11.& 12 Organisation + control of genomes

Genome

The complete set of genetic material in a particular cell

Where is prokaryotic genome located?

Nucleoid region

Where is eukaryotic genome located

Nucleus

What is the appearance of prokaryotic chromosome

One chromosome

Single, circular

What is the number and appearance of eukaryotic genome

More than 1, usually in diploid or more sets of chromosomes

Multiple, linear (REM HUMANS ARE STRAIGHT)

(P vs E) which genome is smaller and fewer?

Prokaryotes

(P vs E) number of origins of replication per chromosome

P: 1 E: multiple

What is the importance of multiple origins of replication in eukaryotic genome

Increase speed of replication due to larger genome size

Why are telomeres not present in bacteria

Circular chromosome, chromosome will not shorten each DNA replication cycle as DNA polymerase is able to replace RNA primer with DNA

Histone like proteins vs histone proteins (P vs E)

P histone like proteins

E is large number and various types of histone proteins

Explain level of DNA packing coiling in PROKARYOTES

Circular DNA (1) folded into chromosomal looped domains by histone like protein DNA association (2) folding further compacted by Supercoiling

Explain higher degree of condensation in EUKARYOTES

Double helix DNA (1) associated with histone proteins [DNA is negatively charged histone are positively charged due to high proportion of lysine and arginine → strong electrostatic interactions ionic bonds] to form nucleosome (2) (DNA would around 8 histone proteins) (10nm fibre, joined by linker DNA) → coil around itself chromatin fibre /solenoid 30nm with the help of histone H1 (3)→ forms looped domains 300nm fibre when associated with scaffold proteins (4) → Supercoiling occurs (5)

How are functionally related genes grouped in prokaryotes

Single Operon (since same metabolic pathway) controlled by single promoter

Non coding regions and introns (P vs E)

Prokaryotes not common, less extensive introns than eukaryotes

Are extrachromosomal DNA (plasmids) present in prokaryotes and eukaryotes

E: maybe P: usually absent (exceptions: mitochondria and chloroplast)

How are functionally related genes grouped in eukaryotic genome

Different chromosomes, each gene has individual promoter

What are non coding regions of DNA

Genomes that do not code for proteins or RNA products

What does tandem repeat sequence mean

Short sequence of nucleotides repeated end to end multiple times within the genome

What’s the only 2 that are non coding tandem repetitive DNA sequence

Centrosome and telomeres

List all rhe non coding sequences

1. Distal control element: enhancer silencer

2. Proximal control element: promoter

3. Terminator

4. Introns

5. Telomeres

6. Centromere

Describe promoter

Location: just upstream of transcription start site

Structure: (critical elements improve efficiency and help recruit RNA polymerase and gTF)TATA box, CAAT box and GC box (last 2 may not be present always)

TATA binding proteins/gTF bind to TATA box and recruit other gTF and RNA polymerase → TIC → initiate transcription → increase basal rate of transcription (general not specialised tf)

function: recognition site for binding of gTFs and RNA polymerase to form TIC

Describe introns

Structure: interspersed between coding region exon to form pre mRNA, splice sites at both ends of introns signal RNA splicing

function: allows particular gene to potentially code for several polypeptides (alternative clicking)

Describe terminator

Location: end of gene

Function: TRANSCRIBES terminator sequence on RNA product that serves as a termination signal to STOP transcription → RNA polymerase release premRNA detach from DNA template

transcription termination in prokaryotes

Enzyme: RNA polymerase

Transcribes: terminator sequence rich is guanines and cytosine followed by repeated adenines

hairpin loop forms in guanine rich portions

jam: RNA polymer made pause, placing it directly above AU pairs

strands bonds and cause molecule to separate from DNA, releasing RNA polymerase

Transcription termination in eukaryotes

after poly (A) signal sequence is transcribed, premRNA contain poly a signal AAUUAAA, downstream 10 - 3* nucleotides downstream protein cut it and release

Explain enhancers and activator EASR

POSITIVE Regulatory/control elements, DNA seq bound by specific TF (protein) activator

Location: within intron or near controlled gene

Function:when activator bind to it, promote assembly of TIC → increase T rate.

Mode of action:

1. Promote assembly TIC: activator protein bind -! Spacer DNA bend → allows direct interaction of activators with RNA polymerase and gTF

2. Increase accessibility to promoter → bound activator protein, chromatin remodeling complex/histone acetylene → deco dense → exposed

describe repressor

Negative control element where TF repressor bind to.

Function: inhibit assembly of TIC at promoter decrease rate of transcription

Mode of action: recruit histone deacetylases DNA bind more tights to histone → repressor interact with proteins of RIC and prevent CORRECT ASSEMBLY of functional TIC at promoter decrease rate→ interfere wirh correct binding of TF and activator to DNA by binding at or near P and E.

When are centromeres visible

Metaphase (contracted region where KC proteins bind so that spindle fibres can attach during nuclear division)

function of centrosome

1. Allow sister chromatids to adhere to each other (help of protein cohesion)

2. Allow spindle fibres attach to KC on centromere of sister chromatid

3. Sister chromatid of HC can be separated to opposite poles

4. During anaphase of mitosis or A2 of meiosis when centromeres divide

Structure and function of chromosome

Structure:

• both ends of linear chromosome

• Consists of multiple tandem repeats of short non coding DNA sequence

• 3’ extends beyond 5’ end forming 3’ ss overhang (no complementary strand) which fold back on itself to form T loop (displaces + binds to complementary seq of other strand)

Function!

1. Ensure genes are not lost/eroded with each DNA replication round due to end replication problem - prevent loss of vital genetic info

2. Maintain stability of chr. by preventing as ends of chr from funding via formation of T and D loops

3. Prevents chromosomal ends activating cell system for monitoring dna damage

4. Protect prevent chromosome ends getting degraded by cullular nuclease via telomeric cap

5. Shorten every cell division once critical length of telomeres reached → apoptosis

6. Prevent cancer development by preventing accumulation of mutations as old cells with shortened telomeres undergo apoptosis

What are spacer DNA

Regions of Un transcribed DNA between genes bend

What is telomerase

Ribonucleoprotein (RNA + protein) : reverse transcriptase(synthesis DNA using RNA) + single RNA molecule (provide template sequence AAUCCC for synthesis of teloemric DNA)

• 3’ overhand of DNA molecule via CBP