M.

01 INTRODUCTION TO BIOCHEMISTRY BIOCHEMISTRY

Dr. Professor || November 5, 2021 LECTURE
Transcribers: Delicano, Alleen Nove
Editors: Delicano, Alleen Nove

B. Overview of Biomolecules
INTRODUCTION TO BIOCHEMISTRY Proteins
A. Definition of Biochemistry ▪ polymers of amino acids joined by peptide bonds
B. Overview of Biomolecules 2. Proteins
C. The Cell ▪ polymers of amino
acids joined by
1. Types of cell: Prokaryotic and Eukaryotic peptide bonds
2. Cell organelles and their Functions

D. Viruses
Learning Outcomes
At the end of this unit, the students are expected to:

1. Define and differentiate biochemistry from other branches ▪ There are 20 different common amino acids, with different
of chemistry chemical properties.
2. Differentiate a prokaryotic cell from a eukaryotic cell in ▪ Essential amino acids ▪ Nonessential amino acids ▪ Amino
terms of its features and the organisms in which these cells Acids are made up of carbon, oxygen, hydrogen, and
are found nitrogen.
3. Identify the organelles found in cells ▪ Different combinations of amino acids give proteins
different properties.
4. Give the function of each cell organelle
Lipids
5. Identify a virus in terms of its structural features and how it ▪ hydrophobic
exists. ▪ composed mostly of carbon and hydrogen
▪ three important types include
A. Definition of biochemistry
• the scientific discipline that seeks to explain life at
the molecular level”

• It uses the tools and terminology of chemistry to

describe the various attributes of living organisms

• Biochemistry is also a practical science: It

generates powerful techniques that underlie
advances in other fields, such as genetics, cell
biology, and immunology.
B. Overview of Biomolecules
Types of Biomolecules
Nucleic Acids
1. Carbohydrates ▪ Nucleic acids = polymers of nucleotides
2. Proteins ▪ Nucleotide = a phosphate + sugar backbone+ a
3. Lipids nitrogenous base
4. Nucleic Acids
Carbohydrates
▪ molecules of carbon, oxygen, and hydrogen
▪ Major source of energy for cells

Page 1 of 8
M.01 INTRODUCTION TO BIOCHEMISTRY

DNA Cell Structure

▪ Bonding between • basic unit of life
bases on opposite • lowest level with all attributes of life
strands follows • organisms composed of one or more cells
strict base-pairing • cell structure correlated to function
rules: • all cells are related
Prokaryotic and Eukaryotic cells
▪ A with T ▪ This unity of life is best explained by a tree of life, with
▪ G with C modern species having evolved from common ancestors.

Organization of the
Human Body

Physical properties of chemicals

Atoms are the smallest units of an element and are
composed of protons, neutrons, and electrons

▪ Protons (positive charge) and neutrons form atomic

nucleus Universal features of living cells

▪ Electrons (negative charge) are outside the nucleus

Elements: fundamental forms of matter ▪ carbon, hydrogen,

oxygen, nitrogen

Prokaryotes
• Bacteria or Archaea
• Size (0.5 – 10 µm)
• nucleoid - DNA not membrane bound
• Circular DNA - plasmid
• lack membrane bound organelles
• no histone proteins
• presence of peptidoglycan in cell wall

- Gram-positive
- Gram-negative

Classification of
Organisms

Page 2 of 8
M.01 INTRODUCTION TO BIOCHEMISTRY

Outside of cell
TEM of a plasma membrane
• Phospholipid bilayer
• Cholesterol
• Proteins
• Carbohydrates

Inside of cell
0.1 mm
Carbohydrate side chains

cholesterol
Hydrophilic
region

Hydrophobic 8 hm
region
Hydrophilic
1 µm 2 µm 5 µm region Phospholipid Proteins
(a) Spherical (b) Rod-shaped (c) Spiral Inside cell
(cocci) (bacilli)
(b) Structure of the plasma membrane
Prokaryotic Reproduction
• Binary Fission
• Genetic Diversity via Horizontal Gene Transfer Plant and Animal Cells
• Transformation
• Transduction
• Conjugation

Gram- Gram-
positive negative
bacteria bacteria
Cell Surface Structures 20 µm
Hans Christian Gram: Gram Staining
Cell Surface Structures
Carbohydrate portion
of lipopolysaccharide
Outer
membrane
Peptidoglycan Cell
Cell
wall layer wall Peptidoglycan
layer
Plasma membrane

Protein Plasma membrane

Protein
Gram- positive bacteria Gram-negative bacteria

(a) Gram-positive: peptidoglycan traps 20 µm

crystal violet. (b) Gram-negative: crystal violet is easily rinsed away,
revealing red dye.

Page 3 of 8
M.01 INTRODUCTION TO BIOCHEMISTRY
Ribosomes Ribosomes
Endomembrane System Free or bound
Protein synthesis

0.25 mm

Free ribosomFigure 6es.10in cytosol

Endoplasmic reticulum (ER) Ribosomes bound to ER
Large
subunit

Small
subunit
TEM showing ER and
ribosomes Diagram of a ribosome

Endoplasmic Reticulum

Nucleus
Nucleolus
• Nucleus Smooth ER Nuclear
envelope
• genetic control Chromatin Rough ER
• DNA synthesis
• RNA synthesis
• Nuclear pores Endoplasmic
• Nuclear envelope
• Inner membrane
Reticulum ER lumen
Cisternae Transitional ER
• Outer membrane Ribosomes
Transport vesicle
Rough ER 200 nm
Smooth ER
Pore Rough ER
complex
Ribosome
• Rough ER
• Smooth ER

Close-up
of nuclear Chromatin
envelope

Rough Endoplasmic Reticulum (RER)

Chromatin – ribosomes
DNA + histone proteins = nucleosome
•– protein
Roughsynthesis
Endoplasmic
Reticulum (RER)
– ribosomes
– protein synthesis

Nucleolus

Golgi apparatus/body/complex
• Golgi apparatus/body/complex
Nucleolus •
•
receives
modifies
• stores
• ships
cis face
(“receiving” side of 0.1 mm
Golgi apparatus)
Cisternae

Nuclear
pores
Nucleolus
Nuclear
Nuclear membrane
membrane

A transmission electron micrograph (X 6,000) trans face

(“shipping” side of TEM of Golgi apparatus
Golgi apparatus)

Page 4 of 8
M.01 INTRODUCTION TO BIOCHEMISTRY

Lysosome Mitochondrion/mitochondria
Vesicle containing • Double membrane Mitochondrion/mitochondria
two damaged 1 mm •• Inner membrane
Double membrane
organelles
• Cristae
• Inner- energy
membrane production
• Matrix - energy
• Cristae production
- energy production
• Lysosome • Matrix - energy production
• intracellular •• DNA
digestion of
fragment DNA
nutrients/dead
•• binary
binaryfission
fission
organelles Peroxisome •• found
foundininallallaerobic
aerobiceukaryotes
eukaryotes
fragment 10 mm
• programmed cell Intermembrane space
destruction Outer Mitochondria
membrane

Lysosome
DNA
Peroxisome Inner
Free Mitochondrial
membrane
ribosomes DNA
in the Cristae

Digestion mitochondrial Nuclear DNA

Mitochondrion matrix
Matrix
Vesicle 0.1 mm
(a) Diagram and TEM of mitochondrion (b) Network of mitochondria in a protist
cell (LM)
(b) Autophagy
Chloroplasts
Chloroplasts
• Thylakoid (granum/grana)
Endomembrane System ••photosynthetic pigments
Thylakoid (granum/grana) • Stroma
Nucleus
• Stroma
• photosynthetic pigments • Uses chemical energy
• Uses chemical energy • Sugar production
• Sugar production
Rough ER
Ribosomes
Smooth ER
Stroma

Inner and outer

membranes
Granum

Plasma DNA
membrane Intermembrane space
Thylakoid 1 mm
(a) Diagram and TEM of chloroplast

Endomembrane System
Nucleus
Central vacuole
Cytosol
Rough ER
Smooth ER

Central
Nucleus vacuole
Cell wall
Chloroplast
Plasma
trans Golgi
membrane 5 mm

Types of Vesicles
Endomembrane System • Storage &
Types of Vesicles
shipping vesicles
Nucleus
• Secretory Harmless
• Storage & shipping
vesicles
waste
Alcohol
vesicles
• Endocytic
• vesiclesvesicles
Secretory Peroxisome
Rough ER – vacuoles
• Endocytic vesicles Cell toxic
Smooth ER – food Golgi
waste
– –vacuoles
contractile apparatus

cis Golgi – •food

expels waste Lysosome
– •contractile
Peroxisomes
– •contain
expels waste
enzymes Residual
• that detoxify
Peroxisomes body
Bacterium
– contain enzymes that
detoxify
Plasma
membrane Plasma
trans Golgi
membrane

Page 5 of 8
 M.01 INTRODUCTION TO BIOCHEMISTRY

Peroxisome
Peroxisome
• single membrane 1 mm
• plants and animals
• single membrane Chloroplast
• detoxifies
• plantscells
and animals Peroxisome
• H2O2• detoxifies cells Mitochondrion
Centrosome Microtubule
• H2O2
Centrioles
0.25 mm

Longitudinal
section of
one centriole

Cytoskeleton

Microtubules Cross section

Vesicle of the other centriole
ATP
Receptor for
motor protein
skeleton
Direction of swimming

Motor protein Microtubule

(ATP powered) of cytoskeleton
(a) Flagella
and cilia
(a) Motion of flagellum 5 mm
Microtubule Vesicles 0.25 mm
Direction of organism’s movement

Power stroke Recovery stroke

(b) Motion of cilia Figure 6.23

15 mm

0.1 mm Outer microtubule Plasma membrane

doublet

(b) Dynein proteins

Central
microtubule
Radial
spoke

Microtubules Cross-linking
proteins between
outer doublets
(b) Cross section of
Plasma motile cilium
membrane
Basal body

0.5 mm 0.1 mm
(a) Longitudinal section Triplet
of motile cilium

(c) Cross section of

basal body

Contractile proteins

Muscle cell
0.5 mm
Actin
filament
Myosin
filament
Myosin
head
(a) Myosin motors in muscle cell contraction

Page 6 of 8
M.01 INTRODUCTION TO BIOCHEMISTRY

Cortex (outer cytoplasm):

gel with actin network
100 mm
Inner cytoplasm: sol
with actin subunits

Extending
pseudopodium

(b) Amoeboid movement

Summary Ebola Polio virions

Prokaryotes
Eukaryotes

Locomotory organelles
Cytoskeleton

Viruses
• nonliving
Influenza A: Enveloped, with
• obligate intracellular parasites – only demonstrate spikes, RNA, multisegmented
characteristics of life while “inside” a host cell: bacterium, genome (8 separate pieces
animal cell, or plant cell of RNA)

• are inert outside a host cell (no enzyme or other activity)

Bacteriophage:
• inside a host cell – viral nucleic acid (DNA or RNA) takes
over the cell and directs the cell to produce new virus
particles (replication)
• Basic virus particle is called a “virion” – intact and infective
virus particle

• Components: Nucleic Acid (DNA or RNA), Protein coat

(capsid) made of individual protein subunits called
capsomeres.

• Some may have and outer envelope or a membrane Viral replication

derived from the host cell.

• The envelope can have specific spikes of protein (H and N

spikes of Influenza) that aid in attachment and makes them
sensitive to chemical actions of disinfectants.

Morphology of viruses
1. Helical (like TMV or Ebola)
2. Polyhedral (adenovirus and polio virus)
3. Enveloped (flu)
4. Complex (bacteriophage)

Page 7 of 8
M.01 INTRODUCTION TO BIOCHEMISTRY

Cultivation of viruses
need living cells, living hosts Tissue cultures, embryonated
eggs, bacterial cultures, live animals

Prions
Prions are infectious proteins, which cause scrappie in
sheep, Kuru in humans, BSE in cattle, and CJD in people
(mad cow in humans).

Page 8 of 8