Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

BIOC1203 > Amino acids and proteins > Flashcards

Amino acids and proteins Flashcards

(62 cards)

Start Studying
1
Q

what are L-amino acids

A

rotate plane polarized light anticlockwise (left)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what are D-amino acids

A

rotate plane polarized light clockwise (right)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

which type of amino acids are found in proteins

A

L

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

in the kyte & doolittle hydropathy table what do negative vs positive vales mean

A

negative - hydrophillic
positive - hydrophobic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

in acids what does f tend towards if pH»pKa

A

f -> 0
mostly deprotonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

in acids what does f tend towards if pH«pKa

A

f -> 1
mostly protonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

in acids what is f if pH=pKa

A

f = pKa (50% ionised negatively charged)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

in bases what does f tend towards when pH«pKa

A

f -> 1
mostly protonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

in bases what does f tend towards when pH»pka

A

f -> 0 mostly deprotonised

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

in bases what is f when pH=pKa

A

f = 0.5 (50% ionised positively charged)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what is a key role of histidine

A

stabilises pH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what are the 4 post translational modifications

A

phosphorylation
glycosylation
lipidation
ubiquination

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what is glycosylation

A

attachment of sugar molecules to surface of proteins (secretory pathway)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what is ubiquitination

A

attaches chains of ubiquitinate with deubiquiting enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what is lipidation

A

attachment of a fatty acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

why is kinase important

A

treatment of cancer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what causes sickle cell anemia

A

caused by variation in the gene that encodes for the beta subunit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

how are amino acids linked together

A

condensation reactions releases water catalysed by peptidyltransferase in ribosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what is the C and N terminus of a polypeptide

A

NH3 is N terminus
COOH is C terminus
(always written N to C terminus)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

why are polypeptides always written N to C terminus not the other way around

A

because they are chiral

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

are the bonds in proteins cis or trans and which amino acid is the exception

A

trans (except proline)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

what is phi

A

rotation about Ca-N bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

what is psi

A

rotation about Ca-C bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

what is the Ramachandran plot

A

deduced thar only certain torsion angles are possible in polypeptide chain others are forbidden due to steric clashes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
what are the three regions on the Ramachandran plot and where can they be found
a (alpha helix) is found bottom left ar (alpha helix left) is found top right B (parallel and antiparallel B strands) is found top left
26
what is the primary structure
amino acid sequence encodes for 3D protein structure can be compared to show evolution
27
what is secondary structure
local arrangement of polypeptide chains that involve extensive H bonds between main-chain amide and carbonyl groups alpha helix and beta strands
28
describe alpha helixes
posesses a dipole sidechains point out and downwards when helix runs upward from N -> C alpha helix capping is when side chain or main chain groups cap the otherwise unsatisfied NH and CO groups on the N and C termini
29
describe B strands
most extended conformation of polypeptide chain sucessive side chains point above/below main chain groups arranged side to side antiparallel and parallel
30
why is antiparallel more stable than parallel beta strands
there is less strain on H bonds in antiparallel
31
how do alpha helix and beta pleated sheet help the stability of molecules
maximises intramolecular H-bonds almost always unstable on isolation because H-bonds between mainchain groups are no stronger than those formed with the solvent
32
what is circular dichorism
a material exhibits differences in absorption of R or L (all chiral molecules display circular dichorism)
33
what is the difference between a loop and a turn
loop - lack of regular psi/phi angles turn - are ordered
34
35
what is the difference between the two types of beta turns
differ in orientation of peptide
36
what is the tertiary structure
folded biologically active conformation of a single polypeptide chain basic unit is a domain
37
what is a domain
a region of polypeptide chain that folds independently into a tertiary structure for a particular function
38
what are motifs I and give examples
combination of secondary structure elements e.g. helix-turn-helix, beta hairpin
39
what are motifs II and give examples
simple motifs combined together to generate more complex motifs e.g. greek key
40
what is a homo-oligomer
multiple copies of the same polypeptide chain
41
what is a heter-oligomer
contains different polypeptide sequences
42
what did crick and Watson say about the need for quaternary structures
quaternary structures provide genetically efficient mechanisms to build large biomolecular architectures with minimal use of genetic code
43
what is allostery
when the structure and function of a protein is regulated through its binding to another molecule
44
what is cooperativity and what is the difference between negative and positive cooperativity
when the occurrence of a transition in one subunit of a complex influences the probability of the other subunit making the same transition negative - less likely positive - more likely (domino effect e.g. O2 binding)
45
why are peptide bonds thermodynamically unstable
because they require ATP hydrolysis in a coupled reaction
46
what are the non covalent interactions
H bonds salt bridges vanderwals interactions hydrophobic interactions
47
what constitutes intramolecular interactions
burial of hydrophobic side chains into a tightly packed hydrophobic core that is shielded from the solvent
48
describe disulfide bridges
found in cell surface/secrete proteins form oxidising conditions don't form cytoplasmic proteins as cytoplasm is a reducing environment
49
what are the suspected roles of disulfide bridges
contribute to the stability of folding pathways intramolecular disulfide of CL domain promotes folding interchain disulfide bonds hold heavy and light chains together
50
what is the typical native state of proteins and why
ΔG of folding = 50kg/mol because it is a delicate balance between burial of hydrophobic residues and entropic penalty of forming higher ordered structure
51
why is marginal stability of proteins useful
because cells need to readily unfold and degrade proteins, protein dynamics and conformational changes are essential for function
52
what is actomyosin
different proteins work together to form a functioning contractile unit
53
explain x-ray crystallography
pure sample of protein is crystallised crystal is short with high energy x-rays analysis of diffraction patterns produce 3D electron density map that can be used to build molecular model of protein can be used to image almost anything but can be hard to form crystals
54
explain cryo-electron microscopy
pure sample applied to grid in thin layer and flash frozen imaged in electron microscope different views combine to give 3D structure (sample must be large)
55
why is the sample flash frozen in cryo-electron microscopy
so that water vitrifies so that the volume doesn't change and the biological molecule is conserved
56
explain NMR (briefly)
isotope labels used to generate distance restraints which can be used to generate ensembles of structures
57
what type proteins can de-novo protein structure determination be carried out on
small proteins
58
explain circular dichroism
reveals secondary structure content of a protein rapid, non-deconstructive and only requires small samples uses circularly polarised radiation in the form of uv radiation measures the difference in absorption between left handed and right handed polarised light all chiral molecules display CD therefor uv CD spectre of proteins is characteristic in their secondary structure content deconvolution
59
how can proteins be unfolded
temperature pH addition of chaotropes
60
why do chaotropes unfold proteins
disrupt H bonds which reduces strength of the hydrophobic effect
61
whats Anfinsen's dogma
the protein structure is unique and thus corresponds to the lowest free energy state
62
why do proteins bury the hydrophobic side chains
shielding from solvent formation of van der walls interacts with hydrophobic core energy driving force for folding

BIOC1203 (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions