proteins Flashcards
2 types of proteins and what makes them different
globular and fibular
-primary sequence of amino acids coded for by DNA
what features of a double bond does the peptide bond have
- 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)
what is the orientation of a polypeptide
N-terminal end: first aa, has NH3+ group
C-terminal: final aa, has COO-
what are the post translational modifications (covalent linkages)
- 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)
examples of peptide sizes, smallest to la
aspartame glutathione glucagon(peptide hormone) / substance P (NT) proteins dystrophin
describe levels of structure
primary: aa sequence
secondary: a helix or B pleated sheet
tertiary: fold upon itself
quaternary: two chains
length of one turn of an a helix
0.54 nm
describe a helix
- H bonds between peptide bond carbonyl-O & H of N-H every 4th peptide
- right haded helix
- R groups on outside
how many residues on an a helix per turn
what is it stabilised by
3.6
H bonds
describe beta sheet
• 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
types of b sheet structurea
1) antiparallel B hairpin bend. widespread in globular proteins (S-snake, continuous)
2) parallel B sheet (all point towards C terminus)
describe collagen
- triple helix
- H bonds between chain
- 3 residues per turn
- Left handed helix
amino acid sequence in collagen
- Gly - X - Y - Gly - X - Y -
X= mainly proline
Y= mainly hydroxy-proline
what structure is Hb made of
60% a helix
what are proteins with high % B sheet
- fibrillar proteins (silk fibres - fibrinogen)
- high strength, no elasticity
what is super secondary structure and give examples
Combinations of α- helix and β-sheet form common domains found in proteins
e.g. – β-barrel
– β-sandwich
– Rossmann fold
define tertiary stucture
How the whole polypeptide (subunit) is folded in 3D, it will consist of a number of different supersecondary structures (domains)
define quaternary structure
How the whole functional protein is formed in 3D, it may consists of a number of subunits e.g haemoglobin α2β2
what forces stabilise protein structure
- covalent: disulphide bridges (not all proteins)
- non-covalent: H bond, electrostatic attraction, VdWaals forces, hydrophobic effect
what are some examples of H bond donors
-O: e.g. O-H (side chain - ser, thr, Tyr
N: e.g. N-H (peptide bond, Trp, His, Arg): NH3+ (Lys, Arg)
what are some examples of H bond acceptors
O: eg. C=O carbonyl (peptide bond)
- 3x covalent bounded N: =N-
e. g. Trp, His
length of H bond
0.28nm
=2.8A
describe electrostatic interactions: between what
-charged side chains
-Asp and glu Glu carboxyl groups are ionised– COO-
-Lys and Arg amino groups are ionised
– NH3+
describe van der Waals forces
sumoftheattractiveorrepulsiveforces between molecules, • Excluding those due to – covalent bonds – hydrogen bonds – electrostatic interaction
eqn for van der waas
d/2 = van der waals radius of atom
hydrophobic effects
regions can’t form Hbonds
what are peptides denatured by
ph
temp
ionic strength
amount of stablization energy in a protein is quite small
what is the protein folding pathway
- 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
what results in misfiled proteins and disease (give examples)
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
Creutzfeldt-Jakob Disease (CJD) initial neuological symp
- difficulties with walking
- slurred speech
- numbness
- dizziness
- visual problems
Creutzfeldt-Jakob Disease (CJD) Initial psychological symptoms
- severe depression • withdrawal
- anxiety
- irritability
- insomnia
explain the mutagenic conversion of PrP
- 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
difference between PrPc ad PrPSc
C: a-helix, no B sheet. susceptible to proteolysis
Sc: less a and B sheet present, protease resistant
non coded amino acids: hydroxylproline
– Hydroxylation of proline
– Important component of collagen
– Allows specific triple helix structure
non coded amino acids: selenocysteine
– “encoded” by a subset of STOP codons
– Contains Se instead of S
– Reduced pKa useful for enzymes in anti-oxidant activity
non coded amino acids: homocysteine
– extra methyl group (R = CH2CH2SH) compared to cysteine
– Needed to synthesise cysteine
– Not found in proteins
