Chapter 2

Molecular Biology
I. Molecules to Metabolism
A. Organic chemistry: chemistry of carbon
compounds

1. Biochemistry: branch of organic

chemistry that attempts to explain the
chemistry characteristics of living
organisms
2. All living things are made up of molecules that
can be grouped into four types

a) carbohydrates
b) lipids
c) proteins
d) nucleic acids

3. Biochemical processes follow certain common

pathways for which common patterns can be studied
(photosynthesis and cellular respiration)
B. Molecular biology is the chemistry of living
organisms

1. Four groups of molecules interact with

each other in a wide variety of ways in
order to carry out the metabolism of each
cell

2. Insulin and plasma

membrane example
Insulin example
C. Carbon-based life

1. Organic chemistry is the study of compounds

that contain carbon, but some compounds that
contain carbon are not organic Ex. Carbon
Dioxide

2. Carbon is the keystone element for life on

Earth since carbohydrates, proteins, lipids and
nucleic acids contain carbon
3. Carbon has six electrons and six protons
a) 2 electrons fill the first inner shell
b) 4 electrons fill the second shell
c) In order to be stable with 8 electrons in
the second shell, it needs to share electrons
with 4 other atoms to form covalent bonds
4. The ability to bond to 4 other atoms allows it
to make many compounds of various sizes

5. Hydrogen, oxygen, nitrogen, and phosphorus

are the other elements common in living
things
6. Large carbon molecules

a) Monomers: small, simple molecules

b) Polymer: repeated, linked units

Polymers

c) Macromolecules: large polymers

Macromolecule
D. Biochemical compounds that are important to
living organisms

1. Important biochemical molecules and their

building blocks
Molecule Building Block

Carbohydrates Monosaccharides

Lipids Fatty acids, glycerol

Proteins Amino Acids

Nucleic Acids Nucleotides

2. Metabolism is the way that the molecules

interact with each other in living things
Molecule Subcategory Example Molecules

Carbohydrate Monosaccharides Glucose, galactose,

fructose, ribose

Disaccharides Maltose, lactose, sucrose

Polysaccharides Starch, glycogen, cellulose,

chitin

Proteins Enzymes, antibodies,

peptide hormones

Lipids Triglycerides Fat in adipose cells

Phospholipids Cell membrane

Steroids Hormones

Nucleic Acids DNA, RNA

E. Metabolism: reactions controlled by enzymes

1. Metabolism: all of the reactions within

all of the cells when molecules collide with
enough energy to cause a reaction

2. Factors that determine if reactions will

occur during a collision
a) Identity of the colliding molecules
b) Orientation of the colliding molecules
c) Speed of the molecules when they
collide
3. Cells use enzymes to increase the chance that a
collision will lead to a reaction

4. Enzyme: protein that have a specific shape into which

a reactant can fit called the active site

a) Enzyme acts as a catalyst to help the

reaction and it is not used up in the reaction

b) Enzyme enables the reaction to occur at a

higher reaction rate and with less collisional
energy (activation energy) then a reaction
without the enzyme

c) Enzyme lowers
the activation energy in the reaction
 Enzyme action

5. Many reactions are occurring inside each

living organism’s cells and most are catalyzed
by enzymes. These are the reactions that
make up your overall metabolism

a) replication of DNA
b) synthesis of RNA and proteins
c) cell respiration to make ATP energy
d) photosynthesis to make carbohydrates
F. Metabolism = catabolism + anabolism

1. Catabolism: enzyme reactions that

convert large, complex molecules like food
into smaller simpler molecular forms

2. Anabolism: enzyme reactions that

convert small, simple molecules into a
large, more complex molecule
3. Animals rely on foods to obtain the building
blocks molecules that they need

a) Food is digested into building blocks

(catabolism)

a) Building blocks are transported to body

cells where they bond together to form
larger molecules (anabolism)
4. Digestion of food takes place in alimentary canal by
digestive enzymes called hydrolysing enzymes

5. Hydrolysis: reactions that requires a water

molecule to split apart a larger molecule

a) hydrolysis of disaccharide to 2
monosaccharides
Ex: lactose + water  glucose + galactose
b) Hydrolysis of polysaccharide to many
monosaccharides
starch + (many) water  many glucose

c) Hydrolysis of triglyceride lipid to glycerol

and fatty acids
triglyceride + 3 water glycerol + 3 fatty acids

d) Hydrolysis of a polypeptide (protein) to amino

acids
Protein + (many) water  (many) amino acids
6. Condensation reactions: water molecules are
produced when monomers are linked together to form
larger molecules

a) Reverse the 4 previous reactions to

show a condensation reaction
Ex: (many)amino acids  protein + water

b) Uses a different enzyme to create covalent

bonds instead of breaking them as in hydrolysis
reactions
G. Summary
1. Organism’s metabolism comprises all of
the reactions that occur within all of its cells

2. Metabolism is the sum of all the reactions

that work to hydrolyse large biochemical
substances into smaller subcomponents
(catabolism)

3. Also includes all the reactions that rebuild

large complex substances from the smaller
subcomponents (anabolism)
II. Water
A. The structure of water molecules and the
resulting polarity

1. Water is the solvent of life

a) Living things have water within
their cells (cytoplasm)
b) Water in the surrounding
environment
2. Aqueous solution: solution in which water is
the solvent

3. Structure of water is important for

understanding the properties of water
a) Hydrogen and oxygen bonds are polar
covalent bonds
b) Unequal sharing of electrons
c) Slight negative charge at the oxygen end
d) Slight positive charge at the hydrogen
end
e) Water is polar
f) Water exhibits dipolarity, causing it to interact
with other water molecules and other molecules

g) Hydrogen bonds: short-lived (ephemeral)

attractions between O and H atoms of different
water molecules
B. Cohesive Properties

1. Cohesion: molecules of the same type are

attracted to each other

2. Positive end of one water molecule

attracts the negative end of another water
molecule forming a hydrogen bond

3. When water freezes the hydrogen bonds become

locked into place

4. Liquid water molecules have faster motion and

water molecules influence each other
5. Ephemeral hydrogen bonding explains a
variety of events

a) why water forms into droplets

b) why water has surface tension to allow
some organisms to “walk on water”
c) how water is able to move as a water
column in the vascular tissue of plants
C. Adhesive properties

1. Adhesion: attraction between

two unlike molecules

2. Water is attracted to cellulose molecules

by hydrogen bonds in vascular tissue of plants

3. Cohesion and adhesion work

together to “pull” up a column of
water through a plant
Cohesion and Adhesion clip
D. Thermal properties
1. Water has thermal properties that are
important to living things.

2. Water has a high specific heat: water can

absorb or give off a large amount of heat
without changing the temperature very much.

3. Specific heat: amount of heat per unit

mass required to raise the temperature 1°C

4. Living things are composed of a great deal

of water, so the water content acts as a
temperature stabilizer
5. Water has a high heat of vaporization: water absorbs a
large amount of heat when it evaporates

a) Acts as a cooling mechanisms

b) Internal body heat results in perspiration

c) Perspiration then evaporates from the skin

d) Heat that turned the water molecules from

liquid to vapor came from your body, so
sweating makes you feel cooler and it actually
lowers your body temperature

6. Heat of vaporization: amount of heat required to

convert a unit mass of liquid into vapor with no increase
in temperature
E. Solvent properties

1. Water is an excellent solvent of other

polar molecules (most molecules inside and
outside cells are polar)
a) carbohydrates, proteins, and
nucleic acids are polar
b) “Likes dissolve likes”
c) lipids are non polar and organisms
have strategies for transporting them
 2. Water is the medium in which most of
the biochemistry of a cell occurs (aqueous
solutions)
Aqueous solution Location Common reactions
Cytoplasm Fluid inside cells but Glycolysis/protein
outside of organelles synthesis

Nucleoplasm Fluid inside nucleus DNA replication/

transcription

Stroma Fluid inside chloroplast Photosynthesis

Blood plasma Fluid in arteries, veins, Loading and unloading

capillaries of respiratory
gases/blood clotting
F. Examples of water as a solvent in plants and
animals

1. Vascular tissue in plants carries water and a

variety of dissolved substances
a) Xylem: carries water and
minerals from roots to leaves
b) Phloem: transports dissolved
sugars from leaves to stems, roots,
and flowers
2. Blood is the most common transport medium
in animals and mostly made up of water

a) Plasma: liquid portion of blood

b) Solutes in blood: glucose, amino acids,

fibrinogen (protein for blood clotting),
hydrogen carbonate ions (transporting
carbon dioxide)
G. Water “loving” or water “fearing” substances

1. Molecules in living systems interact with

water in a variety of ways

2. Hydrophilic: water “loving”- polar

substances that can easily dissolve in water
and the majority of biochemically important
molecules
a) often due to functional groups that
are polar
b) carbohydrates are polar due to
hydroxyl (OH) functional group
3. Hydrophobic: water “fearing” –non-polar
molecules and typically are composed of just
carbons and hydrogens

a) Methane (CH4) is hydrophobic and will

not dissolve in water

b) Biochemically important molecules that

are non-polar: fatty acids found in
triglyceride lipids and phospholipids

c) Carboxyl function group at the end of a

fatty acid does make it slightly polar, but the
long hydrocarbon chain makes the majority of
the molecule non-polar
4. Protein molecules can be differentially polar
depending on the arrangement of the amino acids

a) Some amino acids are relatively polar and some

non-polar

b) Location of each type of amino acid is

important in the 3D structure of the protein

c) Proteins that attach to and extend down into

the cell membrane are hydrophobic and mix with
fatty acid tails of the membrane

d) Proteins that extends out of the membrane are

hydrophilic amino acids that can mix with water
environment either inside or outside the cell or
organelle
H. How does solubility in water affect the mode
of transport of molecules in organisms?

1. Water in living organisms acts as a

mode of transport for the variety of
molecules that must be moved about both
within cells and between cells

2. Due to different polarities, each type of

substance has a different solubility in
whatever aqueous environment it is found
in
 Polarity of Different Molecules
Substance High/low Mode of transport in aqueous /dissolves
solubility in easily if no special mode
water
Glucose Polar: High No special mode
solubility
Amino Acids Vary: reasonably No special mode
soluble
Cholesterol Non-polar: low Transported by blood proteins that have polar
solubility amino acids on outer portion to give water
solubility

Fats Non-polar: low Transported by blood proteins that have polar

solubility amino acids on outer portion to give water
solubility

Oxygen Travels as O2: Hemoglobin

low solubility
Sodium Ionizes: high No special mode
chloride(NaCl) solubility
I. Comparing water and methane

Use the textbook reading and handout to

determine the differences between methane CH4
and water H2O
Explain using hydrogen bonds
III. Carbohydrates

A. Monosaccharide: the building blocks of

disaccharides

1. Monosaccharides: monomer of
carbohydrates and classified by the number of
carbon atoms they contain
a) trioses: 3 carbons with formula C3H6O3
b) pentoses: 5 carbons with formula C5H10O5
c) hexoses: 6 carbons with formula C6H12O6
2. Condensation reaction occurs to join two
monosaccharides together to form a
disaccharide and water clip

a) Two alpha-D-glucose molecules join to form

maltose
clip
b) Alpha-D-glucose and galactose molecules
join to form lactose
c) Glucose and fructose join to form sucrose
B. Monosaccharides: the building blocks of
polysaccharides

1. Repeatedly bonding glucose

monosaccharides by condensation reactions
produces a variety of very large molecules
(polymers)
2. Examples of glucose polymers
a) Cellulose: component of plant cell
walls for rigid support of stem, roots, and
leaves

b) Starch: products of photosynthesis are

stored in plants as starch in roots

c) Glycogen: animal stores excess glucose

as glycogen in liver and muscle tissue
C. Summary list of carbohydrates

1. Monosaccharides: glucose, galactose,

and fructose

2. Disaccharides: sucrose, lactose, and

maltose

3. Polysaccharides: cellulose, starch

(amylose and amylopectin), glycogen
Summary clip
 3D Models of polymers
Cellulose, Starch, and Glycogen

Note the following

1. All are polysaccharides of glucose
2. Bonding numbers such as 1,4 linkages refers to
the carbon numbers that create covalent bonds
3. Starch has 2 subcomponents: Amylopectin and
amylose
4. All three are composed of many thousands of
glucose monomers
Glycogen:
http://www.biotopics.co.uk/jsmol/glycogen.html

Cellulose:
http://www.biotopics.co.uk/jsmol/cellulose.html

Starch: Amylose
http://www.biotopics.co.uk/jsmol/amylose.html

Starch: Amylopectin:
http://www.biotopics.co.uk/jsmol/amylopectin.html
IV. Lipids
A. Fatty Acids: contain a
1. Carboxyl group (-COOH) at one
end

2. Methyl group (CH3) at the other

end

3. Chain of hydrocarbons (hydrogen

and carbon atoms) that is usually 11-
23 carbons long
Lipids
B. Saturated fatty acids: carbons are carrying as
many hydrogen atoms as they can (saturated
with hydrogens)

1. Found in animal products like butter,

bacon, and fat in red meat

2. Solid at room temperature

3. No double bonds between the carbons

4. Straight shape with no kinks or bends in

the chain
C. Monounsaturated fatty acid: one double
bond in the chain of hydrocarbons (two empty
spaces where hydrogen could be)

1. Absence of two consecutive hydrogen

atoms on the same side of the carbon atom
chain causes the molecule to bend at the
zone where the double bond is
D. Polyunsaturated fatty acid: have at least 2
double bonds in the carbon chain

1. Two or more carbons are not carrying

the maximum number of hydrogen atoms

2. Usually liquids at room temperature

3. Usually from plants (olive oil)

4. Can have a very long hydrocarbon chain with
many double bonds which causes the molecule
to have many bends that it starts to curve over
onto itself or twist around itself
E. Hydrogenation: cis and trans fatty acids

1. Hydrogenation: polyunsaturated fats are

hydrogenated by removing or partly eliminating the
double bonds by adding hydrogen atoms
a) occurs in heavily processed foods
b) straightens out the bent shape of
the unsaturated fatty acids

2. Cis fatty acids: naturally curved fatty

acids

3.Trans fatty acids: hydrogenated,

straightened out fatty acids
4. Majority of trans fatty acids are the result of chemical
transformation in food processing (some natural in meat
and dairy)

a) Usually partially hydrogenated and still have one or

more double bonds : partially hydrogenated oils is
usually on the ingredients list of a product

b) Results in a more solid or spreadable fat,

inexpensive, and long lasting, good for use in a deep
fryer

c) Trans fats have been implicated in various

health disorders like obesity, heart disease, stroke,
cancer, and diabetes: can increase your bad
cholesterol (LDL) and decrease your good cholesterol
(HDL)
5. Omega-3: cis fatty acids: the first carbon
double bond occurs at the third carbon: fish are a
good source of omega-3
 Fatty Acids

Curved Straight/straighter

Unsaturated Saturated

Poly Mono Animal fats

Cis Trans

Omega-3 Omega-6 Partially Fully

Hydrogenated
F. Condensation reactions result in the formation
of triglyceride lipids

1. Triglyceride lipids: made up of glycerol

and three fatty acids

a) Animal cells called fats and plants

cells called oils
b) Characteristics of the fatty acids
will determine the overall
characteristics of the fat or oil
2. Condensation reactions create the covalent
bonds between the glycerol portion and the three
fatty acids of a triglyceride lipid
G. Energy storage solutions in humans

1. Chemical strategies to store molecules

in reserve to use for ATP production during
cell respiration

a) storing glucose as glycogen in

liver and muscle
b) storing triglyceride lipids within
adipose fat cells
2. Triglyceride lipids can by hydrolyzed into two
carbon segments that can enter into cell
respiration and efficiently produce ATP (energy)

3. Lipids have twice the energy content per gram

compared with other molecules like
carbohydrates and proteins

4. Another advantage for long-term storage is that

lipids are insoluble in water, so they don’t upset
the osmotic balance of the solutions (blood,
cytoplasm)
H. Calculating the body mass index

1. Body mass index (BMI): indicator of healthy

weight and is a number that reflects both the weight
and the height of a person
(person that is taller should weigh more)

2. Three ways to determine BMI

a) Formula in metric or imperial (English)
BMI = weight (kg)/ (height (m) x height (m)
BMI = weight (lb) / (height (in) x height (in) x703
 b) Nomogram: graph to read the BMI
value from a central intersection point
between weight and height

c) Online calculator that outputs the BMI

after height and weight measurements are
entered

3. Value is then correlated with information that

shows whether a value reflects someone being
underweight, normal weight, overweight, or
obese
Interpreting BMI Values

BMI Description Category

Below 18.5 Underweight

18.5-24.9 Normal weight

25.0-29.9 Overweight

30.0 and above Obese

BMI chart
V. Proteins

A. Formation of polypeptides

1. Cells use the naturally occurring

20 amino acids to synthesize
polypeptides (proteins)

2. Each polypeptide is made under

the control of a gene (segment of
DNA)

3. Peptide bond: covalent bond that

links amino acids together
Proteins
4. Each cell is differentiated to have a specific function
and uses only the genes they need for that cell type
a) Pancreas cell will turn on the gene
for the synthesis of the peptide
hormone insulin

5. Some genes code for proteins involved in common

cell functions of most cells
a) Protein components that make up
ribosomes which are in all cells

6. Total number of active genes in humans is difficult to

determine, but it is thought to be between 20,000 and
25, 000 genes in each of our cells
a) number of genes doesn’t show the organisms
complexity
b) mouse has approximately 30,000 and rice has
51,000
7. All genes are the genetic code for the
possible polypeptides found within the
organism

8. All polypeptides are synthesized from the

same monomers (amino acids)

9. Virtually all organisms use the same

genetic code and use the same 20 amino acids

10. Each amino acid differs in the R or

variable group bonded to the central carbon
atom
11. Polypeptides are synthesized at
ribosomes under the control of genes and it
is a condensation reaction

12. The sequence of the amino acids is

determined by the DNA, but the
condensation reactions are the same.
 Amino Acids

Section 2-3

Amino group Carboxyl group

General structure Alanine Serine

Go to
Section:
B. Polypeptides are highly variable

1. Amino acids are assembled in a certain

ordered determined by triplets of
nucleotides along RNA and is directed by a
ribosome

2. Large choice for the sequence of amino

acids as well as the total number of amino
acids in the polypeptide
a) Each polypeptide has a specific
purpose, its own sequence and own 3D
shape

b) The shape determines the function of the

protein

c) Single change in one amino acid can

change the function of the protein
 A Protein

Section 2-3

Amino
acids

Go to
Section:
C. Levels of polypeptide and protein structure

1. Proteins have many functions in cells

and organisms and have many forms and
structures.

2. The function is closely related to its

structure
 Examples of proteins and their function
Protein Function
Rubisco Enzyme photosynthesis
Insulin Protein hormone to decrease blood
sugar levels
Immunoglobulin Antibody that recognizes an
antigen as part of the immune
response

Rhodopsin Pigment in the retina of the eye for

low light conditions
Collagen Protein in connective tissue like
skin, tendons, and ligaments

Spider silk Fibrous protein spun by spiders for

webs
3. Four levels of organization to protein structure

a) Primary: sequence of amino acids

which will determine the 3D shape

b) Secondary: repetitive shapes of

either helix (spiral staircase) or
pleated sheet
(sheet with corrugated folds)
(ex: spider silk)
D. Some proteins are more than one polypeptide

1. Protein: is an organic substance of

covalently bonded amino acids that is ready
to carry out its function

2. Polypeptide: single amino acid chain

a) if it can carry out its function, it is
a protein

b) some polypeptides cannot serve its

function until they combine with
another polypeptide
(quaternary structure)
c) Tertiary: globular shape
(ex: enzymes)

d) Quaternary: two or more polypeptides combined

together to make a single protein (ex:
hemoglobin)

Structure
Summary
E. Your unique proteome

1. Genome: specific DNA sequence that is

unique to one individual

2. Proteome: specific set of proteins that

is unique to one individual
3. Protein placed in a pH environment out of its
normal range: Lose its 3D shape and function

4. Fluid environment like cytoplasm, blood

plasma can be flooded with H+ (acid) or OH-
(base), the extra charges can prevent normal
hydrogen bonding: protein will not take on its
normal 3D shape and it will not function
normally
F. Proteins can be denatured by heat and alternation of
the pH environment

1. Changes in temperature and pH can disrupt the

intra-molecule bonds that hold together the
secondary, tertiary, and quaternary structure

2. Increase in temperature
a) Increases the molecular motion
causing the hydrogen bonds of secondary
structure to break
b) Protein loses its 3D shape and then its
function
c) If peptide bonds remain intact, the protein
will return to its normal shape and function
if it is returned to normal temperature
VI. Enzymes are organic molecules that act as catalysts

1. Enzymes are proteins: long chain of amino

acids with specific 3D globular shape

2. Active site: section of the enzyme that matches

the substrate (glove fitting a hand: glove is the
active site and hand is the substrate)or (lock and
key: lock is active site and key is substrate)

3. Substrate: substance on which the enzyme acts

a) specific to the enzyme
b) must enter the enzyme with enough rate
of motion that will provide the energy
necessary for the reaction
 4. Activation energy: energy needed to start
the reaction

5. Enzymes lower the activation energy

of the reactions

6. Enzymes are not used up the reactions

and can be used many times

7. Enzymes will not force a reaction that

would not otherwise happen without the
enzyme
Enzyme action
Active site of enzyme

Yellow: substrate
B. Factors affecting enzyme-catalysed reactions:
All chemical reactions require the molecules to collide with a
high enough rate of speed in order to react with each other

1. Effect of temperature: rate of motion of the substrate and

enzyme is dependent on the temperature
a) Higher temperature: molecules are moving faster
and will collide more often and with more energy

b) Reactions with or without enzymes will increase

their reaction rates as the temperature increases

c) Reactions with enzymes do have an upper limit of

temperature: enzyme will lose its 3D shape as the intra-
molecule bonds are stressed and broken by high
temperatures
d) Denaturation: enzyme loses its 3D
shape, can be temporary if the intra-
molecular bonds can re-establish after the
temperature returns to suitable level
2. Effect of pH: change in pH can lead to
the improper charge matching between the
enzyme and substrate causing the enzyme
to become less efficient

a) the active site has amino acids

with areas that are positively or
negatively charged

b) the negative and positive areas of the

substrate much match the opposite
charge when the substrate is in the
active site of the enzyme
pH Scale
Acid: pH = 0-6

Base: pH = 8-14

Neutral: pH = 7

Acids and Bases

c) Acid added: (pH is lowered) more H+
ions bond with the negative charges and
prevents the proper matching

d) Base added: (pH is raised) more OH- ions

bond with the positive charges and prevents
the proper matching

e) There is not one best pH for all enzymes:

many in the human body work best near
neutral (pH=7), but pepsin for digesting food
in the stomach works in an acidic environment
(pH near 2)
Effect of pH on rate of the reactions
3. Effect of substrate concentration: As the
concentration of substrate increases
(with enough enzyme), then the rate of the
reaction will increase to a certain limit

a) more reactant molecules, there are more

to collide and react

b) enzymes have a maximum rate at which

they work, so if every enzyme is working,
adding more substrate will not increase the
reaction rate further
Effect of substrate concentration on
rate of the reactions
C. Use of immobilized enzymes in industry

1. Industrial applications for the use of catalytic

proteins

2. Expensive to extract or produce pure enzymes in

large quantities so enzymes in industry need to be
reused repeatedly

3. Difficult to remove enzymes from liquid

productions in solutions so that the enzyme can be
used further

4. Invent ways to trap the enzymes in place and

prevent them from getting washed out with the
products
5. Calcium alginate: substance in tiny
pores of beads that can hold the enzymes
and immobilize them

6. The alginate beads are recovered in the

industrial process and the enzymes can be
reused
D. Use of immobilized lactase to produce lactose-
free milk

1.Lactose: sugar found in milk and most

humans are born with the ability to digest it by
producing the enzyme lactase in the digestion
system

2. Lactase: enzyme that digests the

disaccharide lactose into two
monosaccharides (glucose and galactose) and
the monosaccharides can be absorbed into the
bloodstream
3. Lactose intolerant: lose the ability to produce
lactase as you get older: milk and dairy products
are not digested and the normal bacterial
colonies in the intestines feed directly on the
lactose

4. The bacteria are being overfeed and this leads

to cramping, excessive gas, and diarrhea

5. Can eat dairy products that have been treated

with lactase before consumption
6. Nutrients in milk are not affected, but the
lactose has been pre-digested so lactose
intolerant people can absorb the
monosaccharide sugars

7. Lactase enzyme molecules are trapped in the

small pores of the alginate beans and then the
milk is exposed to the beads for enough time
for pre-digestion to occur
Interesting fact: There are more people with
lactose intolerance than there are people who do
not have the condition

In genetics: lactose intolerance is consider the

wild-type (Wild-type: most common phenotype
in a natural population)

High incidence of lactose intolerance in some

ethnic groups and low incidence in others: good
example of natural variation in populations
VII.Higher level metabolism

A. Metabolism: sum of all chemical

reactions that occur within you as a living
organism
Anabolic Reactions Catabolic Reactions

Build complex molecules Break down molecules

Are Endergonic Are Exergonic

Are Biosynthetic Are degradative

Ex: photosynthesis Ex: cellular respiration

B. Metabolic pathways: sequences of metabolic
reactions in organisms catalyzed by enzymes

1. Some consists of cycles or chains of

reactions
Substrate A  Substrate B  Final product
( Represents an enzyme)

2. Pathways are usually carried out in

designated compartments of the cell where
necessary enzymes are clustered

3. Enzymes required for pathways are

determined by the cell’s genetic makeup
C. Induced-fit model of enzyme action

1. Lock and key model: 1890 Emil Fischer

proposed the model of enzyme action:
substrate molecules fit like a key into a
rigid section of the enzyme (lock): the
model has been modified
2. Induced-fit model: Enzymes undergo
significant changes in their conformation when
substrates combine with their active site

a) Hand and glove analogy

b) Conformational changes and induced fit are

the result of changes in the R-groups of the
amino acids at the active site of the enzyme, as
the enzyme interacts with the substrate
D. Activation energy (AE): energy necessary to
destabilize the existing chemical bonds in the
substrate of an enzyme-substrate catalyzed
reaction

1. Enzymes lower the activation energy

2. Chemical reactions occur faster because

they reduce the amount of energy needed

3. Enzymes do not alter the proportions of

reactants or products
E. Mechanism of enzyme action

1. Surface of the substrate contacts the

active site of the enzyme

2. Enzyme changes shape to accommodate

the substrate

3. Temporary complex called the enzyme-

substrate complex forms
4. AE is lowered and the substrate is
altered by the rearrangement of the existing
atoms

5. Transformed substrate, the product, is

released from the active site

6. The unchanged enzyme is then free to

combine with other substrate molecules
Equation summarizes enzyme action
E + S  ES   E + P

E = enzyme
S = substrate
ES= enzyme substrate complex
P = products
F. Inhibition: effects of certain types of
molecules on enzyme active site that can alter
the enzyme activity

G. Competitive inhibition: a competitive

inhibitor molecule competes directly with the
usual substrate for the active site of an enzyme

1. Substrate will have fewer encounters

with the active site and rate of the chemical
reaction will be decreased
2. Competitive inhibitor must have a
structure similar to the substrate

3. May be reversible or irreversible

4. Reversible competitive inhibition could

be overcome by increasing the substrate
concentration
5. Example: Sulfanilamide is a drug used
to kill bacteria during an infection

a) Folic acid is need by the bacteria

and is produced by enzyme action on
PABA

b) The drug competes with PABA

and blocks the enzyme

c) Prevents the production of folic acid

resulting in the death of the bacteria
H. Non-competitive inhibition: involves an inhibitor
that does not compete for the enzyme’s active site,
but the inhibitor interacts with another site on the
enzyme

1. Another name for non-competitive inhibition is

allosteric inhibition and the site the inhibitor binds to is
called the allosteric site

2. Binding at the allosteric site changes the shape of

the enzyme making it non-functional

3. Can be reversible or irreversible

4. Some allosteric interactions activating an enzyme

instead of inhibiting it Inhibition
I. End-product inhibition: prevents the cell from
wasting chemical resources and energy by
making more of a substance than it needs

1. Many metabolic reactions occur in an

assembly line type of process so a specific end
product can be made

2. Each step is catalyzed by an enzyme

3. When the end product is in large enough

quantities, the assembly line stops
4. The assembly line is stopped by inhibiting
the action of the enzyme in the first step

5. As the existing end product is used up the

cell, the first enzyme is reactivated

6. The enzyme that is inhibited and

reactivated is an allosteric enzyme

7. When present in high concentrations, the

end product binds with the allosteric site and
causes inhibition to the first enzyme
 8. Lower concentrations of the end product
result in fewer bindings with the allosteric
site and therefore activating the enzyme

End product inhibition