proteins

Question 1

2 types of proteins and what makes them different

Answer 1

globular and fibular

-primary sequence of amino acids coded for by DNA

Question 2

what features of a double bond does the peptide bond have

Answer 2

• shorter than C-N bond length
• rigid CN bond, no rotation or trans arrangement
• partial -ve charge on O atom, +ve on N
• peptides form H bonds with other polar groups in polypeptide chain (eg. alpha-helix)

Question 3

what is the orientation of a polypeptide

Answer 3

N-terminal end: first aa, has NH3+ group

C-terminal: final aa, has COO-

Question 4

what are the post translational modifications (covalent linkages)

Answer 4

• disulfide bridges between 2 cys, (join subunits e.g. insulin)
• glycosylation (OH thr and ser, NH2 asn)
• phosphorylation (signal transduction e.g. insulin receptor tyr; change activity of enzyme)
• methylation via NH2 groups of lys and arg (histones - gene expression)

Question 5

examples of peptide sizes, smallest to la

Answer 5

aspartame
glutathione
glucagon(peptide hormone) / substance P (NT)
proteins
dystrophin

Question 6

describe levels of structure

Answer 6

primary: aa sequence
secondary: a helix or B pleated sheet
tertiary: fold upon itself
quaternary: two chains

Question 7

length of one turn of an a helix

Answer 7

0.54 nm

Question 8

describe a helix

Answer 8

• H bonds between peptide bond carbonyl-O & H of N-H every 4th peptide
• right haded helix
• R groups on outside

Question 9

how many residues on an a helix per turn

what is it stabilised by

Answer 9

3.6

H bonds

Question 10

describe beta sheet

Answer 10

• Side chains in each strand alternately lie above and below the plane of the sheet

• H bonds between peptide chains hold strands tgether
• liner peptide chains

Question 11

types of b sheet structurea

Answer 11

1) antiparallel B hairpin bend. widespread in globular proteins (S-snake, continuous)
2) parallel B sheet (all point towards C terminus)

Question 12

describe collagen

Answer 12

• triple helix
• H bonds between chain
• 3 residues per turn
• Left handed helix

Question 13

amino acid sequence in collagen

Answer 13

• Gly - X - Y - Gly - X - Y -
  X= mainly proline
  Y= mainly hydroxy-proline

Question 14

what structure is Hb made of

Answer 14

60% a helix

Question 15

what are proteins with high % B sheet

Answer 15

• fibrillar proteins (silk fibres - fibrinogen)

- high strength, no elasticity

Question 16

what is super secondary structure and give examples

Answer 16

Combinations of α- helix and β-sheet form common domains found in proteins
e.g. – β-barrel
– β-sandwich
– Rossmann fold

Question 17

define tertiary stucture

Answer 17

How the whole polypeptide (subunit) is folded in 3D, it will consist of a number of different supersecondary structures (domains)

Question 18

define quaternary structure

Answer 18

How the whole functional protein is formed in 3D, it may consists of a number of subunits e.g haemoglobin α2β2

Question 19

what forces stabilise protein structure

Answer 19

• covalent: disulphide bridges (not all proteins)

- non-covalent: H bond, electrostatic attraction, VdWaals forces, hydrophobic effect

Question 20

what are some examples of H bond donors

Answer 20

-O: e.g. O-H (side chain - ser, thr, Tyr

N: e.g. N-H (peptide bond, Trp, His, Arg): NH3+ (Lys, Arg)

Question 21

what are some examples of H bond acceptors

Answer 21

O: eg. C=O carbonyl (peptide bond)

• 3x covalent bounded N: =N-
  e. g. Trp, His

Question 22

length of H bond

Answer 22

0.28nm

=2.8A

Question 23

describe electrostatic interactions: between what

Answer 23

-charged side chains
-Asp and glu Glu carboxyl groups are ionised– COO-
-Lys and Arg amino groups are ionised
– NH3+

Question 24

describe van der Waals forces

Answer 24

sumoftheattractiveorrepulsiveforces between molecules,
• Excluding those due to 
– covalent bonds
– hydrogen bonds
– electrostatic interaction

Question 25

eqn for van der waas

Answer 25

d/2 = van der waals radius of atom

Question 26

hydrophobic effects

Answer 26

regions can’t form Hbonds

Question 27

what are peptides denatured by

Answer 27

ph
temp
ionic strength
amount of stablization energy in a protein is quite small

Question 28

what is the protein folding pathway

Answer 28

• thousands of possible structures only one of which is functional
• The amino acid sequence encodes the final structure but also the pathway that leads to that structure

Question 29

what results in misfiled proteins and disease (give examples)

Answer 29

mutations = misfold
-– Sickle cell disease Glu→Val (charged to hydrophobic)
stablising the polymerization of HbS

stable aggregations of proteins
– amyloid proteins forming plaques in Alzheimer’s Disease – prion protein polymerisation in Creutzfeldt-Jakob Disease

Question 30

Creutzfeldt-Jakob Disease (CJD) initial neuological symp

Answer 30

• difficulties with walking
• slurred speech
• numbness
• dizziness
• visual problems

Question 31

Creutzfeldt-Jakob Disease (CJD) Initial psychological symptoms

Answer 31

• severe depression • withdrawal
• anxiety
• irritability
• insomnia

Question 32

explain the mutagenic conversion of PrP

Answer 32

• Prion Protein (PrP) conversion from the normal cellular form (PrPC) to the pathogenic form (PrPSc)
• Polymerisation of the pathogenic form (PrPSc) to form fibrils
• PrPC alpha- helical
• PrPSc beta sheet

Question 33

difference between PrPc ad PrPSc

Answer 33

C: a-helix, no B sheet. susceptible to proteolysis

Sc: less a and B sheet present, protease resistant

Question 34

non coded amino acids: hydroxylproline

Answer 34

– Hydroxylation of proline
– Important component of collagen
– Allows specific triple helix structure

Question 35

non coded amino acids: selenocysteine

Answer 35

– “encoded” by a subset of STOP codons
– Contains Se instead of S
– Reduced pKa useful for enzymes in anti-oxidant activity

Question 36

non coded amino acids: homocysteine

Answer 36

– extra methyl group (R = CH2CH2SH) compared to cysteine
– Needed to synthesise cysteine
– Not found in proteins