11 - Gene expression in eukaryotes

Question 1

What are the two main differences between prokaryotic and eukaryotic genome organisation?

Answer 1

Prokaryotes have small genomes packaged in circular DNA, where as eukaryotes have large genomes consisting of linear DNA organised into chromatin

Question 2

Why are eukaryotic genomes usually larger than prokaryotic genomes?

Answer 2

Eukaryotes have a larger number of genes (as they are more complex) and lots of non coding DNA

Question 3

What is in non-coding DNA?

Answer 3

• gene regulatory sequences (such as promotors)
• introns
• sequences without a known function

Question 4

2 types of repetitive sequences

Answer 4

1. Interspersed repetitive DNA

2. Tandemly repetitive (satellite) DNA

Question 5

1. Interspersed repetitive DNA

Answer 5

• Repeated units scattered throughout the genome
• Single unit 100-10,000 bp
• Copies not necessarily identical, but closely related
• Makes up 25-40% of most mammalian genomes
• e.g. Alu elements (300 bp repeats) make up 5% of the mammalian genome

Question 6

2. Tandemly repetitive (satellite) DNA

Answer 6

• Can be broadly classified according to the length of a single repetitive region
• Much satellite DNA is located at telomeres and centromeres - suggesting a structural role

Question 7

Chromatin structure

Answer 7

• Chromosomes are composed of chromatin (protein + DNA)

- Chromatin is an intricate form of packaging for DNA (10,000-fold compaction)

Question 8

Chromatin

Answer 8

• DNA in a cell must be packed in an organized manner – to be accessible for transcription and replication
• This involves association with specific proteins (histones) and the formation of chromatin
• Eukaryotic chromatin is much more complex than prokaryotic chromatin
• Each human chromosome contains a single linear DNA double helix ~6 cm long

Question 9

Heterochromatin

Answer 9

highly condensed during interphase, not actively transcribed

Question 10

Euchromatin

Answer 10

less condensed during interphase, able to be transcribed

Question 11

Histones

Answer 11

proteins with positively charged amino acids that bind to the negatively charged DNA

Question 12

What is the first part of DNA packing?

Answer 12

Around 200 base pairs of DNA is wrapped around a core of 8 histone molecules to form a nucleosome bead.
Histone 1 sits on the outside and acts as a linker

Question 13

What happens in the 2nd part of DNA packing (I.e. forming chromatin fibres)

Answer 13

the nucleosome beads are coiled together to create a 30nm chromatin fibre which is looped onto a protein scaffold to form euchromatin

Question 14

Why does euchromatin have an open/looped structure?

Answer 14

To allow for transcription and replication

Question 15

What is DNA methylation and what does it do?

Answer 15

The addition of methyl groups to certain DNA bases, which results in the chromatin compacting which reduces transcription and therefore gene expression.
It also accounts for genomic imprinting in mammals

Question 16

What is histone acetylation and what does it do?

Answer 16

The addition of acetyl groups (-COCH3) to the histone tail which causes the histones to grip DNA less tightly which can in turn activate genes

Question 17

What process is a form of long-term control of gene expression

Answer 17

cellular differentiation

Question 18

Closed chromatin

Answer 18

DNA methylated;

histones not acetylated

Question 19

Open chromatin

Answer 19

DNA unmethylated;

histones acetylated

Question 20

3 different RNA polymerases

Answer 20

• RNA polymerase I (pol I): ribosomal RNA
• RNA polymerase II (pol II): messenger RNA (mRNA)
• RNA polymerase III (pol III): small RNAs e.g. tRNA

Question 21

Promoter

Answer 21

DNA sequences adjacent to the gene (‘upstream’) that:
• Determine where the transcription of the gene is initiated
• Determine the rate of transcription

Question 22

The TATA box

Answer 22

• A key part of the promoter
• Provides the site of initial binding of the transcription initiation machinery
• Located 10-35 bp upstream of the transcription start site

Question 23

Describe the formation of the preinitiation complex

Answer 23

1. TF2D binds to the TATA box
2. TF2A and TF2B then bind as well
3. TF2F and RNA polymerase 2 binds
4. TF2E and TF2H to form the preinitiation complex

Question 24

How do enhancers work?

Answer 24

When the activator binds to the enhancer sequence, the DNA folds to bring the enhancer and promoter together

Question 25

transactivation domain

Answer 25

responsible for recruiting other proteins into the transcription factor complex

Question 26

What happens during the processing of pre-mRNA to form mRNA?

Answer 26

• The 5’ end is capped with GTP
• Polyadenylation of the 3’ end
• splicing to remove introns

Question 27

How can one gene code for more than one protein?

Answer 27

alternative splicing by regulatory proteins can result in different combinations of introns which results in different mRNAs

Question 28

Dscam proteins

Answer 28

• located on the surface of a growing neuron

* Provide a cell recognition mechanism that regulates brain development