Protein function II (antibodies, structural proteins)

Question 1

what is Immunoglobin G?

Answer 1

an antibody! it has two heavy chains and two light chains, it also contains a lot of disulfide bonds, which stabilize the structure. Y shaped structure–organized into complement (Fc) and two antigen binding regions (Fab) consisting of globular beta sheet domains

Question 2

how does immunochemical detection work?

Answer 2

1. The Fab region consists of residues from both heavy and light chains
2. specific binding to the antigens epitope due to complementary surface h bonds and electrostatic forces
3. antibody specificity can be used to detect and quatify selective proteins and other molecules, either directly, ELISA, or following protein synthesis, western blotting.

Question 3

What can antibodies specifically detect?

Answer 3

short regions of proteins sequence, #d conformation elements, and post translational modifications

Question 4

what is ELISA?

Answer 4

enzyme linked immunoabsorbent assay
uses two specific antibodies to label and detect antigen on microtiter paper. It is the most commonly used diagnostic method in the lab for proteins and other molecular biomarkers
can give false positives
bind wash label read

Question 5

What is western blotting?

Answer 5

uses antibodies to specifically label and detect proteins following their separation, usually by SDS PAGE
more specific than ELISA because it provides information on size

Question 6

What are cytoskeletal proteins?

Answer 6

actin, microtubules, and intermediate filaments

Question 7

which is the smallest of the three cytoskeletal elements?

Answer 7

actin, it is a polymer of globular G actin

Question 8

what does F actin have?

Answer 8

polarity! it has a negative and positive end which means it can be reversibly polymerized at both ends and can even treadmill

Question 9

what is F actin organized into?

Answer 9

cables, meshes by over 100 different actin binding proteins

Question 10

what are some functions of F actin?

Answer 10

cellular motility, cortical skeleton underlying the plasma membrane

Question 11

are G actin and F actin in equilibrium?

Answer 11

YES

Question 12

when is ATP hydrolyzed (actin)?

Answer 12

ATP is bound to G actin and is hydrolyzed to ADP after incorporation into F actin which is accompanied by a small conformational change

Question 13

What can block F actin from polymerization at the positive end?

Answer 13

capping proteins, severing proteins break the filaments

Question 14

what treadmilling?

Answer 14

the hydrolysis of ATP–net polymerization at the positive end and removal at the negative end

Question 15

what can stabilize and destabilize F actin?

Answer 15

fungal compounds. Stabilize phalloidin, destabilize cytochalasins

Question 16

what are microtubules?

Answer 16

reversible aggregates of tublin dimer which form hollow tubes

Question 17

what is a contractile bundle of actin?

Answer 17

stress fiber

Question 18

what is a gel like network of actin fiber?

Answer 18

cell cortex

Question 19

what is a tight parallel bundle?

Answer 19

filopodium

Question 20

are microtubules polar?

Answer 20

yes they have a negative and positive end

Question 21

what is the negative end anchored to?

Answer 21

some sort of organizing centre eg: centrosome

Question 22

what are the functions of microtubules?

Answer 22

to form rigid tracks for the movement of chromosomes and vesicles. They also form cilia and flagella

are the target of anti cancer drugs

Question 23

What are intermediate filaments?

Answer 23

large heterogenous family of insoluble fibrous proteins

Question 24

what is the fundamental unit of intermediate filaments?

Answer 24

alpha helical coiled coil which is strengthened by non-polar residues

Question 25

what can cause disassembly of intermediate filaments?

Answer 25

phosphorylation

Question 26

what do intermediate filaments provide the cell?

Answer 26

mechanical strength and shapen

eg: lamins, keratin, neurofilaments

Question 27

how does actomyosin work?

Answer 27

think filament = actin, thick filament = myosin
myosin head begins by being bound to the actin subunit of the thin filament. ATP binds which alters the configuration of the myosin head so that it releases the actin. Myosin then binds to an actin subunit further along the filament which causes Pi and ADP to be released as they leave the myosin lever returns to its original position and the two filaments slide past one and other in the power stroke. ATP replaces the lost ADP and the cycle repeats

Question 28

what is rigor?

Answer 28

absence of ATP causing the myosin head to be attached to the actin and it is stiff

Question 29

what is collagen?

Answer 29

it is the most abundant (fibrous) protein in the body. It is a twisted braid of three extended chains. there is a glycine at every third residue allowing for proximity and stability
the interchain hydrogen bonds are strengthened by hydroxylysine (not AA) and hydroxyproline (AA)

Question 30

what does collagen form?

Answer 30

strong cables and meshes in extracellular matrix, bone and connective tissue

Question 31

what are some diseases of collagen?

Answer 31

scurvy, ehlers-danos, and osteogenesis imperfecta

Question 32

What is elastin

Answer 32

a fibrous protein that is deformable and found in elastic tissue such as lungs

Question 33

what connects the chains in elastin?

Answer 33

lys cross linking

Question 34

what cleaves elastin in the alveolar walls?

Answer 34

elastase which is inhibited by alpha 1-antitrypsin

Question 35

what can the decrease alpha1-AT activity be caused by in emphysema?

Answer 35

genetic mutations (E342K mutant) or environmental factors (M358 oxidation)