3. Proteins

Question 1

Which bonds determine tert structures?

Answer 1

H bonds and/or disulfide bonds of the side chains (R groups) within polypeptide

Question 2

Cystine vs Cysteine

Answer 2

2 cysteines make 1 cystine

Question 3

What aa only makes disulfide bond?

Answer 3

cysteine, NOT METHIONINE

Question 4

What type of rxn does peptide bond make vs what type of rxn does breaking a peptide make?

Answer 4

condensation/dehydration (nucleophilic amino group attacks electrophilic carbonyl, water molec leaves) vs hydrolysis (use water to break bond)

Question 5

Another name of peptide bond

Answer 5

Amide bond

Question 6

Structural proteins vs motor proteins vs binding proteins vs cell adhesion molec (CAM)

Answer 6

Fibrous; collagen, elastin, keratin, actin, tubulin vs generates force thru conformational change, catalytic with ATPase activity; myosin, kinesin, dynein vs bind to substrates to sequester it or hold it at steady state vs bind cells to other cells or surfaces; cadherin, integrins, selectins

Question 7

Are actin and tubulin polar?

Answer 7

Yep. One pos and one neg; neg near nucleus and pos near periphery

Question 8

Where are collagen, elastin, and keratin found?

Answer 8

Extracellular matrix, extracellular matrix, and epithelial cells

Question 9

What do actin, myosin, tubulin, kinesin and dynein do?

Answer 9

Actin and tubulin = polar structural proteins; kinesin, dynein and myosin = motor proteins. Actin has one pos end, one neg end; tubulin has pos end near periphery of cell, neg end near nucleus. Kinesin transports vesicles to pos end of tubulin, dynein transports vesicles to neg end of tubulin. Kinesin helps align chm’s in metaphase and pulls apart microtubules in anaphase. Dynein helps cilia and flagella

Question 10

What do cadherins vs integrins vs selectins do?

Answer 10

Mediate calcium dependent cell adhesion, bind same cells together vs have alpha and beta chains for binding to proteins in extracellular matrix, stabilize epithelium, apoptosis and cell division vs bind to carb molec on cell surfaces, expressed on endothelial cells, inflammation

Question 11

3 types of ion channels

Answer 11

Ungated —> unreg, ligand gated, voltage gated - activated by membrane potential
ION CHANNELS = FOR FAC DIFFUSION; FAC DIFFUSION = FASTER THAN SIMPLE DIFFUSION
Only Ungated maintains resting membrane potential

Question 12

3 domains of enzyme linked receptors

Answer 12

Membrane spanning domain - anchor receptor to cell membrane, ligand binding domain - lets ligand bind and invoke conformational change, catalytic domain. Results in second messenger cascade

Question 13

General mechanism of Gprotein receptors

Answer 13

Ligand binds to inc affinity of receptor to G protein, which stimulates or inhibits function in pathway

Question 14

Gs vs Gi vs Gq

Answer 14

Activates adenylate cyclase to inc cAMP vs inhibits adenylate cyclase to dec cAMP vs activates phospholipase C to cleave phospholipid from membrane into PIP2 which then gets cleaved into DAG and IP3, IP3 opens Ca channels in ER which inc Ca in cell

Question 15

Electrophoresis eqn

Answer 15

migrational vel = (Electric field strength * molec’s net charge)/friction coefficient

Question 16

Native PAGE vs SDS PAGE vs isoelectric focusing vs x-ray crystallography

Answer 16

Analyzes proteins in their native states —> separate by mass to size or mass to charge ratio, you can recover proteins after analysis vs separating proteins based only on mass or size b/c SDS denatures proteins —> gives everything a neg charge, you can’t recover proteins after analysis; SDS = detergent —> amphipathic vs separating proteins based on pI: proteins stop moving when pH = pI (anode is A+ —> anode is acidic and has pos charge) vs detects proteins’ tert structure

Question 17

Edman degradation

Answer 17

Method used to cleave and determine aa seq of a protein in small portions

Question 18

Bicinchonic acid assay, Lowry reagent assay and Bradford protein assay

Answer 18

Methods to find colorimetric changes of proteins before doing UV spec. Bradford is most common: first dye is protonated and is green/brown, then it gives its protons to the amino group of protein and turns into blue; more protein —> more blue

Question 19

As hemoglobin unloads oxygen, what happens to affinity of remaining oxygen?

Answer 19

Lowers affinity

Question 20

Are hydrophobic regions of membrane channels (like used in fac diffusion) only made of lipids?

Answer 20

Nope, they can also be made of nonpolar aa