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B1omed - Molecular biology > Module 3 - Genomes > Flashcards

Module 3 - Genomes Flashcards

1
Q

The human genome

A

Comprises 3200 Mb DNA that is split into 24 linear DNA molecules. The shortest DNA molecule is 48Mb and the longest is 250Mb.

Each bit of DNA is in a different chromosome. Since we have two sets of chromosomes, a normal genome contains 6400 Mb of DNA

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2
Q

E.coli genome

A

4.64Mb of DNA contained in one singular, circular DNA

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3
Q

Replication of E.coli genome

A

Starts at the origin of replication and goes bi-directionally around the DNA

Always at the same location

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4
Q

Replication of human DNA

A

Many origins of replication and each copies around 150kb of DNA

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5
Q

Initiation of E.coli replication

A

DnaA proteins bind close to the origin of replication, causing the DNA to become wound around them

This forces the base pairs to break at the origin of replication and the origin is A-T rich (easier to come apart)

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6
Q

Prepriming complex in E.coli

A

Formed by attachment of DnaB proteins (helicase) to the origin

DnaB breaks more base pairs so the replication forks move away from the origin

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7
Q

Primosome in E.coli

A

Formed by the attachment of two primase enzymes

These make the RNA primers that initiate replication of the two leading strands

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8
Q

DNA B at the replication fork in E.coli

A

Breaks hydrogen bonds between base pairs

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9
Q

SSBs at the replication fork in E.coli

A

Protecting the bare single strands, preventing them from bonding with the other DNA strand again

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10
Q

Topoisomerases at the replication fork in E.coli

A

Unwind the DNA strands

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11
Q

Primase at the replication fork in E.coli

A

Makes primers to signal the initiation of replication on both strands

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12
Q

DNA polymerase III at the replication fork in E.coli

A

Main replicating enzyme

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13
Q

DNA ligase at the replication fork in E.coli

A

Attaches Okazaki fragments together

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14
Q

The gamma complex (clamp loader) at the replication fork in E.coli

A

Attaches and detaches Pol III from the lagging strand

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15
Q

The beta complex (sliding clamp) at the replication fork in E.coli

A

Holds DNA polymerase III onto the template, allowing for continuous replication

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16
Q

Helicase at the replication fork in humans

A

Breaks the bonds between the base pairs

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17
Q

SSBs at the replication fork in humans

A

Protecting the bare single strands, preventing them from bonding with the other DNA strand again

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18
Q

DNA topoisomerase at the replication fork in humans

A

Unwind the DNA strands

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19
Q

Primase/DNA polymerase alpha at the replication fork in humans

A

Makes primers that initiate replication on both strands

20
Q

DNA polymerase delta at the replication fork in humans

A

The main replicating enzyme that synthesizes DNA

21
Q

Flap endonuclease (FEN1) at the replication fork in humans

A

Acts as an endonuclease that is able to remove primers in the 5’ to 3’ direction and joins Okazaki fragments

22
Q

DNA ligase at the replication fork in humans

A

Joins Okazaki fragments

23
Q

Proliferating cell nuclear antigen (PCNA) at the replication fork in humans

A

Acts as a sliding clamp that holds DNA Pol delta tightly onto the DNA, allowing for continuous synthesis of DNA

24
Q

Terminus utilization substance (TUS) proteins in E.coli

A

Bind to the termination sequences

They have two faces, one face allows the replication to continue through it (permissive face), but the other does not allow replication to continue (non-permissive face)

25
Do reading to understand this better
DNA strand separation followed by specific interaction of the Ter C6 base with the Tus lock domain results in replication fork arrest
26
The end of replication forks in humans
Forks just merge together as exact control isn't needed like with a circular piece of DNA
27
Heterochromatin: the two types: Transcriptional activity, dynamic or constant, stable or reversible, what is it rich in, and what does it do?
Facultative chromatin: Can be transcriptionally active, dynamic (changes) and reversible, rich in LINE sequences, affects gene regulation, stained by G bands Constitutive replication: Not transcriptionally active, constant, stable in all cells, rich in repetitive satellite sequences, affects genes near it, stained by C bands
28
LINE sequences
Long interspersed nuclear/ nucleotide elements are a group of non-LTR (long terminal repeat) retrotransposons that are widespread in the genome of many eukaryotes
29
Satellite sequences
Highly repetitive DNA consisting of short sequences repeated a large number of times. It carries a variable AT-rich repeat unit that often forms arrays up to 100 Mb Involved in genome stability
30
Retrotransposons
A type of genetic component that copies and paste itself into different genomic locations (transposon) by converting RNA back into DNA through the reverse transcription process using an RNA transposition intermediate
31
Chromatin
DNA that has been taken out of the nucleus
32
Nucelosomes
Consist of chromatin wrapped around proteins called histones One nucleosomes contains 8 histones
33
Chromatosome
Consists of a nucleosome, DNA, and a linker (H1) histone
34
Importance of histones
Allow vast amounts of DNA to be packed into nucleosomes and other higher order DNA structures
35
Importance of nucleosomes
Chromatin structure can be changed through the reversible chemical modification of histones Nucleosome presence or modification can control gene expression
36
Why DNA packaging into nucleosomes is not permanent but dynamic
Nucleosomes detach or shift to allow transcription of DNA Nucleosomes must fully detach for replication of DNA
37
Euchromatin
Contains active genes, less packed, produces a lighter area in the nucleus.
38
Heterochromatin
Contains inactive genes that are more densely packed, produces a darker area in the nucleus
39
Nucleolus
Contains rRNA as this is the site of ribosome biogenesis in the nucleus for the cell
40
Euchromatin: what is it connected to?
Nuclear matrix and nuclear lamina
41
Nuclear matrix: what is it and what does it do?
Found within the nucleus, contains proteins that are involved in the control of nucleic acids Maintaining the shape of the nucleus and the spatial organization of chromatin
42
Nuclear lamina: what is it and what does it do?
Found outside the nucleus, contains proteins that are involved in the control of nucleic acids Regulates numerous nuclear processes: DNA replication, transcription, and chromatin organization, etc
43
Lamins: what are they and what do they do?
Type V intermediate filament proteins that are part of the nuclear lamina, nuclar interior and lamin-associated proteins Provide a platform for the binding of proteins and chromatin and confer mechanical stability
44
When is the highest level of packaging and why is the packaging so high?
Metaphase Packaging is high so that genetic material can be organised and separated
45
Centromeres: what do they do?
Hold the daughter chromosomes together using a special histone (CENP-A) and gives microtubules attachment points to use to pull the chromosomes apart
46
Telomeres: what do they do?
Protects the ends of chromosomes from exonuclease attack and protects the ends from being mistaken as breaks (DNA repair mechanisms would start trying to repair the chromsomoes and would end up corrupting the genetic information)

B1omed - Molecular biology (13 decks)

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