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BIOC192 > progress test > Flashcards

progress test Flashcards

1
Q

what are the main techniques used to determine protein structure?

A

protein crystallography, cryo-electron microscopy, NMR spectroscopy

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2
Q

what are the key properties of peptide bonds?

A

planar, trans dipoles. covalent bonds

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3
Q

phosphorylation function

A

controls enzyme activity- on/off switch

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4
Q

hydroxylation function

A

prevent connective tissue diseases and scurvy.

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5
Q

carboxylation function

A

needed for blood clotting properties

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6
Q

secondary level protein structure

A

local 3D arrangement of a protein chain over a short stretch of adjacent amino acids.

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7
Q

tertiary level protein structure

A

3D structure of a complete protein chain

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8
Q

quaternary level protein structure

A

interchain packing and structure for a protein that has multiple chains

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9
Q

describe a phi bond

A

N-C bonds, free rotation between 0 and 180 degrees. Creates O-O collisions

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10
Q

what type of bond is a C-C bond?

A

Psi bond, free rotations NH-NH collisions.

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11
Q

describe the omega bond

A

C-N bond, little rotation occurs. Close to 0 or 180 degrees around the peptide bond.

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12
Q

key properties of an alpha helix

A

main chain spirals around the central axis
non covalent interactions H+ bonds between (N+4) which help to stabilise the structure.

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13
Q

what is a beta turn and what are its properties

A

requires to form globular proteins, has high gly and pro content.

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14
Q

name the three protein families with examples of each

A

alpha domain- mostly helical eg globin fold in haem/myoglobin
alpha/beta domain- mis of both alpha and beta, eg barrel with hydrophobic core
antiparallel beta- mostly antiparralel beta structure eg retinal binding protein

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15
Q

factors leading to protein unfolding

A

temperature, PH, detergent and organic solvents

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16
Q

what are some diseases that are caused by unfolding proteins

A

amyloid protein misfolding= type 2 diabetes, alzheimers
prion diseases- PRP protein changes it shape causing brain damage. alpha –> beta transformation results in abnormal protein

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17
Q

how do metal ions aid enzymes?

A

they act as lewis acids through acid base catalysis. they help with positioning reactants exactly where they are needed (precise geometrics)

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18
Q

what are co-enzymes and how are they derived?

A

co-substrates, carriers and often derived from vitamins

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19
Q

what is covalent catalysis?

A

formation of a reactive, short lived intermediate that is covalently attatched to the enzyme

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20
Q

what type of amino acids are likely to be involved in acid base catalysis?

A

ones with ionisable side chains
histadine is particulalry suitable as its easily ionised at physiological PH.

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21
Q

which form of enzyme is best for drug design?

A

transition state analogues as they make ideal enzyme inhibitors.

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22
Q

what type of bonds are there between enzyme and substrate?

A

covalent bonds (rare), hydrogen bonds (side chain O& N act as H+ bond doner/acceptors)
ionic- non covalent
Van der waals interactions (protien and substrates in close proximity)

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23
Q

how is delta G lowered

A

ground state stabilisation and transition state stabilisation (an active site thats shape compliments transition state not substrate)
alternative reaction pathways

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24
Q

what are the 3 main catalytic mechanisms enzymes are involved in?

A

covalent catalysis, acid-base catalysis, metal ion catalysis

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25
Q

what are the two kinetic parametres able to be identified on a V vs (S) curve

A

Vmax= max velocity possible with infinite substrate
Km= substrate concentration which V=Vmax/2

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26
Q

what is plotted on a lineweaver burke plot?

A

y axis= 1/V
x axis= 1/S

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27
Q

what does a y intercept represent on a lineweaver burke plot?

A

1/Vmax

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28
Q

what does an x intercept represent on a lineweaver burke plot?

A

-1/Km

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29
Q

What is the significance of Km?

A

how well as enzyme grabs substrate

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30
Q

What does a high Km indicate?

A

a low affinity for binding substrate.

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31
Q

What does Kcat represent?

A

number of substrate molecules converted into product, per , enzyme per unit of time

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32
Q

how do we define catalytic efficiency?

A

enzymes peak activity
high Kcat
low Km (high affinity for substrate)
overall measure of enzyme efficiency= Kcat/Km

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33
Q

what equation describes the V vs (S) curve for a monomeric enzyme

A

v= Vmax x (substrate)/ Km + (substrate)

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34
Q

what are the three assumptions for the michaelis menten model?

A

1) product isnt converted back into substrate
2) haldones steady state: rate of enzyme formation=rate of enzyme breakdown
3) measuring initial rates means that substrate concentration doesn’t change significantly

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35
Q

what km/kcat values are considered to be a ‘perfect catalyst’

A

10^8s-1 M-1

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36
Q

what are the two classes of inhibitor

A

reversible (not covalently bound to enzyme) leaving enzyme in original condition and irreversible (covalently bound to enzyme) permanently inactivating the enzyme.

37
Q

what happens to vmax value with competitive inhibiton when an infinite amount of substrate is present
(including lineweaver burque axis)

A

no change in Vmax,
infinite amount of substrate outcompetes inhibitor
lineweaver burque= y axis doesn’t change

38
Q

what occurs with substrate binding in non competitive inhibition

A

inhibitor binds at a different site to substrate
enzyme can bind substrate, or inhibitor, or both

39
Q

what effect does mixed non-competitive inhibition have on Km and Vmax

A

it changes both values

40
Q

what are allosteric enzymes?

A

enzymes that have things occuring away from the active site.

41
Q

what are three methods of enzyme regulation

A

covalent modification, allosteric effects, proteolytic cleavage

42
Q

the Fe in a haem group has 6 binding sites, what binds to each of them?

A

4 nitrogens on the pyrole rings, one nitrogen on a histadine group and one oxygen

43
Q

what Po2 levels are heam and myo saturated at and what levels do they release their oxygen at

A

myo= saturated at low PO2 levels and releases it at very low PO2 levels.
Haem= saturated at high PO2 levels and gives the O2 up at low levels

44
Q

what is the affinity for oxygen at T and R states

A

low oxygen affinity at T state (deoxy)
high oxygen affinity at R state (oxy)

45
Q

what does cooperativity require?

A

an oligmer

46
Q

what type of binding curve does myo show and what does haemo show?

A

myo=hyperbolic
haem= sigmoidal due to its cooperativity

47
Q

what are the three allosteric inhibitors?

A

BPG, CO2 and low pH

48
Q

how does shifting from R to T state affect how globin interacts with haem?

A

switching between the states causes changes to the F helix. Keeping F away from the binding site weakens the oxygen binding

49
Q

what happens if allosteric inhibitors aren’t present?

A

Haemoglobin is mostly in the R state and shows little cooperativity. means that we dont have a very sigmoidal curve.

50
Q

how does BPG bind to deoxy-heamo?

A

through electrostatic interactions

51
Q

how does BPG stabilise haemo?

A

I the deoxy-T state it reduces oxygen affinity

52
Q

where is BPG produced and what does it promote?

A

produced during respiration in perpipheral tissues, promoting oxygen release where required.

53
Q

what is the bohr effect and what are its two components?

A

elevated CO2 and H+ in metabolising tissue reduces affinity of haemoglobin for O2.
-lower ph favours cooperativity, as it promotes protination of histadien residues therefore stronger ionic interactions with BPG.
-CO2 can bind the amino (N) terminus and stabilise the deoxy (T state) of haemoglobin.

54
Q

how is foetal haemoglobin different?

A

it includes alternative isoforms with higher O2 affinities so it holds oxygen tighter.
made of 2 alpha and 2 gamma units.
it is less sensitive to BPG

55
Q

what causes sickle cell anemia HbS

A

abnormal hydrophobic interaction between Hb tetramers.
interactions are particularly stabilised in the T state, and it is only in this form that the valine is exposed.

56
Q

what are some treatments for HbS

A

CRISPR based therapies- upregulating the gamma subunit expression which can then replace the beta subunit.
Voxelotor- heamoglobin oxygen affinity modulator which stabilises the oxygenated state increasing oxygen affinity.

57
Q

what are the steps behind activation or inhibition of proteins

A

1) chemical substance travels from its source
2) binds to protein/ receptor
3) activates or inhibits it resulting in a change to cellular response

58
Q

what is an advantage of a receptor being placed on the outer membrane?

A

the ligand that binds doesnt have to pass through the cell membrane and is able to act at cell surface.

59
Q

enzymes vs receptor

A

enzyme= one active site, binds substrate and turns into product
receptor=several binding sites, bind ligands and releases them unchanged

60
Q

what are the three main receptor classes?

A

GPCR, ligand gated ion channel, receptor tyrosine kinase

61
Q

which structural component of starch is responsible for the formation of a dark blue-black colour in the ‘iodine starch test’?

A

amylose in the amylose iodine complex

62
Q

how does high heat affect bond stabilising proteins (eg primary, secondary, teritiary)

A

secondary and tertiary structures are broken down, primary remains as its polypeptide sequence.

63
Q

what is beers law?

A

the concentration of a solution is linearly proportional to the absorbance of that solution

64
Q

what is lamberts law?

A

the instensity of the transmitted light is linearly proportional to the path length.

65
Q

what is plotted on a standard curve and where?

A

concentration on the x axis
absorbance on the y axis.

66
Q

what does alcohol dehydrogenase catalyse the conversion of?

A

ethanol to acetaldehyde

67
Q

what is phosphorylation and de, how is this important for signal transduction?

A

turning protein activity on off, up or down
phosphorylation= protein kinase transfering phospate from ATP to protein
dephosphorylation= protein phosphates remove phosphate from proteins to control signal transduction

68
Q

how does the signal transduction mechanism for insulin receptor differ from muscle/adipose cells vs liver cells

A

muscle cells, insulin binding causes the translocation of GLUT-4 so glucose can enter the cell
liver= binding of insulin causing adaptor protein to result in glycogen synthesis

69
Q

what occurs from signal transduction for a glycogen receptor on liver cells

A

glycogen binds to GPCR glucagon receptor
the signal transduction pathway results in glycogen breakdown

70
Q

what is the role of GLP-1

A

a peptide ligand that acts on pancreatic beta cells

71
Q

what occurs in glucagon receptor signal transduction

A

glucagon binds to a GPCR receptor on a liver cells, resulting in a G protein being activated causing signal transduction leading to glycogen breakdown

72
Q

what occurs in GLP-1 receptor signal transduction

A

on pancreatic beta cells GLP-1 binds to GPRC receptor causing g protein activation and signal transduction resulting in insulin release

73
Q

what is ‘codon redundancy’

A

each amino acid codes for multiple codons
so there is flexibility in changing the gene sequence without changing the protein

73
Q

how does signal transduction occur for a receptor tyrosine-kinase receptor?

A

agonist ligand binds, receptor changes shape and is activated. Receptor autophosporylation occurs and adaptor protein is phosphorylated. Adaptor proteins communicate with other proteins in the cell (phosphorylation cascade)

73
Q

what are the three stages of translation

A

initiation: ribosome, Mrna and trna come together= translation intiation complex
elongation: ribosome moves along Mrna adding amino acids
termination: stop codon reached when the peptide chain has necassary amino acids and the translocation complex breaks apart releasing the polypeptide chain

74
Q

what is transcription control and why is it important ?

A

transcription factors bind to promoter regions
transcription factors controls RNA pol binding therefore RNA synthesis
activators encourage rna pol binding
repressors: prevent rna pol bindig and prevent mrna being made

75
Q

what are the two types of genetic variation

A

single nucleotide polymorphism- change of one nucleotide
indels- insertion or deletions, addition or removal of one or more bases

76
Q

what happens if varation in the promoter region?

A

may change gene expression- how much protein is produced
transcription factors etc not binding in the correct places

77
Q

what happens in variants occur in exons

A

may change amino acid sequence and potentially function
snps that change a codon= different amino acid, or coding for stop which means a shortened protein

78
Q

what do indels cause

A

a frame shift= serious consequences for protein

79
Q

what are restriction enzymes and how are they useful in genotyping?

A

proteins isolated from bacteria that cut dna= bacterial defence mechanism
they recognise a particular sequence and cut it at a certain base

80
Q

what are thetwo types of genes that cause cancer when mutated?

A

proto-oncogenes–> oncogenes
tumor supressor genes

81
Q

what is the normal function for a oncogene

A

accelerator
they encode proteins that promote cell growth
gain of function mutations= cell growth when not required

82
Q

what is the normal function for tumor supressor genes

A

brake
genes with proteins that prevent uncontrolled cell growth, inhibit cell divisions and prevent other mutations
loss of function
new alleles= recessive effect

83
Q

what type of mutations in the two genes have to occur to result in cancer?

A

both tumor suppressor genes (recessive) are damages and one oncogene is damaged (dominant)

84
Q

what are the 5 key components needed in a plasmid for recombinant DNA

A

promotor region- drives gene expression (must be specific to cell type)
antibiotic resistance: survival advantage to cells containing the plasmid
origin of replication: allows initiation using host DNA pol
selectable marker: select for cells sucessfully taken up by the plasmid
restriction sites: site that allows plasmid to be cut open and gene of interest to be glued in

85
Q

outline the process of transformation

A

transferring vectors into bacteria
transformed bacteria selected by antibiotic resistance
expression of vector gene in bacteria
amplyfying and purifying dna for use
*only bacteria that have taken up the recombinant vector can grow)

86
Q

how is the issue of cloning eukaryotic genes in prokaryotes overcome?

A

only coding dna is used as introns are spliced out
Cdna made through reverse transcription from reverse transcriptase

BIOC192 (4 decks)

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