Introns and Exons

Question 1

Characteristics of Prokaryotic cells: (7)

Answer 1

• No membrane bound organelles
• Simple genome organization
• Genes usually do not have introns
• Between 500 and 4000 genes
– M. genitalium has 477 genes
• Great degree of diversity
• Unicellular
• Circular DNA

Question 2

Characteristics of Eukaryotic Cells (9)

Answer 2

• All organelles are membrane-bound (e.g. nucleus)
• Complex genome organization
• Large genome size
• Between 6,000 and 30,000 genes
• Genes have introns (non-coding regions)
• Large amount of regulatory DNA - to control gene expression
• High degree of genetic redundancy
• Unicellular or multicellular
• Linear DNA

Question 3

Proteomics

Answer 3

the large-scale study of proteins that

are produced in a cell using the genome - particularly their structures and functions.

Question 4

Transcriptomics

Answer 4

analysis of transcriptomes (gene expression patterns)

transcriptomes are dynamic – patterns vary with cell type, developmental stage etc.

Question 5

Central dogma of molecular biology

Answer 5

DNA to RNA to Protein

You cannot go Protein to RNA to DNA though you can go RNA to DNA.

Question 6

Process of gene expression

Answer 6

1) transcription - RNA is transcribed from DNA template
2) RNA processing - RNA transcript is spliced and modified to produced mRNA which moves from the nucleus to the cytoplasm
3) Amino acid activation - each amino acid attaches to its proper tRNA via specific enzymes and ATP
4) Translation - tRNA add the amino acids to the polypeptide chain as the mRNA is moved through the ribosome one codon at a time.

Question 7

Steps in transcription

Answer 7

1) initiation - RNa polymerase binds to promoter (starting point) and initiates RNA at the start point of the template strand
2) Elongation - polymerase moves downstream from 5’ to 3’ creating the RNa strand
3) Termination - upon transcribing the terminator at the end of the sequence the RNA polymerase detaches from the DNA and the RNA transcript is released.

Question 8

Difference in transcription between prokaryotes and eukaryotes

Answer 8

• In prokaryotes – the RNA transcript of a protein-coding gene is immediately useable as mRNA
• However, in eukaryotic cells it must first
undergo processing

Question 9

RNA processing

Answer 9

1) a cap (modified guanosine triphosphate) is added to the 5’ end
2) Introns are excised and the exons spliced together
3) 50 to 250 adenine nucleotides are added to the 3’ (called a Ploy (A) tail)

Question 10

Chromatin

Answer 10

The complex combination of DNA, RNA and protein that makes up eukaryotic chromosomes

Question 11

Euchromatin

Answer 11

a lightly packed form of chromatin - that is rich in gene concentration,
and is often (but not always) under active transcription

Question 12

Heterochromatin

Answer 12

a tightly packed form of DNA - little or no gene expression in heterochromatic regions of the genome

Question 13

Role of exons in protein domains

Answer 13

Different exons encode
separate domains of
the protein product.
Each domain, an
independantly folding
part of the protein
performs a different
function in the cell.

Question 14

What the pressence of exons and introns means:

Answer 14

The presence of exons
and introns means that
new proteins can
evolve by exon
shuffling among genes
and therefore the
potential to form new
proteins with novel
functions.

Question 15

Control of gene expression

Answer 15

• The control of gene expression enables
individuals to adjust their metabolism to changes in their external and internal
environment and to carry out each of the functions of the cell only when needed.
• The enzymes that transcribe DNA must locate
the right genes at the right time – otherwise serious imbalances and diseases may occur

Question 16

operon

Answer 16

clustered genes (functionally related)

Question 17

repressor protein

Answer 17

binds to operator and blocks

transcription

Question 18

derepression of transcription

Answer 18

molecules bind to

repressor and lower DNA binding affinity

Question 19

activation possible

Answer 19

e.g. CAP (catabolite-activator
protein) protein binds to promoter and stimulates
RNA polymerase binding

Question 20

2 levels of metabolic control

Answer 20

a) Repress expression of the genes for all the enzymes needed for the pathway,
(b) inhibit the activity of the first enzyme in the pathway (feedback inhibition)

Question 21

trp operon

Answer 21

• Involved in the production of the amino acid
tryptophan (5 genes)
• If E.coli is deprived of tryptophan it activates a
metabolic pathway to make its own from another
compound
• If the environment has lots of tryptophan then the
bacterial cell stops producing it (saving energy)

Question 22

lac operon

Answer 22

• Bacteria can use lactose (sugar in milk) as an energy source or as a source
  of carbon to make other molecules
• The lac transcription unit is under the control of a single operator and promoter.
• A regulatory gene (encoded by lacI) is located outside the operon.

Question 23

Examples of negative control of genes

Answer 23

• The lac operon is an inducible operon – it is
normally off, but when an inducer molecule is
present, the operon turns on
• The trp operon is a repressible operon – it is
normally on but when a repressor molecule is
present the operon turns off

Question 24

Methods of gene expression control in eukaryotes

Answer 24

1) Transcriptional regulation in
eukaryotes – the nuclear envelopeoffers post transcriptional control
opportunities

Question 25

Why eukaryotes respond to environmental changes slowly

Answer 25

Eukaryotic DNA sequestered in nucleus
– Environmental signals must be transmitted from cell surface to
nucleus
– Elaborate intracellular signaling systems to control transcription
– Also intercellular signaling important in transcriptional
regulation of multicellular organisms

Question 26

Transcription factors

Answer 26

The protein which mediates the inititation of transcription by RNA polymerase.

Question 27

Example of Eukaryotic promoters

Answer 27

usually include a TATA box (T and A repeats – usually about 25 bp long)

Question 28

Transcription initiation complex

Answer 28

Additional transcription factors which join the polymerase on the DNA

Question 29

What types of regulation use special transcription factors and where do they bind on the DNA?

Answer 29

Heat
Light
Hormones
STFs bind to DNA sequences called Enchancers and often interact with basal transcription factors and RNA polymerase II

Question 30

Histone Acetylation:

Answer 30

attachment of acetyl groups to certain amino acids of histone proteins. When histones are acetylated they grip the DNA less tightly, therefore easier access of genes in that region

Question 31

DNA Methylation

Answer 31

Attachment of methyl groups to DNA bases after the DNA is synthesized -essential for long-term inactivation of genes that occurs during cellular differentiation

Question 32

Alternative RNA splicing:

Answer 32

Different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which are treated as introns

Question 33

Regulation of mRNA degradation

Answer 33

The life span of mRNA molecules in the cytoplasm is an important factor in determining the pattern of protein synthesis in a cell

Question 34

Prokaryotic mRNA life span

Answer 34

degraded by enzymes after a few minutes –quick response to environmental changes

Question 35

eukaryotic mRNA life span

Answer 35

hours, days or even weeks.
E.g. the mRNAs for the protein haemoglobin polypeptides are unusually stable and are translated repeatedly in developing red blood cells