Biochem Comp 2

Almost all amino acids are chiral, meaning that the

alpha carbon is asymmetric

Biological proteins are composed almost exclusively of

L amino acids

D- alanine, one of the few D amino acids, is found in

peptidoglycan in bacterial cell walls

At neutral pH,

• the carboxyl group has a negative charge

• the amino group has a positive charge

Though amino acids have a positive and negative charge, it is a

neutral molecule called a zwitterion (unstable)

Uncharged hydrophilic amino acids

polar but have no net charge

Glycine doesn’t fit into any category because

it doesn’t have a real R group (R = H) . It is the only AA that doesn’t have an steroisomer

Aliphatic (hydrocarbon side chain) amino acids

valine

leucine

proline

isoleucine

alanine

Valine

Leucine

Proline

Isoleucine

Alanine

Uncharged polar amino acids

Asparagine

Glutamine

Serine

Threonine

Asparagine

Glutamine

Serine (phosphorylation)

Threonine

Aromatic amino acids

Phenylalanine (hydrophobic)

Tyrosine (hydrophilic)

Tryptophan (uncharged hydrophilic)

Phenylalanine

Tyrosine

Tryptophan

Basic Amino acids

arginine

lysine

histidine

Histidine (side group is imidazole)

Arginine

Lysine

Cysteine

• can form a disulfide bond with another cysteine (called a cystine)

Methionine

Sulfur Containing Amino Acids

cysteine

methionine

The peptide bond forms when

the
carboxyl group of one amino acid
joins the amino group of another,
releasing water

The peptide backbone is highly repetitive and
consists of the repeating pattern:

α-carbon → carbonyl carbon → amide
nitrogen

Protein function determined by amino acid sequences, but
also depends on

folding, interactions, modifications, and
cellular environment

Primary level of protein folding

amino acid sequence

Secondary

a helix and b sheet (local folding)

Tertiary

3D shape of one chain

Quaternary

arrangement of multiple chains

Anfinsen's principle

The primary
amino acid sequence contains the
information needed to determine the
protein's final three-dimensional
structure.

Homomeric (quaternary structure)

Composed of two
or more identical subunits.

Molecular chaperones

are
specialized proteins that assist in
the folding process, although the
final structure is ultimately
determined by the primary amino
acid sequence

Alpha-helix

Right-handed helix structure

R-groups project outward

β-sheets

consists of extended polypeptide strands arranged next to one another.
Can be:
• Parallel
• Antiparallel

Polyproline Helices

• Proline-rich sequences

• The outward-facing R-groups
  are often hydrophobic

• important for protein-protein interactions

Protein Domains/motifs

an independently folding,
stable, and compact three-dimensional unit
that acts as a fundamental building block of
protein structure and function

Proteins Denaturation

• loss of a protein’s normal
  shape.

• It happens when heat, acids, bases, or
  chemicals disrupt the protein.

• The protein unfolds and loses its normal
  function.

Protein Misfolding

when a protein fails to achieve
its correct structure.

Collagen

• rich in glycine, proline

• left handed helix

• 3 chains twisted together

Collagen Requirements

• Lysine and proline in collagen are
  modified by hydroxylation.

• This helps collagen molecules form
  strong cross-links.

• Vitamin C is needed for this process.

• Cross-links give collagen strength and
  stability.

• Without enough vitamin C, collagen
  becomes weak.

• Severe vitamin C deficiency can cause
  scurvy

Hemoglobin and myoglobin function as

carriers to bring O2 to the cell to participate in cellular
respiration to produce ATP molecules

Both myoglobin and hemoglobin are classified as

globular proteins

Myoglobin stores the oxygen whereas

hemoglobin brings the oxygen to the tissues

Myoglobin

Has higher affinity to O2 than hemoglobin

Binds and releases O2 to muscle cells

Myoglobin Structure

single polypeptide chain folded into a tertiary
structure known as globin fold (composed of 8 alpha helices)
with one O2 binding site. The helices are folded in a way to
create a hydrophobic O2 binding pocket containing heme group
with an iron atom (Fe+2) in its center

Heme structure

Composed of planner
protoporphyrin ring
composed of four pyrrole
rings the lie with their N
atoms in the center (organic
part) binding an Fe+2
(inorganic atom).

Hemoglobin

Take the O2 from the lungs to the tissues and takes CO2 from the tissues back
to the lugs to be expelled out of the body

Hemoglobin structure

tetrameric (4 polypeptide subunits, 2 alpha subunits and 2 beta subunits). Each
subunit has a heme molecule which means each is bound to Fe+2 (total 4 O2 molecules bound)

Hemoglobin has 2 ___ chains and 2 ___ chains

alpha and beta

The saturation curve of myoglobin has a

hyperbolic shape

The saturation curve for hemoglobin has a

sigmoidal shape (S shape)

Myoglobin becomes more saturated at a

lower
pressure than hemoglobin and requires very low
pressures to release O2

hemoglobin where the binding of one O2 to one subunit in
hemoglobin leads to

increasing the affinity of the other subunits for O2 (allosteric regulation)

Allosteric regulation of hemoglobin results in a conformation change also called

the change from tense (T) state to relaxed (R) state

T state happens when there is

low affinity for O2

R state happens when there i

high affinity
for O2

When O2 binds to the iron (Fe+2) group, it pulls up the Fe+2 into the heme group because it decreases
the electron density around the Fe+2, allowing it to become smaller in size, thus able to fit in the
porphyrin ring. This change in the conformation (the pull)

also pulls the proximal histidine group and
changes the overall interaction between hemoglobin subunits

T to R state

In deoxygenated hemoglobin, the quaternary structure is very constrained (T state). When O2
binds and leads to conformational change, it relieves this strain and allows the molecules to go
into the relaxed state (R state)

At low pressure (low O2), the hemoglobin binding
is slow, but as more O2 is binding,

there is a sharp rise in the curve (the affinity to O2
shoots up and we notice the increase in saturation
with O2)

There are 3 allosteric factors affecting Hb affinity, binding and dissociation to O2:

hydrogen ions

2,3 Bisphosphoglycerate

Covalent binding of CO2

Hydrogen Ion (Bohr effect)

by increasing the concentration of
CO2, the H+ ion conc also increases leading to a
decrease in blood pH thus lowering Hb affinity to
O2

In order for the cells to get rid of CO2,

it will
react with H2O to give carbonic acid by the aid of
an enzyme called carbonic anhydrase. Carbonic
acid then dissociates to H+ and bicarbonate ion (aka Bohr effect)

In the Bohr effect, the affinity and binding of Hb to
O2 is

NOT affected by the pH

How do H+ ions really affect Hb?

H+ ions bind
the Hist 146 on the β subunit and the amino group of the terminal
residue in Hb α 122 positions forming stabilized salt bridges that
leads to changing the conformation of Hb and stabilizing the Hb
in T state, making it more likely to unload O2 to the tissues that
need it

Carbon Dioxide (Haldane effect)

• O2 affects the affinity of Hb to CO2
  and H+

• increases the number of
  the polar bicarbonate ions dissolved in the blood

2,3-Bisphosphoglycerate
(2,3-BPG)

Relatively small molecule that contains multiple
negative charges. These characteristics allow this
molecule to bind in the positive pocket inside Hb

2,3-Bisphosphoglycerate
(2,3-BPG) in regards to Hb and O2

2,3-BPG lowers the affinity of
Hb to O2. Therefore, more Hb will be able to release
O2 in the tissues

Red blood cells can modulate Hb affinity for O2 by
altering

the rate of synthesis or degradation of 2,3-
BPG

2,3-BPG binds to the positive pockets inside the Hb, which are

2 Histidine 143 and 2 Lysine 82 from the B subunits

Fetal Hb subunits are

two α subunits and 2 γ subunits

The difference between γ subunits and is that

γ subunits do NOT have Histidine 143. Instead,
it has serine

Serine is neutral which means the positive pocket in the

fetal Hb is
less positively charged than the maternal/adult Hb

The lower positive charge means the 2,3-BPG binds less to the fetal Hb. The physiological
significance of this is that the

fetal Hb has higher affinity to O2 than maternal/adult Hb (allows for efficiently O2 intake)

Carbon monoxide
(CO) poisoning

• CO binds with Hb at the same binding site of O2

• CO has higher affinity to Hb than O2

• More CO binds that O2 = death

Sickle Cell Disease

• a genetic error occur leading to the substitution of glutamate with valine in the B subunits

• Since valine is non polar, it causes the HB molecules to form a linear shape, resulting in (sickle cell)

Thalassemia

there is unbalanced production of α subunits or ꞵ subunits (the genetic mutations that cause thalassemia affect the synthesis of either α or ꞵ subunits)

ꞵ-Thalassemia major (homozygous ꞵ-Thalassemia)

severe disorder caused by inheriting two alleles of the nutation

ꞵ-Thalassemia intermediate:

Less severe clinical phenotype. Can be the result of two different mild mutations or homozygosity for a mild mutation

ꞵ-Thalassemia minor (ꞵ-Thalassemia trait):

Heterozygous disorder that involves a single mutation.

Signal transduction

the process of converting an extracellular signal to a molecular response inside the cell

1) Release of the primary messenger

The primary messenger release occurs as a result of external or internal stimuli

2) Reception of the primary messenger

The majority of primary messengers bind to proteins in the cell membranes (receptors) that transfer this information to the cell’s interior

Signal molecules are also called

ligands

3) Delivery of the message to the interior of the cell (transduction)

The information from the receptor-ligand complex are transferred to the inside of the cell by second
messengers

Second messengers

small molecules that mediate the next steps in the transduction pathways via the
change in their concentration in response to change in environmental signals

The consequences of using second messengers:

• signal may be amplified

• they are free to diffuse to different sites within the cell and influence other processes

• Used in multiple pathways

Activation of effectors that directly influence the physiological response

This results in the activation (or inhibition) of pumps, channels, enzymes or transcription factors
that affects cellular processes

Termination of the signal:

After the completing of the cell response to the external signal, the transduction pathway must be
terminated (to preserve cell responsiveness to new signals)

What are G protein-coupled receptors
(GPCRs)?

• 7-transmembrane helix proteins

• transduce extracellular signals into important physiological effects

Components of GPCRs

• 7 transmembrane helix

• functional extracellular and intracellular loops

• G proteins (Ga, Gb, and Gy subunits)

G Protein A subunits contains two loops, called

switch I and Switch II

Gs

leads to the stimulation of adenylyl cyclase leading to the conversion of ATP to cAMP

Gi

leads to the inhibition of adenylyl cyclase leading to the prevention of conversion of ATP
to cAMP