Proteins

Question 1

anabolic

Answer 1

building up

Question 2

catabolic

Answer 2

breaking down

Question 3

sequence to get a prot

Answer 3

Question 4

roles of prots

Answer 4

1. stryctural - collagen, keratin, fibroin
2. movement - muscle fibres actin + myosin
3. immune sys - antibodies
4. endocrine sys - hormones + receptors
5. transport - Hb, transferrin (Fe carrier)
6. biological catalysis - enzs

Question 5

general structure alpha aas

Answer 5

Question 6

zwitterions

Answer 6

dipolar ion = no net charge unless R grp charged

aas in sol at normal physiological pH normally zwitterions

Question 7

isomers alpha aas

Answer 7

asymmetric mols so 2 diff forms - optical isomers/enantiomers
* mirror images but can’t be superimposed onto each other

in biology prots only contain L form

Question 8

Types aas

Answer 8

1. electrically charged side chains
2. polar uncharged side chains
3. hydrophobic side chains
4. special cases

Question 9

polar meaning

Answer 9

has pos + neg ends as charge not evenly distributed throughout

Question 10

which aa tends to be found in coils

Answer 10

proline

Question 11

prot primary structure

Answer 11

sequence aas joined peptide bonds bet carboxyl grp 1 aa + amino grp next

occur by condensation reaction where H20 mol removed

by convention: N-terminal on left

Question 12

prot secondary structure

Answer 12

determined + maintained by H bonds bet O + H
* w/in prot backbone, not bet R grps

1. alpha helix = folded into spiral w outer surface covered R grps to interact other prots etc
   * CO grp residue n bonded NH grp residue (n+4)
2. beta-pleated sheets in parallel (sequences same direction) or anti-parallel (opp)
   * can be diff peptide chains or 1 chain folded (therefore antiparallel)

Question 13

prot tertiary structure

Answer 13

arrangement in space of aas, held together by diff interactions determined by sequence aas:
* disulphide bond
* side chain H bonding
* electrostatic attraction
* hydrophobic interactions - hydrophobic R grps sit together to avoid contact w water
* metal ion coordination

Question 14

prot quaternary structure

Answer 14

interactions bet diff peptide chains by same side chain interactions:
* disulphide bond
* side chain H bonding
* electrostatic attraction
* hydrophobic interactions
* metal ion coordination

Question 15

3 main types prot

Answer 15

1. globular
2. fibrous
3. membrane

Question 16

globular prots

Answer 16

• fold into compact structures - often w cleft for small mol
• usually hydrophobic side chains inside, hydrophillic outside to interact w aqueous environ = soluble
• majority prots
• e.g. enzs, antibodies

Question 17

fibrous prots

Answer 17

• multiple strands held together strong bonding
• usually insoluble + structural
• e.g. collagen (skin, bone, tendon), keratin (hair, nails, horn), fibroin (silk)

Question 18

mem prots

Answer 18

• hydrophobic regions sit in cell mem
• transmit mols + signals in/out cells
• e.g. channels + receptors

Question 19

prion disease

Answer 19

disease starting from prot malformation:
genetic switch flipped + prot gradually to mainly beta sheets = sticky + aggregate , causing neuronal cell death

prions = infectious prots

Question 20

bovine spongiform encephalopathy (BSE)

mad cow disease

Answer 20

neurodegenerative prion disease brain + spinal cord
* 2.5-8yr incubation
* transmissable to humans if you eat infected meat

Question 21

role of enz

Answer 21

act as biological catalyst by increasing RoR w/o being changed themselves
* decrease activation E by:
1. bringing substrates together
2. excluding water
3. stabilising transition state
4. transferring chem grps

Question 22

enz active site

Answer 22

3D region of enz that performs catalytic reaction, usually involving making/breaking bonds by binding substrate + converting it to product

binds specific aa side chains by weak forces:
* electrostatic interactions
* H bonds
* Van der Waals forces
* hydrophobic interactions
* sometimes reversible covalent bonds

forms predominantly non-polar environ

Question 23

how are enzs made specific

Answer 23

properties + spatial arrangement relatively few aas at AS determine which mols can bind + so substrates

Question 24

induced fit model for enz-substrate binding

Answer 24

as binds, aas move slightly to pull substrate in, change its structure slightly - for closer fit

so AS shape changes slightly

most enzs have this model

Question 25

types enz-substrate binding

Answer 25

isosteric + allosteric

Question 26

describe isosteric enz-substrate binding

Answer 26

RoR incrreases w substrate conc until enz saturated parameters defining enz activity from 'Michaelis-Menten' plot initial rate + substrate conc, showing how quickly substrate converted product | most enzs

Question 27

allosteric enz-substrate binding

Answer 27

enz changes to increase rate if substrate and/or effectors present * e.g. multiple ASs - substrate binds 1, increasing activity others; or causes change in shape of all to fit (induced fit) * each subunit own AS + allosteric sites where subunits join - something binds there + changes shape ASs so can accept substrate allosteric site = anywhere other than AS where something can bind | don't display Michaelis-Menten kinetics ## Footnote interaction of 1 triggers same conformational change in all subunits = cooperativity

Question 28

allosteric regulation

Answer 28

regulating effectors change enz's shape + function by binding weakly allosteric site - inhibition or stimulation * binding of activator stabilises conformation w functional AS * binding of inhibitor stabilises inactive enz form most have 2 or more polypeptide chains (subunits)

Question 29

enz feedback regulation

Answer 29

metabolic pathway w several enzs + series of reactions to end-product, producing intermediates * end-product can act allosteric inhibitor early stage enz to save E + prevent build-up intermediates

Question 30

types enz inhibitor

Answer 30

1. competitive - binds AS instead substrate 2. non-competitive - binds allosteric site irrespective of whether substrate bound 3. uncompetitive - only binds enz-subs complex 4. allosteric - binds @ allosteric site; could be competitive if near AS, uncompetitive or non-competitive

Question 31

factors affecting enz activity

Answer 31

1. substrate/enz conc 2. pH 3. temp - more can overcome ae 4. post-translational modifications 5. cofactors

Question 32

how post-translational modification affects enz activity

Answer 32

REVERSIBLE COVALENT ATTACHMENT of small non-prot grp, most common phosphorylation-dephosphorylation as causes change 2/3 structure * hydroxy side chains (serine, threonine, tyrosine) phophyd (OH grp to bind to) * rapid reversible switch turn metabolic pathway on/off PROTEOLYTIC ACTIVATION enz synthed as larger, inactive precursor form (proenz/zymogen)

Question 33

how cofactors affect enz activity

Answer 33

many enzs require presence small non-prot unit to function * inorganic ions * complex organic mols (=conenzs) - sometimesreded/oxed during reaction

Question 34

what are proteinases | = proteases

Answer 34

enzs that cleave prots + may activate other enzs e.g. blood clotting cascade where 1 removes prodomain enz + activates, does same for another + so on

Question 35

types proteases

Answer 35

* serine * cysteine * aspartate * metalloproteinases * threonine proteinase

Question 36

serine proteinases

Answer 36

reactive serine residue at AS, e.g. trypsin

Question 37

cysteine proteases

Answer 37

cysteine at AS

Question 38

aspartyl proteinases

Answer 38

aspartate at AS

Question 39

metalloproteinases

Answer 39

metal ion (often Zn2+) at AS

Question 40

threonine proteases

Answer 40

threonine at AS, e.g. proteasome

Question 41

isoenzymes | = isozymes

Answer 41

diff forms of enz that cat same reaction, therefore similar AS * usually derived diff genes + occur diff tissues

Question 42

what is a multi-enz complex

Answer 42

aggregation several enzs/coenzs into single functional unit usually to perform multi-step transformation proximity enzs to each other: * increases RoR * minimises side reactions * intermediates immediately available as susbtrates for next reaction | e.g. fatty acid synthase involved lipid biosynthesis