Topic #2 Molecular
Biology
I.
Molecules to metabolism
A. Molecular biology
1. Molecular biology explains living processes in
terms of the chemical substances involved
2. Many molecules are important to metabolism
a. Simple ones like water
b. Complex ones like proteins and nucleic acids
i. Proteins carry out a huge range of tasks
ii. DNA and RNA are the molecules that make
up genes
I.
Molecules to metabolism
B. Carbon compounds
1. Carbon atoms can form four bonds allowing a
diversity of compounds to exist
a. 15th most abundant element on earth
b. The diversity of carbon compounds is largely
due to the properties of the carbon atom
2. Carbon atoms form covalent bonds with other
atoms
a. Strongest bonds
b. Stability based on carbon results
3. Carbon can form up to 4 covalent bonds
a. Can form double or triple bonds
b. Can bond with itself or other atoms
I.
Molecules to metabolism
C. Classifying carbon compounds
1. Life is based on carbon compounds including
carbohydrates, lipids, proteins and nucleic acids
a. Carbohydrates
i. C, H and O
ii. 2:1 ration of hydrogen to oxygen – always
b. Lipids
i. Insoluble in water
ii. Ex. Steroids, waxes, fatty acids and
triglycerides
iii. Triglycerides are fats if solid at room temp,
oils if liquid at room temp
c. Proteins
i. One or more chains of amino acids
I.
Molecules to metabolism
ii. Contain C, H, O and N
iii. Two different amino acids also contain S
d. Nucleic Acids
i. Made up of chains of subunits called
nucleotides
ii. C, H, O, N and P
iii. Two types: DNA and RNA
D. Metabolism
1. Metabolism is the web of all the enzyme
catalyzed reactions in a cell or organism
2. Most happen in the cytoplasm of cells but some
happen outside of cells
3. It is the sum of all chemical reactions that occur
in a living thing
I.
Molecules to metabolism
4. consists of pathways in which one molecule is
transformed into another
5. even primitive prokaryotic cells like bacteria have
metabolism
E. Anabolism
1. Anabolism is the synthesis of complex molecules
from simpler molecules including the
formation of macromolecules from monomers by
condensation reactions  ?
2. Includes these processes:
a. Protein synthesis using ribosomes
b. DNA synthesis during replication
c. photosynthesis
I.
Molecules to metabolism
d. Synthesis of complex carbohydrates
F. Catabolism
1. Catabolism is the breakdown of complex
molecules into simpler molecules including the
hydrolysis of macromolecules into monomers
2. Large molecules are broken down into small
ones
3. Involves these processes
a. Digestion of food
b. Cell respiration
c. Digestion by decomposers
**Let’s draw some organic molecules if we haven’t
already**
II. Water
A. Hydrogen bonding in water
1. Water molecules are polar and hydrogen bonds
form between them
2. Has a positive side – the hydrogens and a
negative side – the oxygen
3. the atoms are shared unequally
4. both positively charged particles and negatively
charged particles will be attracted to water
5. the attraction between water molecules is called
a “hydrogen bond”
(more an intermolecular force than a bond…)
B. Properties of water
1. Hydrogen bonding and dipolarity explain the
cohesive, adhesive, thermal and solvent properties of H2O
II. Water
1. Cohesive properties
a. Binding together of two water molecules
b. Water molecules stick to each other
c. Useful for transport in plants  water can
move over 100 meters against the force of
gravity
2. Adhesive properties
a. Hydrogen bonds can form between water and
other polar molecules
b. Water will stick to other surfaces
3. Thermal properties
a. High specific heat capacity
i. It takes a lot of energy to raise the
temperature of water
II. Water
ii. To cool down, water must lose relatively
large amounts of energy
iii. Water’s temperature remains relatively
constant so it’s a stable habitat for aquatic
organisms
b. High latent heat of vaporization
i. It takes a lot of energy to cause a water
molecule to become vapor
ii. Gives evaporation a cooling effect
c. High boiling point
i. Goes along with the latent heat of
vaporization
ii. Water is liquid for a wide range of temps
0° - 100°C
II. Water
C. Hydrophilic and hydrophobic
1. Substances can be hydrophilic and hydrophobic
2. Hydrophilic
a. “water-loving”
b. Some substances are attracted to water
c. These substances will dissolve in water
3. Hydrophobic
a. “water-hating”
b. Some substances are not attracted to water
c. These substances are insoluble in water
III. Carbohydrates and lipids
A. Carbohydrates
1. Monosaccharide monomers are linked together
by condensation reactions to form disaccharides
III. Carbohydrates and lipids
and polysaccharide polymers
2. Monosaccharides are single sugar units
a. Glucose
b. Fructose
c. Galactose
3. Disaccharides consist of two monosaccharides
linked together
a. Maltose = glucose + glucose
b. Sucrose = glucose + fructose
c. Lactose = glucose + galactose
4. Polysaccharides consist of many
monosaccharides
III. Carbohydrates and lipids
5. condensation reactions
a. Involves bringing two monosaccharides
together to make a disaccharide
b. Water is lost (condensation)
i. one monosaccharide loses OHii. One monosaccharide loses H+
c. Anabolic process and requires energy
B. Lipids
1. Triglycerides are formed by condensation from
three fatty acids and one glycerol
2. Lipids are diverse molecules
3. Lipids are not soluble in water
4. Triglycerides are one of the principal groups of
lipids
III. Carbohydrates and lipids
a. Fats
i. triglycerides that are solid at room
temperature
ii. Come from animals
iii. Made from saturated fatty acid chains
iv. Butter…lard
b. Oils
i. Triglycerides that are liquid at room
temperature
ii. Come from plants
iii. Made from unsaturated fatty acid chains
iv. Olive oil…corn oil…peanut oil…baby oil
wait…
III. Carbohydrates and lipids
C. Fatty acids
1. Fatty acids can be saturated, monounsaturated
or polyunsaturated
2. Hydrocarbon chain with a carboxyl group at the
end
3. carboxyl group is written –COOH
4. Length of hydrocarbon chain is variable
- most are 14-20 carbon atoms long
5. saturated
- single bonds between the carbons
- saturated with H bonds
6. monounsaturated
- ONE double bond between the carbons
III. Carbohydrates and lipids
7. polyunsaturated fatty acids
- more than one double bond between the
carbons
D. Unsaturated fatty acids
1. Unsaturated fatty acids can be cis or trans
isomers
2. Cis – hydrogen atoms are nearly always on the
same side of the two carbon atoms that are
double bonded
- low melting points
- liquids, therefore oils
3. Trans – hydrogen atoms are on alternate sides
or opposite from each other
- produced artificially
IV. Proteins
A. Amino acids and polypeptides
1. Amino acids are linked together by condensation
to form polypeptides
2. Polypeptides are chains of amino acids that are
made by linking amino acids together with
condensation reactions (Translation)
3. one amino acid loses an H+ and the other loses a
OH4. water is eliminated
5. Dipeptide
a. Made up of two amino acids
b. C-N bond is the peptide bond
6. Polypeptide
a. Chain of amino acids
IV. Proteins
b. Polypeptides are ~250 AA long
c. Some are smaller, others are huge
7. A polypeptide can be different from another
based on three things:
a. Size – how many AA are there?
b. Sequence – what is the order of the AA in the
polypeptide?
c. Type – which AA are in the polypeptide?
B. The diversity of amino acids
1. There are twenty different amino acids in
polypeptides synthesized on ribosomes
2. Amino acids all contain carboxyl groups, amino
groups, hydrogen and an R group
3. The R group provides the diversity
IV. Proteins
C. Polypeptide diversity
1. Amino acids can be linked together in any
sequence giving a huge range of of possible
polypeptides
2. size, sequence, type (like before)
D. Genes and polypeptides
1. The amino acid sequence of polypeptides is
coded for by genes
2. The number of AA sequences that can be
produced is immense
3. Living things actually only produce a small
fraction of the possible sequences
4. The AA sequence of each polypeptide is stored
in a coded form in the base sequence of a gene
IV. Proteins
5. Most genes store AA sequence of polypeptides
6. Three bases are needed to place each AA
E. Proteins and polypeptides
1. A protein may consist of a single polypeptide or
more than one polypeptide linked together
2. Collagen is made up of 3 long polypeptide chains
a. Great tensile strength bc they’re coiled
together
b. Stronger than they would be if they were
apart
c. Make up tendons, ligaments, skin and blood
vessel walls
F. Protein conformations
1. The amino acid sequence determines the three-
IV. Proteins
dimensional conformation of a protein
2. some are elongated with repeating units
3. some are globular and soluble in water
G. Protein functions
1. Living organisms synthesize many different
proteins with a wide range of functions
2. catalysts – enzymes in metabolism
3. muscle contraction – actin and myosin
4. cytoskeletons – microtubules
5. tensile strengthening – fibrous proteins
6. clotting – clotting factors, fibrin
7. transport – hemoglobin transports O2
8. hormones – insulin, FSH, LH
9. receptors – binding sites
IV. Proteins
10. packing of DNA – histone (only in eukaryotes)
11. immunity – antibodies
H. Proteomes
1. Every individual has a unique proteome
2. Proteome: all the proteins produced by a cell, a
tissue or an organism
3. The proteome of an individual is variable bc
different cells make different proteins
4. Within a species, there are strong similarities in
the proteome, but some differences
a. Everyone makes catalase in their blood
b. Daily activities change the release of some
proteins
V. Enzymes
A. Active sites and enzymes
1. Enzymes have an active site to which specific
substrates bind
2. Enzymes are globular proteins
3. Enzymes are biological catalysts
a. Speed up metabolic reactions
b. Do not become part of the end product
4. Convert substrates into products
enzyme
Substrate --------------- Products
5. Enzyme-substrate specificity
a. Many different enzymes are needed
b. Each enzyme catalyzes its own reaction
V. Enzymes
6. active site
a. Special binding region ON THE ENZYME
b. Where the substrate will bind
c. Shape and chemical properties match each
other
B. Enzyme activity
1. Enzyme catalysis involves molecular motion and
the collision of substrates with the active site
2. There are three stages
a. Substrate binds to the active site on the
enzyme
b. While substrates are attached to the active
site, they change into a new chemical substance
c. The products separate from the active site
V. Enzymes
3. the enzyme can be used again and again
4. most enzymatic reactions occur in water as
dissolved substances
http://highered.mheducation.com/sites/0072495855/stude
nt_view0/chapter2/animation__how_enzymes_work.html
 let’s watch it in
action!!
C. Factors affecting enzyme activity
1. Temperature, pH and substrate concentration
affect the rate of activity of enzymes
2. Temperature:
a. When an enzymatic reaction is heated, the
kinetic energy is increased and the rate of
reaction increases
V. Enzymes
b. When enzymes are heated, their bonds
vibrate more and the chance of the bond
breaking increases
c. Once the bonds break, the enzyme shape and
overall structure is disrupted…and it’s not the
same
i. the enzyme won’t function the same
ii. The enzyme is denatured – it’s structure is
destroyed
3. pH:
a. Low pH (0-6) means an acid
b. High pH (8-14) means a base or alkaline
solution
c. Enzymes have an optimum pH where their
V. Enzymes
activity is highest
d. It depends on the enzyme
i. Stomach? Low pH (2-4)
ii. Small intestine? Higher…8
iii. Mouth? 7 – neutral
4. Substrate concentration:
a. As substrate concentration rises, the # of
active sites on the enzymes are occupied
i. The reaction rate increases at first
ii. The reaction rate slows and stops once all
the active sites are occupied
Enzyme activity v pH
Enzyme Activity v substrate concentration
Enzyme Activity v temperature
D. Denaturation
1. Enzymes can be denatured
2. The structure of the protein can be altered to the
point where the molecule can’t function properly any
more
E. Immobilized enzymes
1. Immobilized enzymes are widely used in industry
2. Enzymes can be extracted from living cells and
used in industrial processes
3. enzyme can catalyze sugar into alcohol without
using live cells
4. Advantages
a. Enzyme can be easily separated from the
products – prevents contamination
b. Enzymes can be recycled and used again - $$
D. Denaturation
c. Increases enzyme stability
d. Substrates can be exposed to higher enzyme
concentrations – very fast reaction rate
VI. Structure of DNA and RNA
A. Nucleic acids and nucleotides
1. The nucleic acids DNA and RNA are polymers of
nucleotides
2. Nucleotides:
a. Sugar – 5 carbons (pentose)
b. Phosphate group – this is the acid, PO4-3
c. Base – nitrogen; one or two rings
i. adenine
iii. cytosine
ii. Thymine
iv. Guanine
v. uracil
B. Differences between DNA and RNA
1. DNA differs from RNA in the number of strands
normally present, the base composition and the type
of pentose
2. Sugar
a. DNA – deoxyribose
b. RNA – ribose
3. # of strands
a. DNA – two
b. RNA – one
4. base composition
a. DNA
i. Adenine(A)
iii. Guanine(G)
ii. Cytosine(C)
iv. Thymine (T)
b. RNA
i. A, G, C and Uracil (U)
C. Structure of DNA
1. DNA is a double helix made of two antiparallel
strands of nucleotides linked by hydrogen bonding
between complementary base pairs
2. Each strand consists of a chain of nucleotide linked
by covalent bonds
3. Two strands are parallel but run in opposite
directions = antiparallel
a. One strand is in the 5’-3’ direction
b. The other is in the 3’ – 5 direction
4. The two strands are wound together to form a
double helix
5. The strands are held together by complementary
base pairing between nitrogen bases
a. A-T/T- A
b. C-G/G-C