define the genome
full set of genes in an organism
define proteome
full set of proteins encoded by the genome
define non polar
hydrophobic
define polar
hydrophilic
which amino acids are hydrophobic (non - polar)
glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, proline
which amino acids are polar (hydrophilic)
serine, threonine, cysteine, tyrosine, asparagine, glutamine
which amino acids have electrically charged side chains
aspartate, glutamate, lysine, arginine, histidine
which amino acids are acidic
aspartate, glutamate
which amino acids are basic
lysine, arginine, histidine
where do you find polar or charged amino acid residues in a protein
on the outside
all amino acids are chiral apart from
glycine
which chiral amino acids are found in proteins
only L
what bonds are present causing the a helix
hydrogen bonds form between and N-H every 4 residues
which parts of the tertiary structure are polar (philic) and non-polar (phobic)
the interior of the tertiary structure is usually non polar and the exterior / outside is usually polar (hydrophilic)
what bonds occur between cysteine
disulphide bonds
which disease is associated with alzheimers
amyloid disease
what is the basic pathology of alzheimers
amyloid precursor protein accumulates and aggregates forming insoluble fibrils of amyloid B protein which then form plaques causes atrophy of neurones
what causes Creutzfeldt-jacob disease
prion disease - in may be inherited or caused by ingestion of infectious proteins - causes abnormal PrPsc structure
what is the polarity of globular proteins
polar outside and non-polar inside
what time of binding is o2 to Hb and what shape is the graph
co-operative binding and is sigmoidal
does Mb or Hb have the higher affinity for o2
Mb
what occurs during the T state in Hb
T state - Tense state - more salt bridges and a low affinity for O2 - binding sites aren’t accessible
What occurs during the R state of Hb
Relaxed state - less salt bridges and higher affinity
describe what happens in the bohr effect
increase in H+ means more acidity and and lower ph - this decreases Hb’ affinity for O2 and therefore O2 is released
why does an increase in H+ cause O2 unloading
H+ protonates amino acids (mainly histidine) making them more prone to forming salt bridges ie a better T state
what does BPG do
decreases the affinity of O2 at high altitude and in states of hypoxia
how do BPG bind to O2
binds to the space between the B subunits in the T state only and secures the T state
what is BPG effect on foetal Hb
binds less effectively so HbF has higher affinity for oxygen
what is the terminating amino acid in Hb
proline terminates the helical structure at C2
what is a conservative substitution
a sub to another amino acid with similar properties so there is no effect on function
what is a non conservative substitution
substitution which change the properties of the molecule due to a residue with a different side chain amino acid
how many chains does collagen have
3 chains - 2 a-1 and 1 a-2
what is the structure of collagen
has a glycine every 3 residue so that it can fold easily as glycine is very small - glycine pack inside while proline and 4HP are on the outside
what bonds are formed in collagen
hydroxyproline forms hydrogen bonds and hydroxylysine forms cross linking
in collagen it requires vitamin C for bonding, what does it do
hydroxylation of proline and lysine require ascorbic acid as a co factor which is vitamin C
when does a helix become left handed in collagen?
lysl oxidase deaminates some lysine and hydroxylysine residues to allysine which can form cross links with lysine or allysine (3.3 residues per turn rather than a normal 3.6)
what is dupuytrens contracture
excess collagen production hands - permanently bend fingers
what is osteogenesis imperfecta and what are the different types
mutation in type 1 collagen - brittle bone disease - break easily
type 1 - mild
type 2 fatal after birth
type 3/4 - severe deformities
what is ehlers danlos syndrome type IV
translucent skin around eyes so you can see the veins - lyssl oxidase deficiency
what is sickle cell anaemia
substitution of glutamate to valine causing hydrophobic sticky patches and sickle cell shape causing vein obstruction
what effect would changing lysine with argenine have
no effect - it is a conservative substitution as they are both basic
what are all the bonds that stabilise the secondary structure
they are all weak bonds
what would happen to the affinity for Hb and oxygen if you increased levels of BPG
high BPG = lower affinity for o2 and more unloading
collagen formation requires what
vitamin c
what reaction bonds amino acids in a polypeptide and what are the characteristics
peptide bond via condensation reaction and the production of water - partial double bond which causes rigidity and limited rotation going from CN to CO
differences between alpha helix and beta sheet
alpha helix - stabilised by H bonds - has some elasticity
beta - no elasticity
describe primary secondary and tertiary quaternary
primary - amino acid sequence
secondary - local spatial arrangement of amino acids
tertiary - formation of 3D shape
quat - arrangements of different subunits in a protein
where is myoglobin highest in conc
skeletal muscle and cardiac muscle
difference between myoglobin and haemoglobin
myoglobin has only pone subunit mostly alpha helical
hb - binding is sigmoidal, it is pH and CO2 dependant and regulated by BPG - Mb is not
difference between foetal hb and adult hb
foetal has 2 alpha and 2 gamma chains which bind to o2 more tightly
when o2 is bound to hb which state is the iron in
Fe2+
describe the synthesis of collagen
polypeptide synthesis, post translational modifications, pro collagen triple helix within fibroblasts - secretion from fibroblasts - removal of extension peptides - aggregation of microfibril - cross linking
how long is the half life of collagen
a few months