Biochem exam 2 chapter 5

Proteins act as…

catalysts or enzymes

5 functions of globular proteins

-Storage (myoglobin and ferratin)

-Transport (hemoglobin and serotonin transport)

-Defense againt pathogens (antigens, cytokines)

-Muscle contraction (actin, myosin)

-Biological catalysis (chymotrypsin, lysozyme)

The functions of many proteins involve the — — of other molecules

reversible binding

A molecule bound reversibly by a protein is called a what

ligand

3 characteristics of Oxygen

-Poorly soluble in aqueous solutions

-diffusion through tissues is ineffective over large distances

Transition metals have a strong tendency to bind (iron, copper)

Oxygen can bind to a — Prosthetic group

Heme

What is heme

A protein bound prosthetic group

heme is present in what

Myoglobin and hemoglobin

What does heme consist of

Complex organic ring structure protoporphyrin, with a Fe²+ atom

6 coordination bonds of iron (Fe²+) are comprised of what

-four to nitrogen atom in porphyrin ring

-two perpendicular to porphyrin

One of the two perpendicular coordination bonds in iron is occupied by what

a side chain nitrogen of a highly conserved proximal His residue

One of the two perpendicular coordination bonds in iron is occupied by what

binding site for molecular oxygnen (O2)

-Fe²+ binds O2 reversibly

-Fe³+ does not bind O2

What are globins

widespread protein family

globins are a highly conserved — structures

tertiary: eight alpha helicle segments connected by bends (globin folds)

Most globins function in what

O2 transport or storage

4 types Globins in humans

Myoglobin

Hemoglobin

Neuroglobin

cytoglobin

Myoglobin

monomeric, facilitates O2 diffusion in muscle tissue

hemoglobin

tetrameric, responsible for O2 transport in bloodstream

neuroglobin

monomeric, expressed largely in neurons to protect the brain from low O2 or restricted blood supply

cytoglobin

monomeric, regulates levels of nitric oxide, a localized signal for muscle relaxation

Myoglobin has how many residues

153 + one molecule of heme

His 93

93 residue from amino terminal end

His F8

eighth residue in alpha helix F

Protein-ligand binding can be represented as

P + L ⇌ PL, P is protein, L is ligand

what is Ka

association constant. provides a measure of the affinity of the ligand L for the protein

Higher ka means

Higher affinity

Equation for Ka

Ka= PL/[P][L]= ka/kd

HIgh Kd=

low affinity

Kd corresponds to what

the ligand concentration at which approximately half of the available binding sites are occupied (dissociation constant)

When [L] > > > [ligand binding sites], the binding of the ligand by the protein does what

does not appreciably change

BInding equilibrium

[L]/[L]+ 1/ka (hyperbolic type of graph)

What is fractional saturation

often represented by θ, describes the fraction of protein binding sites occupied by ligand.

θ ranges from

0 to 1

Binding of O2 to Myoglobin

Y= [O2]/ [O2] +kd (kd equals the [O2] at which ½ of teh available ligand-binding sites are occupied, or [O2]0.5

Is partial pressure of O2 (pO2) easier or harder to measure than [O2]

easier

Partial pressure of oxygen at [O2]0.5 as P50:

Y= po2/pO2 +p50

carbon monoxide binds free heme more than — times better than O2 does

20,000

look at slide 26 of chapter 5

What is P50

partial pressure of O₂ at which a protein is 50% saturated. When P50 is lower, O2 has higher affinity. Myoglobin has a low P50

erythrocytes are formed from what

hemocytoblasts (precursor stem cells)

main function of erythrocytes

carry hemoglobin

what percent of arterial blood is saturated with O2

96%

what percent of peripheral blood is saturated with O2

64%

How many heme groups does hemoglobin have

4

adult hemoglobin has 2 globin types

-two alpha chains (141 residues each)

-two beta chains (146 residues each)

slide 31 chapter 5

Two conformations of hemoglobin

-R state

-T state

R state

O2 has a higher affinity for hemoglobin (relaxed)

T state

more stable when O2 is absent, predominant conformation of deoxyhemoglobin

What is T state stabalized by

a greater number of ion pairs (many at which lie at the a1b2 (and a2b1) interface

What triggers a conformational change to the R state

O2 binding to hemoglobin in T state

-causes alpha beta subunit pairs to slide past each other and rotate

-the pocket between the beta subunits narows

-some ion pairs that stabilize the T state break and some new ones form

Hemoglobin has what kind of binding curve

hybrid sigmoid for oxygen

allosteric protein

binding of a ligand to one site affects the binding properties of another site on the same protein

modulators

ligands that bind to an allosteric protein to induce a conformational change

Homotropic

normal ligand and modulator are identical

Heterotropic

modulator is a molecule other than the normal ligand

CO has — fold greater affinity for hemoglobin than does O2

250

Ka and Y for Cooperative Ligand Binding

Y=[L]/ [L]^n + Kd. (n is binding sites)

Hill equation

log(Y/1-Y)= n log [L] - log Kd

nH = 1 in hills plots

no cooperativity with ligand bonding

nH > 1:

nH > 1: positive cooperativity

nH < 1

nH < 1: negative cooperativity

nH means what on a hill plot

slope

slide 47 chapter 5

Two models suggest mechanisms for cooperative binding

MWC model=concerted model

Sequential model

MCW model

all subunits in the same conformation

ligand binds more tightly to the R state

sequential model

each subunit can be in either conformation

equilibrium is altered as additional ligands are bound, progressively favoring the R state

Hemoglobin carries two end porducts of cellular respiration

H+ and CO2

Carbonic Anhydrase

catalyzes the hydration of CO2 to bicarbonate

CO2+h20→H+ + HCO3 (reversable)

What is the Bohr effect

decsribes the effect of pH and [CO2] on the binding and release of O2 by hemoglobin

HHB+ +O2 → HbO2 + H+ (reversible)

the structural effects if H+ and Co2 binding to hemoglobin favor what

T state (less affinity for O2)

when [O2] is high hemoglobin binds what

O2 and releases H+

when [O2] is low hemoglobin releases what

O2, and binds H+

Oxygen binding to Hemoglobin is regulated by what

2,3 Bisphosphoglycerate

2,3 Bisphosphoglycerate is an example of what

heterotrophic allosteric modulation

-binds to a site distant from O2 binding site

-greatly reduces the affinity of hemoglobin for oxygen

When does BPG increase

at high altitudes

Hypoxia

lowered oxygenation of peripheral tissues

-causes BPG to increase

Slide 58 look at chapter 5

what is Fetal Hemoglobin

fetus synthesizes a2Y2 heloglobin

-lower affinity BPG than normal adult hemoglobin

-higher affinityfor O2 than adult

Sickle cell anemia what is it?

Homozygous condition where a single amino acid substitution occurs (Glu6 to Val6). Beta chains produce hydrophobic patch

what happens when hemoglobin becomes deoxygenetad

becomes insoluble and forms polymers that aggregate

Is normal hemoglobin insoluble or soluble upon deoxygenation

soluble

2 types of immunity

-innate

-adaptive

immune response

coordinated set of interactions among many classes of proteins, molecules, and cell types

-eliminates viruses, bacteria and pathogens

-distinguishes molecular “self” from “nonself” and destroys “nonself”

The immune system response consists of 2 complementary systems:

-humoral immune

-cellular immune

Humoral immune system

directed at bacterial infections and extracellular viruses

Cellular immune system

Destroys infected host cells, parasites, and foreign tissues

1. Humoral “fluid” immune system targets what

2. What does it recognize

3. what does it make

4. Key players

extracellular pathogens

foreign pathogens

soluble antibodies

B-lymphocytes, helper T cells

1. Cellular immune system targets what

2. clears up what

3. Key playes

own cells that have been infected

clears up virus particles and infecting bacteria

macrophages, killer T cells, and inflammatory T cells

Antibodies are also called

immunoglobulins (Ig)

what do immunoglobulins do

they bind bacteria, viruses, or large molecules identified as foreign and target them for destruction

antibodies are produced by what

B lymphocytes or B cells

Antigens

substances that stimulate production of antibodies

(recognized as foreign by immune system)

what is an epitope

small region of the antigen where a antibody will bind. One antigen can have several epitopes.

Binding will mark the antigen for destruction or interfere with its function

T lymphocytes (cytotoxic T cells) cellular immune response

recognition of infected cells of parasites involves T cell receptors on surface ofTc cells

Helper T cells (cellular immmune response)

produce soluble signaling proteins called cytokines

-interact with macrophages

-stimulate selective proliferation of Tc and B cells that can bind to a particular antigen (clonal selection)

memory cells (cellular immune response)

permit rapid response to pathogens previously encountered

what are vaccines

consist of weakened or killed virus or isolated proteinsfrom a viral or bacterial protein coat

What is an antigen

molecule or pathogen capable of eliciting an immune response

-can be a virus, bacterial cell wall, or individual protein or other macromolecule

antibodies or t cell receptors bind to a — — within the antigen

antigenic determinant (or epitope)