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MY MCD > Nage > Flashcards

Nage Flashcards

1
Q

How are the prime is used in a numbering of nucleic acid‘s?

A

1’ = attached to base

5’ attached to phosphate

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2
Q

Draw the structure of ribose and deoxyribose noting the differences

A 
Pentode sugar in both w O at top
1 is H
2 is H in deoxyribose
2 is OH in ribose
3 is OH
4 is H and C(OH,H,H)
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3
Q

What is the structural differences between thymine and uracil?

A

Both have carbonyl groups

Only thymine contains methyl group (absent in uracil, only H pres)

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4
Q

How can you identify a cytosine from other bases

A

Cytosine Is the only base to contain an amino group

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5
Q

How can you identify a pyrimidine base

A

This base does not contain any amino groups or carbonyl groups or methyl groups

Amino = cytosine
Carbonyl = thymine and uracil
Methyl = thymine
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6
Q

What is a nucleoside

A

Only base and sugar

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7
Q 
What is the name of the nucleoside for each of the following bases:
A
G
C
U
T
A 
(Deoxy)adenosine 
(Deoxy)guanosine
(Deoxy)cytidine
(Deoxy)uridine 
(Deoxy)thymidine
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8
Q

What is the 3/5’ end?

A 
Phosphate group (head) =5
Ribose =3
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9
Q

What links the chain of nucleotides

A

Phosphodiester links

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10
Q

What do you phosphodiester links link?

A

OH group of ribose

O- of phosphate

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11
Q

How did Watson and Crick discover double helix structure

A

Analysis of x-ray diffraction patterns

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12
Q

Which way do the negative charges of DNA orient

A

They point outwards therefore DNA is negative

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13
Q

How many hydrogen bonds between the bases

A

Three between G and C (more stable)

2 between A and T

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14
Q

How do you melt and re-anneal DNA

A

Melt
High temperature or low salt environment

Re-anneal
Low temperature or high salt environment

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15
Q

What is the other word for melting and re-annealing DNA

A

Denaturing

Hybridising

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16
Q

What is different between the Genome of E.coli and human

A

E. coli
4.6 x 10^6 bp
Single circular double stranded molecule

Human
3 x 10^9 bp
Divided to chromosomes each containing linear DNA

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17
Q

How many chromosomes in diploid human cells

A

22 normal pairs and one pair of sex chromosomes

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18
Q

What is special about abnormal karyotypes

A

Can be extra or reduced number of individual or pairs of chromosomes e.g. trisomy 21 or translocations

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19
Q

How many base pairs of DNA is contained in a nucleosome

A

~200bp DNA (LINKER PLUS CORE DNA)

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20
Q

How do nucleosomes shorten DNA

A

7 fold condensation of DNA

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21
Q

DNA chain packing leads to what after 7-fold condensation of DNA?

A

Further 40 fold condensation

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22
Q

What are the levels of DNA organisation

A 
Short region of DNA double helix (2 nm)
Beads on a string form of chromatin
30 nm chromatin fibre of packed nucleosomes
Chromatin fibre folded into loops
Entire chromosome
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23
Q

What is DNA Primase

A

Enzyme involved in DNA replication
Catalyses the synthesis of a short RNA segment called a primer complimentary to a ssDNA (single-stranded DNA)

= type of RNA polymerase

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24
Q

How is the DNA double helix opened?

A

DNA Helicase uses energy from ATP

💔 hydrogen bonds and unwind DNA helix

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25
Q

What do DNA polymerases do?

A

Add nucleotides to 3’ end of growing chain

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26
Q

What things are required for Protein synthesis

A

Template strand
Oligonucleotide primer
Supply of dNTPs

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27
Q

What is the template strand also known as

A

Antisense

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28
Q

What is the sense strand

A

New strand being synthesised

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29
Q

What is an oligonucleotide primer

A

Short chain of nucleotides already joined, onto which new nucleotides can be added

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30
Q

What are deoxynucleotide triphosphates (dNTPs)?

A

Nucleoside triphosphates containing deoxyribose
= building blocks of DNA
Lose 2x phosphate groups when incorporated into DNA during replication

31
Q

New nuclear tides are added to which end of the chain

A

3’ end

On three hydroxyl groups causing synthesis in the 5 to 3 direction

32
Q

During the enzyme reaction when nucleotides are joined together to form the chain how is energy released ?

A

Energy released by triphosphate hydrolysis

33
Q

What are chain terminators ?

A

Nucleoside analogs

Replace nucleosides yet have no hydroxyl group on the 3’, preventing addition of further bases

34
Q

List examples of chain terminators

A

The following are nucleoside analogs:
Dideoxycytidine (HIV)
Azidothymidine (HIV)
Acyclovir (Herpes)

35
Q

Where does your replication start

A

Origins of replication

This site is called a replication fork

36
Q

Describe the asymmetry in DNA replication

A

Due to antiparallel strand orientation
Leading strand synthesised continuously 5 to 3
Lagging strand synthesised in short Okazaki fragments also 5 to3

37
Q

How is DNA primase involved in the start of replication

A

DNA primase synthesises a short RNA fragment which is transient and allows replication to start at a replication origin
DNA polymerase can then add bases

38
Q

How are Okazaki fragments formed

List steps

A

New RNA primer is required per fragment made by Primase
DNA Polymerase adds nucleotides to RNA primer to finish DNA fragment
Old RNA primer is erased and replaced by DNA
DNA ligase joins new Okazaki fragment to growing chain

39
Q

What removes the old RNA primer used when forming Okazaki fragments and causes it to be erased and replaced by DNA?

A

Ribonuclease removes RNA primer using 5’ to 3’ exonuclease activity
Repair DNA polymerase replaces RNA with DNA
DNA ligase joins fragments using ATP to make continuous strand

40
Q

What is the sliding clamp

A

A ring around DNA to prevent polymerase falling off

41
Q

What do single strand DNA binding proteins

A

Prevent any localised secondary structures forming due to hydrogen bonding

42
Q

What is the proofreading mechanism used during DNA replication to prevent dangerous mutations and any errors

A

DNA polymerase checks previous nucleotide when adding a new nucleotide for correct base pairing

If incorrect DNA polymerase’s exonuclease activity will remove it, new correct replacement is added

43
Q

How is replication in E. coli different to humans

A

E. coli have bidirectional replication from OriC
Creates two replication folks that move simultaneously in opposite directions

Chromosomes have many replication origins each evenly spaced, giving bidirectional replication along the Strand until forks meet

44
Q

Describe the M phase

A

Mitosis
One hour of cell division
Chromatids separate to daughter cells

45
Q

Describe the G1 phase

A

Gap phase 1
10 hours without synthesis of DNA
RNA and proteins synthesised
DNA present as single linear double helix

46
Q

Describe the S-phase

A

Synthesis

Nine hours and DNA synthesised

47
Q

Describe the G2 phase

A

Gap phase 2
Four hours and between synthesis and mitosis
Makes proteins and grows
Each chromatid has two identical sister chromatids

48
Q

At which stage of the cell cycle does the nucleus disintegrate
At which stage of the cell cycle does the nucleus reform

A

Metaphase

Reforms at interphase

49
Q

How many base pairs in the human genome

A

6x10^9

50
Q

What are housekeeping genes

A

Genes that are present in all cells, they are important for normal cell function & viability

51
Q

What is the initial product of gene expression

A

ssRNA

52
Q

List the three steps involved in DNA transcription

A
  1. DNA strands unwind
  2. Ribonucleotides base pair w bases on antisense (template) strand
  3. Bases joined by phosphodiester bonds, with the RNA chain growing one base @ time in the 5 to 3 direction
53
Q

What is the template or antisense strand

A

The Strand upon which the RNA sequence is created

54
Q

What are transcription factors

A

Special gene regulatory proteins

55
Q

List the types of RNA involved in each of the following polymerase roles:
RNA Polymerase I
RNA Polymerase II
RNA Polymerase III

A

rRNA
Used to produce the large ribosomal subunit

mRNA
Used to produce the protein-encoding RNAs & the microRNA

tRNA / 5S RNA
Used to produce each of the tRNAs & the small ribosomal RNA subunit

56
Q

What does the DNA sequence TATA specify

A

The initiation point for transcription after which RNA polymerase II will begin transcription

57
Q

The initiation step is required to build a transcription complex before RNA synthesis occurs, where does the complex assemble

A

Complex assembles at gene promoter, level of transcription is regulated by activity of transcription factors

58
Q

What are the steps involved in formation of the basal transcription complex

A
  1. TF IID (TATA binding protein) binds to minor groove,
    Beginning to unwind DNA to allow more contact with DNA bases; asymmetric unwinding ensures unidirectional transcription
  2. TF IIA & TF IIB bind next
  3. RNA Pol II binds to TF IIB w the TF IIF attached
  4. TF II E,H,J attach to RNA Pol II
    H promotes further unwinding
59
Q

How can transcription factors modulate transcription

A

TFs bend DNA on binding, interacting with each other and the basal transcription complex to modulate transcription

60
Q

How can transcription factors remodel chromatin

A

Recruit proteins with enzymatic activities to modify histones

61
Q

What determines transcription factor expression

A

Cell lineage

Altered by external signals e.g. hormones, growth factors, stress

62
Q

What do mutated or abnormal transcription factors lead to

A

Implications in cancer and disease

63
Q

How many RNA Polymerases does E. Coli have

A

Only have one type of RNA polymerase with all subunits
2 a , 2 B

Promoter = TATAAA

64
Q

What is involved in splicing

A

Introns are removed

Modified nucleotide cap at 5’ end added and Poly-A tail at 3’ end

65
Q

How can you distinguish introns from exons

A

Introns begin w GU & end w AG

Exons also end AG

Exon|Intron = AGGU

66
Q

Where is the splice donor site

A

End 2 bases of the exon and GU of intron

67
Q

What is the splice acceptor site

A

15 pyrimidine bases
Any base
Then CAG

(Pyr15NCAG)

68
Q

What are snRNPs

A

Small ribonuclear proteins
Prod. from snRNA
Numbered and form spliceosome

Eg. U1, U5, U2, U4, U6

69
Q

Explain the steps involved in the formation of the spliceosome

A
  1. U1 binds to splice donor site
  2. U5 binds to splice acceptor site
  3. U2,4,6 bind to middle of intron

Splicing complex forms from U1,2,4,5,6 to cleave splice donor sequence

70
Q

What steps will happen after the formation of the spliceosome?

A
  1. Interval btwn Exon|Intron (AGGU) is cleaved
  2. An “A” residue in intron used as branchpoint to which UG bonds
  3. Branch results in phosphodiester bond btwn 5’ phosphate on G and 2’ OH of A (UGA)
  4. Phosphodiester bond btwn G (on Pyr15NCAG) and Exon cleaved

😁Lariat structure formed from Intron !
Exons=joined by RNA Ligase forming continuous sequence

71
Q

What post transcriptional mRNA modification occurs?

A

CAP struct added 5’ end of mRNA

Poly-A tail to 3’

72
Q

How does 5’ capping occur?

A

Post transcription:
5’ end of mRNA has a nucleotide w a triphosphate on its 5’ CArbon

The terminal phosphoanhydride bond is cleaved to form a diphosphate
The final two phosphates of GTP are removed to form GMP which then attaches to the diphosphate to form a 5-5 phosphate linkage
Finally, the 7 carbon in guanine is methylated
= 7-methylguanylate cap

73
Q

What are the functions of a 5’ cap?

A
  • prevents exonuclease degradation

- allows recognition by ribosomes

74
Q

How do viruses alter euk cells to allow for only the viral mRNA to be translated in host cells

A

Viruses lead to enzymes being produced that remove caps

MY MCD (2 decks)

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