AP bio unit 6 genetics

central dogma

the flow of genetic information in cells, from DNA to RNA, then from RNA to polypeptide (DNA replication, transcription, translation)

retroviruses

viruses that have an RNA genome (instead of a DNA genome), including an enzyme (reverse transcriptase) that allows it to go through REVERSE transcription, using its RNA to synthesize DNA

reverse transcription

rna is used as a template, pairs up with one DNA strand, then DNA replicates to create 2 strands (eg. in HIV, a retrovirus).

nucleus

where does (DNA) replication occur in eukaryotes?

nuceloid

where does (DNA) replication occur in prokaryotes?

multiple linear (multiple strands)

structure of DNA in eukaryotes?

single circular (it literally only has 1 DNA (still double helix))

structure of DNA in prokaryotes?

a, t, c, g

what nitrogenous bases is DNA made up of?

pentose sugars (deoxyribose), and phosphate groups

what is the backbone of DNA made of?

nucleotide

the combination of a pentose sugar, phosphate group, and nitrogenous base

purine

has a double ring structure, includes bases A and G

pyrimidine

has a single ring structure, includes bases C and T (and U in RNA)

2 (hydrogen bonds)

how many bonds do A and T have?

3 (hydrogen bonds)

how many bonds do G and C have?

5’ end

which end of the DNA has the phosphate?

3’ end

which end of the DNA has the hydroxyl group?

yes (think of two lane traffic, cars go opposite each other on different lanes)

are DNA strands antiparallel?

3 to 5

what way is DNA READ?

5 to 3

what way is DNA SYNTHESIZED?

DNA helicase

unwinds the DNA strands by breaking the hydrogen bonds between bases, 1st step in replication

topoisomerase

relaxes supercoiling in FRONT of the replication fork (think when untwisting two strands twisted together, when you pull one side to untwist, the other side gets tighter, or supercoils that’s how it made sense to me)

replication fork

where the DNA separates during replication, in the shape of this utensil

primase

synthesizes the RNA primer (DNA polymerase requires RNA primers to initiate DNA synthesis)

RNA primer

a series of nitrogenous bases (AGCU) created by primase to tell DNA polymerase where to start replication; DNA polymerase goes back and removes/edits these later

DNA polymerase

synthesizes new strands of DNA continuously on the leading strand and discontinuously on the lagging strand

leading strand

synthesized continuously TOWARDS the replication fork (the ‘3 to ‘5 strand)

lagging strand

synthesized discontinuously AWAY from replication fork ( the 5’ to 3’ strand), since DNA polymerase reads 3’ to 5’, it has to keep doubling back and reading/synthesizing as more DNA is unraveled (this needs multiple primers)

ligase

joins the fragments (okazaki fragments) on the lagging strand; “seals the bond” between fragments by joining the 3’ and 5’ ends

okazaki fragments

fragments of DNA synthesized on the lagging strand because DNA polymerase has to keep doubling back

SSBs

proteins that keep the separated single strands from coming/joining back together

DNA replication

a semi-conservative process (keeps the old strands but adds new strands through replication) that makes new DNA

transcription

process of turning DNA into mRNA

nucleus

where does transcription occur in eukaryotes?

nucleoid (cytosol)

where does transcription occur in prokaryotes?

a, u, c, g

what nitrogenous bases is RNA made of?

pentose sugars (ribose), and phosphate groups

what makes up the backbone of RNA?

3 to 5

what way is mRNA READ?

5 to 3

what way is mRNA SYNTHESIZED?

template strand

the 3’ to 5’ strand, the OPPOSITE of its bases make the mRNA strand

coding strand

the 5 to 3 strand, its bases are the exact same as the mRNA strand (except for t replaced with u)

RNA polymerase

separates the DNA strand and synthesizes mRNA molecules in the 5 to 3 direction by reading the template DNA strand in the 3 to 5 direction

promoter

the site where RNA polymerase binds to start transcription (made of series of nitrogenous bases)- just a region

transcription factors

activators/inhibitors that turn on/off gene expression and binds to the DNA, affecting the ability of RNA polymerase to bind

eukaryotes

are post-transcriptional modifications present in eukaryotes or prokaryotes?

post transcriptional modifications

changes that occur to RNA transcripts after they are transcribed from DNA, but before they are translated into proteins, and include processes like capping, splicing, and polyadenylation. 

5’ guanine cap (capping)

signals the “start” of the mRNA transcript for ribosome to bind, facilitates export from nucleus, allows mRNA to come out of the nucleus into where the ribosomes are (cytosol)

splicing

removal of introns from pre-mRNA transcript, cuts out unnecessary sequences/non-coding regions

introns

unnecessary sequences and non-coding regions cut out during splicing (post transcriptional/mRNA modification) in eukaryotes

poly a tail

a bunch of adenines put at the end of the mRNA (3’ end), inhibits DEGRADATION from hydrolytic enzymes in cytosol and prolongs the “life” of mRNA

translation

going from mRNA (RNA) to polypeptide (from one language to another)

NO

do prokaryotes cut out introns?

rRNA (ribosomal RNA)

RNA that makes up ribosomes

large subunit

the subunit of a ribosome that binds tRNA (transfer RNA)

tRNA (transfer RNA)

carries a specific amino acid to the ribosome, to correctly translate from mRNA to polypeptide

small subunit

the subunit of a ribosome that binds mRNA (messenger RNA)

mRNA (messenger RNA)

the RNA that is synthesized from DNA, and brings the genetic “message”/code to correctly code for polypeptides

cytosol and rough ER

where does translation occur in eukaryotes?

cytosol

where does translation occur in prokaryotes?

True

T/F: all ribosomes start out in the cytosol, then receive a message to attach to the rough ER

initiation, elongation, termination

what are the 3 steps of translation?

initiation

start codon “activated” (AUG), methionine created

AUG, methionine

what is the start codon and amino acid for all proteins?

elongation

the polypeptide is “elongated”, base pairs between tRNA and mRNA are attached, and amino acids attached with the tRNA to the growing chain.

termination

the ribosome hits the “stop” codon, and stops making the polypeptide

UAG, UAA, UGA

what are the 3 stop codons for translation?

a site

the site on a ribosome where the amino acid is added in, tRNA comes up to the mRNA and adds the amino acid and attaches the anti-codon which is going to base pairs up with the codon in mRNA

p site

where completed a site attachments (amino acids/tRNA) shifts over, where we have our growing polypeptide chain (this site holds the polypeptide chain together)

e site

an empty space for amino acids ready to exit on the ribosome, final shift/translocation in the ribosome

hydrolysis (signals for a water molecule to come in and break the polypeptide chain)

what happens when the ribosome reaches the stop codon?

yes

can DNA polymerase proofread/check itself?

nuclease (ligase then seals back together)

what does DNA polymerase to use to cut out mismatching bases to fix them?

NO (instead a release factor comes in which signals for water to come in and hydrolyze)

when the ribosome hits the stop codon, does it attach another amino acid?

changes it to DNA

what does DNA polymerase do to the RNA primer?

point mutations

mutations at ONE nucleotide base pairs (UAA→ UCA)

silent mutation

a type of point mutation that doesn’t change the amino acid once translated

missense mutation

a point mutation that changes from one amino acid to another when translated (UUA→GUA) (Leu→Val)

nonsense mutation

a point mutation that results in a premature stop (UUA→UAA) “don’t know the end of the sentence"

frameshift mutation

caused by the insertion or deletion of 1 or 2 nucleotide base pairs- shifts the “reading frame” for codons (UUA→UUGA, now the amino acids will have to group differently)

chromosomal mutation

rearrangement of chromosome parts or changes in chromosome numbers

insertion, deletion, duplication, inversion, translocation

types of chromosome rearrangements possible for a mutation?

nondisjunction, polyploidy

how can you have changes in chromosome number?

polyploidy

when you have a WHOLE nother set of chromosomes (you normally have 2, now you have 3)

operons

made up of a promoter, operator, and genes, which can be turned “on and off” to regulate gene expression and RNA synthesis

promoter

site where RNA polymerase binds

operator

site where repressor binds

repressor

STOPS RNA polymerase/Transcription → “rock on the train track”, does this by INHIBITING RNA POLY. FROM BINDING

repressible operons (this whole process happens in prokaryotes, not eukaryotes, although eukaryotes have a lot of the same parts)

these operons start ON, and a repressor attaching makes them INACTIVE (turned OFF); they usually synthesize something (some sort of anabolic pathways), but when they don’t need anymore, a repressor binds to halt RNA synthesis. EX: Trp operon, synthesizes tryptophan, if there’s too much tryptophan, it will act as a ligand and bind to the repressor to turn it OFF

inducible operons (this whole process happens in prokaryotes, not eukaryotes, although eukaryotes have a lot of the same parts)

these operons start OFF, and a repressor attaching makes them ACTIVE (turned ON); they usually break something down (catabolic pathway) In these cases, the repressor is always bound to the operon, but when a molecule needed to be broken down is present, it attaches to the repressor and the repressor FALLS OFF- ex: lac operon, synthesizes enzymes to break down lactose, always repressed, but if lactose is present, it binds to repressor to inactivate (the repressor), repressor falls off and the operon is turned ON

NEGATIVE

what type of feedback loop are both inducible and repressible operons?

CAP

a positive feedback loop, this is here if we want RNA polymerase to bind more often/effectively and produce more mRNA than it is already, and activated by binding to cAMP, that signals when glucose levels are low and we NEED MORE ATP (cAMP is formed through hydrolyzation of ATP)

gel electrophoresis

separating molecules based on size and charge- power is turned on and DNA fragments migrate though gel, fragments separated by size bc the smaller the fragment, the more it can travel through little holes in the gel and vice versa for larger fragments; thicker band=more DNA there, thinner band=less DNA

PCR (polymerase chain reaction)

makes multiple copies of DNA fragments, done if you’re trying to amplify your DNA

heating, cooling, annealing

steps of PCR in order?

heating

denatures the DNA and pulls it apart into single strands, 1st step in PCR

cooling

allows primers to bind to the specific places we want on the structure, 2nd step in PCR

annealing

this is when the DNA polymerase goes through and synthesizes DNA, 2rd step in PCR

TAQ polymerase

what polymerase do you have to use in PCR because of so many heating and cooling cycles?

bacterial transformation

introduces genetic material (plasmid) to bacteria, put plasmid into solution with bacteria, then heat-shock it to open up the membrane to allow plasmid to come in, then see which of them grow (if they have antibiotic resistance to the plasmid, they’ll still grow in the presence of the antibiotic)

DNA sequencing

using radioactive nucleotides to determine the sequence of a DNA strand, coding each of the different nucleotides

kind of (because they are separated and independently regulated, each with their own promoter regulating multiple genes, ex: the trp operon in eukaryotes controls 3 genes, and synthesizes the mRNA all at once (this is really confusing to me too))

do eukaryotes have operons?