Bio 4 Exam Slideshow

Transcription

DNA to RNA

Nucleotides to nucleotides

Transcription

Translation

RNA to protein

What is the process of transcription

DNA must unwind (called transcription bubble), Template strand (RNA reads this), Non-template strand (coding strand)

Eukaryotic transcription-initiation

Promotors (TATA box), Transcription Factors

Transcription Elongation

RNA polymerase moves along the strand, mRNA transcript elongates (40 nucleotides per second)

What does ribosomes do in translation elongation?

Ribosomes synthesize polypeptides in the N-terminal to C-terminal direction

What does occurs in gene regulation for prokaryotes?

Three processing steps where regulation can occur

What does occurs in gene regulation for eukaryotes?

Four processing steps where regulation can occur

What does histone methylation do in histone modification?

Nucleosomes pack together tightly, transcription factors can’t bind to DNA, and genes are not expressed

Nucleosomes pack together loosely, transcription factors can bind to DNA, and genes are expressed

What does histone acetylation do in histone modification?

What does miRNAs do in eukaryotic post-transcriptional control?

Base pairs with mRNA, can target mRNA for degradation or, prevent initiation complex from forming

Is this positive or negative transcriptional control?

Positive regulation

Is this positive or negative transcriptional control?

Negative regulation

Operons allow bacteria to control when they turn on or turn off expression of genes

What do Operons allow bacteria to do?

What are operons controlled by?

All genes in the operon are controlled by the same regulatory element 

What is the crucial step of a repressor binding?

Repressor binding to operator element is the crucial step of controlling operon function 

What happens to the Lac I repressor protein when it binds to lactose, and how does this affect the transcription of the lac operon?

When bound to lactose, Lac I repressor protein is unable to bind to the lac operator, resulting in transcriptional induction of the lac operon when lactose is present

Transcriptional, post-transcriptional, translational, and post-translational levels

Control of gene expression in eukaryotic cells occurs at which level(s)?

What do Kinases do?

It adds phosphate groups

Remove them and changes the shape and activity of a protein

What do Phosphatases do?

In Post-Translational Control what does control protein folding do?

Cleave part of the amino acid sequence and proenzyme → enzyme

What happens to prokaryotes only in transcription and translation?

Transcription occurs in cytosol and transcription and translation can occur simultaneously

Transcription occurs in the nucleus, and RNA processing occurs before translation

What happens to eukaryotes only in transcription and translation?

It contains promoter regions, and additional proteins assist in the binding of RNA polymerase

What happens to prokaryotes and eukaryotes only in transcription and translation?

What happens to ribosome only in transcription and translation?

It catalyzes peptide bond formation, is made up of two subunits, and binds to start codon

What happens to mRNA only in transcription and translation?

It contains codons and is composed of nucleotides only

What happens to tRNA only in transcription and translation?

It contains anticodons, it binds to a start codon, and is composed of nucleotides only

DNA must unwind, a complicated process that helps regulate gene expression, called a transcription bubble

In transcription, what must DNA unwind?

It is a protein that regulates if a gene is transcribed or not

What is a transcription factor?

Some example of transcription factors are

A vitamin D receptor, retinoic acid receptor, and estrogen receptors

In transcription-elongation what does RNA polymerase do?

RNA polymerase moves along the strand and mRNA transcript elongates

How are splicing done in eukaryotic transcription-RNA processing?

They are done by things called small nuclear ribonuclear proteins (snPNPs). Exons are expressed, but introns are not

In translation, what does ribosomes do?

It has large and small subunits that dissociate when it’s not used

In translation, do ribosomes’ large subunits or small subunits bind first?

Small subunits binds first

Eukaryotic transcription termination

Not as well understood at prokaryotes, terminator equals particular sequences that signals the end of transcription

Eukaryotic transcription RNA processing

Alternative splicing, 5' capping, Poly A tail

5' capping

7 methylguanosine cap

Special codons

AUG (start), UAA, UAG, UGA (stop)

Translation basics

tRNA, transfer RNA, composed of RNA, anticodon is key

translation initiation

Requires initiation factors, small subunit and methionine's tRNA, cap binding proteins recognizes 5' cap, moves 5' to 3' til it gets to AUG, large subunit binds last

Translation elongation

3 compartments (A-aminoacyl site, P-peptidyl site, E-exit site), tRNA enters A (except the first methionine), peptide bond forms in P, E is for exiting

Translation termination

Stop codon signals the end, complex dissociates, protein folding

Protein folding

Some proteins need help folding, often a signal sequence is added as well

What are the components of an amino acid?

center carbon, carboxyl group, amino group, hydrogen atom, R group (side chain)

The central dogma refined

Gene (dna) -> pre-mRNA -> mature RNA -> polypeptide -> functional protein

transcription bubbles

the dna must be opened up and unwound and this is formed

Promoter

Where transcription actually starts

transcription factors

bind to promoter sequence, direct RNA polymerase to begin transcription

terminator

directs the end of transcription, proteins interact with the terminator sequence and cause dissociation of RNA polymerase

5' UTR

untranslated region on the 5' end

3' UTR

untranslated region on the 3' end

direct binding to DNA

estrogen (E2) enters the plasma membrane and binds to nuclear ERS (nERs) then translocates into the nucleus, directly induces transcriptional changes in estrogen-responsive genes

binding to transcription factors

E2-ER complex can interact with transcription factore

anticodon

sequence found at the end of tRNAs that complement a codon

aminoacyl site

receives incoming charged tRNA

peptidyl site

formation of peptide bonds occurs

exit site

uncharged tRNA leaves the ribosome

initiation complex

mRNA + small subunit + Met tRNA, cap binding protein recognizes 5' cap, moves5' to 3' until it gets to AUG, large subunit binds last

Stop codon

signals the end, complex dissociates

release factor

causes the ribosome to disassemble and the synthesized polypeptide is release

bacteria

almost exclusively transcription

eukaryotes

transcription, RNA processing, translation, post-translational

bacteria transcription control

most of bacteria control of regulation is focused on transcription (if it is transcribed it is usually translated and then active), operons

eukaryotes control of transcription

transcription factors, methylation, miRNA

methylation

addition of a methyl group

5' Cap, poly A tail

slow exonucleases, can change rate of degredation

eukaryotes post translational

regulation by adding to proteins (phosphate), kinases add phosphate to proteins, phosphatases remove a phosphate to a protein

acetyl groups

similar to phosphate, addition or removal activates or deactivates

ubiquitin

added to protein, can do many things (degradation, move to different area, alter activity, prevent interactions)

prokaryotes gene regulation

three processing steps where regulation can occur, most occurs on the transcriptional level

Eukaryotes gene regulation

four processing steps where regulation can occur, regulation is distributed across levels, transcriptional regulation is very important though

transcriptional control methods

regulation by environment and cell signaling, epigenetic regulations, depends on transcription factors and regulatory elements

vitamin D receptor

works with vitamin D and the retinoic acid receptor

CpG islands

stable methylation of cytosine, preserved through cell division

chromosome packaging

single human somatic cell can span up to 6.5 ft when untwisted and stretched out, chromosome packaging is highly organized

histone acetylation

adding an acetyl group to histones, nucleosomes pack together loosely, transcription factors can bind to DNA, genes are expressed

miRNAs

micro RNAs, small, non coding, RNA molecules, base pairs with mRNA, can target mRNA for degradation or prevent initiation complex from forming

positive regulation activator

enhances polymerase binding, increasing transcription

negative regulation repressor

blocks transcription

phosphorylation

kinases add phosphate groups, phosphates remove them, changed the shape and activity of a protein, can either activate or deactivate a protein.

What are the types of mutations?

Silent, missense, nonsense, and frameshift

silent mutation

does not change amino acid sequence, usually happens when the mutation is in the 3rd codon

missense mutation

changes the amino acid, it might change the protein or not, depends on the amino acid changed, sickle cell anemia is the result of missense

nonsense mutation

AA -> stop codon, produces truncated protein, usually not good, some types of cystic fibrosis

frameshift mutation

insertion or deletion not divisible by 3, alerts the reading from, changes every AA following the mutation, usually very bad

wild type mutant

most common/consensus/original variant of a gene

spontaneous mutation

results of abnormality in DNA replication or crossing over/anaphase

induced mutation

caused by something environmental, chemical (caused by some kind of chemical, nitrous acid, base analogs), physical (something from the environment, radiation)

germaline

mutation in gametes, passed onto next generation

somatic

occurring elsewhere in the body, not passed on

DNA repair

nucleotide excision, Uvr proteins, proofreading and repair mechanism, removes large section of DNA

nucleotide excision

thymine dimers, modified bases, mismatch + missing bases

proto-oncogene

when mutated becomes oncogene, expressed at high levels, control cell growth and cell division, gain function mutations in proto-oncogenes lead unregulated growth

tumor supressor gene

when functioning prevent cancer

EGFR pathway

controls growth and cell division in some tissues Ras -> Raf -> Mek -> Erk, Ras is a proto-oncogene, missense mutation changes it to an oncogene

P53

Guardian of the genome, half of all cancers connect to p53, controls ability of cell to pass in to G1, can activate apoptosis, tumor supressor

EGF Receptor

part of the signaling pathway with RAS, when activated signals go through cell division, usually responds to epidermal growth factor, but can get stuch on

G1, first gap

cell grows, preparing for DNA replication

S, synthesis

DNA replication