Biochem Exam 2

Myoglobin (Mb)

small protein lacking β structure completely

amino acids are part of eight α helices

hyperbolic binding, high O2 affinity (p50=2.8torr)

His F8 (Proximal Histidine)

The residue that forms the 5th coordination bond directly to the central Fe(II) iron atom

His E7 (Distal Histidine)

Forms a hydrogen bond to the bound O2 molecule

polypeptide chain and heme

what is myoglobin made out of

heme

iron-containing porphyrin derivative

prosthetic group that helps bind oxygen

prosthetic group

an organic compound that allows a protein to carry out some function that the polypeptide alone cannot perform

K: dissociation constant

How can binding of O2 to myoglobin be described?

fractional saturation (Y)

the proportion of myoglobin molecules that have bound O2

Y = (pO2) / (K+pO2)

fractional saturation equation

hyperbola

whats the shape of the saturation (Y) vs pO2 plot for myoglobin?

saturation

point at which all virtually all myoglobin molecules have bound to O2

Y is half maximal, pressure is at 50%

K is the concentration of concentration of O2 at which ____ aka _____

760

how many torr in 1 atm

hemoglobin (Hb)

heterotetramer (2α 2β chains; overlapped 3D structure)

all have a heme group in a hydrophobic pocket, a His F8 that ligands the Fe(II) ion, and a His E7 that forms a hydrogen bon to O2.

sigmoidal curve; cooperative binding; lower O2 affinity (p50 = 26 torr)

invariant residues

those that are identical in all the globins

are essential for the structure and/or function of the proteins and cannot be replaced by other residues

found in all vertebrate hemoglobin and myoglobin

hemocratit (40% F; 45% M)

measures oxygen carrying capacity of the blood

(blood volume occupied by RBC)

anemia

too few RBCs

sigmoidal

whats the shape of the saturation (Y) vs pO2 plot for hemoglobin?

26 torr

pO2 at which hemoglobin is half-saturated (p50)

pO2 corresponds to the part of the hemoglobin binding curve where the O2 affinity falls off most sharply

why is hemoglobins oxygen delivery system efficient?

memorize

myoglobin hemoglobin table

rotation of one αβ unit relative to the other

how do oxygenated and deoxygenated states of hemoglobin change conformation?

T (tense)

deoxyhemoglobin state

low O2 affinity

R (relaxed)

oxyhemoglobin state

high O2 affinity

T → R

1st oxygen molecule binding switches the conformation from ___

R → T

1st oxygen releasing switches conformation

allosteric proteins

proteins with multiple binding sites ex. hemoglobin

he binding of a small molecule (called a ligand) to one site alters the ligand-binding affinity of the other sites

O2 pressure, H+ concentration

factors that affect oxygen binding

they become more acidic and release H+

what happens to the N and C terminus groups when oxygen binds to hemoglobin

Bohr effect

the reduction of hemoglobin's oxygen-binding affinity when the pH decreases (H+ increases) is known as the

Hemoglobin picks up O2 in the lungs.

In the tissues, H+ derived from the metabolic production of CO2 decreases hemoglobin's affinity for O2, thereby promoting O2 release to the tissues.

Back in the lungs, hemoglobin binds more O2, releasing the protons, which recombine with bicarbonate to re-form CO2.

describe oxygen transport with Bohr effect

lungs

where does hemoglobin pick up O2?

tissues, decreases

in the ____ H+ derived from the metabolic production of CO2 _____ hemoglobin's affinity for O2

lungs, bicarbonate

in the ___ hemoglobin binds more O2, releasing the protons, which recombine with ____ to re-form CO2.

2,3-bisphosphoglycerate (BPG)

Allosteric regulator that binds strictly in the central cavity of the T state, stabilizing deoxy-Hb and lowering O2 affinity

stabilizes the deoxy conformation of hemoglobin; O2 would bind too tightly

why is BPG important?

T (deoxy) state

in what state does BPG bind in the central cavity of hemoglobin?

reduces hemoglobin's O2 affinity by stabilizing the deoxy conformation

effect of BPG

dont like BPG

Why fetus hemoglobin has higher affinity than adult hemoglobin?

sickle cell hemoglobin (Hb S)

Individuals with two copies of the defective gene

debilitating condition that predominantly affects populations of African descent

he hydrophobic valine residues(blue) on hemoglobin S are optimally positioned to bind to this patch

this intermolecular association leads to the rapid aggregation of hemoglobin S molecules to form long, rigid fibers

describe sickle cell hemoglobin

Hemoglobin S (Hb S)

Caused by a single point mutation (β6 Glu→Val)

Exposed valine causes hydrophobic aggregation into rigid fibers in deoxy state

mutant hemoglobin C

makes the red blood cells a bit more rigid than normal, leading to mild anemia

Thalassemias

Genetic disorders resulting from a reduced rate of synthesis of α or β globin chains

Globular proteins

hemoglobin and myoglobin are

actin filaments, intermediate filaments, microtubules

3 structural proteins

extracellularly

fibers of the protein collagen provide structural support (intra/extra)

actin monomer

adenosine triphosphate (ATP) slips into a pocket on the protein

ribose hydroxyl groups and the phosphate groups form hydrogen bonds with the protein

F-actin (filamentous actin)

a double chain of subunits in which each subunit contacts four neighboring subunits

the end with the ATP site is known as the (−) end,

and the opposite end is the (+) end

Actin Filament Assembly

Subunits usually add more rapidly to the (+) end, which therefore grows faster than the (−) end

Polymerization of actin monomers

Reversible process, so the polymer undergoes constant shrinking and growing as subunits add to and dissociate from one or both ends of the microfilament

treadmilling

when the net rate of addition of subunits to one end of an actin filament matches the net rate of removal of subunits at the other end, the polymer is said to be ___

Capping, branching, and severing proteins

how is assembly and disassemby of actin filaments regulated

structural support, cell movement, tensile force

functions of actin filaments (3)

tubulin

forms microtubules

microtubule

bout three times thicker and much more rigid than actin because it is constructed as a hollow tube

protein tubulin (α,β)

microtubule structure

guanine nucleotide (GTP or GDP)

what does tubulin bind

protofilament

end-to-end association of tubulin dimers form a short linear

positive (terminating in β tubulin)

which end of tubulin grows faster

at both ends

what end of tubulin does disassembly happen?

Paclitaxel (taxol)

drug stabilizes microtubules, preventing depolarization

colchicine

drug depolarizes microtubules

intermediate filaments

strictly structural, no cell motility

interact with actin filaments and microtubules via cross-linking proteins

dead remnants of epidermal cells

where are intermediate filaments most prominent?

keratin

best known intermediate filament

soft keratins

help define internal body structures,

hard keratins

in, hair, and claws

coiled coil (dimer of α helices)

structure of an intermediate filament

100

how many residues in the α helical chain of a coiled coil?

7 residue repeating; first and fourth residues are predominantly nonpolar

amino acid sequence of intermediate filaments consists of

disulfide

what bond cross links keratin fibers

collagen

extracellular structural protein most abundant in animals

every 3rd amino acid is glycine; rest 30% are proline and hydroxyproline

structure of collagen

its a chiral

why does collagens dominant amino acid have to be glycine?

scurvy

lack of vitamin C (ascorbate)

collagen contains too few hydroxyproline residues and hydroxylated lysine residues, so the resulting collagen fibers are relatively weak.

hydroxyproline and hydroxylated lysine

what amino acids are low in scurvy?

catalyzes proline reaction (collagen can’t form without it)

what does ascorbate (vitamin C) do?

covalently (chem modified)

how are collagen molecules cross-linked?

osteogenesis imperfecta

Defects in collagen type I (the major form in bones and tendons) cause the congenital

disease

motor proteins

act on structural elements such as actin filaments and microtubules to generate the movements that allow the cells to reorganize their contents, change their shape, and even crawl or swim

use ATP to carry out mechanical work

ATP hydrolysis → mechanical energy

myosin works with actin to produce movement by converting

2 large polypeptides form 2 globular heads, 1 tail

muscle myosin structure

actin and adenine nucleotide

each head of myosin contains a binding sit for

neck

what acts as a lever and is stiffened by small light chains (2 polypeptides) in myosin?

In a series of steps that include protein conformational changes and the hydrolysis of ATP, the myosin head releases its bound actin subunit and rebinds another subunit closer to the (+) end of the actin filament.

describe the process of myosin rebinding

thick filament

myosin tails associate to form

thin filaments

heads each consist of an actin filament and actin-binding protein

contraction

when myosin acts on actin to shorten muscle

The conversion of ATP to ADP + Pi triggers conformational changes in the myosin head that are communicated to the actin-binding site as well as to the lever (the neck region).

The chemical reaction of ATP hydrolysis thereby drives the physical movement of myosin along an actin filament.

In other words, the free energy of the ATP hydrolysis reaction is transformed into mechanical work

Describe the Myosin-Actin Reaction Cycle

cytokinesis, transport, tension rods

myosin works with actin for what three things?

Usher syndrome

the most common form of deaf-blindness in the United States

is characterized by profound hearing loss, retinitis pigmentosa (which leads to blindness), and sometimes vestibular (balance) problems.

myosin type VIIa

genetic mutations identified in Usher syndrome

premature stop codons, amino acid substitutions, and deletions—all of which compromise the protein's function

microtubule tracks

what does kinesin move along?

Kinesin

a large protein and has two large globular heads and a coiled-coil tail domain.

light chains

situated at the opposite end of the kinesin protein, bind to proteins in the membrane shell of a vesicle(cargo)

Kinesin moves its cargo toward the (+) end of a microtubule along a single protofilament. Other microtubule-associated motor proteins appear to use a similar mechanism but move toward the (−) end of the microtubule.

The motor activity of kinesin requires the free energy of ATP hydrolysis. However, kinesin cannot follow the myosin lever mechanism because its head domains are not rigidly fixed to its neck regions.

In kinesin, a relatively flexible polypeptide segment joins each head to an α helix that eventually becomes part of the coiled-coil tail. In myosin, the lever is a long α helix that extends from the head to the coiled-coil region and is stiffened by the two light chains.

describe the kinesis reaction cycle

processivity

Kinesin is therefore said to have high ____

its cargo can be moved long distances without being lost.

High processivity is advantageous for a transport engine because

immune system

potentially recognize, respond to, and remember millions or billions of antigens