Gene Structure

Question 1

What is a gene?

Answer 1

A region of DNA used as template to synthesise functional complementary RNA molecule (divided into 2 classes - coding and non-coding)

Question 2

What is a coding gene?

Answer 2

A gene that is transcribed and then translated to generate corresponding polypeptide sequence i.e. messenger RNA (mRNA)

Question 3

What is a non-coding gene?

Answer 3

do not serve as templates for making polypeptides; help regulate expression of other genes

Question 4

What is a pseudogene?

Answer 4

Pseudogenes = non-functional inheritable genetic elements similar to functional genes;

unable to produce functional proteins due to genetic alterations (i.e. frameshift/nonsense variants)

~10,000 in mammalian genome (~20% are transcribed into RNAs)

Question 5

What is an Open reading frame (ORF)

Answer 5

sequence of successive nucleotide triplets read as codons specifying amino acids; begin with initiation (start) codon i.e. AUG (coding for methionine) and end with stop codon (i.e. UAA, UAG or UGA)

Question 6

What are regulatory factors?

Answer 6

required by RNA polymerase to initiate transcription of genes; divided into cis-acting (located on same DNA molecule as genes they regulate) and trans-acting (produced by remote genes - migrate to site of action)

Question 7

Give some examples of cis-acting regulatory factors.

Answer 7

Promoter
Enhancer
Silencer
Insulator

Question 8

What is an example of a trans-acting regulatory factor?

Answer 8

Transcription factors = proteins that control rate of transcription of DNA to mRNA, by binding to specific DNA sequences; e.g. TNFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH (required by RNA polymerase II to form basal transcription apparatus)

Question 9

What is a promoter?

Answer 9

regulator region close to 5′ end of gene to which RNA polymerase binds in order to initiate transcription of gene; consists of core promoter and proximal and distal promoter elements

Question 10

Describe the core promoter and proximal and distal promoter elements

Answer 10

Core promoter = most proximal; contains RNA polymerase binding site, TATA box (DNA sequence {5’-TATAAA-3’} located ~30 bp upstream of mRNA start site where transcription factor proteins and histones bind) and/or initiator element (sequence for RNA polymerase II that specifies transcription initiation), and transcription start site (TSS)

Proximal promoter elements = located ~250 bp upstream from TSS; contains many primary regulatory elements; site where general transcription factors bind; e.g. CCAAT box and GC-rich box

DIstal promoter elements = further upstream from gene; also contains transcription factor binding sites, but mostly regulatory elements

Question 11

What is an enhancer?

Answer 11

Regulatory sequence; modulates rate of transcription of associated gene in response to binding of specific proteins (activators); located at variable distances from the TSS; DNA between promoter and enhancer loops out, bringing 2 sequences together

Question 12

What is a silencer?

Answer 12

Sequence bound by repressors, inhibiting activators and reducing transcription; prevent gene expression during differentiation and progression through cell cycle

Question 13

What is an insulator?

Answer 13

Sequence element that protects genes from inappropriate signals emanating from their surrounding environment either by blocking action of enhancer on promoter (if situated between them) or by acting as “barriers” that prevent advance of nearby condensed chromatin

Question 14

Can multiple genes share a locus control region?

Answer 14

Some genes occur in clusters regulated by a locus control region eg Beta-Globin gene cluster

Question 15

What is Post-transcriptional processing?

Answer 15

RNA (primary) transcript of most eukaryotic genes (complementary to entire length of gene) undergoes series of processing reactions to make mature mRNA/non-coding RNA

e.g. RNA splicing = series of reactions whereby intronic RNA segments (non-coding) are removed and discarded while remaining exonic RNA segments (coding) are joined end-to-end

Question 16

Flanking untranslated regions of a gene are known as..?

Answer 16

5’ and 3’ UTRs.

Question 17

What is 5’UTR?

Answer 17

5’UTR spans region from TSS to nucleotide before mRNA start site; binds ribosome (RNA-protein complex; provides structural framework for polypeptide synthesis)

Question 18

Can gene’s use multiple promoters?

Answer 18

10–18% of genes express alternative 5′ UTRs by using multiple promoters; variations act as switches to regulate gene expression i.e BRAC1 = 2 different transcripts derived from 2 different promoters which differ in their 5′ UTRs - shorter transcript expressed in cancerous and non-cancerous breast tissue and efficiently translated; longer transcript predominantly expressed in breast cancers

Question 19

What is 3’UTR?

Answer 19

3’ UTR - immediately follows translation termination (stop) codon; contains:

• terminator sequence (marks endpoint for transcription and releases RNA polymerase)
• regulatory regions - post-transcriptionally influence mRNA polyadenylation, translation efficiency, localization, and stability, and ultimately gene expression
  i. e. polyadenylation signal (AAUAAA) = directs addition (and cleavage) of poly(A) tail to end of mRNA transcript (important for the nuclear export, translation, and stability of mRNA)

Question 20

How many genes are there in the mitochondrial genome?

Answer 20

37 genes coding for two ribosomal rNAs (rRNAs), 22 transfer RNAs (tRNAs) and 13 polypeptides (all subunits of enzyme complexes of the oxidative phosphorylation system)

Question 21

What 2 chains comprise the mitochondrial genome?

Answer 21

The mitochondrial genome consists of heavy- (G rich) and light chain (C rich) transcribed from different promoter regions, in opposite directions

Question 22

How does mitochondrial gene structure differ from nuclear?

Answer 22

Large primary transcripts are produced and cleaved into RNAs for individual genes

Genes are closely clustered and contain no introns