Unit 6 AP Bio Gene Expression

WE are cooked

purines

double ringed nucleotide structure/adenine and guanine

pyrimidines

single ringed nucleotide structure/cytosine, thymine, and uracil

adenine and thymine

held by 2 H bonds

cytosine and guanine

held by 3 H bonds

Rosalind Franklin

X-ray of DNA, revealing a regular and repetitive pattern in a double helix

Edwin Chargaff

analyzed DNA samples from different species, finding that adenine=thymine and cytosine=guanine always (base pairing)

Watson and Crick

combined Franklin and Chargaff’s findings to create 3D double helix DNA model

DNA

• double stranded helix, sugar phosphate backbone, nucleotide pairs in the center, antiparallel strands

• stores hereditary genetic info

• A=T and C=G

5’ end

free phosphate group

3’ end

free hydroxyl group

eukaryotic DNA

DNA in nucleus, linear chromosomes

prokaryotic DNA

DNA in nucleoid region, circular chromosome

plasmids

• small, circular DNA molecules that are separate from the chromosomes and replicate independently of chromosomal DNA

• primarily found in prokaryotes

• contain genes that may be useful but not required

• genes found on ___ can be exchanged with neighboring bacteria

plasmid

removing ____ from bacteria and inserting a gene of interest to form recombinant ____ DNA

RNA

ribonucleic acid, single stranded, A=U and C=G

conservative model

parental strands are fully conserved

semi conservative model

2 parental strands each make a copy, after one round of replication there’s one parental and one new strand

dispersive model

material in 2 parental strands is dispersed randomly between 2 daughter molecules

Meselson and Stahl

analyzed samples of DNA after generations, found the semiconservative model was accurate

helicase

unwinds DNA strands at each replication fork

single strand binding proteins (SSBPs)

bind to DNA to keep it open

topoisomerase

prevents strain ahead of the replication fork by relaxing supercoiling

primase

initiates replication by adding short segments of RNA (primers) to the parental DNA strand

DNAP III

• attaches to each primer on the parental strand and moves in the 3’-5’ direction

• adding nucleotides to the new strand in the 5’-3’ direction

• creates Okazaki fragments

leading strand

synthesized in one continuous segment, runs 5’ to 3’

lagging strand

moves away from the replication fork, synthesized in chunks, runs 3’ to 5’

Okazaki fragments

segments of the lagging strand

ligase

joins the Okazaki fragments, forming a continuous DNA strand

telomere

repeats units of short nucleotide sequences that don’t code for genes, forming a cap at the end of DNA to postphone erosion

telomerase

enzyme that adds telomeres to DNA

gene expression

• the process by which DNA directs the synthesis of proteins

• 2 stages: transcription and translation (occurs in all organisms)

transcription

synthesis of RNA from DNA, occurs in the nucleus

translation

• synthesis of polypeptide from RNA, occurs in the ribosome

• nucleotide sequence —> amino acid sequence

messenger RNA (mRNA)

• synthesized during transcription using a DNA template

• carries info from the DNA at the nucleus to the ribosomes in the cytoplasm

transfer RNA (tRNA)

• important in translation

• each ____ carries a specific amino acid that the mRNA codon codes for

• can attach to mRNA via their anticodon

• translates into peptide sequence

• each has an anticodon region that is complementary/antiparallel to mRNA

anticodon

three-nucleotide sequence located on a tRNA molecule that binds to a complementary codon on mRNA during protein synthesis

ribosomal RNA (rRNA)

helps form ribosomes and links amino acids together

triplet code

nucleotide sequence coding for proteins is read in groups of 3

template strand

• during transcription, only this one DNA strand is being transcribed

• parent DNA strand guiding the leading strand’s synthesis

• runs 3’-5’

codon

sequences of three consecutive nucleotides in DNA or mRNA that specify a particular amino acid or signal the start/stop of protein synthesis

redundancy

more than one codon codes for each amino acid

reading frame

mRNA codons must be read in correct groupings to synthesize correct proteins (not even one letter can change)

initiation (transcription)

RNAP molecules attach to promoter region of DNA without primer

promoter region

specific sequence of DNA located upstream (5' end) of a gene that acts as a binding site for RNAP and transcription factors in initiation of transcription

eukaryote initiation of transcription

• promoter region called the TATA box

• transcription factors help RNAP bind

prokaryote initiation of transcription

RNAP binds straight to promoter without transcription factors

elongation (transcription)

• RNAP opens the DNA and reads the template strand’s triplet code

• RNAP moves 3’-5’, elongates 5’-3’

• only opens small DNA segments at a time

• growing mRNA strand peels away from DNA template strand and the DNA then reforms

prokaryotic termination (transcription)

• termination sequences causes termination signal

• RNAP detaches

• mRNA transcript released and proceeds to translation without modifications

eukaryotic termination (transcription)

• RNAP transcribes the polyadenylation signal sequence

• codes for a polyadenylation signal

• releases the pre-mRNA from the DNA

• must be modified before translation

pre-mRNA modifications before translation

• 5’ cap: modified guanine nucleotide cap

• Poly A tail: 3’ end receives adenine nucleotides

• RNA splicing: sections of pre-MRNA called introns are removed and exons are joined together

introns

intervening sequence, don’t code for amino acids

exons

expressed sections, code for amino acids

5’ cap and poly-A tail purposes

• help mature mRNA leave nucleus

• help protect mRNA from degradation

• help ribosomes attach to the 5’ end of the mRNA when it reaches the cytoplasm

aminoacyl-tRNA synthetase

enzyme responsible for attaching amino acids to tRNA

A site

• on ribosomal subunit

• amino acid site

• holds the next tRNA carrying an amino acid

P site

• on ribosomal subunit

• polypeptide site

• holds the tRNA carrying the growing polypeptide chain

E site

• on ribosomal subunit

• exit site

initiation (translation)

• begins when the small ribosomal subunit binds to the mRNA

• a charged tRNA binds to the start codon

• large subunit binds

elongation (translation)

• the next tRNA comes to the A site

• mRNA is moved through the ribosomes and its codons are read

• each mRNA codon codes for a specific amino acid

elongation steps (translation)

• codon recognition-the appropriate anticodon of the next tRNA goes to the A site

• peptide bond formation-peptide bonds are formed that transfer the polypeptide to the A-site tRNA

• translocation-the tRNA in the A site moves to the P site, the tRNA in the P site goes to the E site

termination steps (translation)

• stop codon in the mRNA reaches the A-site of the ribosome

• stop codon signals for a release factor

  • hydrolyzes the bond that helps the polypeptide to the P-site

  • polypeptide releases

  • all translation units disassemble

retrovirus

• exceptions to the standard flow of genetic info

• info flows from RNA to DNA using reverse transcriptase

• couples viral RNA to DNA and the DNA becomes part of RNA

operon

• group of genes that can be turned on or off

• 3 parts: promoter, operator, genes

regulatory gene

• produces a repressor protein that binds to the operator to block RNAP from transcribing the gene

• always expressed, but at low levels

allosteric activator

substrate binds to allosteric site and stabilizes the shape of the enzyme so the active sites remain open

allosteric inhibitor

substrate binds to allosteric site and stabilizes the enzyme shape so that the active sites are closed

repressible operon

Ex: trp operon

• can be switched off by a trp repressor

• allosteric enzyme that’s only active when tryptophan binds to it

inducible operon

Ex: the lac operon

• controls lactase synthesis

• default off, allosterically active

histone acetylation

adds acetyl groups to histones, which loosens the DNA

DNA methylation

adds methyl groups to DNA, which causes chromatin to condense

epigenetic inheritance

• reversible modifications

• chromatin modifications do not alter the nucleotide sequences of the DNA but they can be heritable to future generations

mutations

changes in the genetic material of a cell that can alter phenotypes

point mutations

change a singular nucleotide pair of a gene

substitution

the replacement of one nucleotide and its partner with another pair of nucleotides

silent mutation

change still codes for the same amino acid (because of redundancy)

missense mutation

change results in a different amino acid

nonsense mutation

change results in a stop codon (no protein)

frameshift mutation

when the reading frame of the genetic info is altered via in insertion or deletion

nondisjunction

when chromosomes don’t separate properly in meiosis

translocation

a segment of one chromosome moves to another

inversions

a segment is reversed

duplications

a segment is repeated

deletions

a segment is lost

gel electrophoresis

• technique used to separate DNA fragments by size

• DNA is loaded into wells on one end of a gel and an electric current is applied

• DNA fragments are negatively charged so they move towards the positive electrode

polymerase chain reaction (PCR)

• method used in molecular biology to make several copies of a specific DNA segment

• segments of DNA are amplified

• results can be analyzed using gel electrophoresis