Nucleic Acida 3- Gene organisation and transcription 1

Question 1

How are genes organised

Answer 1

DNA is organised into functional units called “Genes”.

The Gene is the unit of inheritance

Genes encode information for making proteins and functional RNA’s

Question 2

How does gene regulation explain cell specialiation

Answer 2

Both Red Cells and lymphocytes are “related” as they develop from a common progenitor cell- stem cell in bone marrow.
B-Lymphocytes make “Antibodies” and function in the immune system
Red Blood Cells contain “Haemoglobin” and function in oxygen transport
These two cells make different proteins
Only B-Cells Make Antibodies
Only Red cells contain Haemoglobin
These two cell types arise from the use of different sets of genes

Question 3

What is the microbiome

Answer 3

“the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space.”

Question 4

What is Down’s syndrome

Answer 4

Down syndrome (DS) or Down's syndrome, also known as trisomy 21, is a genetic disorder caused by the presence of all or part of a third copy of chromosome 21.Down syndrome is the most common chromosome abnormality in humans. Occuring one of every 750 babies born in the UK each.  It is typically associated with physical growth delays, a particular set of facial characteristics and a spectrum  of learning difficulties. 
Don’t need lots of complexity at gene level.

Question 5

What is the genome

Answer 5

The complete DNA sequence of an organism is called a “Genome

Question 6

What are house-keeping genes

Answer 6

Some genes are expressed in all cells. These include
“Housekeeping Genes” - needed for normal cell function
and viability

Question 7

What are tissue-specific genes

Answer 7

25% of genes expressed in the cell are required for cell

specific function- tissue-specific genes- making antibodies in b lymphocytes

Question 8

What is the initial product of gene expression

Answer 8

RNA

Question 9

What are the characteristics of RNA

Answer 9

Cells contain three major species of RNA:

	Transfer RNA (tRNA)

	Ribosomal RNA (rRNA)

		Messenger RNA (mRNA)
Thymine is not a base used in RNA. 
It is replaced by Uracil.
The pentose sugar in RNA is Ribose.
RNA is a single stranded nucleic acid species

Question 10

Describe how RNA can be functional or act as a template

Answer 10

In many cases this RNA is the template for protein translation
(eg mRNA)
In some cases this RNA is functional (eg tRNA, rRNA,snRNA

Question 11

What is transcription

Answer 11

The process in which nucleotide
information in the DNA is copied into RNA
is called TRANSCRIPTION

Question 12

What is the antisense strand

Answer 12

The strand that is complementary to the RNA strand

Question 13

Describe the synthesis of the RNA strand

Answer 13

Ribonucleotide bases are joined by phosphodiester bonds. The RNA chain grows one base at a time in a 5’ ->3’ direction

Question 14

Describe the enzymes involved in transcription

Answer 14

Gene transcription is carried out by enzymes called
“RNA Polymerases”
Gene transcription also involves special gene regulatory
proteins called “Transcription Factors”- regulate ability of rna polymerases.
The “start” of a gene contains DNA sequences that
are important in bringing about Transcription- promoter

Question 15

Describe the 3 types of eukaryotic polymerases

Answer 15

RNA Polymerase I -Transcribes rRNA genes
RNA Polymerase III- Transcribes tRNA and 5S RNA genes
RNA Polymerase II - Transcribes genes encoding proteins
into mRNA

Question 16

Describe how Gene regulation is achieved

Answer 16

The elongation reaction of RNA synthesis requires a separate
and distinct initiation step to build a transcription complex.
The DNA sequences at which the initiation complex assembles is
called a gene promoter .
The amount (level) of transcription from a given gene is regulated by the activity of DNA binding proteins known as Transcription Factors.
More if more is needed- responding to an event- respond to stimuli- altering the expression of genes.

Question 17

Describe the anatomy of a gene promoter

Answer 17

Left- transcription factor binding sites
TATA- specify initiation point for RNA polymerase 11
Bases added.

Question 18

What is the significance of the size of the minor groove

Answer 18

Minor grooves- about the size of the protein- allows DNA to interact with proteins such as transcription factors.

Question 19

Describe the role of TF II D

Answer 19

TF II D contains TATA Binding Protein(TBP) and TBP Accessory Factors (TAF’s). On binding to DNA TF II D:-

Partially unwinds the DNA helix, widening the minor grove to allow extensive contact with bases within the DNA

This unwinding is asymmetric with respect to the TBP-TATA complex,thereby assuring transcription is unidirectional
The unwinding exposes the template strand allowing RNA polymerases to begin transcription- landmark for the subsequent assembly of other proteins at the promoter.

Question 20

What happens after TF II D is bound

Answer 20

Next, TFIIA and TFIIB bind. TFIIB is particularly important,
as it is able to bind to TFIID and RNA Polymerase II
RNA pol II cannot bind to DNA.
RNA polymerase binds to TF IIB with TF IIF bound.
The final steps involve the binding of TFIIE,TF IIH and TFIIJ.
TFII H promotes further unwinding of the DNA helix to
facilitate RNA synthesis by RNA Polymerase II.

Question 21

How is the RNA polymerase released from this complex so that it can begin transcription

Answer 21

RNA polymerase is phosphorylated by transcription factor TFIIH- which contains a kinase in one of its subunits.

Question 22

What is the importance of the basal transcription complex.

Answer 22

In the absence of binding of other Transcription Factors this produces a Basal (low) level of transcription.
Binding of more transcription factors allows the amount of transcription to be regulated depending on stimuli- altering gene expression

Question 23

How do transcription factors interact with DNA

Answer 23

Transcription factors “bend DNA” on binding. They can interact with each other and the Basal Transcription Complex to modulate transcription.
Transcription factors also facilitate transcription by helping to remodel “chromatin”. They do this by recruiting proteins with enzymatic activities that modify histones.
Hyperacetylation- more transcription
Hypoacetylation- less transcription.

Question 24

What factors determine transcription factor expression

Answer 24

Cell lineage is a major determinant of Transcription Factor
expression - what is its cell fate
Transcription Factor expression / activity is altered by signals
external to the cell, eg:

			Hormones
			Growth Factors
			Mechanical Stress
			Heat
			Cell contact
			Light
			Touch
			Voltage

Question 25

Describe the role of transcription factors in inflammation

Answer 25

NF kappa B is a transcription factor- released in response to inflammatory initiators- results in synthesis of cytokines and inflammatory mediators.

Question 26

Describe the role of aspirin in reducing inflammation

Answer 26

Aspirin irreversibly inhibits COX-1 and modifies the enzymatic activity of COX-2. COX-2 normally produces prostanoids, most of which are proinflammatory. Aspirin-modified PTGS2 produces lipoxins, most of which are anti-inflammatory
acts to inhibit the breakdown of IkB. Consequently, NFkB remains in the cytoplasm and is unable to initiate transcription of cytokine genes.
I kappa B is and inhibitor of NF kappa B

Question 27

Describe the role of transcription factors in leukaemia

Answer 27

Over half of Acute Lymphoblastic Leukaemia’s (ALL) involve mutated transcription factors. These mutations are often caused by chromosomal translocations.

Question 28

Describe the role of the oestrogen receptor in Breast Cancer.

Answer 28

Oestrogen is a steroid hormone.

Cells that respond to oestrogen contain a protein called the oestrogen receptor.

The Oestrogen receptor is a transcription factor, that regulates “oestrogen regulated genes”
Breast cancer occurs in ~ 1 in every 10 women

Over half of all breast cancers over express the oestrogen receptor

Breast cancer treatment involves the use of anti-oestrogens, such as tamoxifen

Question 29

What is induced cell pluripotency

Answer 29

Induced pluripotent stem cells (also known as iPS cells or iPSCs) are a type of pluripotent stem cell that can be generated directly from adult cells.

The iPSC technology was pioneered by Shinya Yamanaka’s lab in Kyoto, Japan, who showed in 2006 that the introduction of four specific transcription factors could convert adult cells into pluripotent stem cells.
The 4 transcription factors are: Oct4 (Pou5f1), Sox2, cMyc, and Klf4.

Question 30

What are the levels of the regulation of gene expression

Answer 30

Transcription
RNA processing
RNA transport
RNA turnover
Translational
Protein activity

Question 31

What happens once transcription has begun

Answer 31

The general transcription factors dissociate from the DNA- so that they are available for another round of transcription with a new RNA polymerase molecule.

Question 32

What happens once RNA polymerase has finished transcription

Answer 32

It is released from the DNA, protein phosphatases strip off its phosphate groups- only dephosphorylated forms of RNA polymerase can initiate RNA synthesis.