Region where polymerase binds, known as the promoter, which has

specific sequences for binding transcription factors along with

enhancers and silencers

Which of the following is a definition of a gene?

a) The transcribed (copied) region upstream of the start codon

b)The protein coding region

c)The transcribed region downstream of the stop codon

d) All of the above

Prokaryotes do not have a nucleus, so that the ribosomes - the machines that do the

translation - can bind directly to the mRNA while it is still being made.

In eukaryotes, transcription takes place in the nucleus and translation takes place in the

cytoplasm. Transcription and translation are compartmentally distinct.

1- capping at the 5' end

2- removal of introns

3- poly adenylation of the 3' end

Capping adds a modified guanosine - 7 methyl guanosine - to the 5' end of the

message.

The cap helps protect the mRNA from degradation and is important for

translation in the cytoplasm.

It holds the ends of the exons together and reforms the sugar-phosphate

covalent bond.

There are two steps to the reaction, In the first step RNA is broken at the

boundary between the intron and the first exon, with the intron forming a closed

loop intermediate called the intron lariat. In the second step, the two exons are

joined together and the intron lariat is released and later degraded.

True or False:

RNA and DNA both have polyadenylated tails

RNA, particularly messenger RNA is a copy of the parts of the DNA information that is

needed at any particular time

It primarily directs the synthesis of proteins through translation of the triplet code into

amino acids,

40%protein

60% RNA (4 different strands)

The 'A' Site is where charged tRNAs come into the ribosome. This "aminoacylated (has it's 3' end attached to the carboxyl group of the nucleotide) tRNA contains an anticodon that attaches to the nucleotide triplet on the RNA

The 'P' site is where the 'peptyl tRNA' goes

'E' Site can be thought of as the exit site. The tRNA here no longer carries an amino acid on it's 3' end.

Initiation is when the small subunit of the ribosome attaches to the RNA and allows for the first triplet (the start codon AUG) to be read by the anticodon of an aminoacylated tRNA

Elongation is the process of growing a polypeptide through the "changing of hands" from one tRNA to another. When a charged tRNA is placed in the 'P' site, it's growing polypeptide chain is attached to the amino acid that is attached to the tRNA in the 'A' site.

Termination is when the stop codon triplet appears in the RNA and instead of a tRNA, a 'release factor protein' appears and hydrolyzes the bond between the tRNA and the polypeptide chain. This releases the protein. Also the Ribosome is disassembled.

Point mutation: Mutates a nucleotide. This mutation may include: an addition, deletion, or any change. This only affects one gene.

Chromosomal Mutation: May change a position or orientation of a whole DNA segment on the chromosome. This will not change any of the bases. This could lead to loss or duplication of the DNA that constitutes a gene. This can affect multiple genes.

Silent Mutation, Missense, Nonsense, and Frameshift.

Silent Mutation is when a base is changed in a triplet, but that triplet still codes for the same amino acid (Due to the redundancy of triplets)

Missense Mutation is when a base is changed and it results in the coding of a different amino acid.

Nonsense Mutation is when a base is changed which results in the production of a stop codon. This results in a truncated protein.

Frameshift Mutation is when a base is added or deleted from the reading frame which pushes the whole frame over one unit. The result is the production of an unintended protein.

From 5' -> 3' the genes are in this order on the DNA:

Lac I, Lac Z, Lac Y, Lac A.

Lac I encodes a protein which suppresses the production of β-galactosidase, but the protein has a binding site that binds to lactose. In the presence of lactose, this protein binds to the lactose instead of the operator.

This allows for the transcription of the DNA and the production of β-galactosidase. The operon will express all it's genes.

In this case, the lac I gene would produce it's suppressor protein and it would bind to the operator, blocking RNA polymerase. This would prevent the production of β-galactosidase.

CRP would be produced since the signal cAMP would be initiated from the lack of glucose, but since Lac I would produce it's suppressor protein, no β-galactosidase would be produced.

The E.Coli would digest all the glucose first. Once the glucose levels were properly low, it would produce a signal [cyclic AMP] which would activate the cAMP Receptor Protein (CRP). CRP binds to the DNA upstream of the lac promoter and recruits the RNA polymerase. 

This process allows for the production of β-galactosidase only when the glucose levels are down

Histones comprise octomer core spool that DNA wraps around twice. This protein is used in the compaction 

Histones have N terminus chains that are more often than not positively charged via amino acids (i.e. lysine). These tails can interact with the phosphate-sugar backbone of DNA which is wrapped around the octomer core.

The tails allow the DNA to either be wrapped very tightly or loosely.

The tails are likely to be positively charged with amino acids, wrapping the DNA tightly against the octomer.

The tails can be modified depending on the amino acids to change the strength of the DNA binding.

RNAP II is in eukaryotes

and RNAP is in prokaryotes

5' to 3'

3' to 5'

3' to 5'

5' to 3'

1) Capping of 5' end

2) Removal of introns

3) Polyadenylation of 3' end

Translation- cytoplasm

Transcription- nucleus

What are enhancers/silencers?

Regions in the DNA that bind to specific proteins that can regulate transcription. 

Enhancers/silencers work from up to 20000 BP away from promoter

1) DNA loops around and the enhancer/silencer region can interact with the promoter region

2) The enhancer/silencer region binds to a chromatin remodeling protein that opens the chromatin at the promoter