Nonenzymatic Protein Function and Protein Analysis

Question 1

Describe the function and importance of collagen

Answer 1

a structural protein that makes up most of the extracellular matrix of connective tissue

Question 2

Describe the function and importance of Elastin

Answer 2

a structural protein that stretches and recoils like a spring. located in the extracellular matrix of connective tissue.

Question 3

Describe the function and importance of Keratin

Answer 3

a structural protein important for intermediate filament proteins found in epithelial cells. makes up hair and nails

Question 4

Describe the function and importance of Actin

Answer 4

a structural protein that makes up microfilaments and the thin filaments in myofibrils. Most abundant protein in eukaryotes. Actin has a positive and negative side that gives polarity and allows motor proteins to travel unidiretionally

Question 5

Describe the function and importance of Tubulin

Answer 5

a structural protein that makes up microtubules. important in chromosome separation

Question 6

Describe the function and requirements for motor proteins to function

Answer 6

move molecules, act as ATPases that power conformational changes

Question 7

Describe the function and importance of Myosin

Answer 7

primary motor protein that interacts with actin. involved in cellular transport.

Question 8

Describe the function and importance of kinesins and dyneins

Answer 8

motor proteins associated with microtubules. Have two heads that conformationally change to “walk”

Question 9

What is the difference and function between kinesins and dyneins

Answer 9

kinesins= align chromosomes and vesicle transportation. bring vesicles toward the positive end of a microtubules
dyneins= sliding movement of cilia and flagella and vesicle transportation. bring vesicles toward the negative end of a microtubules

Question 10

True or false motor proteins are enzymatic

Answer 10

True

Question 11

What is the purpose of binding proteins

Answer 11

bind to individual cells to transport them

Question 12

Describe the function and importance of Cell adhesion molecules (CAMs)

Answer 12

binding proteins found on the surface of most cells and air in binding the cell to the extracellular matrix of other cells

Question 13

Describe the function and importance of Caherins

Answer 13

CAMs that are group of glycoproteins that mediate calcium-dependent cell adhesion. mostly epithelial cells

Question 14

Describe the function and importance of Integrins

Answer 14

CAMs that have two membrane spanning chains called alpha and beta. play an important role in cell signaling and impact cell division, apoptosis, or other functions.

Question 15

Describe the function and importance of Selectins

Answer 15

CAMs that bind carbs that project from other cell surfaces. Weakest CAMs bonds. expressed on white blood cells and other endothelial blood vessel cells

Question 16

Describe the function and importance of (antibodies) immunoglobulins

Answer 16

proteins produced by B-cells that function to neutralize targets in the body like toxins and bacteria. Y shaped.

Question 17

What is the function of disulfide linkages in antibodies

Answer 17

hold the light and heavy chain of Y shaped antibodies together.

Question 18

What are the 3 outcomes when an antibody binds to their targets (antigens)

Answer 18

1) neutralizing the antigen, making the pathogen or toxin unable to exert its effect
2) marking the pathogen for destruction by other white blood cells (opsonization)
3) clumping together (agglutinating) the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages

Question 19

What term describes an ion channels main purpose

Answer 19

facilitate diffusion

Question 20

What are the 3 types of ion channels and what is their importance and function

Answer 20

1) ungated channels= unregulated. example- unregulated potassium channels
2) Voltage gated channels= gate is regulated by membrane potential change near the channel.
3) ligand gated channels= the binding of a specific ligand causes the channel to open or close. (neurotransmitters)

Question 21

In response to ligand binding enzyme-linked receptors may display catalytic activity. these enzyme linked receptors have what 3 domains; functions

Answer 21

1) membrane spanning domain= anchors the receptor in the cell membrane
2) ligand binding domain= induces a conformational change that activates the catalytic domain
3) catalytic domain= when activated results in the initiation of a secondary messenger cascade.

Question 22

How are G proteins named

Answer 22

due to their intracellular link to GDP and GTP

Question 23

Describe the function and importance of the 3 main types of G proteins.

Answer 23

Gi= inhibits adenylate cyclase. decreases cAMP
Gs= stimulates adenylate cyclase. increases cAMP
Gq= cleaves phospholipids from the membrane into PIP2, PIP2 is cleaved to form DAG and IP3, IP3 can open calcium channels in the endoplasmic reticulum; increasing calcium levels in the cell

Question 24

describe the function of the subunits that make of G proteins

Answer 24

alpha subunit binds GDP and separates from the beta gamma complex once GDP is replaced with GTP. The alpha subunit alters the activity of adenylate cyclase. The GTP on the alpha subunit become dephosphorylated and will rebind to the beta gamma complex

Question 25

Describe electrophoresis

Answer 25

separates proteins by subjecting compounds to an electric field. (-) charged compounds move towards the positively charged anode. (+) charged compounds move towards the positively charged cathode.

Question 26

formula for migration velocity of proteins

Answer 26

``` v = Ez/f E= electric field strength z= net charge on the molecule f= frictional coefficient ```

Question 27

What is the standard medium for electrophoresis

Answer 27

polyacrylamide gel

Question 28

polyacrylamide gel electrophoresis (PAGE); pros and cons

Answer 28

pros; compares the molecular size or charge of proteins cons; limited by the varying mass-to-charge and mass-to-size ratios of cellular proteins bc multiple different proteins may experience the same level of migration

Question 29

Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE); pros and cons

Answer 29

pros; separates proteins on the basis of relative molecular mass alone. disrupts non-covalent reactions

Question 30

Describe Isoelectric focusing

Answer 30

proteins can be separated on the basis of their isoelectric point (pI). exploits the acidic and basic properties of amino acids. (-) proteins migrate towards the (+) anode where side-chains become protonated (+) proteins migrate towards the (-) cathode where side-chains become deprotonated

Question 31

What is isoelectric point (pI)

Answer 31

the pH at which the protein or amino acid is electrically neutral.

Question 32

what is a zwitterion

Answer 32

individual amino acids with a neutral electricity

Question 33

pI formula for neutral amino acids

Answer 33

pI = (pKa, NH3+ group + pKa,COOH group) / 2

Question 34

pI formula for basic amino acids

Answer 34

pI = (pKa,NH3+ group + pKa,R group) / 2

Question 35

pI formula for acidic amino acids

Answer 35

pI = (pKa, R group + pKa,COOH group) / 2

Question 36

Describe Chromatography

Answer 36

refers to the variety of techniques that require the homogenized protein mixture to be fractionated through a porous matrix. place sample onto a solid medium called the stationary phase or absorbent. depending on the relative affinity of the sample for the stationary and mobile phase different substance will migrate through at different speeds. high affinity for stationary phase = barely migrate high affinity for mobile phase = largely migrate

Question 37

Describe column Chromatography

Answer 37

a column is filled with silica or alumina beads as an adsorbent, gravity moves the solvent and compounds down the column. less polar compound = the shorter the retention time more polar compound = longer the retention time

Question 38

Describe ion-exchange Chromatography

Answer 38

beads in column are coated with charged substances. positively charged column will retain negatively charged protein.

Question 39

Describe Size-exclusion Chromatography

Answer 39

the use of tiny pores will allow small compounds to enter the beads thus slowing them down. large compounds cant fit so they will move around the beads and travel through he column faster.

Question 40

Describe Affinity Chromatography

Answer 40

the use of coating beads with a receptor that binds the protein or specific antibody to retain in the column

Question 41

Edman degradation; purpose and function

Answer 41

used to analyze small proteins; sequences proteins 50-70 AA via cleavage. it removes the N-terminal amino acid of the protein, which can then be analyzed via mass spectroscopy.

Question 42

The Bradford protein assay, bicinchoninic acid assay, and the Lowry reagent assay purpose

Answer 42

used to determine the concentration of an antibody in a blood sample

Question 43

what ions are primarily protein bound

Answer 43

calcium and magnessium

Question 44

which ion channels are responsible for maintaining the resting membrane potential

Answer 44

ungated channels

Question 45

What protein properties allow UV spectroscopy to be used as a method of determining concentration

Answer 45

proteins contain aromatic groups in certain amino acids

Question 46

What property of protein digesting enzymes allows for a sequence to be determined without fully degrading the protein

Answer 46

selectivity