Unit 6 Test

review notes, labs, worksheets, POGIL, past notes (amino acids + protein folding)

DNA location

nucleus (eukaryotes) or cytoplasm (prokaryotes)

DNA structure

double stranded molecule in a double helix shape

RNA structure

single stranded but can be in many different shapes and lengths

types of RNA

mRNA, tRNA, rRNA

messenger RNA

carries info from DNA to ribosome

mRNA location

nucleus and cytoplasm

transfer RNA

carries amino acids to ribosomes

tRNA location

cytoplasm

ribosomal RNA

building blocks of ribosomes

rRNA location

cytoplasm

nucleotide structure

pentose sugar, phosphate group, nitrogenous base

deoxyribose vs. ribose sugar

ribose has OH group at 2’, while deoxyribose has H at 2’

nitrogenous bases

adenine, thymine (DNA), cytosine, guanine, uracil (RNA)

purines

double ringed structures; adenine and guanine

pyrimidines

single ringed structures; cytosine, thymine, uracil

chargaff’s base pairing rules

A to T or U with 2 hydrogen bonds; C to G with 3 hydrogen bonds

why are purines paired to pyrimidines

to keep the 2 strands of DNA equidistant

DNA strands

run antiparallel, 5’ to 3’ and 3’ to 5’ strands

how to count carbons on sugar

start from top oxygen and move clockwise; each “corner” is a carbon

backbone of DNA

made up of alternating deoxyribose and phosphate connected by phosphodiester bonds

what connects a base to a sugar

glycosidic bond

how are new nucleotides added?

the OH at the 3’ end of the deoxyribose allows dehydration synthesis to occur

DNA structure in eukaryotes

multiple linear DNA in nucleus, larger

DNA structure in prokaryotes

single circular DNA in nucleoid region, smaller, may contain plasmids

plasmids

small separate DNA carrying unique genes that give advantages to cell survival; replicated independently from main DNA and can be transferred from one cell to another

when does DNA replication occur

S phase of interphase

why is DNA replication a semi conservative process

each parent strand serves as a template, so each daughter strand has one “old” and one “new” strand

topoisomerase

relaxes DNA, preventing it from supercoiling

DNA helicase

breaks hydrogen bonds to separate 2 strands

RNA primase

adds RNA primer to template strands, helps guide DNA polymerase where to start

DNA polymerase

adds new DNA nucleotides to 3’ end only

DNA polymerase III

builds new strands

DNA polymerase I

removes RNA primers and replaces them with DNA nucleotides

DNA ligase

links DNA fragments together by creating phosphodiester bonds in the backbone

stages of DNA replication

initiation, elongation, termination

initiation (DNA replication)

replication begins at origin of replication (eukaryotes have many, prokaryotes have one)

topoisomerase relaxes strands

helicase unzips DNA, creating replication fork

single stranded binding proteins bind to open strands to keep them from rejoining

RNA primase lays down primer

elongation (DNA replication)

DP3 builds strands by laying down complementary base pairs

leading strand

built continuously towards replication fork

lagging strand

built discontinuously away from replication fork

okazaki fragments

fragments of lagging strand

proofreading techniques during replication

DNA polymerase proofreads as they go, mismatch repair mechanisms identify and correct errors that escape proofreading

termination (DNA replication)

DNA ligase bonds fragments together to create 2 completed daughter strands

telomeres

noncoded, repetitive nucleotides at ends of chromosomes that help protect genetic info and provide stability to the chromosome

what happens to telomeres after each round of replication

they shorten - limits the number of cell divisions

telomerase

enzyme that extends telomeres, counteracting shortening in some cells

central dogma of biology

DNA to RNA to protein

what turns DNA to RNA

transcription

what turns RNA into a protein

translation

gene expression

process that turns genetic information into a protein molecule

transcription location

nucleus (eukaryotes) or cytoplasm (prokaryotes)

transcription

RNA polymerase II uses a single strand of DNA to convert a gene into a complementary strand of mRNA, works in a 5’ to 3’ direction

template strand

DNA strand used to make mRNA, aka noncoding, minus, antisense, negative sense strand

alternate names for mRNA (or the DNA strand complementary to the template strand)

positive sense, positive, sense, coding strands

retroviruses

use reverse transcriptase to make cDNA from mRNA, which integrates into the genome to make proviral DNA, going against the central dogma

example of retrovirus

HIV

transcription process (in eukaryotes)

transcription factors attach to the promoter and help RP2 bind to strands - form transcription initiation complex

RP2 unwinds and opens strands to begin transcribing, continues until a termination sequence is reached, forms hairpin loop

promoter

TATA box, upstream of the gene and help RP2 bind to strands

termination sequence

polyadenylation (poly-A) signal

mRNA processing

aka RNA splicing, post transcriptional modification; edits pre-mRNA to make mature mRNA; only occurs in eukaryotes

steps of mRNA processing

adds poly A tail on 3’ end and G cap on 5’ end, spliceosomes splice introns out and exons join together

poly a tail function

adds stability and prevents degradation against nucleases

nucleases

enzymes that break down nucleic acids in the cytoplasm

GTP cap

modified G nucleotide that protects mRNA and helps it bind to the ribosome

alternative splicing

feature of eukaryotes that allow more than 1 protein to be produced from one gene

translation location

ribosomes in the cytoplasm, produces protein by reading mRNA gene sequence, requires energy

ribosome structure

large subunit with 3 groove sites, small subunit; larger in eukaryotes than prokaryotes

A site

binding site for tRNA molecules

P site

contains growing polypeptide chains

E site

where tRNAs exit after they deliver amino acids

codon

3 nucleotide sequence specifying a specific amino acid; universal code

tRNA structure

carry specific amino acid, has anticodon with complementary bases to the mRNA codon - nonsense codon

initiation (translation)

small subunit binds to 5’ end of mRNA to find start codon, first tRNA attach, large subunit attach, ensuring first tRNA is in P site

start codon and its amino acid

AUG, methionine

reading frame

how mRNA is read by ribosomes in sets of three nucleotides

elongation steps (translation)

codon recognition, peptide bond formation, translocation

charged tRNA

tRNA with an amino acid attached

uncharged tRNA

tRNA without an amino acid

codon recognition

charged tRNA with the complementary anticodon enters through the A site

peptide bond formation

ribosome catalyzes formation of a peptide bond between the amino acids in the P and A site

translocation

ribosome shifts down mRNA, moving the tRNAs into the next site, tRNAs leave through the E site

aminoacyl-tRNA synthetase

attaches correct amino acid to tRNA, “charging” it

termination (translation)

when stop codon reached, release factor blocks the A site, causing the polypeptide chain to be released, all components detach and reused

stop codons

UAG, UGA, UGG

what happens after translation?

polypeptide chain folds based on the arrangement of its amino acids, packaged at ER or modified & packaged by golgi bodies

gene expression in eukaryotes vs. prokaryotes

in eukaryotes, transcription occurs in the nucleus and translation occurs subsequently in the cytoplasm

in prokaryotes, transcription & translation occur simultaneously in the cytoplasm, has no mRNA processing

regulatory sequences

non-coding stretches of DNA that interact with regulatory proteins to control transcription and gene expression

regulatory genes

produce regulatory proteins that interact with regulatory sequences to enhance/suppress transcription; usually upstream of the promoter

gene expression in prokaryotes

controlled by operons

operons

clusters of genes under control of a single promoter

3 parts of an operon

promoter, operator, structural genes

indiucible operons

functions in catabolic pathways and are turned off unless the appropriate inducer molecule is present

example of inducible operon

lac operon in E. coli

lac operon

controls metabolism of lactose

lac operon inducer molecule

allolactose

what happens in the absence of lactose in the lac operon?

the lac repressor protein binds to the operator, preventing transcription by blocking RP2

what happens in the presence of lactose in the lac operon?

allolactose binds to the repressor protein, changing its shape so it can no longer bind to the operator - activates transcription

repressible operons

function in anabolic pathways and are turned on unless a product of the operon is in abundance in the cell

example of repressible operon

trp operon in E. coli

trp operon

contains genes necessary for synthesis of the amino acid tryptophan

what is the corepressor molecule for the trp operon?

tryptophan