Chapter 5 Definitions/Concepts

Question 1

Ligand

Answer 1

A molecule bound reversibly by a protein, can be any kind of molecule

Question 2

Binding Site

Answer 2

Where the ligand binds the protein. Complementary to the ligands size, shape, charge and hydrophobic/hydrophilic characteristics.

Question 3

Binding Specificity

Answer 3

Ligand binding to a binding site is usually highly specific

Question 4

Multiple Binding Sites

Answer 4

Proteins can have more than one binding site to bind more than one kind of ligand

Question 5

Conformational Changes

Answer 5

Conformational changes can be subtle or dramatic and are essential for protein function

Question 6

Induced Fit

Answer 6

A change in the proteins binding site that makes the binding of the ligand more desirable

Question 7

Substrates

Answer 7

The molecules acted upon by an enzyme in a reaction

Question 8

Heme

Answer 8

Prosthetic group for binding oxygen, found in hemoglobin and myoglobin

Question 9

Cooperative Bonding

Answer 9

When one O2 is bound it triggers the other subunits from T state to R state, therefore increasing the affinity for more O2 to bind.

Question 10

T State

Answer 10

Conformation that is more stable in the absence of oxygen

Question 11

R State

Answer 11

Conformation that has a higher binding affinity for oxygen

Question 12

Allosteric Protein

Answer 12

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

Question 13

Oxygen binding pressure

Answer 13

The partial pressure of oxygen in the lungs and tissues affect its ability to bind to hemoglobin

Question 14

Hill Coefficient

Answer 14

Measures the degree of cooperatively. When it equals 1 binding is not cooperative. When it is greater then 1 binding is cooperative.

Question 15

Inverse Hemoglobin Binding Relationship

Answer 15

The binding of H and CO2 is inversely proportional to the binding of O2. When the pH is low and CO2 concentration is high the tissues decrease the affinity of hemoglobin for O2, therefore releasing it into the tissue.

Question 16

H binding on hemoglobin

Answer 16

Doesn’t bind to heme group. Binds to any of the amino acids which causes the structure to favor the T state.

Question 17

CO2 binding to hemoglobin

Answer 17

Doesn’t bind to heme group. Binds to N-terminal end of any of the 4 polypeptide chains

Question 18

CO binding to hemoglobin

Answer 18

Does bind to heme group with higher affinity then oxygen, therefore reducing oxygen concentration in the body

Question 19

Sickle Cell Anemia

Answer 19

Hereditary disease with abnormal shaped and fewer erythrocytes. Caused by amino acid substitution in the beta chains, creating hemoglobin s.

Question 20

Hemoglobin S

Answer 20

Has fewer negative charges, protein aggregates into long fibers

Question 21

Antigen

Answer 21

Molecule or pathogen capable of eliciting an immune response

Question 22

Epitope

Answer 22

The part of an antigen the antibody recognizes

Question 23

Immunoglobin G

Answer 23

Major class of antibody comprised of 4 polypeptide chains, 2 heavy and 2 light. Connected by disulfide bonds and non-covalent interactions to form a y-shaped molecule

Question 24

Fab

Answer 24

Part of the immunoglobin G, has amino acids that recognize and bind antigens

Question 25

Antibody-antigen specificity

Answer 25

Conferred by chemical complementarity between antigen and specific binding site

Question 26

Model of Induced Fit Binding

Answer 26

Conformational changes occur to facilitate the most favorable interactions. Shape can change greatly when antigen is introduced

Question 27

Antibody-Antigen Binding

Answer 27

Kd is very small, they bind tightly

Question 28

Polyclonal

Answer 28

Many different antibodies recognizing different epitopes of the same antigen

Question 29

Monoclonal

Answer 29

A single antibody recognizing a single epitope of an antigen

Question 30

Stationary Phase

Answer 30

Uses antibodies to bind and retain a protein (antigen) of interest

Question 31

Motor Proteins

Answer 31

Characterized by their need for chemical energy, usually ATP

Question 32

Myosin

Answer 32

Has 6 subunits, 2 heavy and 4 light and has a supercoiled alpha helix like keratin. Aggregate to form thick filaments. Coiled coil tails bond with the globular regions at end

Question 33

Myosin N-terminal end

Answer 33

Hydrolyzes ATP

Question 34

Actin

Answer 34

Associates to form a long filamentous thin filament. Each monomer contains an ATP binding site that hydrolyzes ATP to ADP during polymerization

Question 35

Actin/Myosin Binding

Answer 35

Each thin filament can bind one head group of myosin

Question 36

Actin/Myosin Contraction

Answer 36

ATP binds myosin -> dissociates -> conformational change causes dissociation -> reduced affinity for actin