Chapter 3

Question 1

Cytoskeletal Proteins

Answer 1

Structural proteins, anchoring proteins, and a lot of extracellular matrix
* Fibrous with repeating domains
* Function in cellular motility

Collagen, elastin, keratin, actin, tubulin

Question 2

Motor Proteins

Answer 2

One or more heads able to generate force through a conformational change
* Have ATPase activity and binding heads (indicates catalytic activity)
* Function in cellular motility (nonenzymatic)
* Have enzymes (protein/RNA molecules with catalytic activity)

Myosin, kinesis, dynein

Question 3

Binding protein

Answer 3

Bind to specific substrate either to sequester in body/hold its concentration at steady state
* If present in high amounts relative to substrate, almost all substrate will be bound despite low affinity

Question 4

Cadherins

Answer 4

Calcium-dependant glycoproteins that hold similar cells together

Question 5

Integrins

Answer 5

Two membrane-spanning chains
* Allow cells to adhere to proteins in extracellular matrix
* Some have signaling capabilities

Question 6

Selectins

Answer 6

Allow cells to adhere to carbohydrates on surfaces of other cells
* Most commonly used in immune system

Question 7

Antibody to Antigen Bonding

Answer 7

1. Neutralization of pathogen/toxin
2. Opsonization (marking) of antigen for destruction
3. Creation of insoluble antigen-antibody complexes that can be phagocytized and digested by macrophages (agglutination)

Question 8

Enzyme-linked Receptors

Answer 8

Participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades
* Autoactivity
* Enzymatic activity

Question 9

G Protein-Coupled Receptors

Answer 9

New membrane-bound protein associated with trimeric G protein
* Initiate second messenger systems
* Two-protein complex
* Dissociation upon activation
* Trimer

Question 10

Receptor Similarities

Answer 10

• Extracellular domain
• Transmembrane domain
• Ligand binding

Question 11

Ungated Channels

Answer 11

Ion channels that are always open
* Responsible for maintaining resting membrane potential
* Involved in cell signaling and pacemaker potentials but cause deviation from resting membrane potential

Question 12

Transport Kinetics

Answer 12

• Display Km and vmax values
• Can be cooperative like some binding proteins
• No Keq values for reactions because no catalysis

Question 13

Isoelectric Focusing & Ion-Exchange Chromatography

Answer 13

• Seperate proteins based on charge
• Charge of protein in any environment is determined by isoelectric point (pI)
• Isoelectric focusing uses gel with pH gradient that promotes variable charge

Question 14

Native PAGE

Answer 14

Complete protein recovered after analysis
* More accurately finds relative globular size of proteins
* Maintains protein’s shape
* Results are difficult to compare since mass-to-charge ratio differs for each protein

Question 15

SDS-PAGE

Answer 15

Denature proteins and masks native charge so size comparison is more accurate
* Can be used to eliminate conflation from mass-to-charge ratios
* Functional protein can’t be recaptured from gel

Sodium dodecy sulfate (SDS) detergent that will digest proteins to form micelles with uniform negative charges

Question 16

Affinity Chromatography

Answer 16

Uses bound receptor/ligand and eluent with free ligand/receptor for protein of interest

Potential Drawbacks:
1. Protein of interest may not elute from column because its affinity is too high
2. Permanently bound to free receptor in eluent

Inactivations:
* Detergents
* Heat
* pH
* Protein elutes off by binding free ligand
* Binding may not have been reversed so free ligand competes for active site

Question 17

Size-Exclusion Chromatography

Answer 17

• Relies on porous beads
• Larger molecules elute first because not trapped in small pores
• Smaller particles trapped retaining in column

Question 18

Protein Isolation

Answer 18

• First step in analysis
• Protein identity must be confirmed by amino acid analysis/activity
• With unknown proteins, want classification of feautures

Question 19

Activity Assay

Answer 19

Display lower actvity after concentration determination:
1. Contamination with detergent
2. SDS could yield artifically increased protein level leading to lower activity than expected (calculated higher than actual)
3. Enzyme denatured during isolation and analysis

Question 20

Edman Degradation

Answer 20

Required sequential degradation for amino acid sequencing
* Proceeds from amino (N-) terminus

Question 21

Electrophoresis

Answer 21

Uses gel matrix to observe migration of proteins in response to an electric field
* Can only handle small volume of protein
* When isolating protein, want a pH that makes protein A negative while B and C are neutral/positive

Question 22

Antibodies

Answer 22

• Specific to single antigen
• Each B-cell prduces single type of antibody with constant region specific to host and variable region
• Label antigens for targeting by other immune cells
• Can cause aggltination by interaction with antigen
• Have two heavy chains and two light chains

Question 23

Trimeric G Proteins

Answer 23

Have a, B, and y subunits in ALL

a Subunits:
Gs, Gi, Gq (differ depending on G protein-coupled receptor’s function)

Question 24

pI

Answer 24

Determined by relative number of acidic and basic amino acids

Basic Amino Acids:
Arginine, lysine, histidine

Acidic Amino Acids:
Aspartic acid, glutamic acid

Glycine is least contributor of all amino acids

Question 25

UV Spectroscopy

Answer 25

Best used with conjugated systems of double bonds
* Proteins containing aromatic groups allow this technique to work