BIOCHEMISTRY REVIEWER

THE MOLECULES OF CELL

PROPERTIES OF WATER
•Water has a high heat capacity
•Water has a high heat of vaporization
•Water is a solvent.

Calorie - A calorie is the amount of heat energy needed to

raise the temperature of 1 gram (g) of water by 1°C.
Hydrophilic - Molecules that can attract water
Hydrophobic - Nonionized and nonpolar molecules, such as oil,
that cannot attract water
Cohesion - refers to the ability of water molecules to cling to each
other due to hydrogen bonding.
Adhesion - refers to the ability of water molecules to cling to other
polar surfaces.

•Frozen water (ice) is less dense than liquid water.

•They are densest at 4°C
•They form regular crystal lattice at below 4°C including 0°C

ACIDS AND BASES

BUFFERS AND PH - A buffer is a substance that keeps pH within
normal limits. Buffers resist pH changes because they can take up
excess hydrogen ions (H+) or hydroxide ions (OH–).

ORGANIC MOLECULES
Many of the organic molecules that you are familiar with, such as
carbohydrates, lipids, proteins, and nucleic acids, are
macromolecules (also called biomolecules)

Macromolecules (also called biomolecules) - meaning that they

contain smaller subunits joined together
Polymers - A polymer is a substance or material consisting of very
large molecules linked together into chains of repeating subunits.
Monomers - A monomer is a molecule that can react with other
monomers to form polymers.

The chemical reactivity of an organic molecule is determined by

the types and locations of functional groups on the organic
molecule.

FUNCTIONAL GROUPS - A functional group is a specific

combination of bonded atoms that always has the same chemical
properties and therefore always reacts in the same way.

The R indicates the “remainder” of the molecule. This is the

place on the functional group that attaches to the carbon
skeleton.

BIOLOGICAL MACROMOLECULES
Biological macromolecules are large molecules, necessary for life,
that are built from smaller organic molecules.

Four major classes of biological macromolecules:

1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acid

SYNTHESIS OF BIOLOGICAL MACROMOLECULES

Dehydration Synthesis- means to put together while losing water.
Hydrolysis - means “to split water,” a reaction in which a water
molecule is used during the breakdown.

CARBOHYDRATES
Carbohydrates provide energy to the body, particularly through
glucose, a simple sugar that is a component of starch and an
ingredient in many staple foods.

The term carbohydrate (literally, carbonwater) includes single

sugar molecules and chains of sugars.

Molecular Structure
•Carbohydrates (CH2O)n
•n - the number of carbons in the molecule.
•The ratio of carbon to hydrogen to oxygen is 1:2:1 in
carbohydrate molecules.

Monosaccharides - Monosaccharides (mono- = “one”; saccharide-

= “sweet”) are simple sugars, the most common of which is
glucose. In monosaccharides, the number of carbons usually
ranges from three to seven. Most monosaccharide names end with
the suffix -ose.

Examples of monosaccharides: pentoses( 5 carbons), hexoses( 6

carbons)

Glucose - is a hexose sugar found in our blood

Disaccharides - Disaccharides (di- = “two”) form when two

monosaccharides undergo a dehydration reaction (also known as a
condensation reaction or dehydration synthesis).

•When glucose and fructose join, the disaccharide sucrose forms.

•Lactose is glucose combined with galactose.

Polysaccharides - A long chain of monosaccharides linked by

glycosidic bonds is known as a polysaccharide (poly- = “many”). +
•It contains long chains of glucose subunits.
•Due to their length, they are sometimes referred to as complex
carbohydrates.
•Starch and glycogen are large storage forms of glucose found in
plants and animals, respectively.
LIPIDS - Lipids include a diverse group of compounds that are
largely nonpolar in nature. This is because they are hydrocarbons
that include mostly nonpolar carbon–carbon or carbon–hydrogen
bonds. Non-polar molecules are hydrophobic (“water fearing”), or
insoluble in water.

Fats and Oils

A fat molecule consists of two main components—glycerol and
fatty acids.

Glycerol - Glycerol is an organic compound (alcohol) with three

carbons, five hydrogens, and three hydroxyl (OH) groups.
Fatty acids - Fatty acids have a long chain of hydrocarbons to
which a carboxyl group is attached, hence the name “fatty acid.”
Fats - tend to be of animal origin (e.g., lard and butter), and are
solid at room temperature
Oils - which are usually of plant origin
•A fat molecule is sometimes called a triglyceride because of its
three-part structure.
Trans Fats - Trans fats are unhealthy fats that can increase bad
cholesterol and heart disease risk.
Omega Fatty Acids - Essential fatty acids are fatty acids required
but not synthesized by the human body. Consequently, they have
to be supplemented through ingestion via the diet.
Waxes - Waxes are made up of long fatty acid chains esterified to
long-chain alcohols.
Phospholipids - Phospholipids are major constituents of the plasma
membrane, the outermost layer of animal cells.
Diacylglycerol - Diacylglycerol is a lipid composed of glycerol and
two fatty acids, and it can be generated from phospholipids or
triacylglycerols.
Steroids - steroids have a fused ring structure. Although they do
not resemble the other lipids, they are grouped with them because
they are also hydrophobic and insoluble in water

PROTEINS
•Proteins are one of the most abundant organic molecules in living
systems and have the most diverse range of functions of all
macromolecules.
•Proteins may be structural, regulatory, contractile, or protective;
they may serve in transport, storage, or membranes; or they may
be toxins or enzymes.
•Proteins are polymers composed of amino acid monomers.

Amino Acid - An amino acid has a central carbon atom bonded to a

hydrogen atom and three functional groups.

TYPES AND FUNCTION OF PROTEINS

Enzymes - which are produced by living cells, are catalysts in
biochemical reactions (like digestion) and are usually complex or
conjugated proteins.
Substrate - a reactant that binds to an enzyme
Hormones - are chemical-signaling molecules, usually small
proteins or steroids, secreted by endocrine cells that act to control
or regulate specific physiological processes, including
growth, development, metabolism,and reproduction.
Amino Acids - Amino acids are the monomers that make up
proteins. Each amino acid has the same fundamental structure,
which consists of a central carbon atom, also known as the alpha
(α) carbon, bonded to an amino group (NH2), a carboxyl group
(COOH), and to a hydrogen atom. Every amino acid also has
another atom or group of atoms bonded to the central atom
known as the R group.

Peptides - A polypeptide is a chain of amino acids that are joined

to one another by a peptide bond.

NUCLEIC ACIDS
Nucleic acids are the most important macromolecules for the
continuity of life. They carry the genetic blueprint of a cell and
carry instructions for the functioning of the cell.

DNA ( deoxyribonucleic acid ) - is the genetic material found in

all living organisms, ranging from singlecelled bacteria to
multicellular mammals. It is found in the nucleus of eukaryotes
and in the organelles, chloroplasts, and mitochondria. In
prokaryotes, the DNA is not enclosed in a membranous envelope.
RNA ( ribonucleic acid) - a single-stranded nucleic acid
molecule that differs from DNA in sugar and base composition
Nucleotide - A nucleotide is an organic molecule that is the
building block of DNA and RNA.

There are four different types of bases in DNA:

1. adenine (A)
2. thymine (T)
3. guanine (G)
4. cytosine (C).
Lecture 3 – Cellular Energy Transformation
All living organisms require a constant supply of energy to survive
In plants and animals glucose is the main source of chemical
energy.

•Chemical energy is present in the chemical bonds

ATP – ADP cycle
•Adenosine Triphosphate (ATP) is the energy currency of a cell
•ATP is needed for every activity that requires energy
•ATP structure – adenosine attached to a sugar group (ribose),
which is bound to a chain of three phosphate groups
•Nucleotide (sugar, N containing base and a phosphate group)
•Cells make their own ATP in cyclic process
•Energy is then reformed during cellular respiration

CELLULAR RESPIRATION
I. Three terms describe the ways in which cells generate
ATP
A. aerobic respiration – a generally efficient process that
requires O2; most, but not all, organisms can use a form of this
process at least some of the time; also called cellular respiration
B. anaerobic respiration – processes similar to aerobic
respiration but that do not use O2; used mainly by bacteria that
live in anaerobic (O2-deficient) environments
C. fermentation – generally inefficient processes used mainly
when other pathways cannot be used or when ATP is needed
quickly; fermentation processes do not use O2

II. Aerobic respiration: a redox process

A. aerobic respiration - the most efficient form of cellular
respiration, is used by most organisms
B. nutrients (typically glucose) - are catabolized to water and
carbon dioxide, and energy is stored in ATP

This is a redox process – glucose is oxidized to carbon dioxide,

and oxygen is reduced to water

C. aerobic respiration - is a complex series of enzyme-catalyzed

reactions that can be grouped into four types of reactions:

1. substrate-level phosphorylation – coupled reactions that

directly phosphorylate ADP or GDP
2. dehydrogenation reactions – redox reactions that transfer
hydrogen to NAD+ or FAD
3. decarboxylation reactions – carboxyl groups are removed;
CO2 is released
4. preparation reactions – molecules are rearranged to prepare
for other reactions
5. of the above, only substrate-level phosphorylation and
dehydrogenation provide energy for cells

III. Aerobic respiration is conventionally divided into four

stages
A. glycolysis
1. occurs in the cytosol (both in prokaryotes and eukaryotes)
2. overall, glucose is converted to 2 pyruvate molecules (a 3-
carbon molecule)
3. released energy is stored in a net yield of 2 ATP and 2 NADH
molecules
4. occurs under both aerobic and anaerobic conditions (no O2
required)
5. actually a series of ten reactions, each catalyzed by a
different enzyme; broken into two phases (energy investment and
energy capture)
6. first phase requires energy investment
• phosphorylation, using two ATP, charges the sugar with two
phosphates
• 2 molecules of glyceraldehyde 3phosphate (G3P) are formed
7. second phase, the energy payoff phase, yields private
and energy captured in ATP and NADH
• aside: -ate and –ic acid forms are essentially equivalent in
cells; for example, pyruvate and pyruvic acid

B. formation of acetyl coenzyme A (acetyl-CoA) from

pyruvate (AKA pyruvate oxidation)
1. pyruvate is sent to the mitochondria in eukaryotes (stays in
cytosol of prokaryotes)
2. set of three enzymes catalyze the reactions, grouped together
in the pyruvate dehydrogenase complex
3. oxidative decarboxylation: a carboxyl group is removed from
pyruvate (CO2 is produced)

C. CITRIC ACID CYCLE

1. AKA tricarboxylic acid cycle, TCA cycle, Krebs cycle

• note there is no net gain or loss of oxaloacetate in the

cycle

D. oxidative phosphorylation: the electron transport chain

and chemiosmosis

occurs in mitochondria of eukaryotes, and on membrane surface

in prokaryotes

acceptors include flavin mononucleotide (FMN), ubiquinone,

iron-sulfur proteins, cytochromes
hydrogen ions (protons) are pumped across the inner
mitochondrial membrane, creating a concentration gradient with
high proton concentration in the intermembrane space

chemiosmosis produces ATP

• protons are charged and do not readily cross a cell
membrane
• special protein channel, ATP synthase (also called ATP
synthetase) allows proton transport with the gradient
• energy is captured and used to make ATP

IV. Aerobic respiration theoretically yields 36 or 38 ATP

molecules from one glucose molecule

•The actual yield is typically about 30 ATP per glucose.

•Chemiosmosis doesn’t actually give round figures, and some of
the energy from the proton gradient is used for other things too,
like bringing pyruvate into the mitochondrion.
•The overall efficiency of aerobic respiration is typically about
32%

V. Non-glucose energy sources

A. other substances can be oxidized to produce ATP in living
systems
B. along with carbohydrates, proteins and lipids (fats) are
generally major energy sources in foods; nucleic acids are not
present in high amounts in foods and thus aren’t as important in
providing cells with energy
C. proteins are broken into amino acids, which can be broken
down further

1. amino group is removed (deamination)

2. amino group may eventually be converted to urea and
excreted
3. remaining carbon chain enters aerobic respiration at various
points, depending on chain length
4. provide roughly the same amount of energy per unit weight
as does glucose

D. lipids (focus on triacylglycerols)

1. lipids are more reduced than glucose (note less oxygen in
lipids), thus more energetic
2. glycerol is converted to glyceraldehyde-3-phosphate (G3P),
entering glycolysis
3. fatty acids are oxidized and split into acetyl groups that are
combined with CoA to make acetyl-CoA (this process is called
oxidation)
4. typically provides over twice as much energy per unit weight
as glucose
5. as an example, oxidation of a 6-carbon fatty acid yields up to
44 ATP

VI. Anaerobic respiration

A. bacteria that live in environments where O2 is not abundant
perform anaerobic respiration
B. still uses an electron transport chain
C. some other compound such as NO3-, SO42- or CO2 serves as
the ultimate electron acceptor
D. not as efficient as aerobic respiration (exact efficiency varies
depending on the process and the species)

VII. Fermentation

A. involves no electron transport chain

B. inefficient; net is 2 ATP per glucose molecule
(only glycolysis works)
C. if glycolysis only, then NAD+ must be regenerated, thus
fermentation, where NADH reduces an organic molecule

1. alcohol fermentation produces ethanol

• ethanol is a potentially toxic waste product, and is removed
from cells
• yeast (and many bacteria) perform alcoholic fermentation in
low oxygen environments
• used in making alcoholic beverage

2. lactic acid fermentation produces lactate and NAD+

• pyruvate is reduced to lactate to regenerate NAD+
• performed by some bacteria and fungi, and by animals (when
muscles need energy fast)
• used in making cheese, yogurt, sauerkraut

Photosynthesis
I. Organisms can be classified based on how they obtain
energy and how they obtain carbon

A. Energy source
1. Chemotrophs can only get energy directly from chemical
compounds
2. Phototrophs can get energy directly from light (these
organisms can use chemical compounds as energy sources as
well)

B. Carbon source
1. Autotrophs can fix carbon dioxide, thus they can use co2 as a
carbon source
2. Heterotrophs cannot fix co2; they use organic molecules from
other organisms as a carbon source

C. Combined, these lead to 4 possible groups:

1. Photoautotrophs – carry out photosynthesis (use light energy
to fix co2, storing energy in chemical bonds of organic molecules);
includes green plants, algae, and some bacteria
2. Photoheterotrophs – use light energy but cannot fix co2; only
nonsulfur purple bacteria
3. Chemoautotrophs – obtain energy from reduced inorganic
molecules and use some of it to fix co2; some bacteria
4. Chemoheterotrophs – use organic molecules as both carbon
and energy sources; dependent completely on other organisms for
energy capture and carbon fixation; includes all animals, all fungi,
most protests, and most bacteria

II. The electromagnetic spectrum and visible light

A. Visible light is a form of electromagnetic radiation
B. Electromagnetic radiation consists of particles or packets of
energy (photons) that travel as waves
1. Amount of energy carried is inversely proportional to
wavelength (distance from one wave peak to another)
2. Spectrum ranges from short wavelength/high energy gamma
rays to long wavelength/low energy radio waves
C. The portion of the spectrum visible to humans (thus what we
call visible light) ranges from higher-energy violet at 380 nm to
lower-energy red at 760 nm; between lie all the colors of the
rainbow
D. Molecules can absorb photons, thus becoming energized;
typically, an electron absorbs the energy
1. High energy: electron can be freed from the atom it was
bound to (ionization)
2. Moderate energy (of correct amount): electron moves to a
higher-energy orbital
• Electron can then be removed from the atom, going to an
acceptor molecule
• Electron can return to a lower energy level, emitting a photon
(fluorescence) or a series of photons (mostly infrared, experienced
as heat)
• Ground state – when all electrons in a atom fill only the
lowest possible energy levels

III. Chloroplast
A. In photosynthetic eukaryotes (plants and algae),
photosynthesis occurs in chloroplasts
B. Chloroplasts have both an inner and outer membrane
C. Chlorophyll, the main light-harvesting molecule, is found in
the thylakoid membrane
1. Chlorophyll has a porphyrin ring and hydrocarbon side
chain
2. Light energy is absorbed by the ring
3. Chlorophyll-binding proteins associate with chlorophyll in
the membrane
4. Chlorophyll has several forms; in plants, typically chlorophyll a
(chl a) initiates photosynthesis

D. Accessory pigments are also found in the thylakoid

membrane
1. Pigments are compounds that absorb light; we see them as
the main color of light that they do not absorb well (thus they
scatter those colors or reflect them back)
2. All pigments have an absorption spectrum
3. Chl a, a green pigment, absorbs violet-blue and red light
4. Several accessory pigments, with absorption spectra that
differ from chl a, aid in photosynthesis

• Chl b is the main accessory pigment; a slight difference in the

ring shifts its absorption spectrum
• Carotenoids are important yellow and orange accessory
pigments
• Accessory pigments can transfer captured energy to chl a
• They also help protect chl a and other compounds from
excess light energy (high light intensity can cause damage)

E. The relative rate of photosynthesis for a given

radiation wavelength is an action spectrum
1. The action spectrum looks similar to the absorption
spectrum of chl a, but is augmented by the absorption spectrum of
the accessory pigments
2. Blue and red light are most effective for photosynthesis
3. Action spectra can vary depending on species

F. Photosynthetic prokaryotes have plasma membrane folds

that act like thylakoid membranes

IV. Photosynthesis overview

A. Photosynthesis converts energy from light into stored energy

in chemical bonds

B. In the process, CO2 is fixed and used in synthesizing

carbohydrates

1. Light reactions occur in the thylakoids; they capture light

energy and consume water, producing O2; energy is placed in ATP
and NADPH in the stroma
2. The C3 cycle occurs in the stroma; it consumes CO2 and
energy (proved by ATP and NADPH), producing carbohydrates
E. In many ways this is the reverse of aerobic respiration

V. The light reactions of photosynthesis

Light is captured in photosystems that contain antenna complexes
and a reaction center
1. There are two types, Photosystem I and Photosystem II
2. Antenna complexes are highly organized arrangements of
pigments, proteins, and other molecules that capture light
energy
3. Energy is transferred to a reaction center where electrons are
actually moved into electron transport chains
• Photosystem I reaction center has a chl a absorption peak at
700 nm (P700)
• Photosystem II reaction center has a chl a absorption peak
at 680 nm (P680)
4. Chlorophyll molecule + light energy an excited electron in
the chlorophyll
5. The excited electron is captured by a carrier in the
photosynthetic electron transport chain, thus reducing the carrier
and oxidizing the chlorophyll molecule (a redox reaction)
6. The electron can then be transferred down the electron
transport chain, with energy harvest possible

D. Noncyclic electron transport produces ATP and NADPH

1. P700 absorbs energy and sends an electron to an electron
transport chain
2. Eventually, the electron winds up on ferredoxin
3. When 2 electrons have reached ferredoxin, they can be used
to make NADPH from
NADP+ + H+; the NADPH is released in the stroma
4. The electrons are passed down one at a time, and are
replaced in P700 by electrons donated from P680
5. P680 absorbs energy and sends an electron to an electron
transport chain
• This chain differs from the one that P700 uses
• Eventually, the electron winds up on plastocyanin • The
ultimate electron acceptor for this chain is P700
6. + can accept electrons from water in the thylakoid lumen;
thus:
• 2 P680+ + H2O 2 P680 + ½ O2 + 2 H+
• This is a big deal, nothing else in living systems can readily
take electrons from water
• This consumes water and releases O2
7. A proton gradient is established, with high [H+] in the
thylakoid lumen
• H+ produced in the lumen when water is split
• + consumed in stroma when NADPH is made
• H+ pumped into lumen using energy released as electrons
move along the electron transport chain between P680 and P700
• The overall gradient winds up being about a 1000-fold
difference in [H+]
• Gradient provides an energy source for making ATP using ATP
synthase (chemiosmosis)
• Compare this process (photophosphorylation) to oxidative
phosphorylation

E. Cyclic electron transport is possible for P700; all it can

accomplish is to enhance the proton gradient that can be
used to make ATP
F. Overall ATP generation is variable, depending on how
much cyclic electron transport occurs
1. For every 2 electrons moved through the whole P680 – P700
noncyclic electron transport system, one NADPH is produced and
the proton gradient is enhanced enough for ~1 or more ATP
• The net amount of ATP needed for the rest of photosynthesis
comes out to 1.5 ATP per molecule of NADPH; thus the numbers in
the equation at the start of this section
• Cyclic electron transport can be used to make up the
difference in ATP needed for the rest of photosynthesis, as well as
to produce extra ATP
• All of the ATP that is made is released in the stroma

VI. Carbon fixation by the C3 cycle (AKA the Calvin-Benson

cycle or Calvin cycle)

B. Note that this consumes all of the products of the light

reactions except O2, and regenerates much of the reactants for
the light reactions, thus generating the overall result for
photosynthesis:

C. The details of the 13 reactions involved in this process were

described by Calvin and Benson in the 1950s
D. All 13 enzymes are in the stroma; 10 of them are also
enzymes that work in aerobic respiration
1. Enzymes can usually catalyze reactions in both directions –
the intermediate ES complex looks the same in both cases
2. The direction of the reaction depends on thermodynamics,
which is influenced by concentrations of all substances involved in
the reaction
E. C3 cycle is broken into three phases: carbon fixation, carbon
reduction, and rubp regeneration
F. Carbon fixation (AKA CO2 uptake):
1. CO2 combines with the 5-carbon compoun