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Biochem 2

Cell structure

1. Prokaryotes
No membrane-bounded nucleus
No organelles
Include Bacteria & Archaebacteria

2. Eukaryotes
Unicellular or multicellular
Membrane-bounded nucleus
Many organelles, some resembling prokaryotic cells
Animal cells: no cell wall (plants and fungi have cell walls made of

3. Organelles

nucleus, ER, Golgi apparatus, mitochondrion, lysosome, peroxisome

Number of each kind of organelle depends on cell type
each organelle is surrounded by a membrane

Organelles in detail:

ER rough: synthesis of proteins

ER smooth: lipid synthesis
Golgi apparatus: Proteins are delivered from the ER to Golgi
Mitochondria: aerobic metabolism
Lysosomes: contain hydrolytic enzymes, to digest materials ingested by
Peroxisomes: contain oxidative enzymes

Advantages of compartmentation:
Enclosed system can maintain local concentrations of compounds
that would diffuse otherwise
Concentrated substances can react more readily, leading to
increased efficiency for many chemical reactions

Endocytosis (Phagocytosis)

Compartments are dynamic

Fusion Budding
4. Cytoskeleton proteins (Eukaryotic cell)

made from 3 types if fibrous proteins

responsible for cell shape and motility

1. Lipid Bilayer

Built from amphipathic lipids (mainly phosphoacylglycerols and

One-tailed lipids and triacylglycerols have the wrong shape
Cell membranes are composed of lipid bilayer

Phospholipids are mixed with water forming a lipid bilayer

Phospholipids contain hydrophilic head and two nonpolar tails (C-C,
C-H bonds)
Lipids rotate, chains flex, heads bob up & down
Center of bilayer is fluid as hydrocarbon
No covalent bonds involved
Charged heads are oriented towards aqueous interior and exterior of
Nonpolar tails form the hydrophobic interior of membrane (from
insoluble barrier that protects the cell)

Triacylglycerol Phosphoacylglycerol Sphinogyelin

Has three nonpolar Has two nonpolar side Has two nonpolar side
side chains chains tails and one chain tails and one
ionic head ionic head
There are three esters There are two esters Sphingomyelin
formed from three formed with two fatty contains an amide,
fatty acids acids not ester
Glycerol is backbone Phosphodiester bond Phosphodiester bond
is located on terminal is located on terminal
carbon of glycerol carbon of spingosine

Factors that affect bilayer permeability:

Saturation of hydrocarbon tails

unsaturated lipids dont pack as well, bilayer is more fluid

Length of hydrocarbon tails

longer chains pack better

higher temp increases mobility

2. Membrane Proteins

Membrane is 50% protein and 50% lipid, but proportions vary to

membrane type

Functions of membrane proteins

transport of substances in & out

receptors for extracellular signals
synthesis of lipids
some reactions of cellular respiration

Peripheral proteins:
Are embedded within the membrane and extend outward on one
side only
Integral proteins:
Extended through the entire bilayer

3. Fluid Mosaic Model

Proteins float in lipid sea

Nonrandom distribution of proteins and lipids
Two sides may be very different
Carbohydrates are almost always on outside
Proteins do not flip-flop
Cholesterol helps maintain proper fluidity

Cholesterols rigid 4-ring structure

Limits flexibility of neighboring fatty acyl tails (tends to decrease fluidity)
prevents the tight packing of fatty acyl tails (tends to increase fluidity)


solute: the dissolved substance (ion or molecule)

diffusion: movement of solute form area of high concentration to area of

low concentra.
Osmosis: movement of water from a region of high concentration to a region
of low concentration
Bilayer permeability:

Small and nonpolar molecules cross membrane easily

Large, polar molecules cannot cross easily, need facilitated transport

Membrane Transport

Faciliated Transport (passive transport)

a) channels (Cl-, HCO3-, glucose) via integral proteins
b) transport proteins (integral proteins etc)

Active Transport
c) pumps (Sodium-Potassium Pump)
move against concentration gradient (low concentr. to high

a) Channels

For ions & very small polar/charged solutes

Form an open passageway through membrane
Solute moves down concentration gradient
Solute can move into or out of cell
No energy input required

b) Transport Proteins

For polar or charged molecules

Protein alternates between two conformations
Solute moves down concentration gradient
Solute can move into or out of cell
No energy input required

c) Pumps
For specific types of solutes
Solute move up concentration gradient
Transport is one-way only
Cell must spend energy (ATP reaction): the energetically favorable
ATP reaction drags along unfavorable transport reaction (active


1. Energy

There are many forms of energy

Energy cannot be created or destroyed, but can be transformed
Biochemists describe energy changes in terms of free energy

1. Law of Thermodynamics

One form of energy can be transformed into another form

Physical, chemical and biological systems tend to move to states

of lower energy

potential energy measured as heat

Entropy (S)
a measure of disorder or randomness (technically, a measure of how
dispersed the heat is
left picture: high order, low entropy
right picture: low order, high entropy

A reaction tends to proceed if the products have lower energy (heat is


A reaction tends to proceed if the products are more disordered than the
reactants (if entropy increases)

Gibbs free energy

G = H TS

Spontaneous if G < 0 (exergonic)

Not spontaneous if G > 0 (endergonic)

- Combustions of glucose: Heat is given off (H<0) and entropy

increases (S >0)
- An unfavorable H or S can be offset by a more favorable S or H
- If both H and S are unfavorable, the reaction wont happen

Calculate H as H products H reactants

Calculate S as S products S reactants

T is temperature in Kelvin (Celsius + 273)

Units of energy are joules per mols (1 calorie = 4.184J)

If a reaction has an unfavorable free energy (G >0), it will not

occur spontaneously. But it can occur if energy is put into the
2. Reactions

The reactants go on left, products go on right

Living systems are not at equilibrium. They are constantly
obtaining and using energy to build molecules, assemble cellular
structures, etc

3. Oxidation and Reduction

Electrons are transferred

Electrons tend to travel to a more electronegative atom
The compound that becomes oxidized acts as reducing agent
Compound that becomes reduced acts as an oxidizing agent
Electrons often travel with a proton, so it looks like a transfer of an
H atom

Electrons are held loosely by atoms with equal electronegativity (is a

less stable situation, higher free energy)

Electrons are held tightly by atoms with high electronegativity (more

stable situation, lower energy)

Reduced carbon compounds have higher potential energy than

oxidized carbon compounds

Oxidizing a carbon compound releases energy

Reducing a carbon compound requires energy

4. Metabolic Reactions

Metabolism: all the chemical reactions that occur in cells

Catabolism: breaking larger molecules into smaller molecules;
energy is usually released (oxidation of glucose)
Anabolism: building larger molecules from smaller molecules;
energy is usually absorbed

a) What do cells need?

All cells must obtain raw materials (Carbon source, Nitrogen, metals
All cells must find a source of free energy (sunlight, chemical

b) Enzymes accelerate reactions that are already spontaneous but slow

Most reactions in cells never reach equilibrium because new
substrate molecules keep being added and product molecules keep
getting used up
Living things need a constant input of energy in order to not be at

c) What about ATP?

Cells use ATP as an energy currency
ATP is a molecule that undergoes a very favorable hydrolysis
reaction (large negative G value)

The favorable (downhill, exergonic) ATP ADP can drag along an

unfavorable (uphill, endergonic) reaction; such as Na-K pump

The free energy of ATP can be tapped when ATP transfers a

phosphate group to another molecule
Attachment of the phosphate group makes the molecule do
something it would not do otherwise
Net cost to the cell is the free energy in ATP (bond between 2nd and
3rd phosphates)

1. What Enzymes Do

Enzymes are biological catalysts

They accelerate chemical reactions by providing a lower-energy
pathway for reactants to become products
They accelerate a reaction only if the reaction is already

When reactants react, old bonds must break so that new bonds can be
formed. This requires input of energy (activation energy)
The reacting molecules represent a range of energy levels. Relatively few
molecules randomly achieve the higher energy level necessary for them to
Thus, few molecules react per unit time (rate of reaction is slow)

If catalyst is present to help break old bonds and form new bonds, then
the reactants need less energy in order to react (activation energy is lower)
Relatively more reactant molecules have the required energy to react, so
the rate of the reaction is higher
Enzyme provides alternate chemical environment for the reaction

2. How Enzymes work

Enzymes interact with reactants (called substrates)

Active site of enzyme contains functional groups that chemically
participate in reaction (yet emerge unchanged)

Enzymes accelerate reactions by.

a) Bringing reactants together and orienting them optimally for reaction

b) Providing chemical groups to nudge the electronic structure of the
reactants toward the electronic structure of the products
c) Preferentially binding the transition state to make it easier for
reactants to get to shi point

Most Enzymes are proteins, a few are RNA

Name often ends in ase
Most enzymes exhibit extremely high specificity: they act on only one
substrate and produce only one product
An enzyme is not permanently changed by the reaction and can act
over and over
The rate increase can be many orders of magnitude
Many enzymes undergo induced fit

Enzymes are proteins and therefore are sensitive to agents that alter protein

Salt concentration

Some enzymes require a co-factor:

Metal ion such as Zn, Mg, Fe or
small organic molecules (coenzymes) for example FAD,NAD
Many coenzymes are derived from vitamins

3. Enzyme Regulation

Most enzymes are regulated. Cells can turn enzyme activity up or down
Making more enzyme molecules or fewer enzyme molecules
Competitive inhibitors to block enzyme activity
Allosteric regulators to block enzyme activity (noncompetitive)
Allosteric regulators to increase enzyme activity

A competitive inhibitor mimics the substrate, binds in the active site

Allosteric effectors increase or decrease enzyme activity, bind somewhere

other than active site
1. Digestion

Macromolecules (polysaccharides, proteins, triacylglycerol) are broken

down to monomers
Digestion (hydrolysis) is catalyzed by enzymes from saliva, stomach,
Small molecules are absorbed mainly in small intestine and shipped to
liver and other tissues

Digestion begins in the mouth (e.g salivary amylase), continuous in the

stomach (e.g. pepsin) but mostly occurs in small intestine
Stomach acid (pH as low as 1.5) promotes protein denaturation

Glycosidases, proteases (peptidases), and lipases are produced by the

pancreas and released into small intestine; pancreatic juice also contains
HCO3- to neutralize stomach acid
Liver produces bile salts (derived from cholesterol), and gall bladder
stores these before release into small intestine
Bile salts act as detergents to break up lipid clumps

Product of digestion (mono- and disaccharides, amino acids and short

peptides, fatty acids) are transported into intestinal cells
Whatever is not used in intestine is shipped to liver. Liver can store
some (glucose glycogen, fatty acids triacylglycerols)

The rest glucose, amino acids, triacylglycerols circulate throughout

body for all cells to use

2. Overview of Energy Metabolism

Monosaccharides, amino acids, and fatty acids are all broken down
to 2-carbon fragments (acetyl-CoA)
The citric acid cycle converts acetyl groups to 2 CO2
The chemical energy of the original fuel molecule is eventually
converted to the chemical energy ATP

Stages of Catabolism

1. Polymer monomer
2. Glycolisis (or fatty acid oxidation, amino acid catabolism)
3. Citric acid cycle
4. Electron transport/oxidative phosphorylation

Picture explained:
Stage 1: Catabolism begins with digestion (hydrolysis of carbs, fats,
Stage 2 : Molecules are converted to acetyl CoA
Stage 3 and 4: Acetyl CoA enters citric acid cycle and produces reduced
whose energy is stored in ATP

Things to keep in mind:

Fuel catabolism releases a large amount of free energy. If this

occurred in one step (combustion), energy would be released all at
once, mostly heat
Instead, cells undertake combustion in small steps, to conserve
energy in manageable amounts
Each step is catalyzed by a specific enzyme
The product of the first reaction is the substrate for the second
reaction and so on, so series of reactions forms a metabolic
Each reaction must be favorable under cellular conditions
Some chemical energy released from fuel molecules is used directly
to drive the synthesis of ATP from ADP + P. But most of the energy
is used indirectly

Fuel catabolism is carbon oxidation (CO2 is the waste product)

A carbons are oxidized, other molecules (cofactors NAD, FAD)
become reduced (NADH, FADH2)
Eventually, O2 is used to reoxidize the NADH and FADH2
The energy changes in these redox reactions drives ADP + P ATP
reaction in oxidative phosphorylation

3. Glycolysis

Glucose (C6) is converted to pyruvate ( 2 C3)

2 ATP are produced
2 NAD are reduced to NADH
Pathway is anaerobic; no O2 is needed
takes place in cytoplasm
Energy from 2 ATP is used in step 1 and 3 for phosphorylation

Coupled reaction: a favorable process drags an unfavorable process along

(Steps 1 and 10 glycolysis)

Glycolysis steps:

Steps 1-5: Energy-investment phase (adding of 2 phosphate requires

energy input of 2 ATP)
Steps 6-10: Energy-generating phase (2 phosphate bonds are broken, 2
ATP are formed

Step 1:
Phosphorylation of glucose to glucose-6-phosphate
Reaction is unfavorable, thus is coupled with the hydrolysis of ATP to
Step 2:
Isomerization of glucose-6-phosphate to fructose 6-phosphate
Step 3:
Phosphorylation (energy-absorbing rxn), driven by ATP hydrolysis to
form fructose 1,6-biphosphate
Step 4:
Cleavage of 6-carbon chain to form two 3-C products (constitutional
Steps 5:
Isomerization to glyceraldehyde 3-phosphate
Step 6:
Oxidation and Phosphorylation: Oxidizing agent NAD+ is reduced to
Step 7:
ATP is formed

Net result of Glycolysis

Three major products are formed in glycolysis: ATP, NADH, and pyruvate

2 molecules of ATP are used (Step 1 & 3)

4 molecules of ATP are formed (Step 7 & 10)

Net result: Synthesis of 2 ATP molecules

4. Fermentation

Fermentation allows glycolysis to continue to generate ATP

As long as glucose is available
ADP + P are regenerated as ATP is used elsewhere in the cell
NAD is regenerated by converting pyruvate to lactate (NADH NAD)
Blood carries lactate from muscles to liver; liver spends more energy to
convert lactate back to glucose by gluconeogenesis
1. Pyruvate Processing

Pyruvate is still a relatively reduced molecule, so its carbons can be

further oxidized (to CO2)
Pyruvate is processed and linked to coenzyme A, producing acetyl-CoA
Fatty acid and amino acid degradation also yield acetyl-CoA

2. The citric acid cycle

8 enzyme-catalyzed steps
Entire pathway acts as catalyst
Based in mitochondria
Acetyl groups of acetyl-CoA are oxidized to carbon dioxide
Cycle begins when 2 C of acetyl CoA react with 4 C substrate to form
Two carbons are removed to form 2 molecules of CO2 (Step 3,4)
4 molecules of reduced coenzymes NADH and FADH2 are formed
(Steps 3,4,5)
These molecules serve as carrier of electrons to electron transport
One mole of GTP is synthesized (step 5)
By step 4 2 Carbons are lost as CO2 and 2 molecules of NADH are

Net results:
2 molecules of CO2
4 molecules of reduced coenzymes (3 NADH and 1 FADH2)
1 molecule of GTP
Main function of citric acid cycle:
To produce reduced coenzymes that enter the electron transport chain and
ultimately produce ATP

3. The Fate of reduced Cofactors

6 glucose carbons have been oxidized to 6 CO2

some of the energy of these carbons were converted in ATP synthesis.
The direct synthesis of ATP is called substrate level phosphorylation
No O2 has been used
C6H12O6 + 6 O2 6 CO2 + 6 H2O Combustion of glucose

Glucose becomes oxidized, NAD and FAD become reduced to NADH and
Reoxidation of NADH and FADH2 drives more ATP production by an
oxygen-dependent process called oxidative phosphorylation

Oxidative phosphorylation is a process in which ATP is formed as a result of

the transfer of electrons from NADH or FADH2 to O2 by a series of electron
Process takes place in mitochondria, is major source of ATP in aerobic
organisms (generates 26 molecules of ATP)

Electron Transport Chain

Inner mitochondrial membrane contains the components of the electron

transport chain
a variety of chemical groups undergo reduction and reoxidation (lose
Electrons from reduced NADh and FADH2 are transferred through this
series of carriers
The end of the line is O2

begins with reduced coenzymes (3NADH and 1 FADH2)

Enzymes are electron rich and are capable of donating electrons to other
Thus NADH and FADH2 are reducing agents; donate electrons they are
Oxidized NAD+ and FAD can re-enter citric acid cycle
In electron transport chain, electrons are passed down in redox reactions
and small packets of energy is released
Electrons continue to flow form higher-energy to lower-energy situations
At the end of chain, electrons react with inhaled O to form water

2. The Proton Gradient

Complexes I,II,III,IV change conformation as they become reduced and
then oxidized
These changes allow them to pick up a proton in the matrix and
release a proton outside the mitochondrion
Therefore, as electrons are transferred, protons are pumped across the

Electron transport complexes move protons against concentration

gradient (low to high concentration outside of mitochondrion Active
The favorable free energy change of the redox reactions (electron
transport process) drives the proton pumping
Therefore, the energy of reduced compounds (NADH, FADH2) is
transformed to the energy of the H+ gradient

Energy of original fuel molecule (glucose) was transformed to energy of

reduced NADH (glycolysis, pyruvate processing, citric acid cycle)
Energy of NADH was transformed into the energy of proton gradient
(electron transport)
Energy is transformed again when the protons move back toward
Protons interact with membrane embedded protein (ATP synthase)

4. ATP Synthase

The flow of H+ ions down their gradient through ATP synthase powers
the synthesis of ATP from ADP + P
Protons hitching a ride on ATP synthase trigger conformational changes
in protein
As ATP synthase changes shape, it binds ATP and P, and then releases
ATP synthesis is an uphill reaction
It is oxidative phosphorylation because it depends on the energy of
redox reactions

The energy of the proton gradient is transformed to the mechanical

energy of ATP synthase spinning (rotary engine)
Mechanical energy is transformed to chemical energy of ATP
Oxidative phosphorylation produces most of the cells ATP

5. Aerobic Metabolism in Context

Glycolysis alone produces 2 ATP per glucose

Entire respiration process produces 32 ATP
Aerobic metabolism is way more efficient
Glycolysis however, is fast and makes sense when small amounts of
ATP are needed quickly


Dark muscles: lots of mitochondria sustained activity powered by

aerobic metabolism

White muscles: Few mitochondria Bursts of activity powered by

anaerobic glycolysis

Slow-twitch fibers are optimized for aerobic activity

Fast-twitch muscle fibers are optimized for anaerobic activity

1. Carbohydrate Metabolism

a) Gluconeogenesis
Starting materials: lactate, some amino acids, glycerol (no fatty
Pyruvate glucose pathway requires 6 ATP
Only liver and kidneys can do this, then glucose travels in blood to
other tissues
Anabolic pathway; synthesizes glucose from pyruvate
Happens when body used all glycogen and glucose (starvation,

b) Glycogen synthesis
Condensation reaction is uphill, so glucose is first activated by
reacting UTP
Additional enzymes are needed to deal with branch points
Ultimately, the process costs 2 ATP equivalents (2 bonds to
phosphate groups are broken)

2. Lipid Metabolism

a) Glycerol metabolism
Triacylglycerol catabolism begins with hydrolysis
Glycerol backbone can be converted to glycolytic intermediate
Glycerol therefore yields acetyl-CoA or glucose

b) beta Oxidation
Fatty acids come from triacylglycerol or membrane lipid breakdown
Fatty acid is first activated by reaction with ATP and linked
Coenzyme A
Beta Oxidation pathway yields acetyl-CoA, NADH, FADH2
Acetyl-CoA enters citric acid cycle, reduced cofactors go to electron
transport chain
Result: A lot of ATP

Linking fatty acid to CoA costs 2 ATP

Now the fatty acyl-CoA is ready for beta oxidation: 4 enzyme-catalyzed

reactions remove 2 carbons at a time and then repeat
Note: Fatty acid is deconstructed at the CoA (tioester) end, not the CH3

c) FattyAcid Sythesis
Fatty acid chain is built from acetyl-CoA molecules
2 C are added at a time, to the tioester (CoA) end
Reactions are similar to beta oxidation, but in synthesis NADPH is
oxidized to NADP
Fatty acids are then linked to glycerol to form triacylglycerol
Liver and adipose tissue are the main sites of fatty acid synthesis
and storage
d) Ketone Bodies
When glucose (and glycogen) have been depleted, body uses
stored fat as fuel and liver makes glucose form glycerol and
amino acids
Brain requires constant supply of glucose and does not use fatty
acid fuels
To avoid breaking down bodys proteins for gluconeogenesis,
liver converts fatty acids to ketone bodies
Ketogenesis also occurs in other situations where glucose is in
short supply

Acetoacetate and beta-hydroxybutyrate are very soluble, easily

reach brain cells
Brain converts ketone bodies to acetyl-CoA that enters citric acid
Ketone bodies are a more portable form of fatty acids

3. Amino acid Metabolism

a) Amino Group Disposal

1. Transamination: amino group is transferred from an amino acid to
alpha-ketogluatarate, forming glutamate

2. Deamination: Eventually glutamate loses the amino group entirely

(becoming alpha-ketoglutarate again)

3. Free amino groups are incorporated into urea for disposal

Urea synthesis takes place in liver

Urea very soluble travels in blood to kidneys and is filtered out into
Urea also plays a role in kidneys, where water is reabsorbed by

b) Carbon skeleton breakdown

1. Some amino acids are broken down to intermediates of the citric

acid cycle

2. Some amino acids are broken down to pyruvate

3. Some amino acids are broken down to acetyl-CoA