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Medicinal & Biological Chemistry > Molecular Biology > Flashcards

Molecular Biology Flashcards

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1
Q

What is the central dogma?

A

DNA into RNA via transcription and RNA into Proteins via translation

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2
Q

Give 2 amino acids that are acidic

A

aspartic acid, glutamic acid

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3
Q

Give 3 amino acids that are basic

A

histidine, lysine and arginine

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4
Q

give 5 hydrophobic amino acids

A

valine, leucine, isoleucine, methionine and proline

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5
Q

give 3 nucleophilic amino acids

A

serine, threonine and cysteine

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6
Q

What are the two amino acids which contain an amide group

A

asparagine and glutamine

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7
Q

What are the three stages of transcription?

A

initiation, elongation and termination

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8
Q

how does transcription begin in prokaryotes

A

sigma factors associate with RNAP to then bind to a promoter to melt DNA to reveal deoxynucleotide sequence within a gene and NTP bounds to unwound DNA
RNAP catalyses new phosphodiester bonds

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9
Q

What is MFD?

A

transcription repair factor which translocates along DNA and bumps trapped RNAPs out of way

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10
Q

what are sigma factors?

A

they determine the promoters specificity of RNAP in prokaryotes
also regulate the activity of RNAP at different promoter

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10
Q

what are operons?

A

only found in bacteria, groups of genes involved in related cellular functions in which their transcription is controlled by a single promoter, has a termination signal at end of operon

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11
Q

how is transcription terminated in prokaryotes?

A

intrinsic termination like p-dependent termination. p uses energy from ATP binding to bind at the 5’ end of RNA transcript and catches up t RNAP to ump it off DNA

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12
Q

what are the three different types of RNAP in eukaryotes and what do they do?

A

RNAP I is involved in transcription of rRNAs
RNAP II is involved in nuclear transcription, RNAP III is involved in transcription of small RNAs/tRNAs

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13
Q

how does transcription start in eukaryotes?

A

transcription factors must bind to promoters to initiate transcription

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14
Q

how is DNA packaged?

A

packaged within chromatin.
heterochromatin is highly condensed and inaccessible but chromatin is less condensed transcriptionally active

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15
Q

What are the differences exons and introns

A

Exons are the coding regions of the DNA, which make up mRNA
Introns are non-coding regions between exons, theyre transcribed but then removed during splicing so they are not in mRNA

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16
Q

are eukaryotic promoters more complex than prokaryotic promoters?

A

in eukaryotes there may be dozens of TF-binding sites within different promoters which may be proximal or distal (to transcription sites)

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17
Q

how is translation regulated?

A

through promoter sequences, enhancers, repressors, transcription factors, and epigenetic modifications

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18
Q

what do transcription factors do?

A

transcription factors bind to DNA on the TF-binding site in promoter regions (pre-initiation complex), they recognise specific sequences like TATA and CAAT and more factors bind to recruit RNAP to start elongation

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19
Q

what do enhancers do?

A

they increase the likeliness of transcription by binding to transcription factors which then interact with promoter to enhance gene expression
they stabilise RNA polymerase

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20
Q

what are 4 ways of histone modifications which alter chromatin?

A

phosphorylation, acetylation, methylation, ubiquitination.
this effects the stability

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21
Q

explain what is acetylation and why it occurs to alter chromatin

A

acetylation facilitates transcription, done by histone acetylases which transfers acetyl groups.
associated with activation, deacetylation has the opposite effect,
Acetyl-CoA is the donor

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22
Q

explain what methylation is and why it is done to alter the chromatin

A

methylation leads to chromatin formation
done by histone methyltransferases (HMTs) S-adenosyl methionine as donor. tends to silence genes, demethylation has the opposite effect
HMT-Suv39h methylates multiple nucleosomes and so on

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23
Q

what is chromatin remodelling?

A

proteins that impose a fluid state on chromatin that maintains the DNA overall packaging
translocates along chromatin to loosen grip onto DNA
examples are SWI/SNF and RSC complexes

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24
describe the ribosome and tRNA
has 2 subunits, small and large RNA is built into ribosome which acts as recognition storage and catalytic activity contains tRNA which has an anti-codon, ACC region on 3' end which carries amino acid Amino acyl tRNA synthase charges the tRNA with amino acids
25
explain the initiation of translation
initiation factors (proteins) use GTP to drive reactions recruits tRNA associated with methionine and binds to mRNA to start reading codons small and large subunits come together to form initiation complex (EIF-2a) complexed by initiation factors
26
what do elongation factors do?
elongation factors assist in the selection of correct incoming charged tRNA at the A site (EF-1a) also involved in translocation of the mRNA peptidyl tRNA from A to P site (EF-2a) use energy from GTP to GDP
27
what do termination factors do?
termination factors stop the whole process. the entry of a stop codon at the A site promotes binding of a release factor (eRF) to promote cleavage of peptide-tRNA ester bond
28
how can protein synthesis be used as a drug target?
in antibiotics like streptomycin, it binds to the small ribosomal unit and blocks interaction with tRNA and mRNA causing misreading of mRNA and misfolding of proteins
29
what are the secondary structures of proteins?
proteins can fold into alpha-helices or Beta-pleated sheets
30
what does hierarchal folding mean?
structural complexity increase gradually
31
what are chaperons?
proteins that assist in protein folding by stabilizing folding intermediates.
32
how are proteins transported to he cell membrane?
proteins destined for the cell membrane or to be exported out of it are synthesized on membrane-bound ribosomes on ER. they are tagged at the N end by a signal recognition particle (SRP) which halts translation and indicates where the protein is destined for. ribosome then transferred to translocon and SRP is released, protein is then allowed through into ER lumen, then modified and put into secretory vesicles
33
how are proteins imported into mitochondrion?
most mitochondrial protein synthesized by ribosomes in cytosol. N terminal sequences mark proteins for mitochondria, is a positively charged alpha helix that can be recognised by mitochondrial receptor unfolded and transported through membrane by help of chaperons
34
how are proteins transported into the nucleus?
nucleus imports proteins synthesized in the cytosol, targeted for transport by nuclear localisation signals (NLS) which include clusters of basic amino acid sequences. interact with importins which take them through nuclear pores. requires GTP hydrolysis
35
What are the 2 types of glycosylation
N-linked and O-Linked
36
what is N-linked glycosylation
attachment of oligosaccharide to protein through amide nitrogen of asparagine it is cotranslational as it occurs as the protein is synthesized so folding can be effected
37
What is O-linked glycosylation?
involves oligosaccharides attached to proteins through hydroxyl groups of serine or threonine occurs after folded protein has reached the Golgi so is post-translational
38
What is I cell disease
patients with I-cell disease lack GlcNAc-P glycotransferase, they cannot transfer GluNAC-P to the oligosaccharides to protein destined for lysosomes.
39
what is a proteasome?
1 type of protein turnover proteolytic system that removes trash proteins to ensure good quality proteins being used only. is a cylindrical structure containing 28 polypeptides and capped with 19S cap which helps recognise and unfold polypeptides has an ATP dependent core for degradation
40
what is ubiquitin?
a 76-amino acid, highly conserved protein which marks proteins to be degraded. polyubiquinated proteins are easily recognised by proteasome
41
what is the N-end rule?
states that the N-terminal amino acid of a protein determines its half life
42
what molecules carry out splicing? how do they work?
small nuclear ribonuclear proteins (snRNPs / snurps) cleavage at 5' donor site and joining the upstream and down streaming exons all together.
43
what is a lariat intermediate?
5' end of intron loops back ad forms covalent bond with broken 3' OH group to ligate 2 exons together
44
what is RNA capping?
stabilisation of mRNA as soon as mRNA leaves ribosome its subject to enzyme degradation to stop this, the N-terminal (5') end with 3 phosphate groups has 1 removed and guanine triphosphate added forming a 5'-5' triphosphate bond with G residue for stabilisation
45
what is polyadenylation? why does it happen?
polyadenylation of mRNAs gives stability to the mRNA the polyadenylate polymerase complex binds to polyadenylation sequence and cleaves the mRNA of about 20 nucleotides. extends the 3' end by adding a polyA tail
46
what does RNA turnover determine? How does RNA turnover happen?
determines how much RNA is available for translation and so how much protein is being made rates vary in cell types degrades by exonucleases from 5' to 3' cleaving when the polyA tail gets too short cap removal triggered
47
what is epigenetics?
how are genome is regulated without changing the genetic code
48
What is CpG methylation
methylation to chromatin to regulate gene expression and stabilty methylation carried out by DNA methyltransferase 1 (DNMT1) which uses S-adenosyl as Me donor
49
what does anabolic pathways mean?
build up substances from materials using energy in the process
50
what does catabolic pathways mean?
break down substances releasing energy in the process
51
What is glycolysis? give equation
type of carbon metabolism its anaerobic respiration which does not involve oxygen glucose into 2lactate +2ATP + 2H2O
52
What do kinase enzymes do?
kinase enzymes transfers Pi from ATP to another molecule this costs energy (uses ATP to do this)
53
what do isomerase enzymes do?
converts molecules into different isomers of each other, typically reversible
54
what does lyase enzymes do?
reversibly breaks a chemical bond by forming a new bond often used to make glucose from other molecules (gluconeogenesis)
55
what does NAD do?
nicotinamide adenine dinucleotide (NAD+) reductant currency of the cell that can transfer a hydride must be regenerated with another reaction
56
what are the overall products of glycolysis ? explain answer
glycolysis uses 1 molecule of glucose, 2 molecules of ATP and 2 molecules of NAD+ to make 2 molecules of pyruvate, 4 molecules of ATP, and 2 molecules of NADH
57
draw the structure of pyruvate
2keto-propanoic acid
58
what is lactate?
pyruvate but with the ketone as an alcohol
59
what is biosynthesis?
generation of complex molecules from simpler ones typically need ATP
60
what are the 6 steps in the cell cycle? explain them
Gap0- resting phase, cell has stopped dividing but can return to cycle if quiescent Gap1- the cell increases in size, synthesis proteins for DNA made S- cell copies its DNA, also includes histone synthesis, nucleosome and chromosome packing Gap2- cell prepares to divide, rapid cell growth and protein synthesis, DNA repair Mphase- DNA copies separated (mitosis) Cytokinesis- cell splits into 2 daughter cells
61
What does DNA helicase do
splits DNA strands apart by breaking hydrogen bonds between bases uses ATP
62
What does DNA polymerase do
DNA polymerase binds 2 strands of DNA together by forming phosphodiester back bonds also proof-reads bases as it translocates along strand
63
what does DNA gyrase do?
is a heterotetramer, 2 GyrA and 2 GyrB helps the DNA coil into double helix
64
how does mitosis happen?
PMAT order involves mitotic spindle of cytoskeleton composed of tubulin fibres which pulls condensed DNA
65
explain cytokinesis
spitting of the daughter cells, can be symmetric or asymmetric contractile ring composed of actin and myosin splits cell in two
66
what are cyclins?
they regulate and help control cell cycle cyclins form complexes with specific kinases and control their activity in adding phosphates to other proteins
67
What happens when DNA is damaged?
DNA damage activates the transcription factor p53 which activates the gene coding for g21 p21 is a cyclin dependent kinase inhibitor to stop phosphorylation and progression too high p53 levels will cause cell cycle to stop and apoptosis to occur
68
what does the p53 pathway have to do with cancer
is the p53 pathway malfunctions, cancer arises as the DNA is not correct
69
describe the lac operon and its repressing signals
lac operon contains genes needed for lactose metabolism, when there lactose, its not needed so is turned off. LacI is a repressor, it binds to DNA to keep this turned off when LacI binds to lactose, it conformationally changed and releases DNA to activate operon
70
Describe a GPCR
single polypeptide with 7 transmembrane domains extracellular N-terminus an intracellular C-terminus g protein alpha subunit binds GDP and froms compex with Beta and Gamma subunits, whole complex binds to nearby GPCR
71
what happens when an agonist binds to GPCR
undergoes conformational change activating the G-protein which replaces the GDP with GTP which causes subunits to split into two parts-GTP bound alpha subunit and Beta-Gamma dimer these transmit the signal when GTP hydrolysed back to GDP, all reassociate back together
72
what is apoptosis?
regulated cell death where all the contents of the cells are fully engulfed and digested by macrophages, triggered by death signals, loss of growth factors, DNA damage or S-Phase issues
73
what are caspases?
cascade pathway of proteases that catalyse the breakdown of proteins by activating each other
74
explain the death receptor pathway
death ligand binds to death receptor which stimulates complexion of DISC which activates caspase cascade
75
What is BRCA 1 and 2
genes that help repair DNA damage need to keep highly conserved as if mutated can be cancerous
76
explain how GPCRs can be cancerous
as GDP is exchanged for GTP to stimulate cell growth and division, hydrolysis needed to turn off cell growth and division (GTP to GDP). if mutations happen on active site means it ant hydrolyse GTP so remains on/active
77
what is the Warburg effect? what drug can help go against this?
when cancer cells consumer large amounts of glucose and convert to lactate even when oxygen present to form lots of ATP, for more growth and division Ivosidenib
78
what is Rb?
Rb is a tumour suppressor gene that inhibits the cell cycle and with E2F will be inactive. CDK4,6/D activate the Rb and E2F by phosphorylation, promoting cell cycle
79
how does the papilloma virus cause cancer?
E7 (the virus) dissociates Rb-E2F and sends Rb for degradation by proteosome so cell cycle will not be supressed. uncontrolled cell division E6 (the virus) targets p53 and marks for degradation
80
what is imatinib
when Bcr gene fuses with Abl Bcr-Abl formed which is highly active and dysregulated causing leukaemia Imatinib binds to ATP binding site of Abl kinase and inhibits ATP binding so Abl-Bcr is deactivated

Medicinal & Biological Chemistry (2 decks)

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