Gene Structure

Question 1

what is glycocalyx

Answer 1

a glycoprotein, polysaccharide that surrounds the cell membranes of some bacteria, epithelia and other cells

Question 2

what are histones

Answer 2

family of basic proteins that associate with DNA in the nucleus and help condense into chromatin

Question 3

what is UASs

Answer 3

upstream activator sequences

Question 4

what are eukaryotic gene systems

Answer 4

• transport of stable RNA from nucleus to cytoplasm

- transcription in nucleus and translation in cytoplasm

Question 5

what is the eukaryotic gene structure like

Answer 5

DNA: associated with histones, linear, genes may contain introns, in nucleus

Internal structures have membrane-bound organelles (mitochondria, chloroplasts, vacuoles)
Ribosomes are 80S

Question 6

what types of reproduction are there in eukaryotic gene systems

Answer 6

> asexual (mitosis)
sexual (meiosis)
DNA usually paired (diploid or more)

Question 7

what are the two short sequences in the core promoter structure of prokaryotes

Answer 7

> at -10 (Pribnow box, or -10 element) usually 6 nt: TATAAT, and absolutely essential for transcription start
at -35 (-35 element) usually 6 nt: TTGAGA, is present, transcription is very high

Question 8

what is the structure of eukaryote gene DNA

Answer 8

Promoter 
Transcription start
5’ UTR
Exons and introns 
3’ UTR
Transcription end point

Question 9

what do eukaryote promoters contain

Answer 9

1. TATA box (TATAAA) to form RNA polymerase transcription complex
2. CAAT box
3. Enhancers, silencers and other upstream activator sequences (UASs) differs from those of prokaryotic genes

Question 10

what are the promoters like in eukaryotes

Answer 10

diverse and complex; regulatory elements can be several kilo base pairs in length from ATG = bending of DNA

Question 11

what is the termination in prokaryotes

Answer 11

1. Rho-dependent

2. Rho-independent

Question 12

what is the transcription termination in eukaryotes

Answer 12

not known but two models proposed

1. torpedo model
2. allosteric model

Question 13

what is the torpedo model

Answer 13

Protein factors recognise terminator signals associated with RNA polymerase II triggering termination process

Question 14

what is the allosteric model

Answer 14

Poly A signals transcribed to mRNA and two proteins transfer Carboxyl terminal domain of RNA polymerase II to polymerase A signal

Question 15

how is mRNA made in eukaryotes

Answer 15

1. mRNA capped (methyl guanosine at 5’ end)
2. mRNA tailed (polyadenosine at 3’ end, usually 200nt of As)
3. mRNA spliced (intron boundaries are cut and rejoined to remove intron sequences from the nascent mRNA). Eukaryotic nuclear genes, this is carried out by spliceosome. Prokaryotes, introns are much rarer and of different type
4. mature mRNA is transported from nucleus to cytoplasm, where translation will over

Question 16

what is the Shine-Delgarno sequence

Answer 16

AGGAGGU - AUG (3-10 nucleotides)
prokaryotes, consensus sequence in mRNA
to which ribosomes bind

Question 17

what makes up a mRNA cap and where is it

Answer 17

Cap is an extra guanosine triphosphate joined backwards (5’ end to 5’ end) onto front of mRNA

Question 18

what is the capping structure like in prokaryotic mRNA

Answer 18

very few prokaryotic mRNAs, mainly from viruses that infect eukaryotic cells, have specific site in 3’ UTR of mRNA, which ribosome can bind
Most do not, have a cap structure. One subunit of ribosome (plus other factors) binds to cap and move along mRNA looking for first AUG

Question 19

what are the nucleotides like in the original mRNA

Answer 19

Nucleotide and first couple of nucleotides in the original mRNA have methyl groups attached to them

Question 20

how does tailing of mRNA in type II genes occur

effect

Answer 20

no terminator of transcription

• transcription continues beyond end of gene. mRNA is cut and string of couple of hundred adenosines (poly A tail) is added
• ribosome can’t bind to cap until whole set of proteins (initiation factors) have bound there

Question 21

what is molecules are capped and tailed

Answer 21

only mRNA

Question 22

what is the role of cap and tail

Answer 22

help ribosomes bind

Question 23

what occurs if the mRNA cap and tail are removed

Answer 23

removed won’t translate efficiently, or translate at all

Question 24

what does the capping and tailing protect

Answer 24

mRNA from nucleases

Question 25

what determines the end of tRNA and rRNA

Answer 25

specific terminator sequences

Question 26

what are genes transcribed by that don't make functional proteins and why

Answer 26

genes transcribed by RNA polymerase I and those translated by RNA polymerase III do not encode proteins so don’t need to be translated – don’t have these structures or mechanism of termination

Question 27

examples of eukaryote proteins additional processing | and why

Answer 27

usually addition of molecules to them in order to make them functional, e.g. 1. Phosphorylation (addition of phosphate) 2. Methylation (addition of methyl groups) 3. Glycosylation (addition of carbohydrate chains)

Question 28

how can proteins be activated

Answer 28

by post-translational proteolysis (trimming of N or C termini or internal cleavage to yield one, or more smaller polypeptides)

Question 29

how may eukaryote proteins be targeted intracellularly

Answer 29

- out of cell - to the endomembrane system (vacuole, protein bodies or lysosomes) - to other organelles (mitochondria and plastids)

Question 30

why aren't proteins intracellularly targeted the same in prokaryotes as eukaryotes

Answer 30

prokaryotes don’t have most of these cellular compartments