proteins

Question 1

what is the basic amino acid structure?

Answer 1

central carbon atom bonded to hydrogen, carboxyl group, amine group and variable/Rgroup

Question 2

what are the 3 ways of catagorising amino acids?

Answer 2

non-polar, polar and charged

Question 3

all amino acids are ___ except glycine

Answer 3

chiral

Question 4

what type of charaility is present in animals?

Answer 4

L-amino acids

Question 5

what does the charge on amino acids depend on?

Answer 5

Pka/ PI and pH

Question 6

which amino acid is actually an imino acid?

Answer 6

proline

Question 7

why are peptide bonds quite rigid?

Answer 7

they resonate between two forms, giving it partial double bond characteristics

Question 8

what is the structure of an alpha helix

Answer 8

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

Question 9

what are alpha helixes and beta pleated sheets represented as in diagrams?

Answer 9

alpha helix = ribbons

beta pleated sheets = arrows

Question 10

structure of beta pleated sheet

Answer 10

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

Question 11

what is primary structure?

Answer 11

order of amino acids

Question 12

what is secondary structure?

Answer 12

aplha helix and beta pleated sheets = only hydrogen bonding

Question 13

what is tertiary structure?

Answer 13

overall 3D shape of protein subunits

often hydrophobic residues in interior and hydrophillic on exterior

Question 14

what is quarternary structure?

Answer 14

arrangement of multiple subunits

Question 15

what are the forces that stabilise teriary and quarternary structure?

Answer 15

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

Question 16

what are 2 diseases caused by abnormal proteins?

Answer 16

alzheimers and Creutxfeldt jacob disease (CJD)

Question 17

what is the biochemical basis of alzheimers disease?

Answer 17

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

Question 18

what is the biochemical basis of CJD?

Answer 18

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

Question 19

structure and function of haemaglobin

Answer 19

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

Question 20

structure and function of myoglobin

Answer 20

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

Question 21

what is the role of the haem prosthetic group?

Answer 21

oxygen binds to the iron ion in the haem group, allowing haemaglobin to carry oxygen

Question 22

what are the differences between Mb and Hb?

Answer 22

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

Question 23

what happens when oxygen binds to haemaglobin?

Answer 23

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

Question 24

what is the T state and R state of Hb?

Answer 24

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

Question 25

what is the bohr effect?

Answer 25

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

Question 26

regulation by BPG

Answer 26

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

Question 27

what are the critical amino acid residues in Hb?

Answer 27

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

Question 28

what is the difference between conservative and non-conservative subsitution of amino acids?

Answer 28

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

Question 29

what is the structure of collagen?

Answer 29

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

Question 30

describe the synthesis of collagen

Answer 30

collagen synthesis occurs in the fibroblast intracellually (main function is to syntheise collagen and stroma) and extracellularly in spaces of connective tissue

Question 31

describe the assembly of collagen

Answer 31

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

Question 32

how many different types of collagen are ther?

Answer 32

12

Question 33

what do collagenases do?

Answer 33

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

Question 34

name 3 diseases associated with abnormal collagen structure

Answer 34

osteogenesis imperfecta (mutation in collagen chains) Ehlers-danlos syndrome type VI - lysyl oxidase deficiency Scurvy - caused by ascorbic acid deficiency

Question 35

what contains hydroxylated proline and lysine residues?

Answer 35

COLLAGEN

Question 36

what is phosphatidylserine?

Answer 36

a glycerophospholipid

Question 37

is prolactin secretion by the pituitary under inhibitory or excitory control?

Answer 37

inhbitory

Question 38

what is a common technique for karyotyping using light microscopu

Answer 38

G-banding