Proteins lec 2

Question 1

Secondary structure components:

Answer 1

alpha helices
beta sheets
hydrogen bonding of backbone (not side chains)

Question 2

secondary structure depends on ___

Answer 2

hydrogen bonding of backbone

Question 3

Alpha helices
coils \_\_\_(direction)

Answer 3

clockwise spiral (right-handed coils)

Question 4

___ have __ residues per turn

Answer 4

alpha helices

3.6

Question 5

alpha helices

every/most/no/ residue(s) form hydrogen bonds

Answer 5

every

Question 6

alpha helices are often ___ but can be ___ or ___

Answer 6

straight
curved
kinked

Question 7

Proline ____ hydrogen bonds. what does it do?

Answer 7

disrupts

prevents hydrogen bonds forming

Question 8

Fibrous proteins are mainly ___ proteins

Answer 8

secondary

Question 9

___ proteins are mainly secondary proteins

Answer 9

fibrous

Question 10

what type of proteins are mechanically strong

Answer 10

fibrous

Question 11

keratin, collagen, fibroin are examples of what kind of protein

Answer 11

fibrous

Question 12

structure of alpha keratin

Answer 12

globular head

long alpha helix

Question 13

alpha keratin residues specialty?

Answer 13

every 4th residue is hydrophobic (one side hydrophobic)

Question 14

every # residue of ___ is hydro___

Answer 14

4
alpha keratin
phobic

Question 15

___ molecules assemble to form a ___ with ____ sidechains on ___ of the coil

Answer 15

2 alpha keratin
dimer
hydrophobic
inside

Question 16

the filaments of alpha keratin are held together by ____

Answer 16

hydrogen bonds
disulphide bonds
ionic bonds

Question 17

structure of alpha keratin:
protofilament 
monomer
protofibril
dimer

Answer 17

Multiple dimers (2 rows)
long alpha helix and globular head
multiple dimers (multiple rows)
2 monomers coiled together making a coiled coil, heads facing same way

Question 18

the alpha helical domain is located ___ on the alpha helix

Answer 18

on the long chain alpha helix of monomers

Question 19

protofilament vs protofibril

Answer 19

protofilament
multiple dimers (2 rows)

protofibril
multiple dimers (multiple rows)

Question 20

primary structure determines the ___ and __ of the protein/polypeptide

Answer 20

size

shape

Question 21

direction of primary structure?

Answer 21

N to C terminus (positive to negative)

Question 22

what are found at the ends of primary structures?

Answer 22

free carboxyl and amino groups at each end of chain
carboxyl - c terminus
amino - n terminus

Question 23

amino acids linked together by __ therefore shape of molecule___ therefore
still can rotate about 2 bonds another than amide per
residue (torsion) ????? need clarification

Answer 23

peptide bonds
rigid
planar
generally trans
can rotate about 2 bonds per residue?

Question 24

alpha keratin dimer.

_____ chains on the inside and ___ chains on the outside

Answer 24

hydrophobic

hydrophilic

Question 25

pH calculation equation?

Answer 25

pH = -log [H+]

Question 26

Blood pH is usually between __ and ___. anything < or > =____

Answer 26

7.35 and 7.45 | death

Question 27

mechanisms to maintain blood pH balance ?

Answer 27

3 renal system buffer system respiratory system

Question 28

types of blood buffer systems

Answer 28

3 Bicarbonate Phosphate protein

Question 29

Bicarbonate equilibrium system ?

Answer 29

Carbonate Bicarbonate - + H3O+

Question 30

During buffering (in the buffer region ) the conc of ____ ?

Answer 30

Hydrogen ions (H+) remains constant

Question 31

What is the source of bicarbonate in the blood?

Answer 31

CO2 from body tissue (derived from respiration) which combines which H2O to make bicarbonate in the blood capillary

Question 32

Reason why we have multiple systems to maintain ____

Answer 32

balance of blood pH 1) redundancy - in case one breaks down 2) timing - each system varies from seconds to days based on the needs

Question 33

ka aka____ deff____

Answer 33

dissociation constant tells us how likely the weak acid will form the conjugate base and H3O+ Ka = [product]/ [substrate]

Question 34

pka = derrived from _

Answer 34

ka

Question 35

pka calculation equation? why is it important?

Answer 35

pka = -log10 x (ka) | puts pka on the same scale as pH (0 to 14)

Question 36

pka deff =

Answer 36

describes the propensity of a weak acid (amino acid side chain) to lose a proton at a given pH (or conversely to hang on to a proton).

Question 37

HCO3- used for ____

Answer 37

renal regulation

Question 38

weak acid example____

Answer 38

``` aspartic acid (Asp) glutamic acid (Glu) ```

Question 39

pKa tells us ___

Answer 39

what an acid/base side chain in a protein should look at physiological pH (7)

Question 40

____ pH = 7

Answer 40

physiological

Question 41

form of the amino acid side chain of a protein based on ??

Answer 41

pH and pka

Question 42

pH = pKa

Answer 42

50:50 protonated : deprotonated acid : base forms

Question 43

pH > pka

Answer 43

deprotonated | base form

Question 44

pH

Answer 44

protonated | acid form favoured

Question 45

overall charge of amino acid determined/calculated through ____

Answer 45

overall charge of the a.a. side chain only

Question 46

exception of the a.a when using pH and pKa to predict the form and why?

Answer 46

Histidine can exist anywhere between 6 and 8 (between the physiological pH, depending on the conditions). Can act as both a protonated form (acid ) or deprotonated form (base)

Question 47

___ lose proton = (de)protonated?

Answer 47

acids | protonated

Question 48

acids ___ protons = (de)protonated?

Answer 48

lose | protonated

Question 49

base ___ protons = (de)protonated?

Answer 49

accept/attract | deprotonated