L1- Protein structure and function

Question 1

Proteins are macromolecules made of

Answer 1

amino acids

Question 2

amino acids join…. to form a…..

Answer 2

amino acids join to form a polypeptide molecule

Question 3

monomers join to form

Answer 3

polymers

Question 4

amino acid sequence encoded by

Answer 4

gene

Question 5

polypeptide chain folds into complex and highly specific three dimensional structure determined by

Answer 5

amino acids

Question 6

folding depends on

Answer 6

chemical and physical properties of the amino acid

Question 7

central dogma

Answer 7

DNA (transcription) –> RNA (translated) –> proteins

Question 8

AA sequence pf protein encoded by

Answer 8

gene

Question 9

Structure of amino acid

Answer 9

Question 10

amino acids are classified accoring to

Answer 10

R group- changes chemical properties of AA ansd thereofr eth eprotein

Question 11

when amino acids join together what is lost

Answer 11

water is lost- left with amino acid residues

(only amino acid residues in protien and not amino acid)

• peptide bond

Question 12

Ionisations state of amino acid

Answer 12

Question 13

when you add solution to amino acid.. the amino group will

Answer 13

gain a hydrogen

Question 14

when you add solution to amino acid.. the carboxylic acid will

Answer 14

lost a hydrogen

Question 15

bases are

Answer 15

proton receivers- become positve

Question 16

acids are

Answer 16

proton donors- become negative

Question 17

amino acid residues are when the

Answer 17

amino and carboxyl group are lost- when AAs combine

Question 18

pKa value

Answer 18

acid dissociation constant for weak acids e.g. amino acids

e.g. how likely the amino acid will ionise or dissociate (how acidic or basic the R group is

Question 19

high pKa value

Answer 19

less likely to ionise

Question 20

low pKa valie

Answer 20

more liekly to ionise

Question 21

if the pH of the soljution is less (more acidic) than the Pk value then the group

Answer 21

will be protonated.

Question 22

the R group can change the chemical properties e.g.

Answer 22

hydrophobic

hydrophilic

polar

non-polar

acidic

basic

neutral

Question 23

if the pH of the solution is more (more alkali) than the pKa then the group

Answer 23

will be deprontonated

Question 24

example of negatively charged R groups

Answer 24

e.g. lysine have a high PkR value

Question 25

positively charged R groups

Answer 25

e.g. glutamare have a lower PkR (aciddisociation of R group)

Question 26

at pH 7 (physiological) what will be the predominant form of asparate (pK=2.8)?

Answer 26

at pH 7 the equilibrium will move to the right due to the amino acid being deprontonated

Question 27

levels of protein structure

Answer 27

primary secondary tertiary quaternary

Question 28

primary

Answer 28

linear amino acid sequence of the polypeptide chain

Question 29

secondary

Answer 29

local spatial arrnagment of the polypetide backbone - localised structre e.g. helices

Question 30

tertiary

Answer 30

final folded form

Question 31

quaternary

Answer 31

association between different polypeptides and proteins to form a multi subunit protein

Question 32

bond between two amino acids

Answer 32

peptide bond- loss of one water

Question 33

conformation of peptide bond can be

Answer 33

**trans**( alpha casrbons on oppsoite side of peptide bond) and **cis** (alpha carbon on same side of the peptide bond- steric clashes)

Question 34

bonds on either side of the eptide bond are free to

Answer 34

rotate- this define secondary structures

Question 35

amino acid R groups determine how...

Answer 35

the polpeptide folds and ultimately determine the physical natur eof proteins

Question 36

isoelectirc point of proteisn

Answer 36

pH at which there is no overall net charge- proteins ahve different isoelectric points

Question 37

basic proteins

Answer 37

pI (isoelectric point) \>7 contain many positively charge amino

Question 38

acidic proteins have an isolectirc point

Answer 38

pI\<7 contain many negatively (acidic) charged amino acids

Question 39

peptide bonds

Answer 39

planar bonds - alpha carbon, carbon, oxugen and hydrogen align in the same plan - rigid no roation - partial double bond

Question 40

if pH\< pI is

Answer 40

protontated

Question 41

if pH \>pI

Answer 41

is deprotonated

Question 42

size of peptides

Answer 42

a few amino acids in length

Question 43

size of polypeptides

Answer 43

many amino acids

Question 44

biologically active proteins come in a range of

Answer 44

sizes... average weight is 110

Question 45

protein conformation: sequences detmeines structure, structure determines....

Answer 45

function

Question 46

which bonds hold the primary structure togetrher

Answer 46

peptide bonds

Question 47

types of secondary structure

Answer 47

1. alpha helix 2. Beta sheet

Question 48

alpha helix structure

Answer 48

3.6 aa. turn, 0.54 nm pitch and right handed

Question 49

what bonds stabilise the structure of the alpha helix

Answer 49

H bonds run up and down the chain- no othe rbonds holding together --\> backdon of C=O group of one residue is H bonded to the NH group of the residue 4 amino acids away

Question 50

B-strand also known as

Answer 50

the extended conformation

Question 51

B-strand/sheet condormation

Answer 51

- Sheets of of polypeptides held together by H bonds above and below - R groups alternate between opposite sides of chain

Question 52

types of B-sheet

Answer 52

- **antiparallel**- adjacent B-strand srun in opp directions with muiltiple H bonds stabiolising the strcuture - **parallel**- run in same direction - **mixed**- run in mixed direction

Question 53

tertiary structure

Answer 53

when primary and secondary strucutres come together e.g. globular and fibrous protein

Question 54

fibrous protein

Answer 54

a lot of very simple repeating secondary structure- supportive structure e.g. collagen **Role**: support , shape, protect 
 Long strands or sheets 
 Single type of repeating secondary structure 


Question 55

Globular protein

Answer 55

lots of mixed conformation- have many structures e.g. enzymes and transporter molecules e.g. carbonic anhydrase 
 Role: catalysis, regulation 
 Compact shape 
 Several types of secondary structure


Question 56

domains

Answer 56

part of polypeptide chain that fold into a distinct shape- often a speciifc functional role

Question 57

folding of membrane protein

Answer 57

Polypeptide chains fold to so that hydrophobic side chains are buried and polar, charged chains are on the surface e.g. myoglobin • Membrane proteins often show “inside out” distribution of amino acids

Question 58

Quarternary structure

Answer 58

multi-subinit proteins e.g. haemoglobin e.g. ribosomes