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Molecular Biology > Mod 3- Genomes > Flashcards

Mod 3- Genomes Flashcards

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1
Q

What is a genome?

A

The complete set of DNA molecules possessed by an organism

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2
Q

What is the size of the human genome?

A

3200 Mb DNA

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3
Q

How many linear DNA molecules are in the human genome?

A

24 linear DNA molecules

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4
Q

What is the range of sizes for the chromosomes in the human genome?

A

Shortest is 48 Mb, longest is 250 Mb

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5
Q

How many chromosomes are in a normal diploid human cell?

A

46 chromosomes

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6
Q

What is the size of the E. coli genome?

A

4.64 Mb DNA

Contained in a single DNA

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7
Q

What shape does the E. coli genome take?

A

Circular

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8
Q

Where does the replication of the E. coli genome begin?

A

At an origin of replication

Always the same position on the genome as it’s a small genome (IN E.Coli)

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9
Q

How many replication forks are formed during E. coli DNA replication?

A

Two replication forks - bidirectional

One will be the leading strand and one will be the lagging strand

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10
Q

What initiates E. coli DNA replication?

A

DnaA proteins bind close to the origin of replication

The DNA becomes wound round these proteins

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11
Q

What is the role of DnaA in E. coli DNA replication?

A

DNA becomes wound around these proteins

It forces the base pairs to break at the origin of replication due to the stress of DNA winding around the barrel

Original is A-T rich (easier to come apart as it only has 2 hydrogen bonds)

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12
Q

What is the prepriming complex in E. coli DNA replication?

A

The attachment of DnaB proteins to the origin

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13
Q

What forms the primosome in E. coli DNA replication?

A

Attachment of two primase enzymes

These make the RNA primers that initiate replication of the 2 leading strands (on each parent strand)

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14
Q

What is the function of DNA topoisomerase at the replication fork?

A

Unwinds the double helix, preventing DNA supercoiling

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15
Q

What do Single Strand Binding proteins (SSBs) do?

A

Protect the bare single strands of DNA

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16
Q

What is the role of DNA pol III during replication?

A

Synthesizes DNA

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17
Q

What is the function of FEN1 in DNA replication?

A

Removes primers and joins Okazaki fragments

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18
Q

What is the role of the ‘proliferating cell nuclear antigen’ (PCNA) in human DNA replication?

A

Sliding clamp that holds DNA Pol delta tightly onto the DNA

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19
Q

What are terminator sequences in the E. coli genome?

A

Binding sites for Tus proteins

These sequences are directional

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20
Q

What is the function of Tus proteins?

A

Allow the replication fork to pass in one direction but not the other

Permissive face (round side) = allows fork to pass through

Non-permissive face (flat side) = prevents fork from passing through

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21
Q

What results in replication fork arrest in E. coli?

A

DNA strand separation followed by specific interaction of the Ter C6 base with the Tus lock domain

There are 5 terminator sequences on each side = 5 chances to stop the fork (fork may stop at any of these)

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22
Q

What happens at the replication forks in human DNA?

A

Forks just merge, don’t need exact control like in circular DNA

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23
Q

Fill in the blank: The human genome comprises _______ Mb DNA.

A

3200

24
Q

True or False: Each replication fork in human DNA copies about 150 kb of DNA.

A

True

25
Q

What is the length of human chromosome 8?

A

About 3.5 µm or 0.0035 mm

26
Q

How many linear DNA molecules comprise the human genome?

A

24 linear DNA molecules

27
Q

What is the total DNA content in a normal diploid human cell?

A

6400 Mb DNA

28
Q

What is chromatin?

A

DNA extracted from the nucleus

(as DNA is associated with lots of protein)

29
Q

What structure does endonuclease digestion of chromatin reveal?

A

A DNA-protein complex with proteins spaced at regular intervals

30
Q

What is the ‘beads-on-a-string’ structure in chromatin?

A

A structure observed through electron microscopy

The circles/ ‘beads’ are DNA associated with proteins (histones)

These beads are called nucleosomes

31
Q

What are the proteins in chromatin called?

A

Histones

Associated with and package DNA

32
Q

What is a nucleosome?

A

The basic unit of DNA packaging, consisting of an octamer of histones

Two of each histones, H2A, H2B, H3 and H4

33
Q

What is the role of histone H1?

A

It is the linker histone that attaches outside the nucleosome

A linker histones keeps the linker onto the nucleosome

34
Q

Fill in the blank: Nucleosome + DNA + linker histone = _______.

A

Chromatosome

35
Q

What is the next level of DNA packaging after nucleosomes?

A

30 nm chromatin fibre

The 4.9cm molecule in chromosome 8 would now be about 1.2mm in length

36
Q

How much do the beads on a string reduce the length of DNA?

A

By one-sixth as it wraps around the histones

There must be high levels of packaging

37
Q

What stabilizes the 30 nm chromatin fibre?

A

Off-axis asymmetric binding of histone H1

38
Q

What is the importance of histones and nucleosomes?

A
  • Histones allow vast amounts of DNA to be packed into nucleosomes and other higher order DNA structures
  • Chromatin structure can be changed (dynamic) through the reversible chemical modification of histones to allow things to happen to the DNA
  • DNA packaging into nucleosomes is not permanent but dynamic
  • Nucleosomes detach or shift to allow transcription of DNA
  • Nucleosomes must detach for replication of DNA
  • Nucleosome presence or modification can control gene expression
39
Q

What characterizes euchromatin?

A

Contains active genes (probably as 30nm fibres)

Appears light under a microscope

Starts replicating first as it is open and accessible

40
Q

What characterizes heterochromatin?

A

Contains inactive genes

Appears dark under a microscope (more densely packed)

41
Q

What is constitutive heterochromatin?

A

DNA that is always tightly packed in all cells

Never needs to be accessed i.e. one of the X chromosomes in females

42
Q

What is facultative heterochromatin?

A

DNA that is tightly packed only in some cells

Can be opened and used

43
Q

What is the role of the nucleolus?

A

Contains ribosomal RNA genes and is the site of ribosome biogenesis (for translation)

44
Q

What is the highest level of DNA packaging found in dividing cells?

A

Metaphase chromosome which is only found in dividing cells

45
Q

What is the function of centromeres?

A

Hold daughter chromosomes together

Contains special histones = CENP-A instead of H3 (allows DNA to associate)

Serve as attachment points for microtubules that pull chromosomes apart

46
Q

What do telomeres do?

A

Produces buffer sequences

Protect the ends
- From exonuclease attack (which digest ends of DNA)
- from being mistaken for chromosomes breaks and joined together by DNA repair mechanisms (identify ends of real chromosomes)

47
Q

What is a karyogram?

A

A complete set of stained metaphase chromosomes used for mapping gene positions

48
Q

True or False: All bands in a karyogram have names.

A

True

49
Q

What is the significance of the nuclear matrix and nuclear lamina?

A

Nuclear matrix = inside nucleus
Nuclear lamina = around edge of nucleus

They maintain the shape of the nucleus

The 30 nm fibre is attached to these to prevent DNA tangling

50
Q

What diseases are associated with nuclear matrix and nuclear lamina?

A

Progeria, Down’s Syndrome, Huntington disease

51
Q

Where does replication of the human DNA begin?

A

Origins of replication

  • Many on each chromosomal DNA molecule
  • Not always at the same sites
  • Each replication fork copies about 150kb of DNA
52
Q

What is the role of DnaB in E. coli DNA replication?

A
  • The pre priming complex is formed by attachment of DnaB proteins to the origin
  • DnaB is a helicase (separates strands)
  • DnaB breaks more base pairs so the replication forks move away from the origin (starts replication process)
53
Q

What happens at the replication fork in E.coli?

A
  • Helicase (DnaB) breaks base pairs
  • Single strand binding proteins (SSBs) protect the bare single strands to prevent degrading
  • DNA topoisomerase unwinds the double helix preventing DNA supercoiling (works ahead of the leading strand)
  • Primase makes primers on the leading & lagging strands
  • DNA pol III (two copies- on each strand) synthesises DNA
  • DNA pol I and DNA ligase removes primers and joins Okazaki fragments (works on lagging strand)
  • The gamma complex (clamp loader) attaches and detaches Pol III from the lagging strand
  • Beta complex (sliding clamp) holds Pol III onto template allowing it to slide

Gamma and Beta complexes are accessory complexes

54
Q

What happens at the replication fork in humans?

A
  • Helicase breaks base pairs
  • Single strand binding proteins (SSBs) protect the bare single strands (replication protein A)
  • DNA topoisomerase unwinds the double helix preventing DNA supercoiling
  • Primase/ DNA pol Alpha makes primers on leading & lagging strands
  • DNA pol Delta (two copies) synthesises DNA = switches to Pol Delta as Pol Alpha doesn’t have proofreading activity
  • FEN1 (acts on flap) and DNA ligase removes primers and joins Okazaki fragments
  • The ‘proliferating cell nuclear antigen’ (PCNA) sliding clamp holds DNA pol Delta tightly onto the DNA
55
Q

What is special about the replication of the E.coli genome?

A

Can replicate in both directions (as it’s circular)

Replication occurs at different rates = not identical speeds

The replication forks always meet around half way

56
Q

What is special about the replication of the E.coli genome?

A

Can replicate in both directions (as it’s circular)

Replication occurs at different rates = not identical speeds

The replication forks always meet around half way

57
Q

What are the different types of histones?

A

H1
- Molecular mass = 23,000 kD
- 30% basic amino acid content
- Different types of this exist

H2A
- Molecular mass = 14,000 kD
- 20% basic amino acid content

H2B
- Molecular mass = 13,750 kD
- 22% basic amino acid content

H3
- Molecular mass = 15,350 kD
- 23% basic amino acid content

H4
- Molecular mass - 11,300 kD
- 25% basic amino acid content

Molecular Biology (10 decks)

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