Most macromolecules of living cells are broken apart via hydrolysis and are

formed via (condensation) dehydration synthesis.

Lipids

A lipid is any biological molecule that has low solubility in water and high
solubility in nonpolar organic solvents.

There are six major groups of lipids:

1) fatty acids
a) Building blocks for most, but not all, complex lipids
b) Usually an even number of carbons, maximum # of carbons in humans is
24
c) Can be saturated or unsaturated
i. Saturated fatty acids contain only single carbon-carbon bonds
ii. Unsaturated fatty acids contain one or more carbon-carbon
double bonds
d) Oxidation of fatty acids liberates large amounts of chemical energy for the
cell, and most lipids reach the cell in the form of fatty acids and NOT as
triacylglycerols.

2) Triacylglycerols
a) Commonly called triglycerides or simply fats and oils, are constructed
from a three carbon backbone called glycerol, which is attached to 3 fatty
acids
 b) Their function is to store energy and may also provide thermal insulation
and padding to an organism
c) Adipocytes, also called fat cells, are specialized cells whose cytoplasm
contains almost nothing but triglycerides.

- Lypolysis of triacylglycerols take place inside the adipose cells when

blood levels of epinephrine, norepinephrine, glucagon or ACTH are
high!!

3) Phospholipids
a) Are built from a glycerol backbone as well, but a polar phosphate group
replaces one of the fatty acids. The phosphate group lies on the opposite
side of the glycerol from the fatty acids making this lipid polar on one
end and nonpolar on the other end.
b) This condition is called amphipathic, and makes phospholipids especially
well suited as the major component of membranes
4) Glycolipids
a) Are similar to phospholipids, except that glycolipids have one or more
carbohydrates attached to the 3-carbon glycerol backbone instead of the
phosphate group.
b) Are also amphipathic
c) They are found in abundance in the membranes of myelinated cells
composing the nervous system.
d) Also serve as markers for cellular recognition.

5) Steroids
a) are four ringed structures, which regulate metabolic activities.
b) Include some hormones, vitamin D, and cholesterol, an important
membrane component.

6) Terpenes
a) include vitamin A, a vitamin important for vision
b) Their building block is the hydrocarbon isoprene, CH2=C(CH3)-CH=CH2 .
Terpene hydrocarbons therefore have molecular formulas (C5H8)n

Another class of lipids is the 20 carbon eicosanoids

a) Eicoanoids include prostaglandins, thromboxanes, and
leukotrienes
 b) Eicosanoids are released from cell membranes as local hormones
that regulate, among other things, blood pressure, body
temperature, and smooth muscle contraction.
c) Aspirin is a commonly used inhibitor in prostaglandin synthesis

Since lipids are insoluble in aqueous solution, they are transported in the blood via
lipoproteins.
a) A lipoprotein is a biochemical assembly that contains both proteins and
lipids. It contains a lipid core surrounded by phospholipids and
apoproteins.
b) Thus lipoproteins are able to dissolve lipids in its hydrophobic core, and
then move freely through the aqueous solution due to its hydrophilic
shell
c) Are classified according to density. The greater the ratio of lipid to
protein, the lower the density.
d) The major classes of lipoproteins are chylomicrons, very low density
lipoproteins (VLDL), low density lipoproteins (LDL – “bad
cholesterol”), and high density lipoproteins (HDL – “good cholesterol”)
- is arranged according to density.

Lipids are also used as intracellular messengers

Proteins

Proteins are the building blocks from which cells are assembled.

They adopt the philosophy “structure dictates function”

Proteins are assembled from a set of 20 different a-amino acids. They are
called alpha amino acids because the amine is attached to the carbon alpha to the
carbonyl group.

Basic amino acids:

1) lysine
2) histadine
3) arginine

There are also 10 essential amino acids in humans, which means that these amino
acids can’t be formed, so we must ingest them.

A protein molecule is made from a long chain of these amino acids, each linked
to its neighbor through a covalent peptide bond. Proteins, therefore, are also
called polypeptides. Each amino acid in a polypeptide chain is referred to as a
residue.

Digested proteins reach the cells of the human body as single amino acids.

Notes on the Amino Acids:

a) There are twenty standard amino acids, each of which include a

carboxyl group, a amino group, a hydrogen, and a side group all bonded to
a chiral carbon center. And they typically differed only in their side
chain/group, often designated as R group

b) All amino acids residues are L-stereoisomers.

c) All amino acids, other than glycine, have a chiral carbon.

d) The position and nature of charges will depend on the pH of the

solution. Free amino acids are zwitterion at neutral pH. The amino
group is protonated and the carboxylic group is deprotonated.

Generic Structure of a amino acid:

Peptide bonds (linking amino acids together) formed via dehydration:

 

The amino acids are joined by peptide bonds from dehydration from the alpha-
carboxyl group of one amino acid and the alpha-amino group of another. Formed
via a condensation (dehydration) reaction

The peptide bond can exist in two conformations (cis and trans).
a) Peptide bonds are generally in the trans formation!!
b) This key fact influences the types of secondary structure that form.

The sequences of peptides are always written from the N-terminal end to the C-
terminal end.
a) N terminus has your amine exposed
b) C terminal has your carbonyl exposed

Folding patterns of Proteins

The final folded structure, or conformation, adopted by any polypeptide is

determined by energetic considerations: a protein generally folds into the shape
in which the free energy is minimized.
 Ex. Hydrophobic, nonpolar, molecules including the nonpolar side chains
of some amino acids tend to be forced together inside the folded
protein thus avoiding contact with the aqueous cytosol
and not disrupting hydrogen bonds that the hydrophilic,
polar, amino acids are creating on the outside with H2O

**Folding is spontaneous. Amino acid sequence, primary structure, dictates

the folding conformation of the protein and is unique to every protein**

Folding generally occurs in a step by step or hierarchical manner; local secondary

structures come together to form tertiary structure etc

- The number and sequence of amino acids in a polypeptide is called the

primary structure

- Secondary structure in proteins can be one of two (2) conformations,

and result from hydrogen bonding between N-H and C=O:

1) a-helix
- A hydrogen bond is made between every forth peptide
bond, linking the C=O of one peptide bond to
the N-H of another.
- Sometimes 2 a-helices will wrap around each other to
form coiled-coil structure.
- Occurs when the 2 a-helices have most of their
nonpolar side chains on one side, so they
can twist around each other.
 2) B-pleated sheets
- Made when hydrogen bonds form between segments of
polypeptide lying side by side.
- B-pleated sheets can be arranged into parallel B sheets
and antiparallel B sheets
- parallel B sheets both neighboring polypeptides
run in the same direction N  C
terminus’s or
CN terminus’s
- antiparallel B sheets both neighboring
polypeptides run in different directions
NC terminus’s and the other in CN
terminus’s

Secondary folding patterns aren’t uniform, they are usually broken up in the
protein folding pattern with multiple alpha helices and B sheets in the protein.

The amino acid proline will disrupt both a-helix and B-pleated sheets, which
assists in the creation of the tertiary structure.

- Tertiary structure: the curls and folds of secondary structure to form an

overall three-dimensional structure.

Tertiary structure typically seen:

- Most hydrophobic side chains are buried away from water
- Typically compact
- Most charged chains are on the outer face hydrated to water
molecules
- Tertiary structures are stabilized by:

1) Hydrogen bonding  Urea

2) Electrostatic interactions  salt & pH change

3) van der Waals forces

4) hydrophobic forces  organic solvents

5) covalent disulfide bonds, between two cysteine

amino acids on different parts of the chain
 mercaptoethanol
 -The biggest contributing factor to tertiary structure come
from the hydrophobic forces!!

- Quaternary structure: when two or more polypeptide chains bind

together.

- the same 5 forces at work in tertiary structure can also act to form
the quaternary structure

When a cell is exposed to extracellular conditions they will create covalent cross-
linkages , both intra and inter. Most often they are disulfide bonds, and they do
not change the conformation of the protein, but instead reinforce it. Disulfide
bonds occur between 2 cysteine amino acids.

- Disulfide bonds usually don’t form in the cell cytosol, because of a

high concentration of reducing agents

A protein can be unfolded, or denatured, by treatment with certain solvents that

disrupt the noncovalent interactions holding the folded chain together.

Denaturing Agents Forces Disrupted

Urea Hydrogen bonds
Salt or pH change Electrostatic forces
Mercaptoethanol Disulfide bonds
Organic solvents Hydrophobic forces
Heat All forces

- When a protein is denatured all that remain is the primary structure

When the denaturing solvent is removed the protein often refolds spontaneously,
or renatures, into its original conformation, this indicates that the primary
structure is what determines the folding pattern of the protein

Many proteins require helper proteins called molecular chaperones to help fold
into the proper energetically favorable tertiary native structure.

Types of Proteins

There are two (2) types of proteins:

1) Globular
- In which the polypeptide chain folds up into a compact shape like a
ball with an irregular surface. Enzymes are usually globular
proteins.

2) Structure/Fibrous
- relatively simple, long polymers
- maintain and add strength to the cellular and matrix structure

Ex. Collagen, made from a unique type of helix (triple helices of

polypeptides rich in glycine and proline) and is the
most abundant protein in the body. It is very tough
 because it crosslinks with itself. Most common
extracellular matrix protein in the body.

c) Glycoproteins are proteins with a carbohydrate group attached and they are
a component of cellular plasma membranes. Also serve as markers for
cellular recognition.

Proteoglycans are also a mixture of proteins and carbohydrates., buy they

generally consist of more than 50% carbohydrates. Major component of
extracellular matrix.

Cytochromes are proteins which require a prosthetic (nonproteinaceous) heme

group in order to function. Cytochromes get their name from the color they
add to the cell. They are present in the METC and are responsible for electron
shifting there.

Proteins containing nonproteinaceous components are called conjugated

proteins!!!

** When you see nitrogen on the MCAT think protein **

Carbohydrates

Carbohydrates (also called sugars or saccharides) are made from carbon and
water. They have the formula CnH2nOn.

Most saccharides are almost always more abundant in nature as the "D"
form!!

Five and six carbon carbohydrates (pentoses and hexoses) are the most common in
nature. The six carbon carbohydrate called glucose is the most commonly
occurring six carbon carbohydrate.

- All digested carbohydrates reaching body cells have been converted

to glucose by the liver and enterocytes!!

The ring form has two anomers. It is a stereoisomer of a cyclic saccharide that
differs only in its configuration at the anomeric carbon
 The anomeric carbon is important to the reactivity of carbohydrates
because it is the site at which ring opening occurs, becoming the carbonyl
group, the important functional group.
 Anomers are identified as "α" or "β" based on the relation between the
stereochemistry of the anomeric carbon and the furthest chiral centre in the
ring. The α anomer is the one in which these two positions have the same
configuration; they are opposite in the β anomer. Opposite carbon 1 and 6
= alpha; Same carbon 1 and 6 = beta

The cell can oxidize glucose transferring its chemical energy to a more readily
useable form, ATP.

If the cell has sufficient ATP, glucose (a monosaccharide) is polymerized to the

polysaccharide, glycogen or converted to fat.

Glycogen  short term store of energy in animal cells

- This process is called glycogenesis.

- Glycogen contains alpha linkages and is found in all animal cells, but
especially large amounts are found in the muscle and liver cells.

The liver regulates the blood glucose level, so liver cells are one of the few cell
types capable of reforming glycogen back to glucose and releasing it to the
bloodstream. The breakdown of glycogen into glucose is called glycogenolysis

Glucose  Glycogen = glycogenesis

Glycogen  Glucose = glycogenolysis
The method of glucose uptake differs throughout tissues depending on two factors; the
metabolic needs of the tissue and availability of glucose. The two ways in which glucose
uptake can take place are facilitated diffusion (a passive process) and secondary active
transport (an active process which indirectly requires the hydrolysis of ATP).

Only certain epithelial cells (enterocytes) in the digestive tract and the
proximal tube of the kidney are capable of absorbing glucose against a
concentration gradient.

- This is done via a secondary active transport mechanism down the

concentration gradient of sodium!!

ALL THE REST ABSORB GLUCOSE VIA FACILITATED DIFFUSION!!

Insulin increases the rate of facilitated diffusion for glucose and other
monosaccharides.

In the absence of insulin, only neural and hepatic (liver) cells are capable of
absorbing sufficient amounts of glucose via the facilitated transport system.

Plants form starch and cellulose from glucose.

a) Starch comes in two forms: amylose and amylopectin
1) Starch has alpha linkages
2) is a straight chain of glucose molecules

b) Cellulose has beta linkages

Animals have the enzymes to digest alpha linkages but not beta linkages. Some
animals have bacteria in their digestive tracts that release an enzyme to digest the
beta linkages in cellulose

Animals eat alpha linkages, bacteria break beta linkages.

Nucleotides

Nucleotides are composed of 3 units:

1) a five carbon sugar (pentose)

a) deoxyribose in DNA
- In DNA the 2' OH of ribose is replaced by a hydrogen atom
b) ribose in RNA
 - In RNA the there is a hydroxyl group on both the 2' and 3'
position. This contributes to RNA's inherent poor
half- life.

2) a nitrogenous base
a) Purine
- Adenine (found in DNA and RNA)
- Guanine (found in DNA and RNA)

b) Pyrimidines
- Cytosine (found in DNA and RNA)
- Thymine (found in DNA only)
- Uracil (found in RNA only)

3) a phosphate group

In nucleic acids, nucleotides are joined together by phosphodiester bonds.

A phosphodiester bond is a group of strong covalent bonds between the

phosphorus atom in a phosphate group and two other molecules over two ester
bonds.

Diagram of phosphodiester bonds between nucleotides

Nucleotides are written 5’  3’

 - RNA and DNA are nucleotide polymers, both of which are created
in the nucleus!!!

In DNA, two strands are joined by the hydrogen bonds to make the structure
called the double helix. This model was proposed by Watson and Crick.

The members of each base pair can fit together within the double helix only if the
two strands of the helix are antiparallel.

By convention the top DNA strand goes 5’  3’ and the bottom 3’  5’

Going in the 5’  3’ Direction is referred to as going downstream

Going in the 3’  5’ Direction is referred to as going upstream

Adenine (A) and Thymine (T) form two (2) hydrogen bonds, while cytosine (C) and
guanine (G) form three (3) hydrogen bonds.

- the more G-C%, the higher the melting temperature because of this
additional hydrogen bond
 Differences Between DNA and RNA

Structurally, DNA and RNA are nearly identical. However, there are three
fundamental differences that account for the very different functions of the two
molecules.
1. RNA is a single-stranded nucleic acid and no double helix is formed.
2. RNA has a ribose sugar instead of a deoxyribose sugar like DNA.

3. RNA nucleotides has a uracil base instead of thymine.

Other than these differences, DNA and RNA are the same. Their phosphates,
sugars, and bases show the same bonding patterns to form nucleotides and their
nucleotides bind to form nucleic acids in the same way.

RNA
Other important nucleotides include:
4) ATP (adenosine triphosphate - RNA)
5) Cyclic AMP – an important component in many secondary
messenger systems
6) NADH and FADH, the coenzymes involved in the Krebs cycle.

Minerals

Minerals are the dissolved inorganic ions inside and outside the cell. By creating
electrochemical gradients across membranes, they assist in the transport of
substances entering and exiting the cell.

They can combine and solidify to give strength to the matrix, such as
hydroxyapatite in bone. Minerals also act as cofactors, assisting enzyme and
protein function.

Enzymes
Proteins that facilitate chemical reactions are called enzymes. Enzymes are
biological catalysts that convert a substrate to a product. They are typically
globular proteins.

Isozymes catalyze the same reaction but with different kinetic parameters
and possess different subunit composition!!!

Enzymes have three (3) properties:

1) They are active at very low concentrations within a cell.

2) They increase the rate of reaction (by decreasing the Activation
Energy [Ea] of a reaction) towards equilibrium (they catalyze both
the forward and reverse rxn) but they themselves aren’t altered in the
process.
3) They do not change the nature of the products.

Although most enzymes are composed of proteins, many enzymes possess

nonprotein components call cofactors.

- Cofactors can be metal ions or organic cofactors, coenzymes (ex.

Acetyl CoA), which are usually derived from vitamins.
(vitamins are essential, can’t be produced by the body, organic
molecules)

- Coenzymes are divided into two (2) types:

- Prosthetic group is an organic cofactor that is covalently
bonded into an enzyme.

- Cosubstrate reversibly binds to a specific enzyme, and

transfers some chemical group to another substrate
then reverted back to its original form by another
enzymatic reaction. ATP is an example of a
cosubstrate type of coenzyme.

Enzymes that require a cofactor but do not have one bound are called apoenzymes
or apoproteins (are completely nonfunctional).

- Recall that lipoproteins contain a lipid core surrounded by

phospholipids and apoproteins

An apoenzyme together with its cofactor(s) is called a holoenzyme (this is the

active form).
The equilibrium is not changed by enzymes, just the rate at which the
equilibrium is reached. In the process of catalyzing a reaction, the enzyme is
not used up or permanently altered.

- Enzymes don’t affect the direction of the reaction because they

catalyzed both the forward and the reverse reaction at the same
time by reducing the Ea.

Although enzymatic reactions use the same substrate and yields the same product
as the uncatalyzed reaction, it produces a different intermediate at the
transition state!!! Like other chemical reactions, enzyme reactions are reversible,
proceeding through the same set of reaction intermediates.

The position on the enzyme to where the substrate binds, usually with numerous
noncovalent bonds, is called the active site.

First the enzyme (E) and the substrate (S) bind to form the ES complex. After
conversion to transition states (ES* and EP*), the final product (P) is formed and
then is released by the enzyme.

S + E  ES  ES*  EP*  EP  E + P

An enzymatic reaction begins with the substrate binding at a specific location

called the active site. Think of an active site as a pocket into which the substrate
fits. The enzyme can bind the substrate only if it possesses the proper
configuration. Thus enzymes generally have a very high degree of specificity.
Many enzymes act only on one particular substrate.

Fig. 1
The equilibrium between Substrate (S) and Product (P) reflects the difference in
the free energy of the ground states, ΔG. On the other hand, the rate of the
reaction depends on the height of the energy barrier between S and P. The peak of
the barrier represents the transition state of the reaction. The difference between
the energies of the ground states and the transition state is called the activation
energy, ΔG‡. To accelerate a reaction, an enzyme must lower the barrier for
reaction – decrease ΔG‡

Once it binds the substrate, the enzyme induces a change in the molecular
structure of the substrate, and when this occurs it makes the substrate more likely
to spontaneously undergo more significant changes.

Enzyme Kinetics

They exhibit saturation kinetics; as the relative concentration of substrate

increases, the rate of reaction also increases, but to a lesser and lesser degree until
a maximum rate (Vmax) has been achieved.
As we can see from this graph, once we have achieved saturation of the free
enzymes the rate of reaction levels off and it cant go any faster.

Vmax is proportional to enzyme concentration!!

Turnover number – the number of substrate molecules one enzyme active site
can convert to product in a given unit of time when an enzyme solution is
saturated with substrate.

Km is the substrate concentration at which the reaction rate is equal to

1/2Vmax. Km DOESNT vary when the enzyme concentration is changed. Is
a good indicator of an enzyme’s affinity for its substrate.

- Lower the Km the higher the affinity the enzyme has for a
substrate!!!

Environmental Factors alter enzyme kinetics:

1) pH
a) depends on the enzyme
Ex. Pepsin prefers pH of below 2 while trypsin, active in the
small intestine prefers pH between 6 and 7
2) temperature
a) At first, as the temperature increases, the reaction rate goes
up, but at some point, the enzyme denatures, and the
rate of reaction drops off.
3) salt concentration
4) hydrostatic pressure
5) substrate concentration
 - First, environmental conditions can produce changes in weak
bonds that can alter the 3-D structure of the enzyme. For
example, warm temperatures can break bonds that are
necessary to form the active site.

- Second, environmental conditions can alter the ionization state

of critical amino acids within the active site.

- Third, environmental conditions can alter the ability of the

enzyme to undergo structural changes necessary for catalysis.

Enzyme Regulation
Enzyme regulation is very important. You want to control how fast an
enzyme is working based on the ability of substrate so not to be wasteful. On a
fundamental level enzyme activity is controlled by regulating the amount of copies
of a particular enzyme (transcriptional regulation). But more common is:

Irreversible inhibition:

- Agents which bind covalently to enzymes and disrupt their function are
irreversible inhibitors. A few irreversible inhibitors bind
noncovalently.
- Irreversible inhibitors tend to be highly toxic!!!

- Penicillin is an irreversible inhibitor that binds to a bacterial enzyme

that assists in the manufacturing of peptidoglycan cell walls!!!

Competitive Inhibition:

- A molecule similar in structure to the substrate reversibly binds to the

active site and inhibits the enzyme’s activity.

Competitive Inhibition
 Competitive inhibitors raise the apparent Km but do not change the
Vmax !!

Allosteric Modulation (Noncompetitive Inhibition):

Allosteric regulators are molecules that alter enzyme kinetics by

noncovalently binding to the enzymes at locations far away
from the active site, allosteric site. The allosteric regulator thus
alters the 3- D structure of the enzyme.

- Allosteric effectors can activate or inhibit enzyme activity

- Homotropic activation- substrate serves as an activator, and You

achieved the typical S or sigmodical curve found in
describing behavior of enzymes such as hemoglobin.
 Oxygen binds to the most difficult site first. This alters the conformation
of the protein so the next subunit binds oxygen more easily. This
process is then repeated for the other two subunits. This change in
conformation caused by the progressive binding of a ligand is known as
cooperativity and leads to sigmoid kinetics. The binding of one ligand
(substrate or modulator) changes the conformation of the protein. This
can increase or decrease the affinity for further ligands

- Both positive and negative cooperativity exist

Note: Fetal hemoglobin must have a higher affinity for O2 than

adult hemoglobin because it steals the O2 from the
adult

- Heterotropic activation/inhibition- a different molecule other

than the substrate serves as the allosteric activator/inhibitor.
Can either activate or repress enzyme activity. Noncompetitive
inhibitors do not resemble the substrate, so
commonly act on more than one enzyme. Unlike competitive
inhibitors, they can’t be overcome by increasing substrate
concentration the substrate

Heterotrophic Inhibition
How is allosteric modulation used by organisms?
- 1st step of metabolic pathway often catalyzed by allosteric enzyme
- Allosteric effector molecule is most often the final product of the
pathway, and is generally a negative modulator.

With these inhibitors, Km remains the same but they lower Vmax.

Feedback inhibition (falls under allosteric regulation):

- when the supply of final product is sufficiently high, the 1st reaction of
the pathway is slowed down (negative feedback), this type of
regulation is more prevalent than positive feedback.
- You can also have it when the supply of final product is low the 1st
reaction of the pathway is sped up (positive feedback).

Fig – Feedback Inhibition

 Reversible covalent modification:
- Many enzymes are activated or inhibited by the transfer of
inorganic phosphate from ATP or modifier to an acceptor.
Most of the time the modifier is removed via hydrolysis. Ex. AMP -
modifier
- The combination of protein phosphorylation by kinases and
dephosphorylation by phosphatases can afford a fine
level of control over enzyme activity.

- Hexokinase is the enzyme which phosphorylates glucose as

soon as it enters the cell.

Zymogen activation – chymotrypsinogen is one example:

- Proteins typically function extracellularly
- Initially synthesized as inactive precursor – zymogen or
proenzyme. For instance pepsinogen (notice the “-ogen”
at the end indicating zymogen status) is the zymogen of pepsin
and is activated at low pH.
- Is irreversible
- Activated by proteolysis of one or a few peptide bonds
a) Proteolysis is the directed degradation (digestion) of proteins
by cellular enzymes called proteases or by
intramolecular digestion

Control Proteins:
- Control proteins are protein subunits that associate with certain
enzymes to activate or inhibit their activity. Calmodulin or
G- proteins are typical examples of control proteins
Other proteins as well as enzymes undergo types of regulation. Hemoglobin
is a good example that is shown in noncompetitive inhabitance – homotropic
activation.

Enzyme Classification

Enzymes are named according to the reactions that they catalyze. Very often, the
suffix “-ase” is simply added to the end of the substrate upon which the enzyme
acts. For instance, acteylcholinesterase acts upon the ester group in acetylcholine.

Two types of enzymes that we should distinguish are lyases and ligases:

- Lyases catalyze the addition of one substrate to a double bond of a

second substrate and is sometimes called synthase.

a) ATP synthase is an example of a lyase

- Ligases also governs an addition reaction, but requires energy from

ATP or some other nucleotide. Are sometimes called synthetases.

Look for the “-ase” ending. Often a seemingly complicated question asking
about a complicated chemical will depend on the fact that it is an enzyme.
Once you recognize the chemical as an enzyme, you know it contains nitrogen
and it is subject to denaturation.

METABOLISM

There are three (3) main types of pathways that reactions can occur through in the
body:

1) Linear
2) Branch point
3) Cyclic
Metabolism – The sum of all metabolic pathways within a cell, tissue, or
organism.

Of the 3 types of pathways they fall into two (2) categories of metabolic pathways:

1) Catabolic pathways - Oxidizing pathways that generate energy!!!

Large molecules are broken and the energy stored as chemical energy
within the bonds are converted into ATP or transferred into other small
molecule shuttles such as NAD, FAD, and NADPH.

2) Anabolic pathways - Biosynthetic pathways where small molecules

come together to form large macromolecules. The ATP that was
generated during catabolic stages is then used generate the various
molecules that are needed for the survival of cell.

Note: Catabolic and Anabolic pathways are linked with each other so
that energy or molecules gained from catabolic reactions can be
used for anabolic reactions.
Catabolic and Anabolic pathways are not the reverse of each other!! This
would lead to futile cycle where in the end only energy is spent. To avoid these
futile cycle each metabolic pathways contains a committed step. A committed
step makes the pathway unidirectional. The anabolic and catabolic pathways are
usually quite different, which allows for them to be regulated separately.

Catabolic and anabolic pathways are regulated such that they usually
take place in different physical environments!!!

Energy Source for organisms:

- Light (energy from photons) => phototroph
- Molecules (inorganic or organic) => chemotroph

Carbon sources for organisms:

- inorganic (CO2 or Bicarbonate) => autotroph
- organic (carbohydrates, lipids, etc.) => heterotroph

Cell Metabolism Cycles:

You do NOT need to memorize any enzymes or pathway intermediates; they will
make you do that in your professional school biochemistry class.
 - You should also know that oxygen is the final electron acceptor of the
electron transport chain (this is because O2 has a high electron
affinity for electrons as we saw in chemistry lecture 7), and that
anaerobic respiration is insufficient to sustain human life.

- In addition, fermentation produces lactic acid as a byproduct in

humans, and ethanol in yeast. This is what causes muscle
cramping during periods of extreme workout.

- Finally, you should know where in the cell each stage of respiration
occurs.

There are three basic steps of metabolism:

1) Macromolecules are broken down into their constituent parts

2) Constituent parts are oxidized to acetyl CoA, pyruvate or other

metabolites forming some ATP and reduced coenzymes (NADH and
FADH2) in a process that doesn’t directly utilize oxygen

3) If oxygen is available and the cell is capable of using oxygen, these

metabolites go into the citric acid cycle and oxidative phosphorylation
to form large amounts of energy.

The second and third stages, the energy acquiring stages, are called respiration.
If oxygen is used, the respiration is aerobic. If oxygen isn’t used, the respiration is
anaerobic.

Aerobic organisms - Glycolysis is the first step and molecule generates most of
the energy from the oxidation of organic oxygen to molecular oxygen.

Anaerobic organism - They only do glycolysis and fermentation

- Obligatory anaerobes – can only live in enviroments without oxygen

and perform only anaerobic respiration

- Facultative anaerobes – can use both aerobic and anaerobic respiration

to survive
Substrate-level phosphorylation is a type of chemical reaction that results in the
formation of adenosine triphosphate (ATP) by the direct transfer of a phosphate
group to adenosine diphosphate (ADP) from a reactive intermediate. In cells, it
occurs in the cytoplasm (in glycolysis) under both aerobic and anaerobic
conditions.

Unlike oxidative phosphorylation, here the oxidation & phosphorylation is

not coupled!!!

Oxidation  releases energy, oxidation #/state increases

Reduction  stores potential energy, oxidation #/state decreases

Recall: LEO says GER

Glycolysis: (anaerobic, occurs in the cytoplasm)

Can be performed in all cells!

Note: Phosphorylated molecules cannot diffuse through the

membrane!!

The process of ATP production in glycolysis is called Substrate-level

phosphorylation

The overall equation:

Glucose + 2ATP + 2NAD+ + 4ADP + 2Pi = 2pyruvate + 2ADP + 2 NADH

+ 2H+ + 4ATP + 2H2O

Equation Reduced:

Glucose + 2NAD+ + 2ADP + 2Pi = 2pyruvate + 2NADH + 2H+ + 2ATP + 2

H2 O

- 2 net ATP (4 total made, but 2 needed to complete this stage)

 - 2 NADH produced (making 4 ATP in ETC for eukaryotes and 6 ATP
for prokaryotes) via reduction of NAD+!!

- 2 pyruvate (3 carbons) produced

Pyruvate can then be converted into various products:

1. It can be oxidized to give the acetyl group of acetyl-
coenzyme A, which is then oxidized completely to
give CO2.
2. It can be reduced to lactate (a type of fermentation).
3. It can be converted to ethanol and CO2 (another type of
fermentation)

- ADP & AMP is a activator for glycolysis

- ATP and Citrate are inhibitors for glycolysis

In order for glycolysis to continue operating the produced NADH must be

oxidized back into NAD+

Note: Fructose can enter glycolysis as fructose 6-phosphate!!

Fermentation (anaerobic, occurs in the cytoplasm)

- It includes the process of glycolysis

- Animal tissues reduce pyruvate to lactate under anaerobic conditions, at

the same time oxidizing NADH back to NAD+, which is needed
for continued glycolysis. Reaction is catalyzed by lactate
dehydrogenase. Lactate can be recycled; it is carried in blood to the
liver where it is converted back to glucose (in a process requiring the
input of energy). The acidification of muscle explain why continued
exercise can cross cramping, aka Acidosis.

- Yeast produce ethanol and CO2!!!

- 0 ATP is produced.
- Low [NAD+]/High [NADH] is a driver for fermentation

Pyruvate Decarboxylation: (aerobic, occurs in the cytoplasm for prokaryotes,

mitochondrial matrix for eukaryotes)
Both pyruvate and NADH move through the mitochondrial membrane through a
large membrane protein called porin.

The inner mitochondrial membrane, however, is less permeable. Although pyruvate

moves into the matrix via facilitated diffusion, each NADH (depending upon the
mechanism used for transport) may or may not require the hydrolysis of ATP (this
is why the NADH in glycolysis only produce 4 ATP instead of 6)

Pyruvate decarboxylation is the biochemical reaction that uses pyruvate to form

acetyl-CoA, releasing NADH, a reducing equivalent, and carbon dioxide

Total:
- 2 CO2
- 0 ATP produced
- 2 NADH produced, for the decarboxylation of both pyruvate (making
6 ATP in ETC)

TCA/Kreb Cycle: (aerobic, occurs in the cytoplasm for prokaryotes,

mitochondrial matrix for eukaryotes)

The process of ATP production in the Krebs cycle is called Substrate-level

phosphorylation

Fig – Kreb Cycle:

Total:
- 4 CO2 produced
- 2 GTP/ATP produced
- 6 NADH produced (making 18 ATP in ETC)
- 2 FADH2 produced (making 4 ATP in ETC)

Each turn in the kreb cycle produces (1 glucose provides two turns):

- 2 CO2 produced
- 1 GTP/ATP produced
- 3 NADH produced (making 9 ATP in ETC)
- 1 FADH2 produced (making 2 ATP in ETC)

TCA/KREB Cycle Regulation:

The cycle is regulated at the three steps that are highly exergonic:
those catalyzed by citrate synthase, isocitrate dehydrogenase,
and a- ketoglutarate dehydrogenase.

- NADH and ATP are both negative regulators; ADP and

Ca2+are positive regulators (activators)!!!
Triglycerides can also be catabolized for ATP. Fatty acids are converted to acyl
CoA along the outer membrane of the mitochondrion and endoplasmic reticulum
at the expense of 1 ATP. Then 2 carbons are cleaved to make acetyl CoA in the
matrix. This reaction also produces FADH2 and NADH for every two
carbons taken from the original fatty acid. Acetyl CoA then enters into the
Krebs cycle as usual. This is called beta oxidation.

- The fatty acids are linked to Coenzyme A and carried into the
mitochondrial matrix by the g-amino acid L-carnitine. They are then
are oxidized TWO carbons at a time in the KREB cycle, yielding an
NADH, FADH2, and acetyl CoA.

Amino acids are deaminated in the liver!! The deaminated product is either
chemically converted to pyruvic acid or acetyl CoA, or it may enter the Kreb cycle
at various stages depending upon which amino acid was deaminated.

Electron Transport Chain (ETC): (aerobic, occurs across the inner cell
membrane for prokaryotes, inner mitochondrial membrane for eukaryotes)

Oxidative phosphorylation oxidizes NADH to NAD+, which creates a proton

gradiant, via the pumping out of H+, that propels protons through ATP
synthase!!!

- So the intermembrane space has a lower pH/higher [H+

concentration] than the matrix

- The inter-cristal space or the mitochondrial matrix has a low H+

concentration and a high pH
 - NADH oxidation back to NAD and FADH2 oxidation back to FAD
occur along with ATP production, allowing the earlier stages to
continue.

- As electrons move within the ETC each intermediate carrier is

reduced by the preceding molecule and oxidized by the following

- Oxygen is the last electron acceptor in the ETC

- 1 NADH produces 3 ATP molecules

- 1 FADH produces 2 ATP molecules

Summary:

36 net ATP produced in eukaryotes, 38 net ATP produced in prokaryotes

(because the electrons from the NADH produced from pyruvate decarboxylation
do not have to be transported across the mitochondrial membrane in prokaryotes;
doing this causes a net loss of two ATP in eukaryotes)

Products and Reactants for Respiration:

Glucose + O2  CO2 + H2O