proteins Flashcards
what is the basic amino acid structure?
central carbon atom bonded to hydrogen, carboxyl group, amine group and variable/Rgroup
what are the 3 ways of catagorising amino acids?
non-polar, polar and charged
all amino acids are ___ except glycine
chiral
what type of charaility is present in animals?
L-amino acids
what does the charge on amino acids depend on?
Pka/ PI and pH
which amino acid is actually an imino acid?
proline
why are peptide bonds quite rigid?
they resonate between two forms, giving it partial double bond characteristics
what is the structure of an alpha helix
hydrogen bonds between different parts of the same chain, the helix is formed by the backbone, the R groups extend outside of the helix
hydrogen bonds stabilises the helix and are called intrachain hydrogen bonds
what are alpha helixes and beta pleated sheets represented as in diagrams?
alpha helix = ribbons
beta pleated sheets = arrows
structure of beta pleated sheet
polypeptide strands run alongside eachother with hydrogen bonds
between same chain = intrachain hydorgen bonds
between different chain + interchain hydrogen bonds
side chains lie above or below the plane of the sheet
pleated due to tetrahedral bonding
no elasticity
fully extended chain
what is primary structure?
order of amino acids
what is secondary structure?
aplha helix and beta pleated sheets = only hydrogen bonding
what is tertiary structure?
overall 3D shape of protein subunits
often hydrophobic residues in interior and hydrophillic on exterior
what is quarternary structure?
arrangement of multiple subunits
what are the forces that stabilise teriary and quarternary structure?
electrostatic interactions - between oppositely charged side chains
polar bonds - permanent dipoles (due to differing electronegativity)
van de waals forces - tempory/induced dipoles
hydrogen bonds
hydrophobic affect - when non-polar amino acids try to minimise contacts with water and buried in the core of proteins
disulphide bonds - between cysteine or methionine covalent bonds
what are 2 diseases caused by abnormal proteins?
alzheimers and Creutxfeldt jacob disease (CJD)
what is the biochemical basis of alzheimers disease?
amyloid precursor protein accumulates and aggregates forming insoluble fibrils of amyloid beta protein in the brain
these fibrils aggregate to form plaques which damage and destroy nuerones
what is the biochemical basis of CJD?
the protein PrPSc (infectious agent - not a virus) has identical primary structure to normal membrane protein PrPc but has much higher proportion of beta sheets
when PrPSc is in contact with normal PrPc, it gives PrPc the abnormal structure leading to insoluble aggregates
structure and function of haemaglobin
haemaglobin consists of 4 polypeptide chains (2a and 2b) held together by non-covalent interactions. each chain contains a haem group so can bind to 4 oxygen molecules. held together in a tetrahedral array
used to transport oxygen
structure and function of myoglobin
similar structure to subunit of Hb but has a very different primary sequence. it is a single chain polypeptide
used in the storage of oxygen
what is the role of the haem prosthetic group?
oxygen binds to the iron ion in the haem group, allowing haemaglobin to carry oxygen
what are the differences between Mb and Hb?
Mb has 1 chain, Hb has 4
Hb binds to O2,CO2, CO, NO, BPH and H+, Mb only binds to O2
binding of oxygen is cooperative in Hb but not in Mb
affinity for oxygen is affected by pH and CO2 concentration in Hb but not in Mb.
Hb is regulated by BPG whereas Mb is not
what happens when oxygen binds to haemaglobin?
oxygen binding reduces the distance between the helices, the proximal His F8 is pulled in, shifting helix F, EF and FG corners. this alters the shape causing some salt bridges to rupture. the change of one subunit changes the relationship between the 4 subunits and these structural changes increase the affinity of the remaining subunits of oxygen
what is the T state and R state of Hb?
t state = tense state, so has more salt bridges = low affinity for oxygen
r state = relaxed state, so less salt bridges, making oxygen binding sites more accesible = higher affinity for oxygen
what is the bohr effect?
lowing pH decreases Hb affinity for O2
increased CO2 in the blood or increased lactic acid will lower pH
this increases release of O2 to rapidly respiring tissues or muscles releaseing lactic acid
regulation by BPG
BPG is found in high cocentrations in red blood cells (and increase at high altitude and in hypoxia).
BPG decreases the affinity of Hb for O2 so causes more oxygen to be released
BPG binds bewteen beta subunits in the T space
negative charges on BPG interact with positive amino acid residues lining the space
what are the critical amino acid residues in Hb?
only 9 individual residues in Hb are invariant so this means many amino acid changes leave Hb unchanged. each invariant plays an important role in the function of haemaglobin
what is the difference between conservative and non-conservative subsitution of amino acids?
conservative substitution involves substitution of amino acid with another amino acid with similar properties whereas non-conservative substitutes a amino acid with one of different properties
what is the structure of collagen?
fibrous protein forming insoluble fibres with high tensile strength. made of 3 polypeptide chains, roughly 12 different types of collagen
have repeated 3 amino acids (Gly - X - Y)n where X is usually proline and Y is usually Hyp
describe the synthesis of collagen
collagen synthesis occurs in the fibroblast intracellually (main function is to syntheise collagen and stroma)
and extracellularly in spaces of connective tissue
describe the assembly of collagen
polypetide synthesis lead to procollagen
removal of extension peptides forms tropocollagen
aggregation occurs forming a microfibril
cross linking forms collagen fibre
hydroxylaton of proline and lysine residues occurs before chain forms a helix, propyl hydroxylase and lysyl hydroxylase both require ascorbic acids as a co factor. hydroxyproline = hydrogen bond formation which helps stabilise the triple helix
hydroxylysine resiudes are attachment sites for sugar residues and are involved in crosslinking between collagen chaisn
how many different types of collagen are ther?
12
what do collagenases do?
break down collagen. sometimes necessary for instance, in growth and tissue remodelling (pregnancy/after birth). and in tissue repair
important in tumour invasion and metastasis often produced at high levels by tumour cells - successful treatment for dupuytrens contracture
name 3 diseases associated with abnormal collagen structure
osteogenesis imperfecta (mutation in collagen chains)
Ehlers-danlos syndrome type VI - lysyl oxidase deficiency
Scurvy - caused by ascorbic acid deficiency
what contains hydroxylated proline and lysine residues?
COLLAGEN
what is phosphatidylserine?
a glycerophospholipid
is prolactin secretion by the pituitary under inhibitory or excitory control?
inhbitory
what is a common technique for karyotyping using light microscopu
G-banding
