Lecture 5 - Proteins

Question 1

what are polymeric proteins?

Answer 1

chain like molecule made of monomers

Question 2

what are the 8 types of protein?

Answer 2

structural, storage, O2 transport, metabolism, cellular response, movement, protection, catalysis

Question 3

what are proteinogenic amino acids?

Answer 3

the 20 standard amino acids, each have an L and d form

Question 4

what form do most amino acids in the body exist in ?

Answer 4

Zwitterionic form

Question 5

what are essential amino acids?

Answer 5

Amino acids that the body cant make which must be gained through diet

Question 6

which amino acids are polar?

Answer 6

serine, threonine, asparagine, glutamine, cysteine, tyrosine

Question 7

which amino acids are acidic?

Answer 7

glutamic acid and aspartic acid

Question 8

which amino acids are basic ?

Answer 8

histidine, arginine and lysine

Question 9

which amino acids are non-polar ?

Answer 9

glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan and proline

Question 10

Describe the peptide backbone formation of a protein

Answer 10

rigid and planar bonds which initially form a partial double bond - usually trans and rotation at chiral is limited with bulky R groups + space availability

Question 11

Describe the primary structure

Answer 11

Amino acid sequence from N-terminus to C-terminus in which a genetic mutation can result in primary structure being changed therefore change in protein function

Question 12

Describe the alpha helix

Answer 12

flexible, coiled, proline is a helix breaker, stabilised by extensive intra chain hydrogen bonding, 3.6 amino acids per chain, R groups project outwards to avoid sterile hindrance, distance between amino acids = 1.5 A (with circle on top)

Question 13

Describe the beta pleated sheet

Answer 13

5-10 amino acids - parallel to antiparallel or mixed, strong + resilient, distance between amino acids = 3.5 A (with circle on top), frequently a part of enzyme active sites

Question 14

what is an amphipathic alpha helix?

Answer 14

proteins that have hydrophilic and hydrophobic parts which are important in helix formation

Question 15

what are the 6 super secondary structures?

Answer 15

Beta hairpin motif, helix-loop-helix, greek key, coiled coil, zinc finger and beta barrel

Question 16

Describe the beta hairpin

Answer 16

two adjacent antiparallel beta strands joined by a hairpin loop

Question 17

Describe helix loop helix

Answer 17

two alpha helices joined by a loop

Question 18

Describe the greek key motif

Answer 18

three antiparallel beta strands connected by hairpins

4th adjacent to the first and connected to first via longer loop

Question 19

Describe the coiled coil

Answer 19

repeats of 7 residues which results in an amphipathic alpha helices with a strip of hydrophobic residues which coil around similar helices

Question 20

Describe the zinc finger motif

Answer 20

two antiparallel beta sheets followed by an alpha helix stabilised by a zinc ion

Question 21

describe the beta barrel motif and the 3 types

Answer 21

multiple antiparallel beta sheets that twist to form a closed structure

1. up to down - 8 antiparallel beta sheets connected by hairpin loops
2. jellyroll barrel - 8 beta strands arranged as 2 four stranded antiparallel beta sheets wrapped around a hydrophobic interface
3. pore forming- 2 4 stranded antiparallel sheets with polar side chains facing inwards to create a channel for hydrophilic molecules

Question 22

Describe a domain

Answer 22

polypeptide chain that folds independently into a stable structure with its own hydrophobic core
proteins can have several different domains- each one associated with a specific function

Question 23

Describe fibrous proteins

Answer 23

insoluble in water, important in providing support and strength

Question 24

Describe collagen

Answer 24

superhelices of gly-rich triple alpha helices that assemble into fibrils, main protein in connective tissues,, strong and elastic
can produce less due to connective tissue disorder forming hyper-flexibility of joints and fragile skin

Question 25

Describe alpha keratins

Answer 25

coiled coils of two alpha helices that assemble into larger fibres, strong and inextensible, insoluble and chemically inert, disulphide bridges across coiled coils

Question 26

Describe beta keratins

Answer 26

fibroin found in the silk of spider webs - layers of antiparallel beta sheets rich in ala and glycolic residues, small side chains interdigitate allowing close packing

Question 27

Describe globular proteins

Answer 27

mix of irregular folded secondary elements to form a compact 3D shape, soluble in water with inner hydrophobic core, transported easily in body fluids

Question 28

Describe haemoglobin

Answer 28

tetramer - 4 polypeptide chains and 4 ahem groups +myoglobin, transports O2, carbon monoxide poisoning as CO binds more easily

Question 29

Describe sickle cell disease

Answer 29

caused by a single gene defect in beta globing gene changing primary structure of protein, spleen produces red blood cells and filters misshaped cells so because there are lots of misshaped cells with this genetic disorder the spleen has to work harder therefore causing damage
- being a carrier makes you susceptible to malaria

Question 30

Describe immunoglobulins

Answer 30

Y shaped proteins that identify and combat invading foreign organisms
4 chains lined by a disulphide bridge - 2 heavy chains and 2 short chains which can have a variable structure

Question 31

Describe denaturation

Answer 31

proteins lose structure in native state due to changes in environment

Question 32

Describe PH denaturation

Answer 32

change in PH changes interaction with bonds therefore adding pressure and causing bond breakage

Question 33

Describe heat denaturation

Answer 33

increase in vibrations which breaks hydrogen bonds and render proteins insoluble in water,

Question 34

what is pyrexia?

Answer 34

ancient anti viral defence mechanism where some bacteria can survive in extreme environments e.g. thermos aquatics lives in hot springs and produces DNA polymerase at these high temperatures

Question 35

Describe denaturation with solvents

Answer 35

forms new hydrogen bond with R chains therefore breaks intra and inter chain bonds and protein unfolds