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BM210 > Block 1 > Flashcards

Block 1 Flashcards

1
Q

Where is DNA copied into RNA

A

Nucleus

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2
Q

Where is RNA processed and exported to

A

Cytosol

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3
Q

Where does translation take place

A

Cytosol

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4
Q

What is a nucleoside

A

A base conjugated to a sugar by a glycosidic linkage

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5
Q

Name the nucleosides

A

Deoxyadenodine, deoxygaunosine, deoxycytosine, thymide

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6
Q

What is a nucleotide

A

A nucleoside conjugated to one or more phosphoryl group

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7
Q

Name nucleotides in DNA

A

Deoxyadenylate (dATP), Deoxyguanylate (dGTP), Deoxyctidylate (dCTP), Thymidylate (dTTP)

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8
Q

Name nucleotides in RNA

A

Adenylate, Guanylate, Cytidylate, Uridylate

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9
Q

what does RNA have on 2’

A

hydroxyl group

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10
Q

what is the bond between bases

A

hydrogen bonds

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11
Q

what’s on the outside of DNA helix

A

sugar phosphates

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12
Q

what degree are bases at to helix axis

A

90°

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13
Q

what are bases at the core attracted to each other by

A

Van der Waals forces

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14
Q

what makes DNA stable

A

hydrogen bonds

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15
Q

what are introns

A

non-coding regions

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16
Q

what are exons

A

coding regions

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17
Q

when does DNA need to be replicated

A

during cell division

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18
Q

why does DNA replication need to be error free

A

to avoid mutation

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19
Q

what stage of the cell cycle does DNA replication take place

A

S-Phase

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20
Q

What are the phases of the cell cycle

A

S=DNA synthesis, G2=growth and preparation for mitosis, M=mitosis, G1=growth

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21
Q

DNA replication is semi-conservative, what enzyme is involved

A

DNA polymerase

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22
Q

What does DNA polymerase require

A

primer, with a free 3’-OH

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23
Q

what does DNA polymerase do

A

catalyses step-by-step addition of deoxyribonucleotide units to DNA

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24
Q

where does new DNA grow

A

3’ end

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25
Q

what direction is DNA synthesis

A

5’ to 3’

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26
Q

what drives DNA synthesis

A

strongly negative DG° from hydrolysis of PPi to 2 Pi

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27
Q

leading strand direction

A

5’ to 3’

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28
Q

how is the lagging strand copied

A

short sequences of DNA are synthesised then joined together by DNA ligase

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29
Q

Transcription goes from

A

DNA to RNA

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30
Q

Translation goes from

A

RNA to protein

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31
Q

are mRNA and DNA complementary

A

Yes

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32
Q

mRNA

A

template for synthesis of proteins, transcribed by RNA polymerase II

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33
Q

tRNA

A

carries activated amino acids to ribosome, synthesised by RNA polymerase III

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34
Q

rRNA

A

major component of ribosomes, synthesised by RNA polymerase I

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35
Q

3 stages of mRNA synthesis

A

initiation, elongation, termination

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36
Q

mRNA initiation

A

RNA polymerase II and transcription factors assemble at promoter sites; RNA synthesis then initiates

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37
Q

mRNA elongation

A

RNA polymerase moves along DNA template to synthesise mRNA which grows in a 5’ to 3’ direction, sequence of growing mRNA driven by base-pairing to DNA strand- faithful copy of DNA template produced

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38
Q

mRNA termination

A

RNA polymerase II ceases transcription at a defined site. The mRNA transcript is then stabilised by specific modifications

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39
Q

can transcriptions factors turn gene expression on or off

A

yes

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40
Q

are transcription factors specific

A

yes

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41
Q

what are transcription factors activated by

A

phosphorylation and subsequent movement into the nucleus

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42
Q

what is used as a template for protein synthesis

A

mRNA

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43
Q

where does translation occur

A

ribosomes

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44
Q

what codon does protein synthesis always start on

A

AUG

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45
Q

what shape do tRNA’s adopt

A

clover leaf with hydrogen bonds between bases

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46
Q

where do amino acids attach at tRNA

A

amino acid attachment site

47
Q

what is at the base of aminoacyl RNA

A

anti-codon which will base pair with the corresponding codon in the mRNA being translated

48
Q

first step of aminoacyl tRNA synthetases

A

amino activation step
amino acid+ ATP==>Aminoacyl-AMP + PPi

49
Q

second step of aminoacyl tRNA synthetases

A

transfer of aminoacyl-AMP to a specific tRNA
Aminoacyl-AMP+ tRNA==> Aminoacyl-tRNA + AMP

50
Q

third step of aminoacyl tRNA synthetases

A

driven by hydrolysis of pyrophosphate (PPi)
PPi+ water==> 2Pi

51
Q

what are ribosomes made up of

A

50S and 30S rRNA subunits

52
Q

ribosome P site

A

peptide grows here through a ‘tunnel’ in the structure

53
Q

ribosome A site

A

amino acyl-tRNA binds here, bringing in next amino acid

54
Q

ribosome E site

A

exit for empty tRNA

55
Q

what do introns begin and end with

A

GU and AG

56
Q

what is alternative splicing

A

different mRNA’s are generated from the same initial primary transcript

57
Q

how can RNA self-splice

A

they can fold into distinct structures, and can act as an enzyme to splice itself

58
Q

what is intercellular signalling

A

communications between cells. Permits a single cell to influence the behaviour of other cells in a specific way, synaptic transmission

59
Q

what is intracellular signalling

A

signalling within the cell. Responding to extracellular and intracellular stimuli

60
Q

what is a nucleosome

A

single DNA/histone octamer complex

61
Q

what is a chromatin

A

the overall DNA-histone complex

62
Q

what is an octamer

A

four histone subunits assembled

63
Q

chromatin can exist as

A

Euchromatin and heterochromatin

64
Q

what is euchromatin

A

loosely packed form of chromatin, enriched in genes, often under active transcription

65
Q

what is heterochromatin

A

tightly packed form chromatin, generally inactive and inaccessible to RNA polymerases

66
Q

what is the chromatin state regulated by

A

methylation and acetylation of the histones

67
Q

what does “semi-conservative” mean?

A

each new double helix has one newly generated strand and one “old” parent strand

68
Q

what two enzymes are involved in DNA replication and their roles?

A

-DNA polymerase - attaches to template DNA strand and catalyses addition of dNTP units to the strand
- Primase - makes random RNA, allows DNA to copy acts as a primer, free 3’ end, starts synthesis

69
Q

what is the specific reaction mechanism for the addition of new nucleotides?

A

the alpha-phosphate of the new dNTP nucleophilically attacks the 3’ hydroxyl of the already attached nucleotide.

70
Q

as DNA is synthesised in a ….. direction, how is the opposite direction strand generated?

A
  • 5’ to 3’ direction
  • Okazaki fragments (short sequences of DNA) synthesise and are joined by DNA ligase
71
Q

what are the three major RNA molecules, their roles and the enzymes that make them?

A
  • mRNA - template for synthesis of proteins, transcribed by RNA Polymerase II
  • tRNA - carries activated amino acids to ribosomes, synthesised by RNA Polymerase III
  • rRNA - major component of ribosomes, synthesised by RNA Polymerase I
72
Q

what five components are needed for RNA synthesis?

A

ATP, GTP, CTP, UTP

73
Q

what are the three steps of RNA synthesis?

A

Initiation - (RNA Pol. II and transcription factors assemble at promotor sites; RNA synthesis then initiates)
Elongation - (RNA Pol. II moves along DNA template to synthesise mRNA which grows in a 5’ to 3’ direction, sequence of growing mRNA driven by base pairing to DNA strand - ‘faithful’ copy of DNA strand produced)
Termination - (RNA Pol. II ceases transcription at a defined site, the mRNA is then stabilised by specific modifications.)

74
Q

which three base sequences can indicate a promoter region and which strands are they present on?

A

TATA box - -25, coding/sense strand
CAAT - -75, coding or template strand
GC box - coding or template strand

75
Q

…… (transcription factor) binds to the …… box via …… (protein), leading to the assembly of the transcription complex

A
  1. TFIID
  2. TATA
  3. TATA box binding protein
76
Q

which transcription factor opens the double helix and how does it allow DNA Pol II to begin transcription?

A

TFIIH - phosphorylates the carboxyl terminal domain

77
Q

how many base pairs does the complex of the proteins on the strand unwind?

A

~17bp

78
Q

what is an enhancer sequence?

A

sequence of DNA before promoter that allows binding of transcription factors

79
Q

what are repressors and activators?

A

repressor - prevents formation of RNA at start site, blocks transcription
activator - facilitates or enhances transcription and RNA polymerase assembly

80
Q

how are transcription factors activated?

A

phosphorylation and movement into the nucleus

81
Q

which three codons are STOP codons, and which one is part of the initiation signal?

A

-UAA, UAG, UGA
- AUG (start codon)

82
Q

…… means the amino acid is coded for by more than one codon

A

degenerate

83
Q

when an amino acid and a tRNA are linked, this makes an ……. This is catalysed by the enzyme …….

A
  1. aminoacyl tRNA
  2. aminoacyl tRNA synthetase
84
Q

what are the three steps of linking an amino acid and a tRNA?

A
  • amino acid activation (amino acid + ATP —> aminoacyl-AMP + PPi)
  • transfer of animoacyl-AMP to a specific tRNA (aminoacyl-AMP + tRNA —> aminoacyl-tRNA + AMP)
  • driven by hydrolysis of pyrophosphate (PPi) (PPi + water —> 2Pi)
85
Q

what feature of aminoacyl-tRNA synthesis allow for specificity to amino acids?

A

(synthetases) ability to proof read and hydrolyse amino acids that don’t fit its activation site

86
Q

what are four structural features of ribosomes?

A
  • one 50S and one 30S rRNA subunits
  • P site where peptide grows through a ‘tunnel’
  • A site where aminoacyl-tRNA binds which brings in next amino acid
  • E site is an exit site for empty tRNA
87
Q

what are the four components of the initiation complex involved in translation? What is the action of the complex?

A
  • Met tRNA (initiation tRNA containing methionine key), GTP, transcription factors, 30S ribosomal subunit to make a complex
  • complex ‘scans’ mRNA looking for an AUG (start) codon
88
Q

during protein synthesis, tRNA and mRNA molecules are moved through the ribosome by the action of ……..

A

elongation factor G

89
Q

how do pre-mRNA transcripts avoid being degraded?

A

capped, tailed and processed

90
Q

what two modifications are involved in capping?

A
  • methylation of bases
  • formation of a rare 5’ to 5’ triphosphate bridge with GTP
91
Q

which enzyme is responsible for the addition of the poly (A) tail?

A

poly (A) polymerase

92
Q

what three traits of introns allow for splicing?

A
  • all start with GU and end in AG
  • feature a pyrimidine-rich tract (Py)n
  • specific adenine (A) known as the branch site
93
Q

splicing proteins gather at the splice sites to form a …..

A

spliceosome

94
Q

what is the specific chemical mechanism behind intron splicing?

A

5’ splice site is attached by the 2’ hydroxyl group of the branch site (A).
3’ splice site is attached to newly formed 3’ hydroxyl of the upstream exon
the exons are joined and the introns are removed as a lariat

95
Q

what is alternative splicing?

A

process where different mRNAs are generated from the same initial (primary) transcript

96
Q

what is self-splicing?

A

can act as an enzyme as RNA can fold into distinct structures
don’t need a spliceosome to remove introns

97
Q

what is the mechanism behind RNA interference (RNAi)?

A

disrupts gene expression, suppresses transcription of genes that contained sequences present in the original double stranded RNA. ‘silence’ the expression of certain genes

98
Q

what is the mechanism behind genome editing/CRISPR?

A

gRNA (guide RNA) is synthesised that directs an endonuclease enzyme called Cas9 to a specific DNA target sequence, inserts or deletes nucleotides

99
Q

what is the difference between intercellular and intracellular signalling?

A

intercellular - communication between cells
intracellular - signalling within cells

100
Q

what are five categories of cell signalling?

A

autocrine - cell signals target itself
juxtacrine - cells signal through junction
paracrine - cell signals target cells nearby
exocrine - cell releases signal into duct
endocrine - cells signal into bloodstream

101
Q

what is the benefit of signal cascades?

A

one signalling molecule can lead to many cell responses

102
Q

what are four major receptors, their mechanisms and their response times?

A
  • Ligand-gated ion channel - causes a conformational change of proteins (opens channels), ions move in or out of cell due to electrical gradient, alters polarization of cell membrane, significant role in transmission. Milliseconds
  • G-protein coupled - ligand binds to receptor, triggers binding of G-protein and modulation of second messengers eg cAMP, lots of signal amplification. Seconds
  • Kinase-linked - phosphorylate protein substrates once activated, receptor class for many polypeptide growth factors eg. insulin, epidermal growth factors (EGF). Hours
  • Nuclear - intracellular, respond to hydrophobic ligands across the plasma membrane, function with other proteins to regulate gene expression. Hours/days
103
Q

what are signalosomes?

A

large supramolecular complex, unique combos of signal pathway components, allows cells to construct optimum cellular subdomain for signalling

104
Q

what are caveolae?

A

specialised membrane domains that form invaginations in the plasma membrane, organising centres for signalling molecules

105
Q

what is compartmentalisation?

A

separation of metabolic processes that together constitute a metabolic cycle

106
Q

what are epigenetics?

A

additional level of gene expression regulation, ‘above’ genetics

107
Q

what is a CpG island?

A

high density regions of CpG nucleotides, promoter region of genes, methylation alters gene expression (no expression if methylated)

108
Q

the ……. base in CpG can undergo …… by the enzyme ……

A
  1. cytosine
  2. methylation
  3. DNA methyltransferase (DNMT)
109
Q

what is the action of methyl binding proteins?

A

prevents binding of transcription factors

110
Q

what is maintenance and de novo methylation?

A

maintenance - ensure methylation patterns are preserved as cell divides
de novo - allows different methylation patterns during development.

111
Q

what is a histone?

A

a ‘spool’ that DNA is wrapped around

112
Q

a single DNA/histone complex is called a …… The overall structure is …….

A
  1. nucleosome
  2. chromatin
113
Q

what is the difference between euchromatin and heterochromatin?

A

euchromatin - loosely packed form of chromatin, enriched in genes, often under active transcription
heterochromatin - tightly packed form of chromatin, generally genetically inactive and inaccessible to RNA polymerases.

114
Q

chromatin state is regulated by …… and …… of histones

A
  1. methylation
  2. acetylation

BM210 (3 decks)

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