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1014 Biological Chemistry > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

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1
Q

how is the ribose sugar different from the deoxyriboses sugar?

A

deoxyribose sugar does NOT have OH on 2’ carbon

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2
Q

what are the key structural features of DNA

B-DNA

A 
double helix thats righthanded
10 bp per turn
2 complementary antiparallel strands 
complementary base pairing
major and minor grooves
(stable)
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3
Q

what are the key structural features of DNA

A-DNA and Z-DNA

A

11bp per turn
forms when DNA is dehydrated

12bp per turn
Left handed helix

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4
Q

what is the directionality of DNA molecule

A

runs in 5’ to 3’ direction

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5
Q

what bond maks up the sugarphosphate backbone

A

phosphodiester bond makes up the backbone

> dna is negatively charged due to the prescence of phosphate groups

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6
Q

how are adjacent nucelotides linked together?

A

they are linked together by phosphodiester bonds between the 5’ and 3’ carbons

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7
Q

How can you measure denaturation of a DNA moelcule? When can DNA be resisitant to denaturation ?
(its melting point will increase as a result)

A

when DNA is unwound/denatured, it can absorb more U.V light (260nm) in its single stranded form.
>If DNA has large amounts of G—C bonds it can be resistant as it takes more energy to break the bonds
>also is there are cations+ they can reduce the ELECTROSTATIC repulsion between phosphate groups

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8
Q

what are some roles of RNA

A 
RNAs are highlt variable and their strucutural flexiblity means they have many roles
•enzymatic/catalyst
•carrier of information
•transportation
•regulation of gene expression microRNA
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9
Q

DEFINITION
genome and gene

chromosome and chromatin

A

complete set of genes in an organism/cell/organelle
sections of DNA that code for a polypeptide/RNA

long DNA molecule asscoiated with histones
DNA-protein complex in eukaryotic cells which condenses into chromosomes

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10
Q

features of bacterial chromosomes/genomes

A

(multiple copies of) single, circular chromosome made of double-stranded DNA.
they are negatively supercoiled by and achored to a protein to form nucleoid
Plasmids may also be present and NO introns

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11
Q

properties of plasmids

A

smaller than the circular chromosome they carry non-essential genes and

they can pass from cell to cell via pilli in process conjugation

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12
Q

features of eukaryotic chromosomes/genomes

A

DNA packaged into long and linear chromosomes only visible in mitosis/meiosis where
DNA is supercoiled and associated with histones.
genes are split into introns and exons

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13
Q

when are scaffold proteins useful?
(condensind and topoisomerases)

POOP

A

A visible (mitotic/meiotic) chromosome is made from loops of the nucleosomes attached to a scaffold made of non-histone protein.

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14
Q

how do epigenetics and histone proteins relate?

A

Covalent modification of histone proteins can be used as a mechanism for regulating genes.
>acetylation of Lysine residues removes the postive charge and WEAKENS DNA-histone interaction so its morelikely the gene will be transcribed– switched on

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15
Q

what are the 3 main features of genetic code?

A

degenerate
non overlapping
universal - some variation in mitch, protist and mycoplasma e.g UGA = tryptophan instead

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16
Q

what are the key codons in translation?

A

Not all of an mRNA is translated into protein.
the initiation codon: translation starts with AUG
the termination codons: UGA, UAG and UAA
➡ AUG encodes methionine (so all newly made proteins begin with methionine)

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17
Q

what is meant by a reading frame?

A

An mRNA has three possible reading frames, only one of which is “open” and used.
spams from the intiation codon to the stop codon

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18
Q

features of tRNA

A

short with a “clover leaf” secondary structure
have an anticodon, complementary to codon,
an amino acid binding site at their 3′ end (unpaired CCA)
its tertiary structure is inverse L shapes

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19
Q

name given for aminoacid + tRNA

A

aminoacyl tRNA

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20
Q

are the base pairing rules the same for tRNA

A

NO! Some tRNAs can recognise more than one codon due to “base wobble” – reduced base-paring specificity aR the 3rd position of the codon

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21
Q

mitochondrial genome facts

A

may be spread over several circular molecules instead of a single linear one
genome also in chloroplast and nucleus

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22
Q

DNA REPLICATION -

comparison between pro and euk

A

✓ semiconservative, bi-directional
✓ semidiscontinuous (leading and lagging)
✕ only one origin if replication in prokaryotes, multiple in eukaryotes
✕ because of this, eukaryotic DNA polymerases are slower, but overall, DNA replication is faster as there are more working at once

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23
Q

how is DNA stable

POOP

A

base stacking and hydrogen bonds

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24
Q

DNA REPLICATION

where would the sequence of bases be for the origin of repliaciton in bactera?

A

bacterial replication begins at a SINGLE/ONE AT-rich origin
>easier to unwind as fewer hydrogen bonds

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25
``` DNA REPLICATION what enzyme synthesises DNA, and what are their requirements to synthesise? RNA polymerase Reverse transcriptase DNA ligase DNA polymerase RNA primase ```
DNA polymerases. They require deoxynucleoside triphosphates (dAMP, dCMP. dGMP, dTMP), a single-stranded template, and a primer with a free 3′-OH to attach nucleotides to
26
DNA REPLICATION | decribe the exonuclease activtiy of DNA polymerase
a 3′→5′ exonuclease activity (allowing them to proofread). ONLY DNA polymerase I from E. coli has 5′→3′ exonuclease activity allowing it to “overtype” existing DNA or RNA (nick translation).
27
DNA REPLICATION | step by step the process
1. helicase, gyrase counteracts supercoiling, protesin binds to single strands 2. primase synthesizes the RNA primers 3. Synthesis of DNA by DNA polymerase III, some okazi fragments made 4. removal of RNA primers and Nick translation by DNA polymerase 1 5. DNA ligase synthesises the missing phosphodiester bonds/ covelently links fragments(gap fill)
28
DNA REPLICATION | why does DNA polymerase III makes most of the DNA
it has high speed, effciency and processivity (can stay attacthed to chain for long time before it detaches)
29
``` DNA REPLICATION what does the lagging strand consist of? mke wizowski fragments okazi fragments kozac sequences suberin sticky end fragments ```
a series of Okazi fragments
30
DNA TRANSCRIPTION | Step by step process
1. initiation - dna partially unwinds, promoter-RNA 2. elongation- RNA polymerase moves along strand, DNA unwinds 15bp at a time 3. termination - polymerase detachtes, mRNA molecule released
31
what is meant by coding and noncoding strand
coding - RNA sequence is the same expect T is U | non coding - RNA sequence is complementary to DNA
32
DNA TRANSCRIPTION - prokaroyes Explain the significance of the the sigma subunit in RNA polymerases (hexamer vs pentamer)
In E. coli the σ RNA polymerase is needed for promoter recognition/initiation of transcription ~ holoenzyme The σ subunit of RNA polymerase dissociated after initiation, leaving the core enzyme to carry out elongation.
33
DNA TRANSCRIPTION | comparison between pro and eukaryotes
✓ use RNA polymerases but it's 1 vs 3 to make the different RNA molecules ✕ eukaryotic produce pre-mRNA that is spliced ✕ seperate to translation in euk as confined to nucleus but in pro its in cytoplasm ✕ very different promoter sequnces
34
DNA TRANSCRIPTION - euk | Decribe the 3 processes that occur in 1° mRNA to produce mRNA
1. capping - methylated G to 5' end 2. cleavage and polyadenylation - 3' end cleaved and poly AAAAA tail added to stabilise mRNA 3. SPLICING
35
where are promoters found ?
upstream the transcription start site
36
What is a nucleosome? 150bp of DNA wrapped around a 'core particle' 46bp of DNA wrapped around a 'core particle' 146bp of DNA wrapped around a 'core particle' 50bp of DNA wrapped around a 'core particle'
nucleosome is 146bp of DNA wrapped around a 'core particle' consisting of 2xH2A, 2xH2B, 2xH3 and 2xH4
37
``` What elongation factors are required in translation in prokaryotes? A EF-1α and EFG B EF-Tu and EF2 C EF-1α and EF2 D EF-Tu and EFG ```
OPTION D - just the LETTERS! | Elongation factors for translation are EF-Tu and EFG in prokaryotes, and EF-1α and EF2 in eukaryotes
38
``` How many types of DNA polymerase does E.coli have? A 2 B 3 C 4 D 5 E 6 ```
5! but only 1 and 3 do the DNA synthesis, the others re invokved in DNA damage repair
39
which describes a nucleoside? when is a nucleotide formed? A A base linked to the 1' C of the pentose sugar B A base linked to the 5' C of the pentose sugar C A phosphate group linked to the 1' C of the pentose sugar D A phosphate group linked to the 5' C of the pentose sugar
OPTION A > A nucleoside is formed from a nucleotide base linked to the 1' C of the pentose sugar. The nucleotide is then formed when one or more phosphate group is added
40
``` Which of the following Histone proteins is not present in the core particle? A H1 B H2A C H2B D H3 E H4 ```
H1 binds to the DNA on the outside of the core particle, thus sealing the DNA. A nucleosome is DNA wrapped around THE core particle containing two molecules of each of histone H2A, H2B,H3 and H4. The DNA between neighboring nucleosomes (linker DNA) binds histone H1. > The packing ratio of nucleosomes is about 7.
41
WHAT IS THE PACKING RATIO?
lenght of DNA/ length of structure of DNA (so if a chromosome of 2um has 14mm of DNA the packing ratio is 7000 (14000/2)
42
Which of the following enzymes are not involved in the process of joining Okazaki Fragments on the lagging strand together? A DNA Polymerase 1 B DNA Gyrase C DNA Ligase
OPTION B DNA Gyrase stops supercoiling DNA Polymerase 1 is used to remove the primers on the lagging strand (and can do nick translation) DNA Ligase is used to fill the remaining gap between the fragments by foming a phosphodiester bond
43
``` In DNA replication in E.coli, which DNA polymerase is responsible for synthesising new DNA in conjunction with a primer? DNA polyermase number... A 1 B 2 C 3 D 4 E 5 ```
NMUBER 3! does the bulk of DNA synthesis | DNA Polymerase 1 is used for Nick translation after the RNA Primer is degraded by 5'-3' Exonuclease
44
In what order are the enzymes in DNA replication used? DNA gyrase - helicase - DNA polymerase III - primase - DNA ligase Helicase - primase - DNA polymerase III - DNA polymerase I - DNA gyrase - DNA ligase Helicase - DNA gyrase - primase - DNA polymerase III - DNA polymerase I - DNA ligase Helicase - primase - DNA gyrase - DNA polymerase I - DNA polymerase III - DNA ligase
OPTION C Helicase unwinds the DNA DNA gyrase removes the positive supercoils Primase synthesises RNA primers NEEDED for polymerases DNA polymerase III synthesises BULK of new DNA DNA polymerase I removes the RNA primers //may do nick translation DNA ligase joins the Okazaki fragments with new phospohodiester bond
45
``` What factors increase the melting temperature (Tm) of DNA (the temperature needed to denature 50% of DNA molecules)? Anions and GC pairs Cations and AT pairs Cations and GC pairs Anions and AT pairs ```
OPTION C Cations - reduce electostatic repulsion// increase attraction GC pairs - there are 3 H bonds between them which require more energy to disrupt therefore a higher temperature.
46
``` What codon do all tRNAs end with (at the 3' end)? UAG UGA CGU CCA CCU ```
CCA which is unpaired and a free OH so aa can join
47
What is the term for a section of DNA where the base pairs are shielded by the sugar phosphate backbone? major groove minor groove
this is the minor groove
48
how are the 5' and the 3' ends of nucleotides chemcally distinct from each other?
5' has phosphate attatched to one end | 3' has nuclotide attatched to it
49
what causes negative supercoils? | unwinding or overwinding
UNWINDING - DNA is negatively supercoiled as it makes it easier to unwind
50
DNA vs RNA in structure - similar and difference
uracil not thymine ribose not deoxy - extra OH on the 2nd carbon singlestranded > BOTH linked by phosphodiester bonds
51
how is the mitochondrial genome organised?
37genes in a circle! 22 - Trna 13 - Mrna 2 - RRna
52
what 2 amino acids make up the bulk of histones? why?
arginine and lysine - basic (+), good at binding to DNA
53
``` if a gene has 9 exons, how many introns? 6 7 8 9 10 ```
8 introns! | its an exon sandwich
54
5' TAGCC 3' waht is complentary strand?
GGCTA - yaaay runs in 3-5 direction as its antiparallel g g c t a
55
in bacterial cells, is the *origin of replication** rich in A-T or G-C base pairs?
RICH IN a-t | >fewer hydrogen bonds so easier to unwind
56
what is the relationship between DNA denaturation and UV light?
the more DNA is unwound, the increased UV absorbtion occurs
57
``` what are the enzymes that synthesise DNA rna polymerase dna polymerase dna gyrase dna ligase dna helicase ```
DNA POLYMERASES synthesise DNA
58
``` what is NOT needed for DNA polymerase to work? A template/region of ss.DNA B free nucleotides C primers with free 3' -OH group D primers with free 5'-OH group E dCMP, dGMP, dAMP, dTMP ```
OPTION D OH is on the 3' end as DNA is synthesised by adding nucleotides to the 3' end > the primers are made of RNA and made by RNA primase
59
what are the actions of DNA polymerase 1 and 3
3-5 they can both PROOFREAD remving incoorect nucelotides, increasing efficiency of DNA replication 5-3 DNA polymerase 1 can do NICKTRANSLATION as it has an exonuclease to overtype but it relocates the gap >> also removes the RNA primers
60
how long are the lagging stand?
the OKAZI FRAGMENTS are ~ 1000-2000bp in pro and 100-200 in euk
61
how are gaps between Okazi fragments sealed?
by DNA ligase! by making a nre phosphodiester bond!
62
why are okazi fragmetns made?
DNA polymerase only eorks from 5 - 3 so the primers on the lagging strand attach a bit far ahead >> 2 steps forward, one step back
63
what do RNA polyemrases need to do transcription
d.s template with PROMOTER/ribosomal binding and TERMINATOR regions free nucleotides but NO PRIMER
64
DNA TRANSCRIPTION - pro | in e.coli, RNA polymerases work by recognissing 'concencus' /average sequences. give examples of them
pribnow box -TATAAT | -35 hexamer - TTGACA
65
what is the composition of ribosomes?
rRNA and protein in a 2:1 ratio by mass
66
DNA TRANSLATION | what does the small and large ribosomal subunits facilitate
small - binds to mRNA | large - catalyses peptide bond reaction
67
``` how much energy is used for each amino acid during translation 1 atp 2 atp 3 atp 4 atp ```
3 ATP - bidning aminoacylTRNA, linking that to ribosome, translocation > 3 is a magic number
68
DNA TRANSLATION | comparison between pro and euk
✓ elongation and termiantion the same but with different **accessory proteins** ✓ ribosomes react the same to antibiotics ✕ 80S VS 70S ribosomes ✕ intiation/regcognition with the ribosomal binding site or methylated G cap
69
name some 'inducible genes' in prokaryotes
inducible - swictched on only when needed e.g. 3 genes needed to metabolise LACTOSE when there is low glucose THE LAC OPERON
70
PROKARY CONTROL OF GENE EXPRESSION | when lactose isnt present, the lac repressor protein binds to the operator. What happens to LRP when lactose is present?
lactose isomer -> allolactose this causes confomational change in LRP and transcription can happen >> allolactose can induce transcription
71
what does CAP (in the lac operon) stand for? what is its role and how is it activated?
CATABOLITE ACTIVATOR PROTEIN | activated by high cAMP levels when glucose level is low and **stimulates transcription**
72
which combination would result in transcription of LAC OPERON happening but at a slow rate? no lactose and glucose present lactose and glucose present lactose and no glucose present
lactose and glucose present why waste the resources when glucose is there! allolactose will form but CAP won't be activated as there are only low levels of cAMP

1014 Biological Chemistry (8 decks)

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