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_Sem 1. MCBG NOTES > Lecture 9 > Flashcards

Lecture 9 Flashcards

1
Q

DNA stands for…

A

Deoxyribonucleic acid

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2
Q

When can you see the chromosomes?

A

When DNA is dividing

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3
Q

Number of chromosomes

A

23 pairs of chromosomes (46 total)
23 from mother, 23 from father

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4
Q

How to ‘count’ the chromosomes

A

Count the centromeres!

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5
Q

Label the key things in this picture…

A
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6
Q

What is the human genome?

A

A complete set of nucleic acid sequences for humans encorded as DNA within the 23 chromosome pairs

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7
Q

How does DNA go from double helix to invididual bases?

A

double helix
chromatin
chromosomes
genes
genomes
GATC

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8
Q

Why is DNA packaging needed?

A

2 metres of DNA needs to fit into 6 micrometre cell nucleus

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9
Q

What is the 1st level of packaging?

A

Beads-on-a-string

DNA + histone -> nucleosome

DNA is looped around a histone core, basic unit of DNA and a histone is called a nucleosome.

Nucleosome = the histone core with 2 legnth of DNA wrapped around it

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10
Q

Structure of the histone

A

Each histone has 8 subunits (the DNA wrapped around the subunits has 147 base pairs)

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11
Q

Second level of DNA packaging

A

Beads-on-a-string nucleosome -> solenoid (wrapped more tightly)

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12
Q

Beads-on-a-string nucleosome - what is the other name?

A

Euchromatin

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13
Q

What is the name of DNA wrapped in as a solenoid?

A

Heterochromatin

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14
Q

What does euchromatin and heterochromatin look like in a nucleus

A
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15
Q

Are genes expressed in euchromatin or heterochromatin?

A
  • Genes are expressed in euchromatin
  • this is becuase DNA is much more accessible
  • Genes are much harder to access in solenoid fibres
  • In general, heterochromatin genes are not expressed
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16
Q

What makes up chromosomes?

A
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17
Q

What is a gene and where are genes located?

A
  • Genes carry the code for proteins
  • Genes have a chromosomal location (they have the same position in all people!)
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18
Q

What is the genome?

A

Genome is the entire DNA sequence of a species Human Genome the following -
22 autosomes plus 2 sex chromosomes X and Y

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19
Q

Can line up all the chromosomes

A
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20
Q

Can graph the number of genes carried by each chromosome

A
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21
Q

How many base pairs in the human genome?

A

3,200,000,000 bp

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22
Q

Which cell doesn’t carried DNA?

A

RBC (doesn’t have a nucleus!)

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23
Q

What type of molecule is DNA

A

DNA is a polynucleotide

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24
Q

What are nucleotides and nucleosides?

A

Nucleoside - base and sugar

Nucleotides - base, sugar and phosphate

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25
Q

What are the two types of pentose sugars?

A

DNA - deoxyribose sugar

RNA - ribose sugar

(must learn the difference between these and the carbon numbering)

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26
Q

What are the two groups of nucleotides

A

Purine and pyrimidine

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27
Q

What are purines, what are their structure?

A

2 ring structure
Guanine, adenine

28
Q

What are pyrimidines and what are their structure?

A

1 ring structure
Cytosine, thymine, uracil

29
Q

Need to be able to recognise each base

A
30
Q

How are polynucleotides formed?

A
  • Nucleosides are precursors for nucleotides
  • Nucleosides form when:
    pentose and nitrogenous base -> nucleoSides
  • Nucleosides are then phosphorylated to make nucleoTides
31
Q

What is the last step of nucleotides forming?

A

Nucleosides are phosphorylated to nucleotides

32
Q

Nucleic acid nomenclature (of nucleosides and nucleotides)

A
33
Q

What is the difference between dAMP and AMP?

A

dAMP = deoxyadenosine monophosdate (made from deoxyribose pentose sugar)

AMP = Adenosine monosphosphate (made from ribsoe pentose sugar)

34
Q

How are nucleotides monomers joined?

A

Nucleotides form polynucleotides. The join with a phosphodiester bond.

35
Q

What is the chain polarity? What are the distinct ends?

A

​• Chain has polarity: 5’ to 3’
• Chain has distinct ends: 5’P and 3’OH

36
Q

Base pairing - what goes with what?

A

Guanine (purine) and cytosine (pyrimidine)

37
Q

Base pairing between G-C

A

GC - 3 hydrogen bonds form

38
Q

A-U base pairing

A

2 hydrogen bonds

39
Q

Number of bonds between each bases

A

​• G-C basepair has 3 hydrogen bonds
• A-T basepair has 2 hydrogen bonds
• A-U basepair has 2 hydrogen bonds

40
Q

Secondary structure of DNA, describe all the bondings

A

DNA strands complimentary and anti-parallel
• Each single strand held together by covalent bonds between sugars -phosphates
• The double strand held together by hydrogen bonds formed by the complementary base pairs

41
Q

Tertiary structure of DNA

A

RIGHT-handed double helix with anti-parallel strands

Base pairings are tightly stacked, van der Waals forces holding them together

42
Q

Quarternary structure of DNA

A

Double helix and the histones (nucleosomes)

43
Q

Convention of writing DNA sequences

A
44
Q

If DNA doesn’t state it’s prime ends, what are it’s prime ends? e.g. ACCT

A

5’ACCT3’

45
Q

How does nomenclature depict a duplex sequence

A

By convention the top letters go from 5’ to 3’ (often the bottome strand is left out - if I know the top strand which is 5’ to 3’ can work out bottom strand)

46
Q

NOTE - All single letters for DNA are depicting a double stranded molecule, e.g. it might say 5’TAGCT3’, it will not say the other half (the complementary strand) - 3’ATCGA5’

A
47
Q

Q: Many nucleoside analgues are frequently used as anti-viral and anti-cancer durgs. Why do you think nucleoside analogues are used instead of nucleotide analogues, after all, nucleotides are the basic units of DNA and RNA

A
  • Nucleosides are nucleotides without a phosphate group
  • Phosphates have a negative charge
  • This means nucleotides can’t travel through the semi permiable plasma membrane due to this negative charge on the phosphate group
  • Therefore, if the phosphate is removed, nucleosides can pass through the membrane
  • This is important as viruses and cancers are inside cells and the drug is needed where the viruses and cancers are.
  • Nucleosides are converted to nucleotides once they are inside the cell or organelle.
48
Q

DNA - name of the two strands in DNA replication

A

Template strand
Coding strand

49
Q

Draw out the cell cycle - at which stage does DNA replication take place?

A

Takes place during the S phase

50
Q

What does semi-conservative mean in DNA replication?

A

Each old DNA strand acts as template for a new DNA strand

51
Q

The reaction that occurs between nucleotides in DNA replication

A
52
Q

Write the formula for DNA replication

A

(DNA)n = DNA strand with n as the number of nucleotides
dNTP = d stands for deoxyribose sugar. N either either adenosine, thymine, cytosine, guanine. T stands for ‘tri’.
At the start of the equation the monomers aren’t yet nucleotides as nucleotides have 1 phosphate group attached
(DNA)n+1 = after adding the monomer e.g. dATP
PPi = the two phosphate released

53
Q

The reaction showing the formation of the nucleotides - which 2 main enzymes are involved?

A
  • catalysed by DNA polymerase
  • hydrolysis of PPi by pyrophosphatase drives the reaction (as it reduces PPi levels)
  • dNTPs needed
  • separation of double-stranded DNA template
  • stepwise reaction
  • synthesis from 5’ to 3’
54
Q

What are the three stages in DNA replication?

A
  • Initiation
  • Elongation
  • Termination
55
Q

What happens in initation (DNA replication)

A
  • Recognition of origin of replication
  • Requires recruitment of DNA polymerase (+ other proteins)
  • Requires a ‘kick-start’ by DNA primase (making a short RNA primer) as DNA polymerase can only extend a 3’end (needs ‘kick-starting’ as DNA polymerase can’t start on it’s own)
  • One origin of replication results in two replication forks
56
Q

Which way does DNA polymerase synthesis?

A

DNA polymerase synthesises DNA from 5’ to 3’, therefore it needs to read the template in the opposite direction (reads it from 3’ to 5’ from the template strand)

57
Q

How does DNA polymerase have a proof-reading ability?

A

DNA polymerase has an exonuclease domain - the exonucleases function is to proof-read, it is able to recognise mispaird bases/wrong bases, it then deletes these bases and ensures it is being replaced by the correct base (it catalyses the removal of this single nucleotide). It can only catalyse the removal of the nucleotide at the end of the strand, therefore if a mutation goes unnoticed and it is incorporated in the DNA (so not at the end anymore), the DNA polymerase is not able to ‘fix’ this problem.

58
Q

Where does the DNA polymerase ‘sit’ in each of the chains?

A
59
Q

What does it mean when it says that DNA primase ‘kick starts’ the DNA replication?

A

DNA primase comes along to give it a ‘kick-start’. Makes a little bit of RNA and then DNA polymerase can continue to make new DNA

60
Q

What happens in DNA elongation?

A
  • Moving replication forks
  • DNA helicase - unwinds DNA strand. This exposes more of DNA template for replication
  • DNA replication occurs
  • The lagging strand has to be replicated in the opposite direction (from right to left)
  • DNA ligase joins the Okazaki fragments of the newly made discontinous strand together
    (see next flashcard for the other picture showing DNA ligase joining the okazaki fragments together
61
Q

Role of DNA helicase?

A

Unwinds the DNA strand, this exposes more DNA strand for replication

62
Q

What is the role of tropoisomerase?

A

This enzyme works with DNA helicase. DNA helicase unwinds the DNA, this however, puts tension on the DNA
Tropoisomerase releases this tension by ‘cutting through the DNA’ strand, releasing pressure

63
Q

DNA replication - elongation cont - final parts of this stage?

A

DNA ligase:
RNA bits are removed, the Okazaki fragments are then fused together by an enzyme called DNA ligase

64
Q

What is the direction of replication in this picture? (elongation step)

A
65
Q

DNA replication - termination

A

(when the replicated strands meet, termination can then occur)

  • When two facing replication forks meet
  • DNA ligase joins the two final fragments
  • Resulting in two identical DNA molecules
66
Q

DNA replication in eukaryotes -

A
  • There are many origins of replication in eukaryotes e.g. 3 here
  • Replication forks will meet each other (think of termination step)
  • Eventually the whole chromosome will be replicated
67
Q

Draw out what a replicated chromosome looks like

A

_Sem 1. MCBG NOTES (11 decks)

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