of another amino acid.
• The length of the amino acid chain can vary from a few amino acids
to hundreds of amino acids.
• Such a chain of covalently-linked amino acids is called a peptide.
• The covalent bonds between amino acids in a peptide are called
peptide bonds (amide).
Peptide
(amide)
H H H O bond H
+
NH 3+ COO- + NH 3 COO- NH 3+ C N COO-
R1 R2 R1 H R2

PROTEINS
Section 20.7
Peptides
• Dipeptide: bond between two amino acids

• Oligopeptide: bond between ~ 10 - 20 amino acids
• Polypeptide: bond between large number of amino acids
• Every peptide has an N-terminal end and a C-terminal end
+H N-aa-aa-aa-aa-aa-aa-aa-aa-aa-COO-
3
OH
N-terminal end
O O CH2 O
+
H H
H 3N CH C N CH C N CH C O-
CH3 CH2 C-terminal end
Alanine Phenylalanine Serine

PROTEINS
Section 20.7
Peptides
Peptide Nomenclature
• The C-terminal amino acid residue keeps its full amino
acid name.
• All of the other amino acid residues have names that end
in -yl. The -yl suffix replaces the -ine or -ic acid ending of
the amino acid name, except for tryptophan, for which -yl
is added to the name.
• The amino acid naming sequence begins at the N-
terminal amino acid residue.
• Example:
– Ala-leu-gly has the IUPAC name of
alanylleucylglycine

PROTEINS
Section 20.7
Peptides
Isomeric Peptides
• Peptides that contain the same amino acids but present
in different order are different molecules (constitutional
isomers) with different properties
– For example, two different dipeptides can be formed
between alanine and glycine
• The number of isomeric peptides possible increases
rapidly as the length of the peptide chain increases
O H O H
+
+
H3 N CH C N CH COO- H3 N CH C N CH COO-
CH 3 H H CH 3
Ala-Gly Gly-Ala

PROTEINS
Section 20.8
• Many relatively small peptides are biochemically active:
– Hormones
– Neurotransmitters
– Antioxidants
• Small Peptide Hormones:
– Best-known peptide hormones: oxytocin and vasopressin
– Produced by the pituitary gland
– Nonapeptide (nine amino acid residues) with six of the residues held in
the form of a loop by a disulfide bond formed between two cysteine
residues

PROTEINS
Section 20.8

• Enkephalins are pentapeptide neurotransmitters
produced by the brain and bind receptors within the brain
• Help reduce pain
• Best-known enkephalins:
– Met-enkephalin: Tyr–Gly–Gly–Phe–Met
– Leu-enkephalin: Tyr–Gly–Gly–Phe–Leu

PROTEINS
Section 20.8
Small Peptide Antioxidants

• Glutathione (Glu–Cys–Gly) – a tripeptide – is present is in high levels in
most cells
• Regulator of oxidation–reduction reactions.
• Glutathione is an antioxidant and protects cellular contents from oxidizing
agents such as peroxides and superoxides
– Highly reactive forms of oxygen often generated within the cell in
response to bacterial invasion
• Unusual structural feature – Glu is bonded to Cys through the side-chain
carboxyl group.
O
H2 H2 H H
+
H 3N CH C C C N CH C N CH COO -
COO- O H2 C H
SH
Glu Cys Gly

PROTEINS
Section 20.9
• General definition: A protein is a naturally-occurring, unbranched

polymer in which the monomer units are amino acids.
• Specific definition: A protein is a peptide in which at least 40 amino
acid residues are present:
– The terms polypeptide and protein are often used
interchangeably to describe a protein
– Several proteins with >10,000 amino acid residues are known
– Common proteins contain 400–500 amino acid residues
– Small proteins contain 40–100 amino acid residues
• More than one polypeptide chain may be present in a protein:
– Monomeric : Contains one polypeptide chain
– Multimeric: Contains 2 or polypeptide chains

PROTEINS
Section 20.9
Protein Classification Based on Chemical Composition

• Simple proteins: A protein in which only amino acid residues are
present:
– More than one protein subunit may be present but all subunits
contain only amino acids
• Conjugated (complex) proteins: A protein that has one or more non-
amino acid entities (prosthetic groups) present in its structure:
– One or more polypeptide chains may be present
– Non-amino acid components - may be organic or inorganic -
prosthetic groups
– Lipoproteins contain lipid prosthetic groups
– Glycoproteins contain carbohydrate groups,
– Metalloproteins contain a specific metal as prosthetic group

PROTEINS
Section 20.10
Four Types of Structures

– Primary Structure
– Secondary Structure
– Tertiary Structure
– Quaternary
• Primary Structure: Primary structure of protein refers to
the order in which amino acids are linked together in a
protein
• Every protein has its own unique amino acid sequence
– Frederick Sanger (1953) sequenced and determined
the primary structure for the first protein - Insulin

PROTEINS
Section 20.10
Primary Structure of a
Human Myoglobin

PROTEINS
Section 20.10
• Proteins of the same organism always same sequence.

• Same protein from different sources:, e.g., Insulin from pigs, cows,
sheep, humans, are similar but not identical.
• Some differences:
Species Chain A Chain B
AA #8 AA #9 AA #10 AA #30
Human Thr Ser Ile Thr
Pig (porcine) Thr Ser Ile Ala
Cow (bovin e) Ala Ser Val Ala
• Due to the differences, insulin may show some difference in response

over time.
• Now human insulin produced from genetically engineered bacteria

PROTEINS
Section 20.11
• Arrangement of atoms of backbone in space.

• The two most common types : alpha-helix (a-helix) and the
beta-pleated sheet (b-pleated sheet).
• The peptide linkages are essentially planar thus allows only
two possible arrangements for the peptide backbone for the
following reasons:
– For two amino acids linked through a peptide bond six
atoms lie in the same plane
– The planar peptide linkage structure has considerable
rigidity, therefore rotation of groups about the C–N bond is
hindered
– Cis–trans isomerism is possible about C–N bond.
– The trans isomer is the preferred orientation

PROTEINS
Section 20.11
Alpha-helix (a-helix)
• A single protein chain
adopts a shape that
resembles a coiled spring
(helix):
– H-bonding between
amino acids with in
the same chain –
intramolecular H-
bonding
– Coiled helical spring
– R-groups stay outside
of the helix -- not
enough room for them
to stay inside

PROTEINS
Section 20.11
Beta-Pleated Sheets
• Completely extended amino acid chains
• H-bonding between two different chains – inter and/or
intramolecular
• Side chains below or above the axis

PROTEINS
Section 20.12
• The overall three-dimensional shape of a protein

• Results from the interactions between amino acid side
chains (R groups) that are widely separated from each
other.
• In general 4 types of interactions are observed.
– Disulfide bonding
– Electrostatic interactions
– H-Bonding
– Hydrophobic interactions

PROTEINS
Section 20.12

• Disulfide bond: covalent, strong, between two cysteine
groups
• Electrostatic interactions: Salt Bridge between charged
side chains of acidic and basic amino acids
– -OH, -NH2, -COOH, -CONH2
• H-Bonding between polar, acidic and/or basic R groups
– For H-bonding to occur, the H must be attached to O,
N or F
• Hydrophobic interactions: Between non-polar side chains

PROTEINS
Section 20.12

PROTEINS
Section 20.13
Quaternary Structure of Proteins
• Quaternary structure of protein refers to the organization

among the various polypeptide chains in a multimeric
protein:
• Highest level of protein organization
• Present only in proteins that have 2 or more
polypeptide chains (subunits)
• Subunits are generally independent of each other -
not covalently bonded
• Proteins with quaternary structure are often referred
to as oligomeric proteins
• Contain even number of subunits

PROTEINS
Section 20.14
Protein Hydrolysis
• Hydrolysis of proteins - reverse of peptide bond

formation:
– Results in the generation of an amine and a
carboxylic acid functional groups.
– Digestion of ingested protein is enzyme-catalyzed
hydrolysis
– Free amino acids produced are absorbed into the
bloodstream and transported to the liver for the
synthesis of new proteins.
– Hydrolysis of cellular proteins and their resynthesis is
a continuous process.

PROTEINS
Section 20.15
Protein Denaturation
• Partial or complete disorganization of protein’s tertiary structure

• Cooking food denatures the protein but does not change protein
nutritional value
• Coagulation: Precipitation (denaturation of proteins)
– Egg white - a concentrated solution of protein albumin - forms a
jelly when heated because the albumin is denatured
• Cooking:
– Denatures proteins – Makes it easy for enzymes in our body to
hydrolyze/digest protein
– Kills microorganisms by denaturation of proteins
– Fever: >104ºF – the critical enzymes of the body start getting
denatured

PROTEINS
Section 20.16
• Three types of proteins: fibrous, globular, and membrane

• Fibrous proteins: protein molecules with elongated shape:
– Generally insoluble in water
– Single type of secondary structure
– Tend to have simple, regular, linear structures
– Tend to aggregate together to form macromolecular structures, e.g., hair, nails,
etc
• Globular proteins: protein molecules with peptide chains folded into
spherical or globular shapes:
– Generally water soluble – hydrophobic amino acid residues are in the protein
core
– Function as enzymes and intracellular signaling molecules
• Membrane proteins: associated with cell membranes
– Insoluble in water – hydrophobic amino acid residues on the surface
– Help in transport of molecules across the membrane

PROTEINS
Section 20.16
Fibrous Proteins: Alpha-Keratin

• Provide protective coating for organs
• Major protein constituent of hair, feather, nails, horns
and turtle shells
• Mainly made of hydrophobic amino acid residues
• Hardness of keratin depends upon -S-S- bonds
– More –S-S– bonds make nail and bones hard and
hair brittle

PROTEINS
Section 20.16
Fibrous Proteins: Collagen

• Most abundant proteins in humans (30% of total body
protein)
• Major structural material in tendons, ligaments, blood
vessels, and skin
• Organic component of bones and teeth
• Predominant structure - triple helix
• Rich in proline (up to 20%) – important to maintain
structure

PROTEINS
Section 20.16
Globular Proteins: Myoglobin

• Globular Proteins: Myoglobin:
– An oxygen storage molecule in muscles.
– Monomer - single peptide chain with one heme unit
– Binds one O2 molecule
– Has a higher affinity for oxygen than hemoglobin.
– Oxygen stored in myoglobin molecules serves as a
reserve oxygen source for working muscles

PROTEINS
Section 20.16
Globular Proteins: Hemoglobin

• An oxygen carrier molecule in blood
• Transports oxygen from lungs to tissues
• Tetramer (four polypeptide chains) - each subunit has a
heme group
• Can transport up to 4 oxygen molecules at time
• Iron atom in heme interacts with oxygen

PROTEINS
Section 20.17
• Proteins play crucial roles in most biochemical

processes.
• The diversity of functions exhibited by proteins far
exceeds the role of other biochemical molecules
• The functional versatility of proteins stems from:
– Ability to bind small molecules specifically and
strongly
– Ability to bind other proteins and form fiber-like
structures, and
– Ability integrated into cell membranes

PROTEINS
Section 20.17

• Catalytic proteins: Enzymes are best known for their catalytic role.
– Almost every chemical reaction in the body is driven by an
enzyme
• Defense proteins: Immunoglobulins or antibodies are central to
functioning of the body’s immune system.
• Transport proteins: Bind small biomolecules, e.g., oxygen and other
ligands, and transport them to other locations in the body and
release them on demand.
• Messenger proteins: transmit signals to coordinate biochemical
processes between different cells, tissues, and organs.
– Insulin and glucagon - regulate carbohydrate metabolism
– Human growth hormone – regulate body growth

PROTEINS
Section 20.17

• Contractile proteins: Necessary for all forms of movement.
– Muscles contain filament-like contractile proteins (actin and
myosin).
– Human reproduction depends on the movement of sperm –
possible because of contractile proteins.
• Structural proteins: Confer stiffness and rigidity
– Collagen is a component of cartilage a
– Keratin gives mechanical strength as well as protective covering
to hair, fingernails, feathers, hooves, etc.
• Transmembrane proteins: Span a cell membrane and help control
the movement of small molecules and ions.
– Have channels – help molecules to enter and exist the cell.
– Transport is very selective - allow passage of one type of
molecule or ion.
PROTEINS
Section 20.17

• Storage proteins: Bind (and store) small molecules.
– Ferritin - an iron-storage protein - saves iron for use in the
biosynthesis of new hemoglobin molecules.
– Myoglobin - an oxygen-storage protein present in muscle
• Regulatory proteins: Often found “embedded” in the exterior surface
of cell membranes - act as sites for receptor molecules
– Often the molecules that bind to enzymes (catalytic proteins),
thereby turning them “on” and “off,” and thus controlling
enzymatic action.
• Nutrient proteins: Particularly important in the early stages of life -
from embryo to infant.
– Casein (milk) and ovalalbumin (egg white) are nutrient proteins
– Milk also provide immunological protection for mammalian
young.
PROTEINS
Section 20.18
Glycoproteins
• Conjugated proteins with carbohydrates linked to them:

– Many of plasma membrane proteins are glycoproteins
– Blood group markers of the ABO system are also glycoproteins
– Collagen and immunoglobulins are glycoproteins
• Collagen -- glycoprotein
– Most abundant protein in human body (30% of total body
protein)
– Triple helix structure
– Rich in 4-hydroxyproline (5%) and 5-hydroxylysine (1%) —
derivatives
– Some hydroxylysines are linked to glucose, galactose, and their
disaccharides – help in aggregation of collagen fibrils.

PROTEINS
Section 20.18
Glycoproteins
Immunoglobulins
• Glycoproteins produced as a protective response to the
invasion of microorganisms or foreign molecules -
antibodies against antigens.
• Immunoglobulin bonding to an antigen via variable
region of an immunoglobulin occurs through hydrophobic
interactions, dipole – dipole interactions, and hydrogen
bonds.

PROTEINS
Section 20.19
Lipoproteins
• Lipoprotein: a conjugated protein that contains lipids in addition to

amino acids
• Major function - help suspend lipids and transport them through the
bloodstream
• Four major classes of plasma lipoproteins:
– Chylomicrons: Transport dietary triacylglycerols from intestine
to liver and to adipose tissue.
– Very-low-density lipoproteins (VLDL): Transport triacylglycerols
synthesized in the liver to adipose tissue.
– Low-density lipoproteins (LDL): Transport cholesterol
synthesized in the liver to cells throughout the body.
– High-density lipoproteins (HDL): Collect excess cholesterol from
body tissues and transport it back to the liver for degradation to
bile acids.

MARCH 2022
CARBOHYDRATES
Carbohydrates
BIOCHEMISTRY
CARBOHYDRATES
CARBOHYDRATES
Section 18.2
Carbohydrates
CARBOHYDRATES
CARBOHYDRATES
Section 18.2
Carbohydrates
• Most of the matter in plants, except water, is
carbohydrate material.
• Carbohydrates account for 75% of dry plant material
and are produced by photosynthesis.
– Cellulose: structural element.
– Starch/glycogen: energy reservoir.
- small amount in human body.
• Plant products are source of carbohydrates.
- Average human diet contains 2/3 of carbohydrates.
CARBOHYDRATES
Section 18.2
Photosynthesis
• A process in which plants produce carbohydrates using
carbon dioxide, water and solar energy.
Chlorophyll
CO2 + H2O + Solar Energy Carbohydrates + O2
Plant Enzymes

CARBOHYDRATES
Section 18.2
Functions of Carbohydrates in the Human Body

• Carbohydrate oxidation - provides energy
• Carbohydrate storage, in the form of glycogen, provides a
short-term energy reserve
• Carbohydrates supply carbon atoms for the synthesis of other
biochemical substances (proteins, lipids, and nucleic acids)
• Carbohydrates form part of the structural framework of DNA
and RNA molecules
• Carbohydrates linked to lipids are structural components of
cell membranes
• Carbohydrates linked to proteins function in a variety of cell–
cell and cell–molecule recognition processes

CARBOHYDRATES
Section 18.3
• Simpler Formula:
– CnH2nOn or Cn(H2O)n (hydrates of C).
– n= number of atoms.
• Carbohydrates are polyhydroxy aldehydes or ketones or
compounds that produce such substances upon
hydrolysis.

CARBOHYDRATES
Section 18.3
Monosaccharide
• Contain single polyhydroxy aldehyde or ketone unit
• They can’t be broken down into simpler substances by
hydrolysis (reaction with water) reactions
• Contains 3-7 C atoms
• 5 and 6 carbon species are more common
• Water soluble white crystalline solids

CARBOHYDRATES
Section 18.3
Oligosaccharides
• Contains 2-10 monosaccharide units - covalently bonded
to each other
• Free oligosaccharides are less common in nature
• Usually found associated with proteins and lipids in
complex molecules.
– Serve structural and regulatory functions

CARBOHYDRATES
Section 18.3
Disaccharides
• Contains 2 monosaccharide units covalently bonded to
each other.
• Disaccharides are crystalline and water soluble
substances
• Table sugar (sucrose) and milk sugar (lactose) are
common disaccharides
• Upon hydrolysis they produce monosaccharides

CARBOHYDRATES
Section 18.3
Polysaccharides
• Contains many monosaccharide units covalently bonded
• Polymers: May contain a few 100s to > million
monosaccharide units
• Examples:
• Cellulose: Paper, cotton, wood
• Starch: Bread, pasta, potatoes, rice, corn, beans,
peas, etc.

CARBOHYDRATES
Section 18.4
Objects and handedness
• Most biological molecules,

including carbohydrates,
exhibit the property of
“handedness” (isomerism)
• Most monosaccharides exist
in two forms: a “left handed”
and “right handed” form -
same as two hands that are
“mirror images” of each other.

CARBOHYDRATES
Section 18.4
Mirror Images
• Mirror Image: the reflection of an
object in a mirror
• Two types of objects:
- Superimposable mirror images:
Images that coincide at all
points when the images are
laid upon each other -- Achiral
- Non-superimposable mirror
images: Images where not all
points coincide when the
images are laid upon each
other -- Chiral (handedness)

CARBOHYDRATES
Section 18.4
Chirality
• Chiral Center: C atom attached to 4 different groups
• A molecule with chiral center is a chiral molecule
– Best way to visualize - look at all C atoms and see if there are at
least two H atoms then that can’t be a chiral center
– C atoms with less than one H atoms are worth looking at for
their chirality.
• Be careful as a C atom may apparently look similar but may not
have four DIFFERENT groups.
– E. g. 3-bromopentane – has no chiral carbons, whereas
bromochloroiodomethane has a chiral carbon.
– A chiral C is usually denoted by *

CARBOHYDRATES
Section 18.4
Practice Exercise
Indicate whether the circled carbon atom in each of the
following molecules is a chiral center.
Answers:
a. Not a chiral center
b. Not a chiral center
c. Chiral center
d. Not a chiral center
CARBOHYDRATES
Section 18.4
Responses of Left and Right Handed Forms of a Molecule in a
Human Body
– Both may be active, one may be more active or one

may be active and other non-active
– Example: Right handed hormone epinephrine is 20
times more active than left handed form
– Almost all monosaccharides are right handed
– Amino acids are almost always left handed

CARBOHYDRATES
Section 18.5
Stereoisomers
• Stereoisomers are isomers that have the same molecular and
structural formulas but differ in the orientation of atoms in space.
• Two types:
– Enantiomers: stereoisomers whose molecules are non-
superimposable mirror images of each other. Molecules with
chiral center.
– Diastereomers: stereoisomers whose molecules are not mirror
images of each other. Cis-Trans isomers

CARBOHYDRATES
Section 18.5

CARBOHYDRATES
Section 18.6

• Fischer projection formula: - A two-dimensional structural
notation for showing the spatial arrangement of groups
about chiral centers in molecules.
• In a Fischer projection formula a chiral center (Carbon) is
represented as the intersection of vertical and horizontal
lines
• Functional groups of high priority will be written at top
CHO CHO
H OH HO H
CH2OH CH2OH
D-Glyceroldehyde L-Glyceroldehyde
(-OH on right side) (-OH on left side)

CARBOHYDRATES
Section 18.6

• We now consider Fischer projection formulas for the
compound 2,3,4-trihydroxybutanal - a monosaccharide
with four carbons and two chiral centers
• There are four stereoisomers for this compound—two
pairs of enantiomers

CARBOHYDRATES
Section 18.6

• The D,L system used to designate the handedness of
glyceraldehyde enantiomers can be extended to other
monosaccharides with more than one chiral center
• The carbon chain is numbered starting at the carbonyl group end of
the molecule, and the highest-numbered chiral center is used to
determine D or L configuration
• Epimers: Diastereomers whose molecules differ only in the
configuration at one chiral center

CARBOHYDRATES
Section 18.7
Constitutional Isomers and Diastereomers

• Constitutional isomers differ in most chemical and
physical properties -- they have different boiling points
and melting points.
• Diastereomers also differ in most chemical and physical
properties --They too have different boiling points and
freezing points.
• In contrast, nearly all the properties of a pair of
enantiomers have the same chemical and physical
properties
– Two differences:
1. Their interaction with plane polarized light
2. Their interaction with other chiral substances
CARBOHYDRATES
Section 18.7
Interaction of Enantiomers with

Plane-Polarized Light
• Properties of light
– Ordinary Light: Move in all directions
– Plane polarized light move only in
one direction (see Figure on right
side)
• Plane polarized light is rotated clockwise
(to right) or counterclockwise (to left)
when passed through enantiomers
• Direction and extent of rotation will
depend upon the enantiomer
• Same concentration of two enantiomers
rotate light to same extent but in opposite
direction

CARBOHYDRATES
Section 18.7
Interaction of Enantiomers with Plane-Polarized Light

CARBOHYDRATES
Section 18.7
Dextrorotary and Levorotatory Compounds

• Enantiomers are optically active: Compounds that rotate plane
polarized light
• Two Types:
– Dextrorotatory:
• Chiral compound that rotates light towards right (clockwise; +)
• (+)-glucose - dextrorotatory – to the right - clockwise
– Levorotatory:
• Chiral compound that rotates light towards left
(counterclockwise; -)
• (-)-glucose - levorotatory – to the left - counterclockwise
– There is no correlation between D, L and +, -
• In D and L system you need to look at the structure
• + and – can be determined using a polarimeter
CARBOHYDRATES
Section 18.7
Interactions Between Chiral Compounds

• Right and Left handed baseball players can’t use same
glove (chiral) but can use same hat (achiral)
– Two members of enantiomer pair (chiral) react
differently with other chiral molecules
• Enantiomeric pairs have same solubility in achiral
solvents like ethanol and have different solubility in chiral
solvent like D-2-butanol
• Enantiomers have same boiling points, melting points
and densities - all these are dependent upon
intermolecular forces and chirality doesn’t depend on
them

CARBOHYDRATES
Section 18.8
Monosaccharides
• Classification based on # of carbon atoms:
– Triose --- 3 carbon atoms
– Tetrose -- 4 carbon atoms
– Pentoses – 5 carbon atoms
– Hexoses -- 6 carbon atoms
• Classification based on functional groups:
– Aldoses: Monosaccharides with one aldehyde group
– Ketoses: Monosaccharides with one ketone group
• Combined # of C atoms and functional group:
– Example:
Aldohexose: Monosaccharide with aldehyde group and 6 C atoms
Ketopentose: Monosaccharide with ketone group and 5 C atoms

CARBOHYDRATES
Section 18.8
• Other Example:
– Aldohexose:
CHO CH2OH
Monosaccharide with
aldehyde group and 6 C H OH O
atoms – D-glucose HO H HO H
– Ketohexose: H OH H OH
Monosaccharide with
H OH H OH
aldehyde group and 6 C
atoms – D-fructose CH2OH CH2OH
D-Glucose D-Fructose
(aldohexose) (ketohexose)

CARBOHYDRATES
Section 18.8
Exercise
Classify each of the following monosaccharides according
to both the number of carbon atoms and the type of
carbonyl group present.
Answers:
a. Aldopentose;
b. Ketohexose;
c. Aldohexose;
d. Ketopentose

CARBOHYDRATES
Section 18.8
Aldoses

CARBOHYDRATES
Section 18.8
Ketoses

CARBOHYDRATES
Section 18.9
Glucose and Fructose

CHO
H OH 1. Most abundant in nature

HO H 2. Nutritionally most important
H OH 3. Grape fruit good source of glucose (20 - 30%
H OH
by mass) -- also named grape sugar, dextrose
CH2OH
and blood sugar (70 - 100 mg/100 mL of blood)
D-Glucose 4. Six membered cyclic form
(aldohexose)
CH2OH
O
1. Ketohexose
HO H
2. Sweetest tasting of all sugars
H OH
3. Found in many fruits and in honey
H OH
4. Good dietary sugar-- due to higher sweetness
CH2OH
D-Fructose
(ketohexose)

CARBOHYDRATES
Section 18.9
Galactose and Ribose
1. Milk sugar
2. Synthesize in human
3. Also called brain sugar-- part of brain and
nerve tissue
4. Six membered cyclic form
1. Part of RNA
2. Part of ATP
3. Part of DNA

CARBOHYDRATES
Section 18.10
Cyclic Hemiacetal
Forms of D-Glucose
• Dominant form of
monosaccharides
with 5 or more C
atoms is cyclic -
cyclic forms are in
equilibrium with
open chain form
• Cyclic forms are
formed by the
reaction of carbonyl
group (C=O) with
hydroxyl (-OH)
group on carbon 5

CARBOHYDRATES
Section 18.10
Cyclic Hemiacetal Forms of D-Glucose

• 2 forms of D-glucose:
– Alpha-form: -OH of C1 and CH2OH of C5 are on opposite sides
– Beta-form: -OH of C1 and CH2OH of C5 are on same sides
6 6
CH2 OH Anomeric CH 2OH
O Carbon O OH
5 5
4 1
OH 4 OH
1
2 OH 2
OH OH
3 3 Anomeric
OH OH Carbon
a-D-Glucose b-D-Glucose
– Anomers: Cyclic monosaccharides that differ only in the position

of the substituents on the anomeric carbon atom.

CARBOHYDRATES
Section 18.10
• Intramolecular cyclic hemiacetal formation and the

equilibrium between various forms are not restricted to
glucose.
• All aldoses with five or more carbon atoms establish
similar equilibria, but with different percentages of the
alpha, beta, and open-chain forms.
• Fructose and other ketoses with a sufficient number of
carbon atoms also cyclize.

CARBOHYDRATES
Section 18.10
Pyranose and Furanose

• A cyclic monosaccharide containing a six-atom ring is
called a pyranose, and one containing a five-atom ring is
called furanose because their ring structures resemble
the ring structures in the cyclic ethers pyran and furan
respectively.
Pyran Furan
O
O
CH2 OH
CH2OH CH2OH
OH CH2OH O
O
OH OH
OH
OH
a-D-Glucose OH
OH
OH OH
OH
a -D-Fructose a -D-Ribose
Pyranose Furanoses
CARBOHYDRATES
Section 18.11
• A Haworth projection formula is a two-dimensional

structural notation that specifies the three-dimensional
structure of a cyclic form of a monosaccharide.
CH2 OH
O CH2 OH
CH2 OH CH2 OH
O O
OH
OH
OH OH
OH
OH
OH OH
OH OH
a-D-Glucose a -D-Fructose a -D-Ribose

CARBOHYDRATES
Section 18.11
Alpha and Beta Configuration

• Alpha or Beta configuration is determined by the position of the —
OH group on C1 relative to the CH2OH group that determines D or L
series.
• In a Beta configuration, both of these groups point in the same
direction
• In an Alpha configuration, the two groups point in opposite
directions.

CARBOHYDRATES
Section 18.11
OH Group Position
• The specific identity of a monosaccharide is determined by the
positioning of the other —OH groups in the Haworth projection
formula.
• Any —OH group at a chiral center that is to the right in a Fischer
projection formula points down in the Haworth projection formula
and any —OH group to the left in a Fischer projection formula points
up in the Haworth projection formula.

CARBOHYDRATES
Section 18.11
Practice Exercise
• Which of the monosaccharides glucose, fructose, galactose, and

ribose has each of the following structural characteristics? (There
may be more than one correct answer for a given characteristic)
a. It is a pentose.
b. It is a ketose.
c. Its cyclic form has a 6-membered ring.
d. Its cyclic form has two carbon atoms outside the ring.
Answers:
a. Ribose
b. Fructose
c. Glucose, galactose
d. Fructose

CARBOHYDRATES
Section 18.11
Glycoside Formation
• Glycoside formation: Cyclic forms of monosaccharides
are hemiacetals, they react with alcohols to form acetals:
– Monosaccharide acetals are called glycosides
• A glycoside is an acetal formed from a cyclic
monosaccharide by replacement of the hemiacetal
carbon —OH group with an —OR group:
– A glycoside produced from glucose - glucoside
– A glycoside produced from galactose – galactoside

CARBOHYDRATES
Section 18.11
Glycoside Formation
– Glycosides exist in both Alpha and Beta forms

CARBOHYDRATES
Section 18.13
Disaccharides
• Two monosaccharides can react to form disaccharide

• One monosaccharide act as a hemiacetal and other as
alcohol and the resulting ether bond is a glycosidic
linkage.

CARBOHYDRATES
Section 18.13
Disaccharides
Cellobiose
• Cellobiose is produced as an intermediate in the
hydrolysis of the polysaccharide cellulose:
– Cellobiose contains two beta - D-glucose
monosaccharide units linked through a beta (1→4)
glycosidic linkage.

CARBOHYDRATES
Section 18.13
Disaccharides
Maltose
• Maltose also known as malt sugar
• Structurally maltose made of 2 alpha-D-glucose units linked via an
alpha 1→4 linkage.
• Maltose is digested easily by humans because we have enzymes
that can break alpha (1→4) linkages but not beta (1→4) linkages of
cellobiose. Therefore cellobiose cannot be digested by humans.
• Baby foods are rich in maltose.

CARBOHYDRATES
Section 18.13
Disaccharides
Lactose
• Lactose is made up of beta-D-galactose unit and a beta-D-glucose
unit joined by a beta (1→4) glycosidic linkage.
• Milk is rich in lactose disaccharide..
– Lactose intolerance: a condition in which people lack the
enzyme lactase needed to hydrolyze lactose to galactose and
glucose.
– Lactase hydrolyzes beta (1→4) glycosidic linkages.

CARBOHYDRATES
Section 18.13
Disaccharides
Sucrose
• Sucrose (table sugar): The most abundant of all disaccharides
and found in plants.
• It is produced commercially from the juice of sugar cane and
sugar beets.

CARBOHYDRATES
Section 18.13
Disaccharides
Practice Exercise
• Which of these disaccharides, i.e., maltose, cellobiose, lactose, and

sucrose, have the following structural or reaction characteristics?
(There may be more than one correct answer for a given
characteristic)
a. Two different monosaccharide units are present.
b. Hydrolysis produces only monosaccharides.
c. Its glycosidic linkage is a “head-to-head” linkage.
d. It is not a reducing sugar.
Answers:
a. Lactose, sucrose
b. Maltose, cellobiose, lactose, sucrose
c. Sucrose
d. Sucrose

CARBOHYDRATES
Section 18.14
Oligosaccharides
• Carbohydrates that contain 3-10 monosaccharide units

boded to each other via glycosidic linkages.
• Not as common as disaccharides in nature. Generally
present in association with other complex molecules.
• Examples:
• Raffinose: made of one each of galactose, glucose
and fructose.
• Stachyose: made of 2 galactose, 1 glucose and 1
fructose units.
• Commonly found in onions, cabbage, broccoli and
wheat.

CARBOHYDRATES
Section 18.15
• Polymers of many
monosaccharide
units bonded with
glycosidic linkages
• Two types:
– Linear and
branched, homo-
and hetero-
polysaccharides

CARBOHYDRATES
Section 18.15
• Polysaccharides are not sweet

• Limited water solubility
• Examples:
– Cellulose, starch in plants
– Glycogen in animals
– Chitin in arthropods

CARBOHYDRATES
Section 18.16
Starch
• A plant storage polysaccharide that is a storage form for
monosaccharides and is used as an energy source in
plant cells.
• Glucose is the monomeric unit

CARBOHYDRATES
Section 18.16
Starch
• Amylose: Straight chain polymer - 15 - 20% of the starch and has
alpha (1 → 4) glycosidic bonds
– Molecular Mass: up to 1000 glucose units)
• Amylopectin:
– Branched chain polymer - 80 - 85 % of the starch alpha (1→4)
glycosidic bond for straight chain and alpha (1→6) for branch
– Molecular Mass: up to 100,000 glucose units) - higher than
amylose
– Amylopectin is digested more readily by humans (can hydrolyze
alpha linkages but not beta linkages)

CARBOHYDRATES
Section 18.16
Starch

CARBOHYDRATES
Section 18.16
Glycogen
– Human and animal storage polysaccharide
– Contains only glucose units
– Branched chain polymer – alpha (1→4) glycosidic bonds in
straight chains and alpha (1→6) in branches
– Molecular Mass: up to 1,000,000 glucose units)
– Three times more highly branched than amylopectin in starch
– Excess glucose in blood stored in the form of glycogen

CARBOHYDRATES
Section 18.17
Cellulose
• Linear homopolysaccharide with beta (1→4) glycosidic bond
• Up to 5000 glucose units with molecular mass of ~900,000 amu
– Humans don’t have enzymes that hydrolyze beta (1→4) linkages - so
they can not digest cellulose -- animals also lack these enzymes but
they can digest cellulose because they have bacteria in their guts to
hydrolyze cellulose
– Cotton ~95% cellulose and wood ~50% cellulose
HO
HO O O
OH
HO O O
OH b(1-4) OH
O O
HO
OH b (1-4)
O O OH
OH b(1-4)
O OH
OH

CARBOHYDRATES
Section 18.17
Chitin
– Similar to cellulose in both function and structure
– Linear polymer with all beta (1→4) glycosidic linkages - it has a
N-acetyl amino derivative of glucose
– Function is to give rigidity to the exoskeletons of crabs, lobsters,
shrimp, insects, and other arthropods
HO
HO O O
OH
HO O N-Acetyl
O
OH HN b-D-Glucoseamine
O O
HO
OH HN O
O O
O OH HN O
HN O

CARBOHYDRATES
Section 18.18
• Acidic polysaccharides - polysaccharides with a repeating

disaccharide unit containing an amino sugar and a sugar with a
negative charge due to a sulfate or a carboxyl group.
• Structural polysaccharide present in connective tissue associated
with joints, cartilage, synovial fluids in animals and humans
– Primary function is lubrication necessary for joint movement
– These are heteropolysaccharides - have more than one type of
monosaccharide monomers is present.
• Examples:
– Hyaluronic acid
– Heparin

CARBOHYDRATES
Section 18.18
Hyaluronic Acid and Heparin

• Hyaluronic acid:
– Alternating residues of N-
acetyl-beta-D-glucosamine
and D-glucuronic acid.
– Highly viscous - serve as
lubricants in the fluid of
joints and part of vitreous
humor of the eye.
• Heparin:
– An anticoagulant-prevents
blood clots.
– Polysaccharide with 15–90
disaccharide residues per
chain.
CARBOHYDRATES
Section 18.20
Glycolipids and Glycoproteins: Cell Recognition
• A glycolipid is a lipid molecule that has one or more
carbohydrate (or carbohydrate derivative) units
• A glycoprotein is a protein molecule that has one or
more carbohydrate (or carbohydrate derivative) units

APRIL 2022
AMINO ACIDS:
Building Blocks For Proteins
BIOCHEMISTRY
AMINO ACIDS
CHARACTERISTICS OF PROTEINS
• Human cells -- 9 000 different proteins
‒ Most abundant molecules in the cells (15% of the
cells overall mass)
• Human body– 1 00,000 different proteins
• Elemental composition- Carbon (C), Hydrogen (H), Nitrogen (N),
Oxygen (O), and Sulfur (S)
‒ Also present are Iron (Fe), Phosphorus (P) and some metals in
some specialized protein
• A protein is a naturally-occurring, unbranched polymer which the
monomer units are amino acids.
AMINO ACIDS LESSON 6
AMINO ACIDS: THE BUILDING BLOCKS OF PROTEINS

• Amino acids are organic compounds that contain both an amino (NH2)
and a carboxyl (-COOH) group attached to same α-carbon atom.
• All amino acids share the same basic structure but differ in their side
chains (-R).
There are 20 common (standard) amino acids divided into four

groups based on the properties of their side chains (-R)
‒ Nonpolar amino acids
‒ Polar neutral amino acids
‒ Polar acidic amino acids
‒ Polar basic amino acids
NONPOLAR AMINO ACIDS

• Contain one amino group, one carboxyl group, and a nonpolar side chain
• Hydrophobic (water-fearing); found in the interior of proteins.
POLAR NEUTRAL AMINO ACIDS

▪ Contain one amino group, one carboxyl group, and a side chain that
is polar but neutral.
POLAR ACIDIC POLAR BASIC

AMINO ACIDS AMINO ACIDS
▪ Contain one amino ▪ Contain two amino group
group and two carboxyl and one carboxyl groups,
groups, the second the second amino group
carboxyl group being being part of the side chain
part of the side chain
Practice Exercise
Classify the following amino acids based on the
polarity of their R-groups.
nonpolar polar neutral polar acidic nonpolar

polar basic
ESSENTIAL AMINO ACIDS NON-ESSENTIAL AMINO ACIDS

▪ Needed in the human body ▪ Can be synthesized by the
for protein synthesis that human body.
must be obtained from
dietary sources. Non-Essential Amino Acids
Glycine Asparagine
Essential Amino Acids Alanine Glutamine
Lysine Methionine Proline Tyrosine
Histidine Phenylalanine Serine Aspartic acid
Isoleucine Threonine Cysteine Glutamic acid
Leucine Tryptophan Arginine
Valine
CHIRALITY AND AMINO ACIDS

▪ Four different groups are attached to the α-carbon atom in all of the
standard amino acids except glycine (R-group is hydrogen)
▪ Molecules with chiral centers exhibit enantiomerism (left- and right-
handed forms)
CHIRALITY AND AMINO ACIDS
▪ Amino acids found in nature as well as in proteins are L isomers.

▪ Rules for drawing Fischer projection formulas of amino acids:
— --COOH group (top)
— R group (bottom)
— Positioning –NH2 on the left (L isomer)
— Positioning –NH2 on the right (D isomer)
ZWITTERIONS
▪ The amino (-NH2) and carboxyl group (-COOH) allow amino acids to
have amphoteric properties.
▪ Both the -NH2 and –COOH groups in an amino acid undergo
ionization in neutral solution (water).
▪ Zwitterion is bipolar and carries both positive and negative charges
with a net zero charges.
ZWITTERIONS
▪ Zwitterion structure changes when the pH of a solution changed
from neutral to either acidic (low pH) or to basic (high pH).
ISOELECTRIC POINTS
▪ pH at which the concentration of

zwitterion is maximum – no net charge.
▪ Different amino acids have different
isoelectric points.
▪ At isoelectric points, amino acids are not
attracted towards an applied electric
field because they carry net zero charge.
ELECTROPHORESIS
▪ Process of separating charged molecules on the basis of their
migration toward electrodes associated with an electric field.
CYSTEINE
▪ The only standard amino acid that has a side chain that contains a
sulfhydryl group (-SH).
▪ Dimer is a molecule that is made up of two like subunits.
PEPTIDES
▪ Amino acids can bond together to produce an unbranched chain of
amino acids.
▪ The length of the amino acid chain can vary from a few amino
acids to hundred of amino acids.
▪ Peptide - chain of covalently-linked amino acids.
PEPTIDES
▪ Dipeptide: bond between two amino acids
▪ Oligopeptides: bond between ~10-20 amino acids
▪ Polypeptide: bond between large number of amino acids
PEPTIDE NOMENCLATURE
▪ The C-terminal amino acid residue keeps its full amino acid name.
▪ All of the other amino acid residues have names that end in -yl. The
-yl suffix replaces the -ine or -ic acid ending of the amino acid
name, except for tryptophan, for which -yl is added to the name.
▪ The amino acid naming sequence begins at the N-terminal amino
acid residue.
Example:
‒ Ala-leu-gly has the IUPAC name of alanylleucylglycine
Practice Exercise
Assign IUPAC names to each of the following peptides.
a. Glu-Ser-Ala glutamylserylalanine
b. Gly-Tyr-Leu-Val glycyltyrosylleucylvaline
c. Asp-Leu-Phe aspartylleucylphenylalanine
ISOMERIC PEPTIDE
▪ Peptides that contain the same amino acids but present in
different order are different molecules (constitutional isomers) with
different properties.
▪ The number of isomeric peptides possible increases rapidly as the
length of the peptide chain increases.
BIOLOGICALLY IMPORTANT SMALL PEPTIDES

Small Peptide Hormones
▪ Oxytocin and vasopressin (pituitary gland) - nonapeptide
▪ Oxytocin regulates uterine contractions and lactation.
▪ Vasopressin regulates the excretion of water by the kidneys.

▪ Enkephalins are pentapeptide neurotransmitters produced by the
brain that bind at receptor sites in the brain to reduce pain.
▪ Met-enkephalin
▪ Leu-enkephalin

Small Peptide Antioxidant
▪ Glutathione (Glu-Cys-Gly)
CELL THEORY LESSON 1
THANK YOU!
MAY 2022
NUCLEIC ACIDS
Friedrich Miescher
BIOCHEMISTRY
NUCLEIC ACIDS
Nucleic Acids
▪ Complex molecules containing elements of carbon,
hydrogen, oxygen, phosphorus, and nitrogen.
▪ Two types of nucleic acids:
‒ DNA: Deoxyribonucleic Acid
• Found within the nucleus
• Storage and transfer of genetic information
• Passed from one cell to another during cell division
‒ RNA: ribonucleic Acid
• Occurs in all parts of the cell
• Primary function is to synthesize the proteins
▪ Monomer units are nucleotides
NUCLEIC ACIDS
Nucleotide Building Blocks
▪ Nucleic Acids: Polymers in which

repeating unit is nucleotide
▪ A Nucleotide has three components:
‒ Pentose Sugar - Monosaccharide
‒ Phosphate Group (PO43-)
‒ Nitrogenous Base
NUCLEIC ACIDS

Pentose Sugar
▪ Ribose is present in RNA and 2-deoxyribose is present in DNA
▪ Structural difference:
‒ a —OH group present on carbon 2’ in ribose
‒ a —H atom in 2-deoxyribose
NUCLEIC ACIDS

Nitrogenous Bases
NUCLEIC ACIDS

Phosphate
▪ Derived from phosphoric acid (H3PO4)
▪ Under cellular pH conditions, the phosphoric acid is fully
dissociated to give a hydrogen phosphate ion (HPO42-)
NUCLEIC ACIDS
Nucleotide Formation
NUCLEIC ACIDS
Nucleotide Nomenclature
NUCLEIC ACIDS
Primary Nucleic Acid Structure
▪ Two nucleotides are joined through

phosphodiester bond to give a
dinucleotide.
▪ Sugar-phosphate groups are the
nucleic acid backbone
▪ Sugars are different in DNA and RNA
NUCLEIC ACIDS
Primary Nucleic Acid Structure
Nucleic Acid vs. Protein

NUCLEIC ACIDS
‒ Nucleotide polymer in which

R each of the monomers contains
ribose, a phosphate group, and
N one of the nitrogenous bases
A adenine, cytosine, guanine, or
uracil.
‒ Nucleotide polymer in which

each of the monomers contains
D
ribose, a phosphate group, and
N one of the nitrogenous bases
A adenine, cytosine, guanine, or
thymine.
NUCLEIC ACIDS
DNA Double Helix

▪ Two strands/ polynucleotide
chains run anti-parallel
(opposite directions: 5’-3’ and
3’to 5’) and coiled around
each other to form a double
helix
▪ Discovered by Watson and
Crick in 1953
DNA Double Helix
NUCLEIC ACIDS
DNA Double Helix
Base Pairing
▪ A pyrimidine is always
paired with purine
▪ Fits inside the DNA double
strand
▪ Hydrogen bonding is
stronger with A-T and G-C
▪ A-T and G-C are called
complementary bases
NUCLEIC ACIDS
DNA Double Helix

▪ DNA Sequence: the sequence of bases on one polynucleotide is
complementary to the other polynucleotide.
▪ Complementary bases are pairs of bases in a nucleic acid structure that can
hydrogen-bond to each other.
▪ Example :
‒ List of bases in sequential order in the direction from the 5’ end to 3’ end
of the segment:
‒ 5’-A-A-G-C-T-A-G-C-T-T-A-C-T-3’
‒ Complementary strand of this sequence will be:
3’-T-T-C-G-A-T-C-G-A-A-T-G-A-5’
NUCLEIC ACIDS
Practice Exercise
Predict the sequence of bases in the DNA strand
complementary to the single DNA strand shown below:
5’ A–A–T–G–C–A–G–C–T 3’
Answer:
3’ T–T–A–C–G–T–C–G–A 5’
NUCLEIC ACIDS
DNA Replication
▪ DNA molecules produce exact copies of themselves
▪ takes place when a cell divides producing two identical daughter cells
each containing the same number of chromosomes as the original cell
NUCLEIC ACIDS
DNA Replication
NUCLEIC ACIDS
DNA Replication
NUCLEIC ACIDS
DNA Replication
NUCLEIC ACIDS
Protein Synthesis
NUCLEIC ACIDS
Types of RNA
▪ Heterogenous nuclear RNA (hnRNA):
Formed directly by DNA
transcription.
▪ Messenger RNA (mRNA):
Carries instruction for protein
synthesis (genetic information) to
the sites of proteins synthesis.
▪ Small nuclear RNA (snRNA):
Facilitates the conversion of
heterogenous nuclear RNA to mRNA.
NUCLEIC ACIDS
Types of RNA
▪ Ribosomal RNA (rRNA): combine with specific proteins to form
ribosomes, the physical sites for protein synthesis.
▪ Transfer RNA (tRNA): Delivers amino acids to the sites for protein
synthesis; the smallest
NUCLEIC ACIDS
Transcription: RNA Synthesis

▪ A process by which DNA directs the
synthesis of mRNA molecules
▪ Two-step process
a. synthesis of hnRNA
b. editing to yield mRNA molecule
▪ Gene: A segment of a DNA base sequence
responsible for the production of a specific
hnRNA/mRNA molecule
▪ Genome: All of the genetic material (the
total DNA) contained in the chromosomes
of an organism
Transcription:
RNA Synthesis
NUCLEIC ACIDS
Splicing
NUCLEIC ACIDS
Alternative Splicing and Transcriptome

NUCLEIC ACIDS
4
42=16
43=64
Codon
Transcription:
RNA Synthesis
Characteristics:
• highly degenerate
• there is a pattern to the
arrangement of synonyms
• almost universal
• an initiation codon exists
The Universal Genetic Code

NUCLEIC ACIDS
Practice Exercise
Using the genetic code, determine the sequence of amino
acids encoded by the mRNA codon sequence shown below:
5’ GCC–AUG–GUA–AAA–UGC–GAC–CCA 3’
Answer:
Peptide: Ala-Met-Val-Lys-Cys-Asp-Pro
NUCLEIC ACIDS
Practice Exercise
Sections A, C, and E of the following base sequence section of a DNA
template strand are exons, and sections B and D are introns.
a. What is the structure of the hnRNA transcribed from this template?

b. What is the structure of the mRNA obtained by splicing the hnRNA?
Answer:
a.
b.
NUCLEIC ACIDS
Practice Exercise
The structure of an mRNA segment obtained from a DNA template
strand is
What polypeptide amino acid sequence will be synthesized using this

mRNA?
Answer:
Anticodon and tRNA Molecules
• The 3’ end of tRNA is where an amino acid

is covalently bonded to the tRNA.
• The loop opposite to the open end of tRNA

is the site for a sequence of three bases
called an anticodon.
Codon-Anticodon Relationship
A tRNA molecule has the anticodon 5’
AAG 3’.
a. With which mRNA codon will this
anticodon interact?
b. Which amino acid will this tRNA
molecule carry?
Leucine, Leu
NUCLEIC ACIDS
Translation: Protein Synthesis

▪ A process in which mRNA codons are
deciphered to synthesize a protein molecule
▪ Ribosome
• an rRNA–protein complex that serves as
the site of protein synthesis
• Contains 4 rRNA molecules and ~80
proteins - packed into two rRNA-protein
subunits (one small and one large)
▪ A ribosome’s active site – Large subunit
▪ The mRNA binds to the small subunit of the
ribosome.
NUCLEIC ACIDS

Activation of tRNA
Initiation
NUCLEIC ACIDS

Elongation
NUCLEIC ACIDS
Termination
NUCLEIC ACIDS
Post-Translation Processing
NUCLEIC ACIDS
Efficiency of mRNA Utilization

NUCLEIC ACIDS
Mutations
▪ An error in base sequence reproduced during
DNA replication
▪ Errors in genetic information is passed on
during transcription.
▪ The altered information can cause changes in
amino acid sequence during protein synthesis
and thereby alter protein function.
▪ Mutagen – substance or agent that causes a
change in the structure of a gene
• Radiation and chemical agents
NUCLEIC ACIDS
Viruses
▪ Tiny disease causing agents with outer protein envelope and inner
nucleic acid core
▪ Invade their host cells to reproduce and in the process disrupt the
normal cell’s operation
▪ Many human diseases are of viral origin, e. g. common cold,
smallpox, rabies, influenza, hepatitis, and AIDS
Vaccines
NUCLEIC ACIDS
Recombinant DNA and Genetic Engineering

▪ Genetic Engineering (Biotechnology): A
process in which an organism is
intentionally changed at the molecular
(DNA) level so that it exhibits different traits.
▪ Recombinant DNA: DNA molecules that
have been synthesized by splicing a
sequence of segment DNA (usually a gene)
from one organism to the DNA of another
organism.
▪ First genetically engineered organism are
bacteria (1973) and Mice (1974)
▪ Insulin producing bacteria - commercialized
in 1982.
Recombinant DNA and Genetic Engineering
Recombinant DNA Production

using Bacterial Plasmid
NUCLEIC ACIDS
Polymerase Chain Reaction

▪ A method for
rapidly producing
multiple copies of
a DNA nucleotide
sequence (gene).
▪ This method
allows to produce
billions of copies
of a specific gene
in a few hours.
Polymerase
Chain Reaction
DNA Sequencing
▪ a method by which the

base sequence in a DNA
molecule (or a portion of
it) is determined
NUCLEIC ACIDS
THANK YOU!
Question 1
Which of the following is a correct characterization for the monosaccharide glucose?
Response: Aldohexose
Question 2
The structure of fructose and glucose differ at which carbon atom?
Response: Carbon 1 and carbon 2
Question 3
Which of the following disaccharides produces both D-glucose and D-fructose upon
hydrolysis?
Response: Sucrose
Question 4
In which of the following disaccharides has β(1-4) glycosidic linkage?
Response: Lactose
Question 5
In which of the following pair of carbohydrates do both members of the pair have the
same type of glycosidic linkage?
Response: Glycogen and amylopectin
Question 6
In which of the following pairs of polysaccharides are both members of the pair storage
polysaccharides?
Response: Glycogen and starch
Question 7
The carbohydrate portion of glycolipids and glycoproteins that are involved in cell
recognition process is which of the following?
Response: Oligosaccharide
Question 8
Which substance is not a polymer of glucose?
Response: Cholesterol
Question 9
Muscle cells store energy in the form of _______.
Response: Glycogen
Question 10
Classify the given monosaccharide according to both the number of carbon atoms
and the type of carbonyl group present.
Response:
Aldopentose
Question 11
Which of the following statements about the polysaccharide hyaluronic acid is incorrect?
Response: All monosaccharide units present are glucosamine derivatives.
Question 12
A trisaccharide toxin produced by potato plants is called __________.
Response: solanine
Question 13
The following are reducing sugars except:
Response: sucrose
Question 14
Any -OH group to the left of a chiral center in a Fischer projection formula points in
which of the following directions in a Haworth projection formula?
Response: points up
Question 15
The cyclic forms of an aldohexose are based on a ring system containing ___________.
Response: 5 Carbon atoms and 1 Oxygen atom
Question 16
Choose "True" if the statement is correct. If otherwise, change the underlined word/s to
make the statement correct.
Fructose has the same chemical formula as glucose.

Response: True
Question 17
A glycosidic bond is a type of ionic bond that joins a carbohydrate molecule to another.
Response: False, Covalent
Question 18
Cellulose is the major substance in plant cell walls.

Response: True
Question 19
Glycogen has similar structure to amylose having α-1,4 and α-1,6 glycosidic bonds.
Response: False, Amylopectin
Question 20
Sucrose can be hydrolyzed into galactose and fructose.

Response: False, Glucose
Question 21
Acidic polysaccharides are heteropolysaccharides.

Response: True
Question 22
The cyclic hemiacetal forms of D-glucose result from the intramolecular reaction
between the carboxyl group and the hydroxyl group on carbon 5.
Response: True
Score: 0 out of 1 No
Question 23
The more specific name for α-D-glucose is α-D-glucofuranose.
Response: False, Dextrose monohydrate
Question 24
In Haworth projection formulas for monosaccharides that are pentoses and hexoses, all
except two of the carbon atoms carry a hydroxyl attachment.
Response: False, Four
Question 25
Structurally, chitin is identical to amylose, except the monosaccharide present is the

glucose derivative N-acetyl-D-glucosamine rather than D-glucose itself.
Response: False, Cellulose
Score: 1 out of 1
Question 1
Which of the following statements concerning the handedness of the standard amino
acids found in proteins is correct?
Response: All except one of them exhibit handedness.
Question 2
What group is positioned at the top of the Fischer projection formula for a standard
amino acid?
Response: carboxyl group
Question 3
The joining together of two amino acids to form a dipeptide involves the chemical
reaction between ______________.
Response: two amino groups
Question 4
The number of carboxyl groups and amino groups present, respectively, in a nonpolar
amino acid is, __________.
Response: 2 and 1
Question 5
At isoelectric point point of an amino acid,
Response: the number of of positive charges will equal the number of negative charges.
Question 6
What functional group is present in the bond formed when two amino acids are joined
together to form a dipeptide?
Response: amide
Question 7
How many isomeric peptides can be formed from three molecules of valine and one
molecule of serine?
Response: 6
Question 8
Which of the following statements concerning tripeptide Gly-Ala-Val is correct?
Response: The C-terminal amino acid residue is Gly.
Question 9
Which amino acid does not contain a charged side chain?
Response: Proline
Question 10
Which of the following statements is most likely to be true of nonpolar R groups in
aqueous solution?
Response: They are hydrophobic and found on protein surfaces.
Question 11
The central carbon of an amino acid is called chiral carbon.

Response: False, Alpha
Question 12
Isomeric peptides have similar physical and chemical properties.

Response: False, Differ
Question 13
Threonine possesses two chiral center/s.

Response: True
Question 14
Phenylalanine has a side chain bonded to both the α-carbon atom and the amino
nitrogen atom, giving a cyclic side chain.
Response: True
Question 15
The presence of nitrogen in proteins set them apart from carbohydrates and lipids.
Response: True
Question 16
Assign an IUPAC name to the small peptide below. TYPE YOUR ANSWER IN
CAPITAL LETTERS.
Leu-Lys-Trp-Met
_____
Response: LEUCYLLYSYLTRYPTOPHYLMETHIONINE
Question 17
CAPITAL LETTERS.
Tyr-Gln-Asp
_____
Response: TRYROSYL-A-ASPARAGYLGLUTAMINYLHISTIDIN
Question 18
CAPITAL LETTERS.
Phe-Met-Glu-Asn
_____
Response: CODONMETHIONYLGLUMAMICASPARAGYL
Question 19
CAPITAL LETTERS.
Met-Asp-Gln-His
_____
Response: METHYLTHIOASPARAGYLGLUTAMINE
Question 20
CAPITAL LETTERS.
Val-Ser-Cys
_____
Response: VALYLSERYLCYSTEIN
Question 21
Match the given amino acids in COLUMN A to their classification in COLUMN B.
Response: Glutamine => polar acidic amino acid
Response: Trytophan => nonpolar amino acid
Response: Arginine => polar neutral amino acid
Response: Aspartic acid =>
Response: Threonine => polar basic amino acid
Score: 1 out of 5
Question 1
Choose "YES" if the given organelle is present in a prokaryotic cell, and choose "NO" if
otherwise.
Response: cell wall => YES
Response: centrioles => NO
Response: mitochondria => NO
Response: nucleus => NO
Question 2
Choose "YES" if the given organelle is present in a typical animal eukaryotic cell, and
Response: cell wall => NO
Response: centrioles => YES
Response: mitochondria => YES
Response: nucleus => YES
Question 3
Response: True
Question 4
Response: False, Bent

Question 5
Response: True
Question 6
Response: False, Nonpolar

Question 7
Response: False, London dispersion forces

Question 8
Which of the following structures would be found in a plant cell but not in a bacterial
cell?
Question 9
Response: dipole-dipole interaction
Question 10
Why can water have no net charge but have slight charges in different parts of the
molecule?
Response: The oxygen end is slightly negative and the hydrogen end is slightly positive.
Question 11
Potassium chloride dissolved in water is an example of what type of intermolecular
force?
Response: Ion-dipole interaction
Question 12
Response: relates the pH of a solution to the pKa and the concentrations of acid and
conjugate base.
Score: 1 out of 1
Question 1
Match the organelles in COLUMN A to their functions in COLUMN B.
Response: Cell membrane => controls the entry and exit of certain substances
Response: Cytoskeleton => gives the cell its shape
Response: Lysosomes => serves as recycling centers for redundant and damaged
organelles
Response: Nucleus => acts as a control center that directs all the activities of a cell
Response: Nucleolus => synthesizes ribosomal RNA
Response: Golgi Apparatus => receives, stores, modifies, and packages proteins and
lipids arriving from the RER and SER
Response: Rough Endoplasmic Reticulum => synthesizes protein
Response: Smooth Endoplasmic Reticulum => synthesizes lipids
Response: Mitochondria => provides energy a cell needs for all its activities
Response: Vacuoles => removes excess water and some wastes from the cell
Question 2
Response: False, Mitochondria

Question 3
Response: True
Question 4
Response: True
Question 5
Response: True
Question 6
Response: False, Watson and Crick

Question 7
Response: Process and deliver proteins
Question 8
A cell with relatively few energy needs will probably have a relatively small number of
__________.
Question 9
The organelle which acts as the centers of cellular respiration is called _________.
Question 10
These scientists proved that organic molecules formed from inorganic molecules
present in the Earth’s early atmosphere when given energy from lightening.
Response: Milley and Urey
Question 11
This bacteria formed 3.5 billion years ago and was photosynthetic and release oxygen
into the atmosphere.
Response: Cyanobacteria
Score: 1 out of 1

Biochem Lek Endterm Notes

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FEBRUARY 2022

A Brief History of Earth and Life

• Earth was formed about 5 billion

A Brief History of Earth and Life

A Brief History of Earth and Life

• The first cells are thought to have arisen from aggregations of

A Brief History of Earth and Life

• The oxygen-rich ozone layer was also established, shielding the

• This further provided our planet for appearance and inhabitation

A Brief History of Earth and Life

• First venturing beyond Africa about 70,000 years ago.

A Brief History of Biochemistry

• In 1780’s, Antoine Lavoisier proposed that the combustion of a

• For the first time a physiological process was explained with

A Brief History of Biochemistry

• Now an obsolete scientific doctrine, vitalists argued that it was the

A Brief History of Biochemistry

• Friedrich Wöhler disproved this belief (i.e., vitalism) in 1828 by

• Many science historians said that in vitro synthesis of urea by

A Brief History of Biochemistry

A Brief History of Biochemistry

• The Miller-Urey experiment showed that a variety of organic

A Brief History of Biochemistry

• In 1850s-1890s, carbohydrates, lipids, and nucleic acids were

• The term “biochemistry” was coined by German chemist Carl

Life in Biochemistry Point of View:

• Hundreds of biochemical reactions and biochemical processes

• The main focus of biochemistry is to understand how biological

NUCLEUS ❑Nuclear Envelope

THE PROTOPLASM AND ITS ORGANELLES

MITOCHONDRIA: POWERHOUSES OF THE CELL

Rough Endoplasmic Reticulum (RER)

PROKARYOTIC CELLS EUKARYOTIC CELLS

❑ From Greek word: ❑ From Greek word:

PROKARYOTIC CELLS EUKARYOTIC CELLS

❑ No nucleus or nucleoli ❑ Have nucleus

PROKARYOTIC CELLS EUKARYOTIC CELLS

PROKARYOTIC CELLS EUKARYOTIC CELLS

❑ Cell divides by binary ❑ Cell divides by mitosis or

PROKARYOTIC CELLS EUKARYOTIC CELLS

PLANT CELL VS ANIMAL CELL

Plant Cell Both Animal Cell

• Water and Polarity

The formation and function of molecules

• Atoms with incomplete valence shells can share or

• These interactions usually result in atoms staying

• A molecule is consist of two or

• Atoms in a molecule attract electrons to varying degrees.

• Electronegativity is an atom’s attraction for the electrons in a

• The more electronegative an atom, the more strongly it pulls

• Oxygen and nitrogen, more

• In a nonpolar covalent bond, the atoms share electron equally.

• In a polar covalent bond, one atom is more electronegative, and

• Unequal sharing of electrons causes a partial positive or

What makes water polar?

Polar Bonds and Molecules

• Molecules such as CO2 have

What makes water polar?

Solvent Properties of Water

• Atoms sometimes strip electrons from their bonding partners.

Hydration Shells Surrounding Ions in Water

Ion-dipole and Dipole-Dipole Interactions

• Ion-dipole and dipole-dipole interactions help ionic and polar

Induced Dipole-Induced Dipole Interactions or