Biology Final Exam Material

Gene regulation vs gene expression

Regulation is the control of where and when gene expression (transcription and translation) occurs because all cells in an organism have the same DNA sequences it just depends on which one is being expressed

Most gene regulation occurs

At transcription

Epigenetic change

Changes to the DNA structure to alter gene expression

Genetic changes

When the DNA sequence changes and it is a mutation

What has to happen for transcription to occur

The transcription factor has to be able to bind to DNA so that RNA polymerase can be attracted and know where to start

Chromatin remodeling

The more relaxed they are, the more transcription will occur

The more compacted they are, the less transcription will happen

Histone tail modification

The more open they are or loose, the more transcription will occur

The more closed they are or tight around the DNA the less transcription will occur

Promoter methylation

Adding methyl to bases and it compacts the DNA

The less there are the more transcription will occur

The more there are the less transcription will occur

Transcription factors

They bind to specific DNA sequences using weak interactions to attract the RNA polymerase to the specific spot and it is regulated

Phosphorylation and binding of other molecules are other processes that change the shape of it

RNA polymerase and general transcription factors

Bind to DNA, the promoter sequence

For gene expression, they regulate and recruit general transcription factors like mediators to initiate transcription just after the promoter sequence (TF=promoter, RNA polymerase= activator)

Activator (positive TF)

Proteins that bind to DNA enhancer sequences and recruit TFs and RNA polymerase

Help RNA polymerase and general TFs bind to DNA to increase transcription

TFs in Ras pathway, steroid hormone receptors, p53

Negative transcription factors

Binds to DNA, proteins bind to silencer DNA sequences and blocks binding of general transcription factors to the promoter sequences and prevent RNA polymerase to do transcription

RNA processing proteins

Unprocessed RNA, also called primary transcript or pre mRNA

Looks like 5’ end and 3’ end tail of RNA with exons and introns

This will eventually produce mature processed mRNA that can exit the nucleus and be translated

What the product is from transcription

Ribosome

Binds to final copy of mRNA (5’ end specifically) and translate mRNA to produce polypeptide

mRNA destroyer

Binds to the UTRs in mRNA

They are part of the mRNA that are not turned into protein, but play. A big role and right before the start and stop codon; 3’ UTR has sequences that act like binding sites for molecules to decide mRNAs fate

Overall process of gene regulation

It occurs in the DNa with epigenetic changes, then transcription in nucleus where different genes are getting expressed, then it is turned into mRNA where it is the primary transcript and splices for specific proteins and then is turned into mature mRNA that will be translated and specific proteins will be made

Splicing

Produces different proteins from the same gene by cutting out introns that will not be coded for translation for proteins

Only the shaded region, the ORF, is used to make the actual protein and the amino acid sequence, everything else will just alter the mRNA sequence

Increases protein diversity without needing more DNA

Mature mRNA

From the pre- mRNA

5’cap is added (promoter sequences is gone) and it is the UTR, start codon, then exons only and some are shaded to code for the protein; stop codon, UTR, then 3’poly tail added to increase stability

Prokaryote attributions

Transcription= cytosol, translation= ribosome and at same time with no RNA processing

For all the genes= 1 strand of mRNA but then a protein for every gene present

Genes are generally on until they are turned off

Operon

Multiple genes under the control of one regulatory region

Each gene has a start and stop codon so multiple RNA polymerases can make different proteins

Tryptophan (trp)

Bacteria needs this to make proteins; when levels are high in the cell, then none of this is produced but when it is low it is produced because gene expression needs energy so it has to be worth it

5 genes in the operon

trpO

The operator of the trp operon so TrpR is the repressor and if tryptophan attaches to the TrpR then it will bind to this operator and no transcription

Ptrp

The promoter of the trp operon where the RNA polymerases will bind to if there is no tryptophan for the repressor to be activated

Lac operon

This is expressed only when lactose is high and glucose is not available; this encodes genes to metabolize lactose only but there is no benefit to express these genes when lactose is not available

When lactose is in cell

Binds to Lacl and it is not repressing the cell so transcription can happen

When glucose is in the cell

Then cAMP is low and will not bind and change CRP’s shape so it cannot bind to CBS and not promote RNA polymerase

Lacl

It is the operator that binds to the operator sequence lacO; it repressed transcription of lac operon and lactose can bind to this and change shape so that it DOES NOT bind to operator and transcription occurs

CRP

It goes on the CBS binding site which is the promoter

Helps activate transcription and cAMP will bind to it when glucose is low to change the CRP shape so it binds to CBS and calls RNA polymerases which has a low affinity and needs this transcription factor

Allosteric regulators

Binding of these changes the shape and function of a protein

EX: trp, cAMP, and lactose

Lac Y

Gene that allows lactose to be imported into the cell/ makes lac permeate

Lac Z

This gene makes beta galactosidase which breaks down lactose into glucose and galactose

High glucose and high lactose

So lactose binds to the Lacl and so it is not repressed

But because glucose is high, cAMP is not produced and so it does not bind to CRP and not to promoter CBS sequence so no transcription of lac operon

Lactose high, glucose low

Optimal environment where the lactose binds to lacl and so it does not repress and cAMP binds to CRP and binds to CBS to attract RNA polymerase and transcription occurs

No sugars present

Because glucose is absent, cAMP is active ad binds to CRP which binds to CBS but no lactose so it does not lift lacl from repressor sequence

High glucose, no lactose

No cAMP so no promoter sequence and no lactose so lacl is on repressor so no transcription

Mutation

A heritable change to the DNA, it is when errors/ damage are replicated then they are mutations

2 causes of mutations

1. Replication errors made by DNA polymerases which that are not corrected

2. DNA damage that is not corrected

How to repair during the synthesis of DNA

When DNA polymerase makes mistake it detects structural distortions in DNA and then goes back to take out wrong base and inserts correct one

How to repair during replication in S phase

Detected by DNA polymerases which, proofreads when it is actively working and catches the error

How to repair damage just after replication

Specialized enzymes detect mismatch remove daughter strand sequence near mistake and DNA polymerases which replaces with correct sequence based on parent strand and then DNA ligase completes the DNA backbone

Depurination of adenine in G0

N glycosidix bond between adenine and sugar phosphate backbone breaks at AP site; very easy to fix it just sees where the release of free adenine at AP sites

Deamination of cytosine to uracil in G0

Spontaneous hydrolysis of amino group from nitrogenous base; frequent; when cytosine is deaminatedm it makes uracil and it is very easy to fix because uracil should not be in DNA and recognize it quickly so DNA polymerase fixes it

Deamination of 5 methyl cytosine to thymine

Methyl group added to certain cytosine bases and when methylated it turns into thymine;

Not easily fixed because DNA will make a T:A bond when it should be G:C so the daughter cell will be different

What do UV rays do to DNA?

Crosslink thymine bases and create covalent bonds between them so it distorts helixes

What does tobacco smoke do to DNA?

This environmental mutagen adds bulky side groups added tot he bases and changes the helix

What do X rays do to DNA?

Most dangerous because it will break the double stranded DNA backbone

Synonymous mutations

Mutation hat changes one base pair, but it still produces the same amino acid

Does not affect the primary protein structure

Nonsense mutation

A base pair changes and creates a stop codon earlier in the sequence

Affects primary and tertiary protein structure

Frameshift mutation

When a base is inserted or deleted from the sequence= shifts all of the bases to make completely new amino acids; best when added or subtracted by groups of three

Affects primary and tertiary protein structure a lot

Missense mutation

A base changes so the new amino acids has different properties than he one previous

Affects primary and tertiary protein structure

Conservative/ neutral mutation

When a base changes the amino acid but they both have the same properties;

Only affects the primary protein structure but not the tertiary structure because it has the same properties so same folding

Blood type enzyme

This enzyme encodes which sugars to match on the proteins on the surface of red blood cells so this tells you what type of blood you have

Type A sugar, Type B sugar, and no sugar (type O) also can have type A and B sugars on

What mutations affect transcription?

In the promoter, enhancer, and silencer sequence that affect RNA polymerase and TF binding

What mutations affect the length of mRNA?

Mutations to exons (whether translated or not)

What mutations affect translation/ proteins?

Mutations to UTRs o capping tails

What mutations affect the sequence/ length of a protein?

Mutations to translated regions of exons