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Biomed > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

What is miRNA?

A

binds to mRNA - promotes degradation/inhibiting translation

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2
Q

what is snRNA

A

Involved in RNA splicing

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3
Q

What is the function of holoenzymes?

A

Act as a primer for RNA polymerase

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4
Q

What is a Pritbrow box, and what does it act as?

A

is a promoter region comprised of high A-T concentration

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5
Q

What does a termination sequence look like in terms of bases?

A

G-C rich region followed by an A-T rich region

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6
Q

What is the mass of each prokaryotic ribosomal subunits and the total ribosome mass

A

50s and 30s

total is 70s

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7
Q

At what codon does translation initiation commonly occur?

A

AUG

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8
Q

What 2 amino acids cannot be included in an alpha-helix structure and why?

A

Glycine - too flexible for the structure

Proline - too kinky because its angle it 10 degrees off for the optimum structure for an alpha helix structure

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9
Q

What is the optimum angles for Psi/Psh bonds to be for an alpha helix?

A

60

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10
Q

What is the purpose of randomly coiled parts of a polypeptide chain?

A

allows ligand binding and acts to connect different different protein domains

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11
Q

Function of beta-ME?

A

breaks di-sulphide bridges in tertiary-structures

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12
Q

How did Anfinsen fully unfold a protien?

A

8micromililitres of urate

excess beta-ME

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13
Q

What are the 4 driving forces of protein folding?

A

hydrophobic affect
Pi-Pi bonds between aromatic rings
electrostatic interactions
hydrogen bonds

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14
Q

What amino acids are phosphorylised in a quaternary structure?

A

serine/threonine/tyrosine

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15
Q

What is acetylisation and how does it do it?

A

compensates for the positive charge of lysine by forming acetyl-lysine

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16
Q

What is palmitoylation and what amino acids are involved?

A

long lipid groups help anchor proteins in the membrane

glycine, cysteine, lysine

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17
Q

How does AAT deactivate elastase?

A

AAT lures in elastase then, rotates it 180 degrees

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18
Q

What is the function of scaffolding proteins?

A

allows other proteins to bind to for compartmentalisation

also used for cell signalling

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19
Q

What is a glycosaminoglycan

A

amino acid within a polysaccharide

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20
Q

Proteoglycan function?

A

holds together protein placement in connective tissue

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21
Q

What are peptidoclycans formed from?

A

polysaccharide-peptide complex

alternating N-acetylglucosamine and N-acetylmuramic acid

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22
Q

In bacterial cell walls What forms the bridges between the amino acids in the structure?

A

penta-glycine bridges

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23
Q

What is the defintion of a ligand?

A

a molecule that binds to a macromolecule to form a complex which initiates a conformational change to generate a signal

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24
Q

What is a juxtacrine signal?

A

A signal that is only between 2 neighbouring cells

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25
Q

What is an autocrine signal, and what is the distinction between intracrine signal?

A

an autocrine signal is one where the signalling cell and the target are the same cell
intracrine signals are a type of autocrine signal but the signal remains within the cell

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26
Q

What does NO cause?

A

chronic relaxation

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27
Q

What type of signal is hydrophobic but cannot diffuse into a cell, how is it transported into the cell and where is its receptor located?

A

thyroxine signals
transporter proteins
in the nucleus

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28
Q

What are ligand-gated ion channels composed of?

A

4 polypeptides, 3 hydrophobic, and 1 aliphatic, lines the pore

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29
Q

What happens when G-protein releases GDP and gains GTP?

A

alpha-G dissociates from beta-G and the both become active

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30
Q

What are the functions of activated G-aplha?

A

Activates adenyl-cyclase

can also deactivate adenyl-cyclase

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31
Q

What does calcium bind to for intracellular messaging, and what does that bind to?

A

calmodium, then CaM-kinase

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32
Q

what is the function of calmodium-dependent kinase

A

regulates many proteins activity

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33
Q

How does protease modify an enzyme?

A

cleaves a peptide chain on the active site

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34
Q

how does a kinase modify an enzyme and how is this reversed?

A

the kinase can phosphyrale the enzyme

reversed by any phosphotase

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35
Q

what is a K-type modification?

A

an enzyme binds to a substrate to increase the affinity of that substrate for another enzyme

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36
Q

define a plasmid?

A

small circular DNA found in bacteria

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37
Q

what DNA polymerase can be used for PCR

A

Taq-DNA polymerase

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38
Q

outline the function of restriction enzymes?

A

detect the specific sequence of DNA to cut

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39
Q

what are the required components for PCR

A

ds DNA template
pair of oligonucleotide primers
DNA polymerase
Nucleotides

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40
Q

Why don’t restriction enzymes cleave bacterial DNA

A

ECO RI methylase methylates the DNA sequence which prevents restriction enzymes from cleaving the sequence

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41
Q

why does ECO RI methylase only methylate bacterial DNA?

A

when already methylated DNA undergoes semi-conservative replication, there is a strand that is not methylated and one is
ECO RI only methylates hemi-methylated DNA, so it methylates the other strand and wont methylate non-bacterial DNA

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42
Q

What is the difference between type I/II/III restriction enzymes?

A

Type 1 cuts DNA 1000 base pairs away from its recognition site
Type II cuts DNA at the recognition site
Type III cuts DNA 25 base pairs away from the recognition site

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43
Q

Function of DNA ligase

A

catalyses phosphodiester bonds and used to stick DNA to a plasmid

44
Q

what do you do when the gene and the vector do not contain compatible enzymes

A

use nuclease to create blunt ends that can be inserted into the plasmid
use DNA pol to fill in ends of the gene to create a blunt end

45
Q

how do you prepare a competent cell for a plasmid, and what is the purpose of the second step?

A

50mM CaCl2

heat shock of 42C for 2 minutes to increase membrane fluidity so the plasmid can pass through

46
Q

how do you calculate specific enzyme activity and what does it indicate?

A

enzyme activity/total amount of protein

indication of purity

47
Q

What is Vmax and how do you find out the Km

A

V-max - maximum possible rate
Km - half of Vmax on a V-[S] graph and do a line from half the Vmax to the line, and then go down to the x-axis, and thats the Km

48
Q

what is Kd, and what does a small Kd indicate?

A

Kd is the affinity for substrate and the lower the Kd the higher the substrate affinity

49
Q

outline the micheales-menten model

A

E + S ES E + P

K1/K-1 Kcat

50
Q

how does a competetive inhibitor affect the Km and Vmax?

A

Vmax stays the same, Km is larger

51
Q

how does a non-competetive inhibitor affect the Km and Vmax?

A

Vmax is smaller, Km stays the same

52
Q

how do uncompetetive inhibitors affect the Km and Vmax

A

both Vmax and Km are smaller

53
Q

what are some enzyme strategies to reduce the activation energy and why do they work

A

destabilise of substrate and stabilisation of the transition state
basically makes it more energetically favourable for the substrate to enter the transition state

54
Q

what amino acids form a catalytic triad

A

serine, aspartate, histidine

55
Q

what are is the main cause for Turner/Klinefelter syndrome

A

non-disjunction - chromosomes fail to seperate for gamete formation

56
Q

what is philadelphia chromosome

A

translocation of material between chromosome 9 and chromosome 22

57
Q

what is cystic fibrosis

A

when chloride ions don’t move outside the cell, causing mucus to build on top of it

58
Q

what causes sickle cell disease

A

A is changed to T at position 17 for the beta-chain of haemoglobin.
changes glutamic acid to valine

59
Q

key features of B-DNA

A

right-handed
10 base pairs per turn
3.4nm per turn
2nm in diameter

60
Q

features of A-DNA

A

right handed
formed when DNA is dehydrated
wider, tilted, offset from its axis

61
Q

features of Z-DNA

A

left handed

formed by high G-C concentration

62
Q

at what nanometre does DNA absorb maximally

A

260nm

63
Q

difference between sucrose density centrifugation and cesium chloride density gradient centrifugation

A

sucrose density - not an equilibrium method - everything eventually sinks
cesium chloride - is an equillibrium method - material floats in its corresponding position of density

64
Q

what makes the primer and what is it made from

A

primase

made of RNA

65
Q

what are the short fragments of DNA from the lagging strand called and what joins them together

A

okazaki fragments

DNA ligase

66
Q

what does the missing OH mean for dideoxynucleotide triphosphate mean in terms of PCR

A

can be added to the DNA chain but causes chain termination because a nucleotide (e.g. dATP) cannot bind to it

67
Q

what dye is used to visualise DNA strands in agarose gel

A

ethidium

68
Q

what is added to polyacrylamide and why, what is used to visualise the DNA fragments

A

8M of urea to seperate single stranded DNA

autoradiography/addition of a fluorescent group via covalent bonding

69
Q

what is the difference between the sanger and next generation methods in sequencing

A

in the next generation sequencing method an image is taken after addition of each nucleotide
reversible terminator cleaves off the fluorescent dye allowing addition of another dNTP - continuing PCR

70
Q

what is the difference between DNA and RNA

A

RNA contains ribose sugar

contains an extra OH group at the 2’ carbon

71
Q

what are promoters and where pribnow boxes located

A

sequences that determine the start for transcription

prokaryotes

72
Q

how fast does transcription occur

A

50 bases per second

73
Q

how many bases does RNA polymerase bind to

A

30 bases

74
Q

how is RNA modified to form tRNA

A

some bases and sugars are modified

CCA is added at the 3’ end

75
Q

difference between RNA I/II/III in eukaryotes

A

1 - involved in rRNA
2 - involved in mRNA
3 - involved in tRNA and 5S rRNA

76
Q

why is a poly-A tail added to the 3’ end of pre-mRNA

A

increases stability and specifies it for export into the cytoplasm

77
Q

what is the ‘cap’ added to pre-mRNA

A

a 5’-5’ triphosphate link to 7-methyl-G

78
Q

function of fibronectin mRNA and what synthesises it

A

is an mRNA that include EIIB and EIIA

produced by fibroblasts

79
Q

what does abnormal processing of beta-globin in RNA transcript cause

A

anemia due to defect in haemoglobin synthesis

80
Q

what is the difference between constitutive and regulative expression

A

constitutive - genes expressed all the time

regulative - genes expressed under certain conditions

81
Q

difference between inducible and repressible gene expression

A

inducible - molecule binds to repressor protein to remove it from the operator region to activate transcription (lactose)
repressible - bind to repressor protein so that it binds to the operator region (tryptophan) aka a corepressor

82
Q

difference between promoter and promoter-proximal regions

A

promoter - common in most genes (TATA box)

promoter-proximal - specific for particular gene

83
Q

difference between basal and regulatory transcription factors

A

basal - bind to promoter regions

regulatory - bind to proximal-promoter regions

84
Q

function of streptomycin

A

freezes initiation complex and causes misreading in mRNA

85
Q

function of tetracycline

A

prevents binding of incoming amino-acyl tRNA

86
Q

function of erythromycin

A

binds to 50s sub-unit and prevents translocation

87
Q

function of puromycin and why can’t it be used as an antibiotic

A

mimics the terminus of amino-acyl tRNA so is added to onto the chain-causing premature termination
not selective to ribosomal ribosomes, will fuck up eukaryotic ribosomes

88
Q

why can there be no rotation around the planar peptide bond

A

resonance gives a partial double bond

89
Q

definition of protein domain

A

area of a protein that folds independently

90
Q

what enzymes acetylate and deacetylate lysine

A

acetylate - KAT’s

deacetylate - KDAC’s

91
Q

what is a zymogen

A

precursors of enzymes that are activated after a proteolytic cascade

92
Q

when is PKR activated and by what and what causes this and what is that thing a sign

A

activated when double stranded RNA is detected - a sign of infection
activated by dsRNA

93
Q

function of porphryin rings

A

prosthetic group in proteins involved in coordinating transition metals

94
Q

what is Fe2+ coordinated by in haemoglobin

A

histidine residues

95
Q

effect of CO2 on haemoglobin

A

CO2 dissolves in water to form carbonic acid
decreased pH leads to protonation of histidine in beta-haemoglobin
causes the chain to be more likely to enter T-state
Bohr effect

96
Q

structure of hemicellulose

A

beta 1-4 xylopyranose

97
Q

structure of pectin

A

mixture of branched polysaccharides

rich in alpha 1-4 galacturonic acid

98
Q

structure of agaraose

A

D-galactose linked with beta 1-4 galactose

has an ether bridge

99
Q

structure of chitin

A

polymer of N-acetylglucoseamine

100
Q

function of a GPI anchor

A

helps binding of proteins to lipids at the lumenal or surface membranes

101
Q

what diseases are caused by dis-functioning Ca2+/K+ channels

A

Ca2+ - malignant hyperthermia/Darier disease

K+ - long Q-T syndrome

102
Q

what are beta-barrel structures

A

form hydrophobic porins in the outer membrane of bacteria and mitochondria

103
Q

difference between endo and exonucleases

A

endo - break nucleic acids at the interior

exo - removes nucleotides from the ends

104
Q

what type of ligase is most used for preparing plastids

A

T4-DNA ligase

105
Q

what % of cells take up the DNA

A

0.01%

106
Q

function of tetracyclin and how does it distinguish

A

acts as a selectable marker to distinguish recombinant and self-ligated vectors.
recombinant if there is no tetracyclin resistance

107
Q

do bacteria glycosylate proteins

A

no

Biomed (9 decks)

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