Eukaryotic Genome

Question 1

Describe how DNA is organised to form chromosomes ?

Answer 1

NUCLEOSOME
- ionic attraction between positively charged histone proteins and negatively charged DNA

• DNA winds round 8 histone proteins to form a nucleosome, stabilised by H1 histone

CHROMOSOME
- chain of nucleosome s are joined by linker DNA and coiled into a helical structure called chromatin

• chromatin associate with nuclear matrix scaffold of protein forming looped domains
• Further coil and condense into chromosomes

Question 2

What is the importance of ionic attraction between histone octamer and DNA ?

Answer 2

Stabilised the structure of DNA to prevent DNA damage

Question 3

What is the importance of forming nucleosome ?

Answer 3

Alllows long DNA to be coiled tightly thus can pack into nucleus

Question 4

What is her significance of having DNA bound to histone proteins ?

Answer 4

Allows regulation of gene expression as DNA bound to histone proteins are transcriptionally inactive while those found at linker DNA are transcriptionallly active

Question 5

What cause transcriptionally active DNA regions ?

Answer 5

• Histone acetylation
• DNA demethylation

Question 6

What causes transcriptionally inactive DNA regions ?

Answer 6

• Histone deacetylation
• DNA methylation

Question 7

Describe histone acetylation

Answer 7

Acetylation of free lysine residues on N-terminal of histone protein, catalysed by histone acetylase.

Decrease net positive charge of histone, lowering affinitng with DNA

Forms euchromatin

General transcriptional factor and RNA polymerase greater accessibility to underlying DNA sequences, facilitate binding to promoter

Question 8

Describe histone deacetylation

Answer 8

Deacetylation of free lysine on N-terminal of histone protein catalysed by hostine deacetylase.

Increase net positive charger on histone, higher affinity to DNA

Form heterochromatin

General transcription factors and RNA polymerase less accessible to underlying DNA sequences

Question 9

What is euchromatin ?

Answer 9

Chromatin thread that is less tightly coiled and is less condensed due to lower affinity of histone and DNA as net positive charge on histone decreases.

Question 10

What is heterchromatin ?

Answer 10

Chromatin that is more tightly coiled and more condensed due to higher affinity of histone and DFNA as net positive charge of histone increases.

Question 11

Describe DNA methylation

Answer 11

Addition of methyl group to DNA catalysed by DNA methyltransferase

Methyl group blocks binding of transcription factors greater

Induces histone deacetylation as histone deacetylation recognise and binds to regions with methylated DNA, forming heterochtomatin

Question 12

Why histone methylation (histone acetylation + DNA methylation) occurs over larger areas of chromatin

Answer 12

When ells differentiate, only a specific set of genes coding for tissue specific proteins is expressed.

Many other genes like stem cell specific genes and non-housekeeping genes are not expressed.

histone methylation occur over a larger area to make chromatin. More condensed t silence genes that are not required

Question 13

What are the control elements ?

Answer 13

1. Promoter
2. Enhancer
3. Silencer

Question 14

1. Where is promoter located
2. What TF binds to it

Answer 14

1. Upstream proximal to gene it regulates
2. General transcription factors

Question 15

Describe promoter control

Answer 15

GTF binds to promoter via TATA box and recruits RNA polymerase to form TIC

Question 16

1. Where is enhancer / silencer located
2. What TF binds to them

Answer 16

1. Distal up or downstream
2. Activators and Repressors

Question 18

Describe enhancer control

Answer 18

Activator binds to specific enhancer

Trigger DNA looping mechanism aided by DNA bending proteins

Bring activator close to promoter to interact with TIC

Upregulating activity of RNA pol

Question 19

Describe silencer control

Answer 19

Repressor bind to specific silencer

Trigger DNA looping mechanism aided by DNA bending proteins

Bring repressor closer to promoter to interact with TIC

Downregulates activity of RNA pol

Question 20

Explain the difference between chromatin level and transcriptional level control

Answer 20

(Chromatin: chromatin remodelling)
(Transcriptional: control elements)

Chromatin level control is more long term
- certain genes are transcriptionally inactive regions will never be expressed

Transcriptional level
- certain genes will be expressed at different times in response to a stimuli (binding of repressor, activator)

Question 21

What are the post-transcriptional control ?

Answer 21

1. 5’ capping
2. 3’ polyadenylation
3. Splicing (alternative splicing)

Question 22

Describe 5’ capping and its effects

Answer 22

7-methylguanosine added to 5- end of pre-mRNA
Catalysed by mRNA guanyltransferase

Effects:
Protect against degradation by 5’ exonuclease for more translation

Direct movement of mRNA out of nucleus and binding to ribosome

Question 23

Describe 3’ polyadenylation and its effects

Answer 23

Adenine nucleotides added to 3’ end of pre-mRNA to form poly-A-tail
Catalysed by poly(a) polymerase

Effects:
Protect against degradation of 3’ exonuclease for more translation

Direct movement of mRNA out of nucleus

Question 24

Describe splicing

Answer 24

snRNAs recognise and binds to splice sites via CBP to position spliceosome

Introns loop into a lariat and excised by spliceosome

Exons are spliced together

Question 25

Describe alternative splicing and its effects

Answer 25

Exons spliced together in different combinations Effects: Produce mature mRNA with diff, producing diff proteins for diff functions

Question 26

Describe the roles of telomerase

Answer 26

1. buffer DNA to protect the organism’s genes from being eroded after successive rounds of DNA replication - (so critical proteins will still be synthesised despite the shortened chromosomes) 2. Prevent fusion between exposed ends of chromosomes - (preventing chromosomal aberration which disrupt regulatory control of genes on the adjoined chromosomes) 3. Limits number of cell divisions as cells will undergo apoptosis when a critical length of the telomere is reached - (which limits the extent of accumulated mutations and prevents development of cancer)

Question 28

What explains diff genes being expressed in different tissues ?

Answer 28

Genes have diff methylation patterns in different tissues.