Gene Expression And Regualtion In Eukaryotes

Question 1

Central dogma

Answer 1

Flow of information from dna to ran to make a protein

Question 2

3 stages of the central dogma

Answer 2

Dna replication
Transcription
Translation

Question 3

Dna replication

Answer 3

-helicases unwind the double helix
-single strand binding proteins stabilise the unwound paternal dna
-The leading strand is synthesised continuously in the 5’-3’ direction by dna polymerase
-the lagging strand is synthesise discontinuously.Primase synthesis a short rna primer which is extended by dna polymerase to form an Okazaki fragment
-after rna timer is replaced by dna, dna ligase joins Okazaki fragment to the growing strand

Question 4

Okazaki fragment

Answer 4

Sequences of dna nucleotides which are synthesise discontinuously and joined by dna ligase

Question 5

Okazaki fragment

Answer 5

Sequences of dna nucleotides which are synthesise discontinuously and joined by dna ligase

Question 6

Transcription

Answer 6

-initiation
-Elongation
-Termination

Done by rna polymerase
Processing of primary mrna into mature MRNA in the nucleus

Question 7

Translation

Answer 7

-it is the synthesis of proteins on ribosomes in the cytoplasm
Initiation
Elongation
Termination

Question 8

Key stages where gene expression may be regulated

Answer 8

-chromatin modification
-transcription initiation
-post transcription
-post translation

Question 9

Regulation of gene expression On a dna level(chromatin)

Answer 9

-genes within heterochroamtin are usually not expressed
-active genes are within euchromatin are usually expressed
-chemical modifications to the histones regulates expression,Histone modification include:
1)histone acetylation:it unwinds dna as acetyl groups are attached go lysine in history tails acetylation adds negative charge ,reduces attraction to dna loosens the structure and permits transcription

2)histone methylation:
- The addition of methyl groups (methylation, CH3) to histone tails can reduce transcription – Transcription repression
-nucleosomes pack tightly together,transcription factors cannot bind dna,genes are not expressed
• No change to charge of the histone protein
• Methylation can attract other chromatin remodelling proteins to either
loosen the structure or block TF binding
• Less dynamic than acetylation but can be reversed
• Mono, di- or tri methylation

-Dna methylation
• Attaching a methyl group (-CH3) to a cytosine nucleotide base within a cytosine- guanosine (CG) sequence (CpG island)
• Methylation of CpG sites in promoter regions, prevents the DNA from being transcribed = Gene silencing
• Roles in cellular differentiation and long term inactivation of genes e.g. expression of maternal or paternal alleles, X chromosome inactivation, imprinting

Question 10

Chromatin

Answer 10

-it’s a complex of equal parts of DNA and
proteins that forms chromosomes

-The nucleosome (beads) is the fundamental subunit of chromatin
• 8 protein molecules (histones)
• Positively charged AAs bind to negatively charged DNA
-Chromatin could be heterochromatin or euchromatin

Question 11

Heterochromatin

Answer 11

-deeply stained
-Very comfort/condensed dna
-genes not likely to be expresses

Question 12

Euchromatin

Answer 12

-Lightly stained
-Less compact
-Loosely packed DNA = accessible!

Question 13

Regulation of gene expression:transcription

Answer 13

Characteristics involved:

UPSTREAM of gene
• Promoter and Transcription factors
• Proximal control elements
• Enhancer (distal control elements)

DOWNSTREAM of gene
• Poly-A signal sequence
• Transcription termination region

Transcription initiation:

1. Activator proteins bind to distal control elements (enhancer)
2. A DNA bending protein brings the bound activators close to the promoter
3. The activators bind to general transcription factors to form an active transcription initiation complex,
4. Promotes RNA Pol binding to the promoter and transcription begins

Question 14

Regulation of Gene Expression: Post-transcription

Answer 14

1. 5’ cap (methylated Guanosine)
2. poly-A (adenine) tail at the 3’
   primary (pre) mRNA
   
   3. RNA Splicing: removal of introns (intra-genic regions) by spliceosome
      Next step: translocation to the cytoplasm from the nucleus
3. Alternative RNA splicing
   Variable processing of exons creates a family of proteins / spliced variants

Question 15

Function of The 5′ cap has in post transcriptional gene expression

Answer 15

1. Regulate nuclear export of mRNA;
2. Prevent degradation of mRNA by exonucleases;
3. Promote translation by facilitating ribosome attachment
4. Promote 5′ proximal intron excision/splicing out

Question 16

Function of the 3’ poly-A tail in post transcriptional gene expression

Answer 16

1. promote the export of mRNA from the nucleus
2. protect the mRNA from degradation
3. facilitate ribosome attachment to mRNA

Question 17

Other non-coding (nc) RNAs

Answer 17

• rRNA (ribosomal) and tRNA (transfer) are non-coding RNAs – NO
protein!
• Long nc RNA (lncRNA) >200 nucleotides, diverse functions
• Micro RNAs (miRNAs) – small, single stranded RNA molecules, bind to complementary mRNA sequences. Lead to degradation of the target mRNA or block its translation- post transcriptional gene silencing
• Small interfering RNAs (siRNAs)– similar to miRNAs, ~20bps in length, block gene expression via RNA interference (RNAi) – gene silencing

Question 18

Regulation of Gene Expression: Post-translation

Answer 18

Protein processing and protein degradation
• Proteolytic (protein) processing e.g. pre-pro-hormones
• Chemical modification (introducing functional groups)
e.g. phosphorylation, glycosylation, targeting for transport
• Protein degradation(ubiquitination)

Question 19

Protein degradation: Ubiquitination

Answer 19

• Ubiquitin is added to proteins destined for degradation
• A marker (76aa) ‘Death tag’
• Recognised by proteosome
• The proteosome, breaks down proteins in to smaller fragments (7-9 aa)

Question 20

How is Prokaryotic and Eukaryotic Gene Expression
similar?

Answer 20

1)Both require the participation of regulatory proteins known as transcription factors
• prokaryotes: activator and repressor
• eukaryotes: activator proteins act on enhancer

2) In both prokaryotes and eukaryotes, control of gene expression can occur at the level of:
• transcription
• translation
• protein activity (post-translation)

Question 21

How is Prokaryotic and Eukaryotic Gene Expression different?

Answer 21

Prokaryotes: Mostly On
• Most genes of a bacterium constitutive.
• The majority of products are constantly made
• Repressible systems are more common than inducible systems.
Eukaryotes: Mostly Off
• The vast majority of genes in a mature eukaryotic cell are turned off.
• Specific proteins and environmental conditions are necessary before a gene can • be turned on

Question 22

How is Prokaryotic and Eukaryotic Gene Expression different?

Answer 22

1)
-Prokaryotes: Mostly On
• Most genes of a bacterium constitutive.
• The majority of products are constantly made
• Repressible systems are more common than inducible systems.
-Eukaryotes: Mostly Off
The vast majority of genes in a mature eukaryotic cell are turned off.
• Specific proteins and environmental conditions are necessary before a gene can
• be turned on

2) Prokaryotes: Naked DNA
Eukaryotes: Nucleosomes
• Eukaryotic DNA is packaged as chromatin: octomer of histones + DNA

3)

Prokaryotes: One RNA polymerase
Eukaryotes: Three RNA polymerases
• The proteome is transcribed by RNA polymerase II. • RNA polymerase I rRNA
• RNA polymerase III tRNA

4)

Prokaryotes: No modification of mRNA transcript
• What you see is what you get.
Eukaryotes: Extensive modification of mRNA transcript • 5’ ends capped
• 3’ Poly A tail
• introns removed and exons spliced
Prokaryotes:
• Transcription and Translation take place simultaneously
Eukaryotes:
• Transcription and RNA processing in the nucleus; translation in cytoplasm