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Genomics > Genome Structure > Flashcards

Genome Structure Flashcards

1
Q

What regions are involved in a gene?

A

A non-coding, coding and regulatory region

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2
Q

Why does the phosphate group give the DNA it’s overall charge?

A

The phosphate groups negativity is dominant since the ribose sugar and nitrogenous bases are neutral

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3
Q

What attaches to the 5th and 3rd carbon of every nucleotide monomer in DNA?

A

The 5th and 3rd carbon are both attached to the phosphate group

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4
Q

In what direction do you write the sequence of DNA?

A

From the 5’ to 3’ direction (number from the 5’ C to 3’ C of each pentose sugar)

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5
Q

What interact with the major/ minor grooves of the DNA?

A

Enzymes and DNA

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6
Q

What is the total length of DNA in every cell?
How many cells are there in the body?
What is the average diameter of a cell?

A

2m; 40 trillion; 50 micometres

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7
Q

How does DNA end up compacted into a chromosome?

A
  1. DNA is wrapped around histone proteins to form nucleosomes - the beads on a string structure
  2. This is winded into chromatin and then further winding forms extended sections of a chromosome
  3. Then, loops of chromatin form which eventually form a full-sized chromosome
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8
Q

What are histones?

How many histones form a nucleosome?

What are the 4 types of histones?

How many BPs of DNA per nucleosome?

Which histone interacts with linker DNA (DNA between nucleosomes)?

Where is DNA in relation to histones?

A

Proteins that bind DNA; 8; 2a, 2b, 3 and 4 (2 of each); 146BPs; histone 1; wound around the outside

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9
Q

What determines the shape of a chromosome and what are it’s shapes?

A

The position of the centromere; metacentric have the centrosome in the middle where as submetacentric have the centrosome off centre and acrocentric has no short arms of the chromosome at all, instead the centrosome is so off to one side that the end bits are given a different name - ‘satellites’

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10
Q

What is a karyotype and when are cells used for it?

A

A karyotype is the number and appearance of chromosomes in the nucleus of a eukaryotic cell.

Cells are stopped in metaphase (when the chromosomes are aligning at the equator of the cell in mitosis i.e. before cell division) and are spread out and analysed in a karyotype

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11
Q

What is the exome? How much of the overall genome does it make up?

A

All the coding sequences of DNA/ all the gene sequences of DNA (including the coding parts)

This is a tiny part of the overall genome

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12
Q

What is the primary DNA sequence?

A

The 2 strands of DNA before the bonds between the bases have occurred; encodes all gene products necessary for an organism + regulatory signals (to turn the expression of genes on/off)

Much of the DNA sequence does not have an assigned function as yet

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13
Q

What is a gene?

A

All the DNA that is transcribed into RNA + all the cis-linked control regions (regions physically close to exons on the DNA strands) which control appropriate tissue specific expression of the final protein

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14
Q

What does the promoter region of a gene control?

A

If the gene is expressed, where it is expressed, when it is expressed, the quantity of expressed product. It is also the signpost for cellular machinery to come and start transcription of a gene

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15
Q

What does the stop codon region of a gene ensure?

A

That transcription of the gene stops at the right time, so the RNA is what it is meant to be

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16
Q

How many genes in the human genome and how much of this makes up the whole genome?

A

20,000; <2% of the whole genome

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17
Q

How many genes do simpler organisms such as flies, yeast and bacteria have?

A

Flies - 10,000
Yeast - 4,000
Bacteria - 1,000
But genome size is not strongly related to the complexity of an organism

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18
Q

Do genes stand out despite being of such low proportion of the whole genome?

A

They do not stand out fam

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19
Q

Do genes vary in size?

A

Yes - the globin gene is 1.8kb whereas the dystrophin gene is 2.4Mb

20
Q

What are intergenic regions and what can they contain?

A

The sequences between genes with no known function; include repetitive DNA, endogenous retroviruses (remnants of retroviruses that have been incorporated there) and pseudogenes

21
Q

What are retroviruses?

A

A group of RNA viruses which insert a DNA copy of their genome into the host cell in order to replicate, e.g. HIV

22
Q

What is gene clustering? What does this allow for? Why does this occur?

A

Genes tend to cluster together in families e.g. the globin gene clusters
This allows for regulation of them together
Perhaps happened as the genes duplicated in time that way i.e. due to evolution

23
Q

What is a transcription unit and what does it contain?

A

The part of the gene that can be transcribed into RNA; containing exons, introns and a promoter at it’s start

24
Q

Why is RNA processed and how is this done?

A

In order to target it correctly/ so it is resistant to cellular machinery; processing is capping and polyadenylation

25
Q

What do promoters do with RNA polymerase?

A

They recruit the RNA polymerase to a DNA template, which then moves from the 5’ to 3’ direction

26
Q

What are examples of 2 regulatory signals in the promoter region of a gene and what do they do?

A

The CAAT and TATAA boxes

Th TATAA box recruits TFs and RNA polymerase

The CAAT box is the binding site for an RNA TF

Other regulatory elements in the promoter region
Have binding sites for TFs
That help regulate the recruitment of RNAP

27
Q

What are untranslated regions of a gene?

A

Parts at the start and end of a gene that are transcribed to form RNA, but not translated to form the final protein

28
Q

What does RNA polymerase do?

A

It unwinds the DNA strands to separate them at a local level

It matches RNA bases (which includes uracil instead of thymine) to complimentary DNA bases on the DNA strand

This is during transcription

29
Q

What are the 3 RNA polymerase enzymes in eukaryotes and their functions?

A

RNAPI - needed to transcribe rRNA genes
RNAPII - needed to transcribe mRNA
RNAPIII - needed to transcribe tRNA/ other small RNAs

30
Q

Is it only RNA polymerase involved in expressing a gene?

A

No, general transcription factors, cofactors, activators and repressors all work together

31
Q

What is the process of transcription?

A
  1. RNA polymerase recruits to a closed DNA complex and unwinds it
  2. It moves down the DNA strand to synthesize more RNA (elongation)
  3. When the termination signal is reached, the RNA strand dissociates
  4. The DNA reforms it’s double helix
32
Q

How do introns vary?

A

They vary in number (0 to 311), size (30bps to 1Mbp) and can contain other genes (if of larger size)

33
Q

What is the average RNAPII elongation rate?

A

60 bases per second so transcription of some long introns lasts many hours

34
Q

What are examples of regulatory regions of a gene and their functions?

A

Enhancers upregulate gene expression and are targets for TFs (activators)
Silencers downregulate gene expression and are targets for TFs (repressors)
Insulators prevent enhancers/ silencers from influencing other genes (adjacent)

35
Q

Enhancers and silencers are position independent - what does this mean?

A

Some occur well upstream of the promoter, some are in the promoter, some are in introns and some are in the terminator region (sequence in DNA that marks the end of a gene)

36
Q

How is the RNA strand produced modified after transcription?

A

Capping at the 5’ end, polyadenylation at the 3’ end and splicing to remove introns

37
Q

What is the 5’ cap and what is it’s purpose? When is it added?

A

The cap is 7 methyl guanosine and it protects the RNA strand from being degraded by enzymes. It is added soon after RNAP begins transcription

38
Q

What is the process of the poly A tail being added?

A

The termination signal to stop the RNA strand (pre MRNA) from forming is transcribed along with the exons and introns in the gene. It is an AAUAAA and G/U rich region.

Cleavage factors bind this region and cleave everything after the AAUAAA region, including the G/U rich region.

Then polyadenylate polymerase (PAP) adds a lot of Adenine bases (approx. 250) to protect that end from degradation + help target the RNA strand out of the nucleus

What you are left with now is known as the ‘primary transcript’

39
Q

What happens after the cap is added and polyadenylation occurs?

A

Splicing to remove introns - the spliceosome (a big protein complex) removes the intron between 2 exons, then joins the exons together.

The intron forms a lariat structure with 2’-5’ linkage and is degraded

40
Q

What is alternative splicing?

A

Different introns can be spliced out/ exons can be skipped, leaving different variations of mRNA and so variations of a protein (isoforms) can be produced from the same gene

41
Q

What is an exon junction complex?

A

A protein complex which forms on a pre-messenger RNA strand at the junction of two exons which have been joined together during RNA splicing

42
Q

What happens upon exon junction complexes binding the pre-mRNA?

A

The TREX export complex binds the cap

The TREX and EJCs suggest to the nucleus to transport the mRNA out to the ER to be translated

43
Q

How does translation occur?

A

The ribosomes on the ER/ cytoplasm catalyse the joining of the amino acids from tRNA to form a polypeptide.

The tRNA has complimentary anticodons to the mRNAs codons to enable the correct amino acids to join together

44
Q

What are pseudogenes?

A

Genes that have been at least partially inactivated by the loss or gain of sequence that disrupt their correct transcription and/or translation

45
Q

What is an example of a pseudogene?

A

Glucocerebrosidase has an adjacent pseudogene that only differs in the coding region by one 55bp deletion and a few single base changes; so the gene still forms a transcriptional nit but not a functional protein

Processed pseudogenes are thought to be mRNA copies that have been recopied back into the genome (so have no promoter, no introns) (recopying known as retrotranscription)

Genomics (7 decks)

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