Bio Exam 4

what is a telomerase

• dna polymerase

what does telomerase do

• it makes DNA from an RNA template

• adds in noncoding DNA

is telomerase always active

• no, in early development it is but if it gets reactivated things like cancer develop

• the “immoorality” trick

what does exonuclease do

• it proofreads mistakes in the 3 to 5 direction

• and also removes primers in the 5 to 3 direction

what is used when there is a mistake in the middle

• an endonuclease

stem cells = divider cells that can do a lot of dividing

basic definition of transcription

• RNA polymerase and proteins work to make RNA versions of the info encoded in a gene

• spontaneous reaction

what is the strand read by a RNA polymerase called in transcription

• the template strand

what is the complementary strand found in transcription

• the non-template or coding strand

where does transcription start

• at the promtor

  • RNA polymerase moves away from the promotr as it reads the gene

upstream meaning

• where and what happens before transcription begings

• what RNA polymerase hasn’t already transcribed

• ex. before promotor

downstream meaning

• what happens after transcription has begun

how does transcription end

• terminator sequence that tells it to cut

translation = synthesizing proteins

what do tRNAs carry

• anticodons

  • that are complementary to the mRNA strand

uncharged vs charged tRNA

• has an amino acid vs doesn’t

what recharges a tRNA

• aminoacyl tRNA synthetase

what are ribosomes made up of

• ribosomal RNA (rRNA)

• have a small and large subunit (together when doing translation, apart when not occuring)

describe ribosome

• has a site for the tRNA to leave

• has a site for the mRNA to enter

• has a site at the top for peptide bonds to go out of

can mRNA be reused after translation

• yes, it

what prevents mRNA from rapid degradation

• 5’ cap and poly-A tail

what is a poly-A tail

• adenine containing nucleotides that are added to the 3 end of a mRNA

• added after transcription

• prevent degradation

• increases translation efficiency

what does the coding strand tell you

• the sequence of nucleotides that the RNA product will have

how is transcription terminated

• terminator sequence

explain transcription and upstream and UTR

• transcription begins upstream BEFORE the AUG codon

  • which makes the UTR region

with translation it starts at the start codon which is never usually the first bases so there is an untranslated region that just isn’t made into a protein

where does the ribosome attach in translation

• 5 end and it keeps going until it finds the start codon

which subunit the small or the large binds to the mRNA

• small

small vs large subunit

• small

  • reads the mRNA

• large

  • holds the tRNA’s in place

  • helps form the peptide bonds

is the release factor used in transcription or translation

• translation

what is a release factor

• a protein

• same shape as a tRNA and triggers the release of the mRNA from the ribosome

• binds to the stop codon

the ribosome is not an enzyme but a ribozyme

• it can just do certain chemical reactions

translocation = moving down (ex the mRNA moving through)

what is the start codons and the name

• ATG or AUG

• methionine

the different steps and their polarity

• dna template

  • read from 3 to 5

• mRNA is made from 5 to 3

• then an anticodon is made 3 to 5

  • but read 5 to 3

are ribosomes involve din transcription

• no! only in translation

what is unique about prokaryotes and transcription and translation

• they can happen at the same time

where do transcription and translation happen (prokaryotes & eukaryotes)

• transcription = nucleus in eukaryotes, cytoplasm in prokaryotes

• translation = cytosol in the ribosomes for both

when looking at the genetic code cart are you reading 3 to 5 or 5 to 3

• you are reading the mRNA 5 to 3

all newly translated proteins start with Met but there can be modfiications or some are lose it over time

after the first MET is added from AUG, any other AUG’s will be just making MET for funsies

how many different codons are there and why

• 61

  • because tRNA’s don’t recognize stop codons or give them an amino acid

release factors bind to and recoginze stop codons NOT tRNA’s!

what is telomerase only for

• LINEAR CHROMOSOMES

What is a mutation

• any change in DNA or genetic information

difference between mutations in germ and somatic cells

• in germ you can pass it to the next generation (think meiosis_

• in somatic you pass it to your daughter cells and not offspring

there are new mutations whenever DNA replicates

• but not only from replication

  • can get mutations from mistakes in meiosis, dna damage (chemical)

missense mutation

• single base change that affects amino acid

nonsense mutation

• translation stops early from a single base

• protein is smaller than usual

silent mutation

• single base that changes mRNA codon but not amino acid

• occurs because o

why do silent mutations happen

• because of the redundancy of the genetic code

are silent mutations always silent

• no because it can still affect splicing

  • like progeria

what is another name for silent mutations that dave likes

• synonymous mutations

  • because its technically not phenotypically “silent”

frameshift mutation

• alters reading frame

do frameshift mutations get affected in the upstream or downstream direction

• downstread in the 3’ direction

mutation is always random!!

where do new alleles come from

• mutations

mutagens

• something that causes mutations

a signal binds where

• to the receptor on the target cell

• and then the target cell changes shape and therefore its activity

do hormones travel short or long distances

• they travel long distances

what is a ligand

• any molecule that binds to a receptor

what are the three groups of chemcial messengers for animals

• amines

  • amino acids

• peptides

  • small proteins

• steroids

  • lipids

where do lipid soluble ligands bind and where do non lipid soluble ligands go

• to receptors insdie the cell

• if not lipid soluble bind onto the outer membrane

In steroid hormone signaling, nonpolar steroid ligands diffuse directly across the plasma membrane and bind to intracellular receptors in the cytoplasm or nucleus

. Once inside the nucleus, the ligand-receptor complex binds to specific DNA sequences to directly regulate gene expression by stimulating the transcription of target genes

transcription and translation can be influenced by cell signalling

mobile loop = covers active site when nothing is it in it

signal transduction

• events that convert one type of signal to another

• an outside signal to the inside

kinase

• an enzyme that catalyzes the aditiion of a phosphate group from ATP to another molecule

are hormones present in low or high levels

• low levels but they can be amplified and create a large response

signal amplification in signal transduction

• a primary messenger can trigger the release of secondary messengers that can amplify the original signal

the hormone receptor complex can interact with DNA

what is a secondary messenger

• an ion or a small molecule

amino acids are highly polar

• because of their r groups

when does full replication of dna only happen

• when it is being signaled to divide for mitosis or meiosis

is dna only sometimes semi-conservative?

• no it is ALWAYS semi conservative

when DNA is replicating the old the new strand is identical to the orginial strand it was paired with

• before the mRNA part

what were the three hypothesis for how DNA replication

1. semiconservative

2. conservative

3. dispersive replication

describe conservative replication

• there is one strand that is the orignial

  • it opens up and is used as a template and then closes itself and the new ones come together and the old go back to the way they were

dispersive replication

• along the length there is some old and some new

every newly addded nucleotide is bringing energy from its phosphates

what direction do RNA and DNA polymerase read and make their strands

• read it from: 3’ to 5’

• make it from": 5’ to 3’

• (built by 5’ to 3’ moving along a 3’ to 5’ template)

do both DNA and RNA need a template

• YES

is there a DNA polymerase that works without a template

• yes, one exception

• and it makes random sequences

• but just remember every one has it

does DNA or RNA polyermarese neeed primer? or both

• DNA polymerase needs primer

• RNA polymerase doesn’t need any primer

all RNA and DNA synthesis is 5 to 3

where does replication begin for circular and linear chromosomes

• at the origin of replication

there are two forks at every origin

• one on each side

eukaryotes can have multiple origins of replication

what does exonuclease do

• replaces the primers

what makes primer

• primase

what is a challenge for linear chromosomes and not circular ones

• that for linear ones they have ends that aren’t replicated

• circular ones don’t have this problem because no ends

what would happen if there was no telemoerase

• then the chromsoome would get shorter and shorter each generation

what is telomerase (function and actually what it is too)

• an enzyme

• it carries an RNA template to extend the DNA template

you can’t just extend the end of a linaer chromosome with more primer because it will keep being the last thing there, and you also cant just put bases there because there is no primer to do that

is the issue of having unfinished replication in the leading and lagging strand?

• this is only an issue in the lagging or discontinuous strand

what type of polyermase is primase

• an RNA polymerase

what is the key to immortality

• telomerase

what is different about cancer cells and telomerase

• it is always activated and there is indefinite (always) division

DNA polymerase essentially always needs an area that is already double stranded so it can work

• because the primase makes a sequence to the template strand

  • leaving it double stranded

primase adds RNA nucleotides