Molecular building blocks of life Flashcards
primary protein structure
sequence of nucleotides joined by peptide bonds in condensation reactions
amino acid structure
positive amino end N-terminus
negative carboxyl C-terminus
zwitterion
only L isomers found in proteins
zwitterion
having one of each charge but no net charge
amino acid isomers found in proteins
L
(L=living)
law for L isomers
CORN going clockwise
peptide bonds
rigid
partial double bond character
can undergo cis-trans isomerisation
trans vs cis frequency in proteins
trans 1000* more common than cis
chloramphenicol
antibiotic for eye infections/ penicillin-resistant meningitis.
prevents peptide bond formation by binding to bacterial ribosome
chloramphenicol acetyl transferase
enzyme used by resistant bacteria to prevent chloramphenicol ribosome-binding
negatively charged amino acids
carboxylate side chains
aspartate (D/Asp)
glutamate (E/Glu)
positively charged amino acids
primary amino groups
arginine (R/Arg)
lysine (K/Lys)
hydrophobic amino acids
proline (P/Pro)
leucine (L/Leu)
valine (V/Val)
isoleucine (I/Ile)
phenylalanine (F/Phe)
methionine (M/Met)
tryptophan (W/Trp)
aromatic amino acids
tryptophan (W/Trp)
phenylalanine (F/Phe)
tyrosine (Y/Tyr)
small amino acids
glycine (G/Gly)
alanine (A/Ala)
serine (S/Ser)
cysteine (C/Cys)
smallest amino acid
glycine (G/Gly)
charged/ polar amino acids
aspartate (D/Asp)
asparagine (N/Asn)
glutamate (E/Glu)
glutamine (Q/Gln)
arginine (R/Arg)
histidine (H/His)
glycine
2 hydrogens attached to a carbon
no D/L form
found in flexible regions of protein
neurotransmitter
Cysteine
thiol group (H lost more easily)
binds to other cysteine via disulfide bonds
binds to metal in proteins
disulfide bonds characteristics
increase stability of proteins
histidine
acts as a base> not strongly charged in body
can bind metals as well
aromatic amino acids characteristics
largest
hydrophobic
found in protein core
absorb light (used in spectroscopy)
required for diet of humans
phenylketoneuria
inability to break down excess phenylalanine > aspartame avoided
residue
each amino acid in a sequence
peptide backbone
w exposed carbonyls and amides
rigid planar peptide due to partial double bond w resonating electrons
secondary protein structure
structure of a protein molecule resulting from regular coiling/ folding of amino acid chain
alpha-helix
H bonding between oxygen of carbonyl group of one N on amino acid and hydrogen of NH group of another amino acid 4 places ahead (3.6 residues)
successive side-chains point 100 degrees apart
exist singly/ grouped/ in coils
beta pleated sheet
looser/ straighter alpha helix
parallel/ antiparallel
depend on H bonds/ L amino acid/ rigidity of peptide bond
side chains alternate 180 degrees up/ down
2 res repeat
hydrogen bond
intermolecular interaction between hydrogen atom bonded to atom more eneg and another atom in another molecule (usually O/N/F)
H bond strength compared to covalent
H 1/10 strength of covalent
eneg series
O>N>C=H
electronegativity
tendency of an atom to attract a bonding pair of electrons
parallel vs antiparallel frequency
parallel less common due to poor H-bonding
myoglobin structure
tertiary
1 unit
haemoglobin structure
tertiary/ quarternary
4 units > 2 alpha 2 beta
myoglobin function
binds haem group
haem group
contains iron
red pigment
binds oxygen in muscle
haemoglobin
binds oxygen in lungs and releases in tissue
acts cooperatively to deliver oxygen to tissues
multiple interacting sites
structure changes upon binding
myoglobin at normal oxygen delivery
high saturation
myoglobin at low oxygen supply to tissues
low saturation
haemoglobin graph shape
saturation at lungs/ tissues?
sigmoidal
high sat in lungs
low sat in tissues
sickle cell anaemia
low oxygen structure polymerizes Hb
E6>V mutation in beta sub-unit
blockages in peripheral blood vessels
homozygous recessive
SC trait > malaria resistant
mad cow disease
bovine spongiform encephalopathy
beef carcasses heat treated and fed back to cattle
brain damage
human variant developed
mad cow disease propagation
2 beta sheets sticking together
prion protein transformation diseases
GSS
Alzheimers
CJD
F-F insomnia
prion protein transformation
alpha-helix stable
exposed H-bonds on beta provide sticky ends
amyloid disease
uncontrolled protein growth
- can be controlled by single atom changes
diseases caused by missing protein
cystic fibrosis (missing CF transmembrane regulator protein)
muscular dystrophy (missing dystrophia)
phenylketoneuria (phenylalanine hydroxylase missing)
haemophilia (missing blood clotting factor proteins)
cancer (missing tumour suppressor genes)
type 1 diabetes (insulin-producing cell destruction)
TPP2 protein
glycine500 > aspartate
G500D mutation
complex quarternary structure
insulin action mechanism
present as hexamer at high conc in pancreas, dissociates in blood to form single monomer active in blood
bind to receptor
influence cell metabolic activity
novonordisk insulin replacement
insulin aspart
weaker hexamers due to proline> aspartate mutation
binding site for taxol
kinesins
microtubules
tubulin proteins form helix w 13 vertical filaments around hollow core
filamentous actin
polymer of globular proteins assembling to form long polymers
titin
largest protein preventing muscles over-stretching
30,000 amino acid residues
silk beta pleated sheet design
ala/ gly residues interlocking
rigid/ inextensible structure
A-keratin
coil of alpha helices
stretchy/ flexible w few disulfide bridges
collagen
coiled coil of three strands
gly-pro-pro sequence
100 res long
e.g. cartilage/ teeth/ skin/ bone
enzyme function
structure
contractile
defence
catalytic
regulatory
transport
storage
enzyme inhiibtor examples
tamiflu
penicillin
aspirin
statins/sarin
microcystin
tamiflu/ relenza
neuraminidase inhibitors
remove neuramic acid residues from host cell surface, easing virus life cycle release stage
tamiflu resistance
lysine to arginine mutation
penicillin mechanism
binds to enzymes producing bacterial cell wall
equilibrium constant
[C][D]/[A][B]
proportional to energy released by reaction
change in Gibbs free energy
-RT(LnKeq)
gas constant
8.314
catalysis mechanisms
proximity
orientation
strain (on bond)
acid-base catalysis (donation/ acceptance of protons)
covalent
active site specificity
3D shape
H-bonding
2 specificity mechanisms
lock and key (binding site complementary to substrate)
induced fit (binding site and substrate contact induces active site shape change)
specificity types
absolute
bond
group
stereo
enzyme reaction types
oxidation/ reduction
transferase
hydrolases
lyases
isomerases
ligases/ synthases
catalysis constant
(turnover number)
no. substrate molecules that can be converted to product by one enzyme in 1 second
equipment for measuring activity
spectrophotometer
activity measurement
product appearance
reactants disappearance
initial rate
rate at specified substrate concentration
Vmax[S]/(Km+[S])
michaelis constant
indicates affinity of an enzyme for a substrate as well as ES-complex stability
high Km
low affinity
low Km
high affinity
Km
[S] at Vmax/2
Vmax calculation
(only found at infinite [S])
1. line of best fit from least squares fitting programme
2. use linewaver-burk plot (double reciprocal)
types of enzyme inhibitors
irreversible
reversible: competitive, non-competitive, uncompetitive
irreversible enzyme inhibitor
irreversible binding of enzyme via covalent bonding to amino acid side chain (ser/cys) at/ near active site
permanent enzyme inactivation/ substrate binding inhibition
sarin
nerve gas covalently binding to ser residue on AChesterase (no ACh breakdown)
irreversible inhibitors examples
aspirin
penicillin
beta lactamase
aspirin
inhibition of cyclooxygenase I/II and therefore prostaglandin H2 synthase via acetyl group transfer to S530
penicillin
Ser res binding in glycopeptide transpeptidase, preventing peptidoglycan synthesis
Beta lactam
irreversible inhibition of bacterial cell wall enzymes
beta lactams resistance
beta lactamase
resistant bacteria product breaking down beta lactams
augmentin
amoxycillin/ beta lactamase combo
competitive inhibitors
compete w substrate active site
similar structure to substrate
overcome by [S]^ until outcompeted
competitive inhibition Vmax
unchanged
drugs as competitive inhibition
tamiflu (flu)
acarbose (T2 diabetes)
statins (hepatocytes rather than HMG-CoA reductase, reduces mevalomic acid as cholesterol precursor)
non-competitive inhibition
binds away from active site w same affinity, modifying reaction rate
influences catalysis capacity
non-competitive inhibition Km/Vmax
both decrease
when does pH affect enzyme activity
alteration of 3D active site structure
substrate binding group changes charge
