Remedial– Biology

Topic 1 – Organic Compounds and

Enzymes
 Details for Biology Exam

• Test Duration: 90 minutes

• Questions: 50 questions

• Questions Types: Multiple Choice Questions

Learning objective 1:
• Structure and function of organic compounds
• The role of enzymes in the formation and dissociation of organic compounds
• Atoms
• Molecules
• Polymerization and
degradation of
monomers
 Atoms
• All organisms consist of atoms and molecules organized in specific
ways that give them properties different from those of nonliving
things.

• The acronym CHNOPS stands for the most important elements

(atoms) found in living things
Hydrogen –symbol H (atomic number 1)
The simplest element found. It combines with oxygen to form water, an essential abiotic
substance for living things. Gas at room temperature.

Carbon- symbol C (atomic number 6)

Ubiquitous element on this planet that forms the basis for all living things. It can form the
most number of bonds in chemical combinations. Used for fuel and materials. Solid at
room temperature (black).

Nitrogen- symbol N (atomic number 7)

An essential component of proteins and nucleic acids. Gas at room temperature.
Oxygen- symbol O (atomic number 8)
Necessary for aerobic respiration to take place and for the formation of many organic molecules. Gas at
room temperature.

Phosphorous- symbol P (atomic number 15)

Necessary for nucleic acid structure (found in RNA and DNA) and energy transformations (ATP). Also
important in membrane structure. Present in foods. Essential for bones and teeth. Solid at room
temperature (red/white).

Sulfur- symbol S (atomic number 16)

Forms sulfide bridges that are found in proteins – essential for building DNA. Solid at room temperature
(yellow).
 Compounds or Molecules
• Most atoms - including those common to living things – react with
one another by chemical bonds to form compounds and/or molecules

• An example is the reaction of hydrogen and oxygen to form a water

molecule within the water compound
 Organic molecules
• Organic molecules are those that contain both carbon (C) and
hydrogen (H) atoms

• There are four major classes of organic compounds in any living thing:
• Carbohydrates

• Lipids

• Proteins

• Nucleic Acids
 Biological Macromolecules
• Carbohydrates, lipids, proteins and nucleic
acids are called macromolecules because of
their large size

• You are very familiar with these molecules

because certain foods are known to be rich in
them

• When these foods are digested, they get

broken down into subunit molecules -
monomers

• The human body then takes these subunits and

builds from them the macromolecules –
polymers - that make up the body’s cells
 Majority of macromolecules are polymers, built from
monomers

• A polymer is a long molecule

consisting of many similar building
blocks ​

• The repeating units that serve as

building blocks are called monomers
 Synthesis and degradation of polymers

• A cell uses a type of condensation

reaction to synthesize any type of
macromolecule (polymers); this
reaction is called a dehydration
reaction
• a water molecule is removed when two
monomers are joined

• To degrade a macromolecule
(polymers), the cell uses an opposite
type of reaction, called hydrolysis
reaction
• A water molecule is added to break the
bond holding monomers together
Polymer formation:
Dehydration -
Removal of water
molecule

Polymer degradation:
Hydrolysis - Addition
of water molecule

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 Polymerization (dehydration synthesis) and Digestion
(hydrolysis)

For dehydration and hydrolysis reactions to take place in a cell, an enzyme must be present to speed up the
reaction by bringing the reactants together
Lipids are not considered polymers
because they do not have true monomers.
 Carbohydrates
• An immediate energy source in living organisms
• Composed of carbon, hydrogen, and oxygen
atoms
• CnH2nOn
• Most of the carbon atoms in carbohydrates are
linked to a hydrogen atom and a hydroxyl group
(OH)
• Plays structural roles in a variety of organisms
• The term carbohydrates include single sugar
molecules and chains of sugars.
• A glycosidic bond is formed when two or more
monosaccharides are joined together
 Carbohydrates
• Monosaccharides
• Building blocks of carbohydrates, e.g.,
• Glucose
• Fructose
• Galactose

• Disaccharides
• Made of two monosaccharides
• Sucrose = Glucose + Fructose [table sugar – found in fruits, manufactured from sugar cane]
• Maltose = Glucose + Glucose [malt sugar – comes from plants and grains]
• Lactose = Glucose + Galactose [milk sugar – comes from milk]

• Polysaccharides
• Made of multiple monosaccharides
• Starch (storage carbohydrates in plants)- can be digested by humans from potatoes, rice etc
• Cellulose (cell wall of plants)- can not be digested by humans
• Glycogen (energy storage in animals)
Proteins
 Antibodies help in fighting
infections Hormones signal various
cells across body
Protein
20%
Muscle movement is Hemoglobin transports
controlled by proteins Water oxygen
70%
(actin and myosin)

Digestive enzymes helps

break down food

Keratin found in skin,

hair and nails Forms channels for substances to
move through membrane
 Proteins

• Composed of C, H, O, N, and small amounts of other

elements, such as S

• Amino acids are the monomers of proteins

o Common structure with variable R-group
o There are 20 different amino acids varying in R group
(remainder)
o Side-chain (R) determines structure and function
o Carbons are bonded to a hydrogen atom, an amino
group -NH2, an acidic group -COOH, and an R group
 Proteins: Peptide bond formation
• Amino acids are joined by dehydration or
condensation reaction through a “peptide bond.”

• Peptide: Two or more amino acids bonded

together

• Polypeptide: Chain of many amino acids joined by

peptide bonds

• Proteins are made up of 1 or more polypeptides

• Peptide bonds are broken apart by hydrolysis

(need to add an H2O molecule to break the bond)
 Protein Structure
• Primary: A linear amino acid sequence

• Secondary: Chemical and physical

interactions cause folding into coils and
folds (hydrogen bonds within the
polypeptide sequence)

• Tertiary: Folding gives complex three-

dimensional shape

• Quaternary: Made up of 2 or more

polypeptides in a tight arrangement
Nucleic Acids
 Nucleic Acids

Responsible for the storage, expression, and transmission of genetic information and have a role in
directing protein synthesis.

Two classes
1. Deoxyribonucleic acid (DNA)
o Store genetic information coded in the sequence of their monomer building blocks
(nucleotides) – essential for the development, growth, and reproduction of all
organisms

2. Ribonucleic acid (RNA)

o Involved in decoding this information into instructions for linking together a specific
sequence of amino acids to form a polypeptide chain
• Nucleoside = Nitrogenous base + Sugar

There are two families of nitrogenous bases:

• Pyrimidines (cytosine, thymine, and uracil)
have a single six-membered ring

• Purines (adenine and guanine) have a six-membered ring fused to a

five-membered ring

In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose.

• Nucleotide = Nucleoside + Phosphate group

 Flow of genetic information
Central Dogma
• Each gene along a DNA molecule directs the
synthesis of a messenger RNA (mRNA)

• The mRNA molecule interacts with the cell’s

protein-synthesizing machinery to direct the
production of a polypeptide

• The flow of genetic information can be

summarized as follows:

DNA → RNA → Protein

 • mRNA
Genetic material • tRNA
• rRNA
 DNA vs. RNA

DNA RNA
Deoxyribonucleic acid Ribonucleic acid
Deoxyribose Ribose
Thymine (T) Uracil (U)
Adenine (A), guanine (G), cytosine (C)
used in both
2 strands- double helix Single strand
1 form Several forms
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Lipids
Function of Lipids

(Adipose tissue)

(cell membrane)

(Adipose tissue)

(Reserve fuel)
Lipids (C, H, and O)
• Are the one class of large biological molecules that are
not regarded as polymers

• The unifying feature of lipids is that they mix poorly, if

at all, with water

• Lipids are hydrophobic because they consist primarily

of hydrocarbons (C and H), which form nonpolar
covalent bonds

• The most biologically important lipids are fats,

phospholipids, and steroids
 Fats
• Fats are constructed from two types of
smaller molecules: glycerol and fatty
acids
• Glycerol is a three-carbon alcohol with
a hydroxyl group (-OH) attached to
each carbon
• A fatty acid consists of a carboxyl
group (-COOH) attached to a long
carbon skeleton
• Assembled by dehydration reactions
(ester bond formation)
• The primary function of fats is energy
storage (like fuel)​ energy from 1gm fat
> 2x energy from 1gm sugar
 PHOSPHOLIPIDS

Two FA+ phosphate group + Glycerol

Hydrophilic -> Phosphate groups

Hydrophobic -> 2 FA
• When phospholipids are added to water, they
self-assemble into double-layered structures
called bilayers (Micelles).
Hydrophobic tails stay away from water

• Amphipathic molecules.

• At the surface (membrane) of a cell,

phospholipids are also arranged in a bilayer,
with the hydrophobic tails pointing toward the
interior. Hydrophilic head stays towards water layer

• The existence of cells depends on

phospholipids.
 STEROIDS
• Steroids are lipids characterized by a carbon
skeleton consisting of four fused rings but
do not contain fatty acid. Insoluble in water,
used as hormones and for other purposes.

• Cholesterol, a type of steroid, is a

component in animal cell membranes and a
precursor from which other steroids are
synthesized.

• Needed for bile formation, hormone

synthesis, and cell membrane
 No true
Monomers
 Macromolecules

Category Example Subunit(s)

Carbohydrates Polysaccharide Monosaccharide

Proteins Polypeptide Amino acid

Nucleic Acids DNA, RNA Nucleotide

Enzymes
 Enzymes
• Reactions do not occur randomly in cells; they are usually part of
metabolic pathways, a series of linked reactions

• Metabolic pathways begin with a particular reactant and end with an

end product

• For those metabolic pathways to occur, enzymes are needed

• An enzyme is a protein molecule that functions as an organic catalyst

to speed a chemical reaction
 Enzymes
• The following diagram can represent a metabolic pathway:

• In the first reaction, A is the substrate for Enzyme 1 and B is the

product, then B becomes the substrate for Enzyme 2, and C is the
product; this process continues until the final product D forms.

• In other words, the products of the previous reaction become the

reactants of the next reaction.
 Energy of activation

• Molecules usually do not react with one another unless they are
activated in some way

• The energy that must be added to cause molecules to react with one
another is called the energy of activation (Ea)
 Energy of activation

• Enzymes lower the amount of energy required for activation to occur

by bringing the substrate into contact with one another and by even
participating in the reaction at some times
 Enzyme-substrate complex

• An enzyme has an active site where the substrates and enzyme fit
together in such a way that the substrates are oriented to react

• Following the reaction, the products are released, and the enzyme is
free to act again
 Enzymes Names for their substrate

• Every reaction in a metabolic pathway requires its specific enzyme

• Because enzymes only form a complex with their specific substrate,
they are named for their substrate

Substrate Enzyme
Lipid Lipase
Urea Urease
Maltose Maltase
Ribonucleic acid Ribonuclease
Lactose Lactase
Cellulose Cellulase
 Factors Affecting Enzymatic Speed

1. Substrate concentration: enzyme activity increases as substrate

concentration increases because there are more collisions between
substrate molecules and the enzyme
2. Temperature and pH: As the temperature rises, enzyme activity
increases to a certain point, then decreases because the enzyme
denatures and becomes inactive. Under extreme conditions of pH,
denaturation also occurs.
3. Enzyme concentration: The higher the enzyme concentration
in a reaction mixture, the greater the number of active sites
available and the greater the likelihood of enzyme-substrate
complex formation, as long as there is sufficient substrate
available
3. Enzyme concentration, presence of inhibitors and enzymes
cofactor are other factors that effect the activity of an
enzyme
• Inhibitor: a molecule that binds to an enzyme and
decreases its activity
• Cofactor: some enzymes require a helper molecule to
bind to them so they can act as catalysts