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progress test Flashcards

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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
what are the two kinetic parametres able to be identified on a V vs (S) curve
Vmax= max velocity possible with infinite substrate Km= substrate concentration which V=Vmax/2
26
what is plotted on a lineweaver burke plot?
y axis= 1/V x axis= 1/S
27
what does a y intercept represent on a lineweaver burke plot?
1/Vmax
28
what does an x intercept represent on a lineweaver burke plot?
-1/Km
29
What is the significance of Km?
how well as enzyme grabs substrate
30
What does a high Km indicate?
a low affinity for binding substrate.
31
What does Kcat represent?
number of substrate molecules converted into product, per , enzyme per unit of time
32
how do we define catalytic efficiency?
enzymes peak activity high Kcat low Km (high affinity for substrate) overall measure of enzyme efficiency= Kcat/Km
33
what equation describes the V vs (S) curve for a monomeric enzyme
v= Vmax x (substrate)/ Km + (substrate)
34
what are the three assumptions for the michaelis menten model?
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
35
what km/kcat values are considered to be a 'perfect catalyst'
10^8s-1 M-1
36
what are the two classes of inhibitor
reversible (not covalently bound to enzyme) leaving enzyme in original condition and irreversible (covalently bound to enzyme) permanently inactivating the enzyme.
37
what happens to vmax value with competitive inhibiton when an infinite amount of substrate is present (including lineweaver burque axis)
no change in Vmax, infinite amount of substrate outcompetes inhibitor lineweaver burque= y axis doesn't change
38
what occurs with substrate binding in non competitive inhibition
inhibitor binds at a different site to substrate enzyme can bind substrate, or inhibitor, or both
39
what effect does mixed non-competitive inhibition have on Km and Vmax
it changes both values
40
what are allosteric enzymes?
enzymes that have things occuring away from the active site.
41
what are three methods of enzyme regulation
covalent modification, allosteric effects, proteolytic cleavage
42
the Fe in a haem group has 6 binding sites, what binds to each of them?
4 nitrogens on the pyrole rings, one nitrogen on a histadine group and one oxygen
43
what Po2 levels are heam and myo saturated at and what levels do they release their oxygen at
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
what is the affinity for oxygen at T and R states
low oxygen affinity at T state (deoxy) high oxygen affinity at R state (oxy)
45
what does cooperativity require?
an oligmer
46
what type of binding curve does myo show and what does haemo show?
myo=hyperbolic haem= sigmoidal due to its cooperativity
47
what are the three allosteric inhibitors?
BPG, CO2 and low pH
48
how does shifting from R to T state affect how globin interacts with haem?
switching between the states causes changes to the F helix. Keeping F away from the binding site weakens the oxygen binding
49
what happens if allosteric inhibitors aren't present?
Haemoglobin is mostly in the R state and shows little cooperativity. means that we dont have a very sigmoidal curve.
50
how does BPG bind to deoxy-heamo?
through electrostatic interactions
51
how does BPG stabilise haemo?
I the deoxy-T state it reduces oxygen affinity
52
where is BPG produced and what does it promote?
produced during respiration in perpipheral tissues, promoting oxygen release where required.
53
what is the bohr effect and what are its two components?
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
how is foetal haemoglobin different?
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
what causes sickle cell anemia HbS
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
what are some treatments for HbS
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
what are the steps behind activation or inhibition of proteins
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
what is an advantage of a receptor being placed on the outer membrane?
the ligand that binds doesnt have to pass through the cell membrane and is able to act at cell surface.
59
enzymes vs receptor
enzyme= one active site, binds substrate and turns into product receptor=several binding sites, bind ligands and releases them unchanged
60
what are the three main receptor classes?
GPCR, ligand gated ion channel, receptor tyrosine kinase
61
which structural component of starch is responsible for the formation of a dark blue-black colour in the 'iodine starch test'?
amylose in the amylose iodine complex
62
how does high heat affect bond stabilising proteins (eg primary, secondary, teritiary)
secondary and tertiary structures are broken down, primary remains as its polypeptide sequence.
63
what is beers law?
the concentration of a solution is linearly proportional to the absorbance of that solution
64
what is lamberts law?
the instensity of the transmitted light is linearly proportional to the path length.
65
what is plotted on a standard curve and where?
concentration on the x axis absorbance on the y axis.
66
what does alcohol dehydrogenase catalyse the conversion of?
ethanol to acetaldehyde
67
what is phosphorylation and de, how is this important for signal transduction?
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
how does the signal transduction mechanism for insulin receptor differ from muscle/adipose cells vs liver cells
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
what occurs from signal transduction for a glycogen receptor on liver cells
glycogen binds to GPCR glucagon receptor the signal transduction pathway results in glycogen breakdown
70
what is the role of GLP-1
a peptide ligand that acts on pancreatic beta cells
71
what occurs in glucagon receptor signal transduction
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
what occurs in GLP-1 receptor signal transduction
on pancreatic beta cells GLP-1 binds to GPRC receptor causing g protein activation and signal transduction resulting in insulin release
73
what is 'codon redundancy'
each amino acid codes for multiple codons so there is flexibility in changing the gene sequence without changing the protein
73
how does signal transduction occur for a receptor tyrosine-kinase receptor?
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
what are the three stages of translation
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
what is transcription control and why is it important ?
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
what are the two types of genetic variation
single nucleotide polymorphism- change of one nucleotide indels- insertion or deletions, addition or removal of one or more bases
76
what happens if varation in the promoter region?
may change gene expression- how much protein is produced transcription factors etc not binding in the correct places
77
what happens in variants occur in exons
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
what do indels cause
a frame shift= serious consequences for protein
79
what are restriction enzymes and how are they useful in genotyping?
proteins isolated from bacteria that cut dna= bacterial defence mechanism they recognise a particular sequence and cut it at a certain base
80
what are thetwo types of genes that cause cancer when mutated?
proto-oncogenes--> oncogenes tumor supressor genes
81
what is the normal function for a oncogene
accelerator they encode proteins that promote cell growth gain of function mutations= cell growth when not required
82
what is the normal function for tumor supressor genes
brake genes with proteins that prevent uncontrolled cell growth, inhibit cell divisions and prevent other mutations loss of function new alleles= recessive effect
83
what type of mutations in the two genes have to occur to result in cancer?
both tumor suppressor genes (recessive) are damages and one oncogene is damaged (dominant)
84
what are the 5 key components needed in a plasmid for recombinant DNA
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
outline the process of transformation
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
how is the issue of cloning eukaryotic genes in prokaryotes overcome?
only coding dna is used as introns are spliced out Cdna made through reverse transcription from reverse transcriptase

BIOC192 (5 decks)

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