Chapter 7: Protein Function

Question 1

The functions of proteins are determined by the reversible binding of molecules called?

Answer 1

ligands

Question 2

Ligands

Answer 2

can be any molecule including another protein that binds to another molecule
*binds to the binding site on a protein

Question 3

Bind and chemically transform other molecules-they catalyze reactions

Answer 3

Enzyme

Question 4

Induced Fit

Answer 4

Protein structure typically changes upon binding to a ligand

Question 5

What do enzymes bind to?

Answer 5

Substrates in a catalytic site or active site.

Question 6

Why can’t oxygen travel through the body without a protein?

Answer 6

Doesn’t dissolve in aqueous solutions easily and cannot diffuse through tissues easily.

Question 7

Fe and O2 alone would damage our DNA, so it is sequestered in a protein to make it less reactive…the protein-bound prosthetic group heme is born!

Answer 7

Fax

Question 8

Heme consists of?

Answer 8

a.) complex organic ring structure
b.) protoporphyrin IX (porphoryin)
c.) bound iron atom in its ferrous (Fe+2) state

Question 9

Which iron state can bind O2?

Answer 9

Fe+2 binds O2 reversibly, Fe+3 cannot bind O2

Question 10

Myoglobin is made up of -

Answer 10

a.) 1 polypeptide chain
b.) 1 heme group
c.) capacity to bind and release their ligands

PRIMARILY FOUND IN MUSCLE TISSUE

Question 11

How does Ka play a role in protein-ligand interactions?

Answer 11

Provides a measure of the affinity of the ligand L for the protein.

HIgher Ka = stronger affinity for L and. protein

Question 12

What does a small Kd value mean?

Answer 12

The protein binds TIGHTER to its ligand.

Question 13

What is Kd representing?

Answer 13

The state of the protein when half of the ligand binding sites are occupied. Used to describe strength of protein’s ability to bind its ligand.

Question 14

Theta θ means…

Answer 14

a.) fraction of binding sites occupied by ligand
Kd = θ = 0.5

Question 15

What does x represent?

Answer 15

Greator affinity for ligand, binds tighter than protein Y

Question 16

t/f

Carbon monoxide will outcompete Oxygen all the time

Answer 16

TRUE

Question 17

What else effects how ligands bind?

Answer 17

The protein function, and its steric effects

Question 18

Erythrocytes

Answer 18

Red blood cells, does not contain nucleus

Question 19

Hemoglobin

Answer 19

a.) Contained within erythrocytes

b.) Transports oxygen throughout our blood supply

c.) Takes O2 from lungs and carries it to all the extremities

d.) 4 subunits (2 alpha and 2 beta)

e.) Beta subunit is very similar to structure of myoglobin

Question 20

What bonds play a role in the quarternary structure of hemoglobin?

Answer 20

Hydrophobic interactions

Hydrogen Bonds

Salt bridges

Question 21

What are the 2 conformations of hemoglobin?

Answer 21

R and T states

Question 22

Talk about R state (relaxed) of Hemoglobin

Answer 22

a.) Binds oxygen more easily than T state

b.) Binding of oxygen causes heme to assume a more planar conformation

Question 23

Talk about T state (tense) of Hemoglobin.

Answer 23

a.) More stable than R state

b.) Called deoxyhemoglobin, stabilized by the greater number of ion pairs

c.) When bound to O2, conformation is changed to R state

Question 24

What is the high affinity state of hemoglobin (sigmodial)?

Answer 24

When multiple O2 molecules are bound

*only occurs with multi-subunit proteins

Question 25

A sigmodial curve represents:

Answer 25

proteins binds to multiple ligand

Question 26

# t/f affinity of hemoglobin should drop as it travels through peripheral tissue

Answer 26

true

Question 27

Allosteric proteins

Answer 27

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

Question 28

Can interconvert more-active and less-active forms of the protein

Answer 28

Modulator

Question 29

When the ligand and modulator are the same, it is called

Answer 29

homotropic ex. O2

Question 30

When the ligand the modulator are different, it is called

Answer 30

heterotrophic

Question 31

**concerted model** (interconversion of inactive and active forms of a protein during cooperative ligand binding)

Answer 31

This model is based on the assumption that the subunits of a cooperatively binding protein are functionally identical, that each subunit can exist in two confirmations and the all subunits undergo the transition from one conformation to the other simultaneously.

Question 32

sequential model

Answer 32

Ligand binding can induce a change of conformation in an individual subunit. This change causes a change in the next door neighbor

Question 33

What happens when blood pH is low?

Answer 33

There are high CO2 levels, affinity of hemoglobin for O2 decreases and affinity increases for CO2

Question 34

What happens when blood pH is high?

Answer 34

Low CO2 levels, affinity of hemoglobin for O2 increases

Question 35

Hemoglobin binds CO2 which binds as a _______ group to the a-amino group at the amino-terminal end of each globin chain, forming ________ residue. These bound carbamates form additional ______, which stabilize the T state to help promote the release of _____.

Answer 35

carbamate carbamino-terminal salt bridges O2

Question 36

What is hemoglobin and O2 binding regulated by?

Answer 36

BPG (2,3-biphosphoglycerate)

Question 37

An example of heterotropic allosteric modulation?

Answer 37

BPG binding to hemoglobin

Question 38

Characteristics of BPG?

Answer 38

1.) reduces the affinity of hemoglobin for O2 2.) BPG concentrations in the blood will rise in response to a person’s change in O2 concentration 3.) more BPG will bind Hb to stimulate the release of O2 (HYPOXIA).

Question 39

BPG and deoxyhemoglobin relationship?

Answer 39

1.) stabilized the T state of deoxyhemoglobin 2.) negatice charges of BPG interact with positive charge groups that surround subunits in T state 3.) Binding pocket for BPG disappears on oxygenation, following transition to the R state

Question 40

White blood cells- detect and deal with infections or foreign molecules that enter your body

Answer 40

Leukocyte

Question 41

Ingest large particles and cells by phagocytosis (absorbs)

Answer 41

Macrophage

Question 42

A type of white blood cell that is part of the immune system. There are two main typesdcx: B cells and T cells

Answer 42

Lymphocyte

Question 43

Fights pathogens that are free in the bodily fluids, relies on antigens to detect these pathogens

Answer 43

Humoral Immune System

Question 44

Involve the destruction of infected cells by cytotoxic T cells, or the destruction of intracellular pathogens by macrophages. The activation of naive T cells in response to antigen, and their subsequent proliferation and differentiation.

Answer 44

Cellular Immune System

Question 45

A protein produced by an animal’s immune system in response to the introduction of a foreign substance (an antigen)

Answer 45

Immunoglobulins (antibodies)

Question 46

Produce and secrete antibodies

Answer 46

B lymphocytes

Question 47

Interact with indected host cells through receptors on T-cell surface

Answer 47

T lymphocytes

Question 48

Involved in direct killing of intracellular pathogens and mutated/cancerous cells

Answer 48

cytotoxic T cells

Question 49

Integral membrane proteins that acitivate T cells in response to an antigen

Answer 49

T-cell receptors

Question 50

Interact with macrophages and secrete cytokines that stimulate T cells, helper T cells, and B cells to proligerate

Answer 50

Helper T cells

Question 51

Random mutations that cause production of B cells with increased antibody-binding affinity for their antigens

Answer 51

Clonal selection

Question 52

A substance that elicits an immune response (production of antibodies) when introduced into an animal

Answer 52

Antigen

Question 53

regions of proteins that can trigger a cell immune response to generate antigenic response and bind antibody

Answer 53

Epitope

Question 54

Structure of Immunoglobulin G

Answer 54

* 2x anti-binding site * Papain cleavage sites (Fc) (links it all together)

Question 55

What are antibinding sites made of?

Answer 55

1 light chain, 1 heavy chain *antigen binds to these antibinding sites in between light and heavy chain

Question 56

# t/f confirmational flexibility is important to maintain function.

Answer 56

True | Fc portion of antibody contains bound carbohydrate

Question 57

Is antigen and antibody binding an induced fit for IgG?

Answer 57

Yes, needs to be bound tight

Question 57

Immunoglobulin M (IgM)

Answer 57

First antibody secreted by B cells in response to an infection. It can be secreted as a pentameric structure.

Question 58

IgA

Answer 58

Is found in saliva, tears, and milk.

Question 59

IgD

Answer 59

Function not clear, but it has the same antigen binding site as IgM and is secreted second

Question 60

IgG

Answer 60

MOST ABUNDANT/ ALWAYS IN SYSTEM Secreted by memory B cells, and are made from the cells “memory.”

Question 61

IgE

Answer 61

Bind to allergens and causes an increase in histamine secretion.

Question 62

Process of IgG and macrophage phagocytosis?

Answer 62

Fc region binf to Fc receptors on macrophage surface, truggering macrophage to eat and destroy virus.

Question 63

______ antibodies are produced by many different B lymphocytes responding to one antigen. Antibodies are produced that bind to many different epitopes within the antigen.

Answer 63

Polyclonal antibodies

Question 64

_____ are produced by identical B cells grown in cell culture. The antibodies produced all recognize the same epitope on the same antigen.

Answer 64

Monoclonal antibody

Question 65

What do motor proteins do?

Answer 65

1.) underlie the contraction of muscles 2.2.) migration of organelles 3.) rotation of flagella 4.) movement of some proteins along DNA

Question 66

How is myosin composed?

Answer 66

2 heavy chains, carboxyl termini forming an extended coiled coil (tail), amino termini habing globular domains (heads) with 2 light chains on each head.

Question 67

Is muscle made up of thick and thin filaments?

Answer 67

Yes, myosin and actin

Question 68

Myosin (in sense of filament)

Answer 68

aggregates to form a bipolar strucute called thick filament

Question 69

Filamentous assemblage of G-actin monomers that polymerize two by two, giving the appearance of two filaments spiraling about one another in a right-handed fashion

Answer 69

F-actin

Question 70

What are muscle fibers made of?

Answer 70

myofibrils surrounded by membranous sarcoplasmic reticulum (striated appearance)

Question 71

When muscle contracts ...

Answer 71

I bands narrow and Z disks get closer together

Question 72

Give a short description of how thick and thin filaments work in muscle contraction.

Answer 72

Thick filaments are bipolar structures created by the association of many **myosin molecules**. Muscle contraction occurs by the sliding of the thick and thin filaments past each other so that the Z disks in neighboring I bands draw closer together. The thick and thin filaments are interleaved such that each thick filament is surrounded by six thin filaments.

Question 73

Step mechanism for muscle contraction:

Answer 73

1.) ATP binds to myosin head, causing dissociation from actin 2.) Tightly bound ATP is hydrolyzed, a conformational change occurs. ADP and Pi remain associated with the myosin head 3.) Myosin head attaches to actin filament, causing release of Pi 4.) Pi release triggers a "power stroke", a conformational change in the myosin head that moves actin and mypsin filaments relative to one another. ADP is released in this process

Question 74

Tropomyosin + Troponin main function include:

Answer 74

Bind to F-actin in the thin filaments In relaxed muscle, they arrange around actin to block binding sites for myosin.

Question 75

Troponin I

Answer 75

prevents binding of myosin head to actin

Question 76

Troponin C

Answer 76

Has a binding site for Ca+2

Question 77

Troponin T

Answer 77

Links the entire troponin complex to tropomyosin

Question 78

When the muscle receives a neural signal to initiate contraction, then ...

Answer 78

Ca2+ is released from the sarcoplasmic reticulum and binds to troponin C. This causes a conformational change in troponin C, which alters the positions of troponin I and tropomyosin so as to relieve the inhibition by troponin I and allow muscle contraction.