AP Bio Unit 6 (ch 16-18, 20)

gene expression & regulation

what is a virus

additional DNA/RNA enclosed by a protective coat (often protein)

how does a virus reproduce

by infecting a cell and overtaking its metabolic machinery

what is a bacteriophage

infects and replicates within bacteria

what did Hershey and Chase discover

that DNA made up chromosomes and not proteins

why are sugar-phosphates outside the double helix

because they are negatively charged, hydrophilic, polar

what do sugar-phosphates do to DNA

stabilize DNA

why are nitrogenous bases inside the double helix

because they are non-polar and hydrophobic

how does the inside of the double helix affect the nitrogenous bases

it protects them from water

which bases are purines

adenine and guanine

which bases are pyrimidines

cytosine, thymine, uracil

what type of bases pair together

purines and pyrimidines

where does replication begin

origins of replication

how many origins of replication do eukaryotes have

multiple

how many origins of replication do prokaryotes have

one

where are the origins of replication located on prokaryotes

on their circular chromosome

how is the “beginning” different in prokaryotes and eukaryotes

prokaryotes only have one origin of replication while eukaryotes have multiple

what are DNA polymerases

enzymes that build new DNA strands by adding nucleotides

where do DNA polymerases add nucleotides

the 3’ end of the new chain

what does anti-parallel mean in regards to DNA

the 2 strands of DNA are oriented in opposite directions to each other

what does DNA being anti-parallel mean for the 2 new strands formed during replication

they will be anti-parallel to their template strands

how does the antiparallel structure of the double helix affect replication

allows DNA polymerase to add nucleotides to the free 3’ end of a primer of a growing DNA strand

what is a leading strand

new DNA strand synthesized continuously across a template towards the replication fork in the 5’ to 3’ direction

what does the leading strand allow DNA polymerase to do

add nucleotides as the helix unwinds

what is a lagging strand

new DNA strand formed discontinuously along a template strand away from the replication fork

what are the segments of a lagging strand

okazaki fragments

why is the lagging strand created in okazaki fragments

because DNA polymerase can only build the strand in the 5’ to 3’ direction

what is the function of DNA polymerase I

removes the primer from the 5’ end of fragment 2 and replaces it with nucleotides added to the 3’ end of fragment 3

what is the function of DNA polymerase III

synthesize leading and lagging strands and add nucleotides to the 3’ end of the fragment 5 primer in the replication fork

what does DNA polymerase ensure

genetic information is accurately passed on or fixed if damaged

what is the function of helicase

unwinds parental double helix into 2 strands

what is the function of topoisomerase

prevent tangles in the 2 strands ahead of the replication fork

what is the function of ligase

joins the 3’ end of fragment 2 to the 5’ end of fragment 1

what is the function of single-stranded binding proteins

prevent the 2 strands from binding together

what is the function of primase

begin synthesis of RNA primer for the 5th okazaki fragment

why are there very few errors in the final copy of DNA

because DNA polymerase proofread each nucleotide against its template strand as soon as it is bonded to the growing strand

why do linear DNA molecules have problems replicating the ends of their DNA

because their usual replication machinery can’t complete the 5’ end of daughter DNA strands due to not having a 3’ end of a pre-existing polynucleotide

what is the result of linear DNA molecules being unable to replicate the ends of their DNA

rounds of replication are repeated and produce shorter DNA molecules with uneven ends

what is a telomere

protective caps at the end of eukaryotic chromosomal DNA molecules

what is the function of a telomere

prevent the ends of chromosomes from degrading or fusing

what do telomeres allow to happen

genomic stability and cell division

how can telomeres protect from cancer

by limiting the number of divisions somatic cells can undergo

how does the telomeric DNA of an older person compare to that of a younger person

it’s shorter in older people

what is transcription

when a cell copies a DNA segment to transfer the genetic information using an mRNA from DNA to RNA

what does RNA polymerase do

read a DNA template strand and synthesize a complementary RNA strand by adding nucleotides

what are the 3 steps of transcription

initiation, elongation, termination

what is translation

cell decodes an mRNA template into an amino acid sequence

what is formed after translation

polypeptide chain that folds into a protein

where does transcription and translation happen in prokaryotes

cytoplasm

where does transcription and translation happen in eukaryotes

nucleus, cytoplasm

what are codons

mRNA nucleotide triplets

how are codons read

in the 5’ to 3’ direction

what is unique about the AUG codon

it’s duel coded

what is unique about the UAA, UGA, and UAG codons

they code for a stop signal

what does a stop codon do

terminate the codon and ends translation

what macromolecule is RNA polymerase II

enzyme/protein

what does RNA polymerase II do

transcribe protein-coding genes into mRNA precursors

what is the function of RNA polymerase II

split DNA template strand, join RNA nucleotides complementary to template strand

what macromolecule is the promoter

nucleic acid

what does the promotor do

signal where to start making RNA

what is the function of the promotor

serve as a binding site for RNA polymerase and transcription factors

what macromolecule is the terminator

nucleic acid sequence

what does the terminator do

signal RNA polymerase to stop synthesizing RNA (end of transcription)

what does the terminator prevent

excessive transcription, improper gene expression

what is a transcription unit

DNA segment that gets copied into a single RNA molecule

what are the components of a transcription unit

promotor, structural gene, terminator

what does a transcription unit do

initiate transcription, code for RNA, regulates RNA output, ends transcription

what is a transcription factor

protein that controls gene activity

what does a transcription factor do

bind to DNA sequences and turn genes on and off

what is the transcription initiation complex

protein assembly of general transcription factors and RNA polymerase bound to the promotor

what does the transcription initiation complex do

act as the “on” switch for an enzyme to unwind DNA and synthesize the RNA copy

what is the TATA box

DNA sequence in the promotor region

what does the TATA box do

act as a landing/binding site for proteins that initiate transcription

what does upstream mean

direction opposite of transcription

what does downstream mean

direction of transcription

how does initiation occur in transcription

RNA polymerase binds to promotor region

what results from initiation

DNA unwinds and complementary mRNA strand begins getting synthesized

what happens during elongation of transcription

RNA polymerase unwinds forward and rewinds DNA behind it, synthesizes complementary mRNA strand in the 5’ to 3’ direction

what happens during termination of transcription

RNA polymerase stops transcribing and detaches from DNA template, releasing the new RNA molecule

what modification is added to the 5’ end of the RNA transcript

5’-cap (G-cap)

what modification is added to the 3’ end of the RNA transcript

poly-A tail

what does the G-cap do

protect mRNA from getting degraded by enzymes

what does the poly-A tail do

help mature mRNA move from nucleus to cytoplasm

what are UTRs

parts of mRNA that aren’t translated into proteins but serve other functions

what are introns

non-coding segments of nucleic acids

what happens to the introns

they get spliced out by spliceosomes

what are exons

regions that are expressed by translating amino acid sequences

what happens to the exons

they get joined together after the introns are spliced out

how do tRNA molecules differ from each other

they have different anticodons, amino acid binding sites, and if they have wobble base pairing

what do anticodons do

translate mRNA sequences to amino acid sequences

what is wobble base pairing

flexible non-standard base pairing often at the 3rd position of an mRNA codon

what is the structure of a ribosome

large subunit, small subunit, made of proteins and rRNAs

what is the function of a ribosome

read mRNA and synthesize proteins by linking amino acids in the right sequence

what happens in initiation of translation

small ribosomal subunit, mRNA, and first tRNA assemble at the start codon and form a pre-initiation complex

what happens in elongation of translation

ribosome adds amino acids to form a polypeptide chain through decoding, peptide bond formation, and translocation

what is alternative splicing

where a single gene can produce multiple different proteins in/excluding exons during mRNA formation

how does translation terminate

when a stop codon enters a ribosome’s A site

why do some proteins fold to create a functional protein

because its primary structure (amino acid sequence) forms a protein with a 3D molecule containing a secondary and tertiary structure

what are post-translational modifications

chemical changes to a protein after it has been synthesized from mRNA

what do free ribosomes do

synthesize proteins inside the cytosol

where are free ribosomes located

suspended in the cytosol