proteins

Question 1

what are proteins made up of?

Answer 1

amino acids

Question 2

what catalyses the reaction of amino acids forming polypeptides?

Answer 2

ribosomes

Question 3

what type of reaction is peptide bond formation?

Answer 3

condensation

Question 4

what does peptide bond formation require and where does this come from?

Answer 4

energy from GTP

Question 5

what does the structure of a polypeptide look like?

Answer 5

has a polypeptide backbone with amino acid side chains radiating out

Question 6

what are the levels of structure of proteins?

Answer 6

primary
secondary
tertiary
quaternary

Question 7

what is the primary sequence?

Answer 7

the connection between amino acid residues

Question 8

what does the secondary structure do?

Answer 8

determines how the proteins locally fold

Question 9

what is folding determined by in proteins in the secondary structure?

Answer 9

interactions between amino acids

Question 10

why does folding occur in proteins?

Answer 10

to minimise overall structure

Question 11

what is the tertiary structure?

Answer 11

combination of secondary structures (it is the polypeptide chain)

Question 12

what is the quaternary structure?

Answer 12

a complex of one or more polypeptide chains or subunits

Question 13

what is the bonding like in an alpha helix?

Answer 13

N-H of every peptide bond forms hydrogen bonds to the C=O of a neighbouring peptide bond located 4 amino acids away

Question 14

what is a beta sheet?

Answer 14

several strands of a polypeptide chain are held together by hydrogen bonding between peptide bonds in adjacent strands

Question 15

what are the amino acid side chains like in a beta sheet?

Answer 15

project alternately above and below plane of sheet and adjacent chains can run parallel or antiparallel

Question 16

what sort of structure do beta sheets form?

Answer 16

rigid

Question 17

where are beta sheets found?

Answer 17

at the core of many proteins

Question 18

what type of protein conformations are there?

Answer 18

alpha helix
beta sheets
unstructured regions

Question 19

what is a subunit?

Answer 19

each polypeptide chain in a protein

Question 20

what is the simplest protein like?

Answer 20

dimer

Question 21

what is a dimer? what about trimer? tetramer?

Answer 21

dimer - two folded polypeptides that are identical
trimer - 3
tetramer - 4

Question 22

what are the forces in protein?

Answer 22

electrostatic
ionic
dipole-dipole interactions
hydrogen bonding
hydrophobic
disulphide bond

Question 23

what is a disulphide bond?

Answer 23

covalent bond between 2 SH groups

Question 24

what are the hydrophobic/hydrophilic parts like in protein in the cytosol?

Answer 24

hydrophilic parts turned towards the outside
hydrophobic parts inside

Question 25

what are the hydrophobic/hydrophilic parts like in protein in the membrane?

Answer 25

hydrophobic parts turned to outside hydrophilic parts inside

Question 26

what are good indicators for which part of a polypeptide chain is in contact with the aqueous solvent?

Answer 26

amino acid side chain hydropathy

Question 27

what do disulphide bonds do and why is this needed?

Answer 27

stabilise 3D structure of protein relative hostility of extracellular environments requires extra stability

Question 28

what alters the stability of disulphide bonds and why?

Answer 28

cytoplasm reduces stability cytoplasm is relatively reducing

Question 29

where are most proteins with disulphide bonds secreted to and why?

Answer 29

more oxidising extracellular destinations where disulphide bonds are effective in stabilising protein structure

Question 30

what is the difference between interchain and intrachain disulfide bonds?

Answer 30

interchain - between S atoms on separate chains intrachain - between S atoms on the same chain

Question 31

what are proteins highly susceptible to and why?

Answer 31

denaturation proteins have low conformational stabilities so their weak nonbonding forces that maintain structure can be altered

Question 32

what are examples of denaturation of proteins?

Answer 32

changes in temperature and pH detergents organic substances salts chaotropic agents

Question 33

how can changes in temperature effect proteins?

Answer 33

can cause total loss of 3D structure

Question 34

how can changes in pH effect proteins?

Answer 34

causes ionisation of side groups to change

Question 35

how can detergents effect proteins?

Answer 35

change hydrophobic interactions

Question 36

how can organic substances effect proteins?

Answer 36

interfere with hydrophobic interactions

Question 37

how can salts effect proteins?

Answer 37

can stabilise

Question 38

what does zwitterionic mean?

Answer 38

opposite charges

Question 39

how many acid-base groups do amino acids have?

Answer 39

two, or three if it has an ionisable side group

Question 40

which amino acid residues are ionisable in proteins?

Answer 40

those with positive or negatively charged side groups

Question 41

what does amphoteric mean?

Answer 41

can act as both an acid and base

Question 42

what is amino acids's structure like at neutral pH?

Answer 42

both ionisable groups are ionised - in zwitterionic form

Question 43

what is amino acid's zwitterionic form?

Answer 43

NH2 group becomes NH3+ COOH group becomes COO-

Question 44

what happens to amino acid's structure as pH decreases from 7?

Answer 44

concentration of the form where both ionisable groups are protonated increases, concentration of zwitterionic form decreases

Question 45

what happens to amino acid's structure as pH increases from 7?

Answer 45

concentration of the form where both ionisable groups are deprotonated increases, concentration of zwitterionic form decreases

Question 46

what are charged amino acids often involved in?

Answer 46

active site of enzymes

Question 47

what pH are many organisms maintained at?

Answer 47

7.4

Question 48

what do chaotropic agents do?

Answer 48

increase solubility of non polar substances in water so can disrupt hydrophobic interactions

Question 49

what are two examples of chaotropic agents and what concentrations are they used in to denature proteins?

Answer 49

guanidinium urea 5 to 10M

Question 50

what is the structure of guanidinium ion?

Answer 50

C attached to 3 NH2 groups by a single bond and partial bond all has a 1+ charge

Question 51

what is the structure of urea?

Answer 51

C attached to 2 NH2 groups and double bonded to O

Question 52

what type of process is the denature of proteins using chaotropic agents?

Answer 52

reversible

Question 53

what can the denature of proteins using chaotropic agents be used for?

Answer 53

to purify proteins

Question 54

what are motifs?

Answer 54

sequences of amino acids that are repeated frequently

Question 55

what is an example of an amino acid motif?

Answer 55

RGD

Question 56

how can proteins be grouped?

Answer 56

functionally structurally cellular localisation

Question 57

what are the types of proteins when classifying functionally?

Answer 57

enzymes structural transport defense

Question 58

what do enzyme proteins do?

Answer 58

accelerate biochemical reactions

Question 59

what do structural proteins do?

Answer 59

form biological structures

Question 60

what do transport proteins do?

Answer 60

carry biochemically important substances

Question 61

what do defence proteins do?

Answer 61

protect body from foreign invaders

Question 62

what are the types of proteins when classifying structurally?

Answer 62

globular fibrous

Question 63

what are globular proteins?

Answer 63

complex folds, irregularly shaped tertiary structures

Question 64

what are fibrous proteins?

Answer 64

extended, simple folds

Question 65

what are the types of proteins when classifying by cellular localisation?

Answer 65

membrane soluble

Question 66

what are membrane proteins like?

Answer 66

in direct physical contact with a membrane generally water insoluble

Question 67

what are soluble proteins like?

Answer 67

water soluble can be anywhere in cell