Molecular Genetics DAT Ch6

Nucleoside

Ribose Sugar and Nitrogenous Base

Nucleotide

Ribose sugar, Nitrogenous Base, and Phosphate Group

Adenine and Guanine

Purines

Cytosine, Thymine, Uracil

Pyrimidines

T or U

A binds to

C

G binds to

G-C H bonds

3

A-T H bonds

2

Strongest base pair bonds

G and C

RNA

single stranded with ribose sugar (2’ and 3’ OH)

DNA

double stranded with deoxyribose sugar ( 3’ OH)

Nucleosomes

complexes of DNA wrapped around Histone proteins

Histones

positively charged proteins that bind with negatively charged DNA for organization

Chromatin

overall packaging of DNA and histones

Euchromatin

nucleosomes are “loosely packed” so DNA is readily accessible for transcriptions

Heterochromatin

nucleosomes are “tightly packed” so DNA is mostly inactive

Acetylation

removes some positive charge on Histones, relaxing the DNA histone attractions and increasing transcription (Euchromatin)

Deacylation

increasing positive charges on Histones, tightening the DNA histone attractions and decreasing transcription

Methylation

adds methyl groups to Histones, can increase or decrease transcription depending on the gene. Contributes to keeping inactivated genes turned off

Origin of Replication

where the DNA strands first separate to initiate DNA replication

Circular DNA

One origin of Replication in ____

Linear DNA

Two origins of replication in ____

Semiconservative Replication

each new double helix produced by replication has one “new” strand and one “old” strand

Terminal phosphate

5’ end

Terminal hydroxyl

3’ end

Initiation of Replication

form at A-T rich DNA segments (weaker)

Helicase

first replication enzyme, unzips DNA by breaking H bonds between DNA strands creating a replication fork

Supercoiling

tensions ahead of replication fork

Topoisomerase

relieves supercoiling ahead of replication fork

Single Strand Binding Protein (SSBP)

bind to uncoiled DNA strands after helicase to precent reattachment of the strands

Primase

places RNA primers along the template strands to create 3’ ends for nucleotide addition

Sliding Clamp Proteins

hold DNA polymerase onto the template strand

DNA polymerase

adds free nucleotides to 3’ ends. Can only add to hydroxyl group, need primase on 3’ to 5’ strands

Leading Strand

5’ to 3’, produced continuously, 3’ facing away from the replication fork, DNA polymerase can function on its own

Lagging Strand

3’ to 5’, produced discontinuously because 3’ end is facing away from the replication fork. Requires RNA primase to add short segments of RNA to create free 3’ hydroxyl groups, okazaki fragments

Okazaki fragments

found on the lagging strand, DNA fragments

DNA ligase

glues together the separated fragments of DNA after DNA polymerase

Termination

replication fork cannot continue, ending DNA replication

Telomeres

sections of non coding DNA repeated nucleotide sequences at the ends of linear chromosomes so that genetic information is not lost on lagging strands

Telomerase

enzyme that extends telomeres to prevent DNA loss

G1 Phase

Transcription occurs during this part of the cell cycle

Genes

instructions within DNA that code for proteins, first they must be transcribed into RNA before being translated in new proteins

Promoter region

found in both DNA replication and transcription, an area where initiation or replication fork or transcription bubble can be found

mRNA

single stranded messenger RNA transcribed from proteins

Transcription location

Eukaryotes in nucleus, mRNA is then shuttled outside

Prokaryotes in the same place at the same time

Transcription Initiation

promoter sequence next to the gene attracts RNA polymerase to transcribe the gene

Transcription Elongation

transcription bubble forms and RNA polymerase travels 3’ to 5’ direction on the template strand. RNA is created in the 5’ to 3’ direction

Transcription Termination

signals to RNA polymerase to stop transcribing the gene

Template/Antisense/Noncoding Strand

template strand used to transcribe the mRNA

coding/sense strand

almost equivalent to the transcribed RNA beside Uracil

Cystol

Prokaryotes transcription occurs in the ____

Operon

group of genes that function as a single unit that is controlled by one promoter, and an operator region that is near the operon promoter

Repressors

bind to the operator regions

Activators

bind to the promoter sites

lac operon

inducible operon containing LacZ, lacY, and lacA in lactose metabolism

Inducible Operon

must be induced to become active, in a resting state it is inactive

Glucose, Lactose

lac operon will only be induced when there is low ____ and presence of ____

lac repressor protein

constitutively expressed (always on) and bound to the operator blocking transcription of lac operon

Allolactose

derivative of lactose binds to the lac operon repressor protein, removes it from the operator allowed transcription to occur

cAMP and CAP

second level of lac operon regulation, CAMP levels are inversely related to the presence of Glucose. When low glucose cAMP binds to CAP which then binds to the lac promoter region to help attract RNA polymerase and promote transcription

trp operon

prokaryotic operon that is responsible for the production of the amino acid tryptophan, repressible operon

repressible operon

always active and coding for tryptophan synthetase unless there is a high presence of tryptophan

trp repressor protein

tryptophan induces it, attaches to the operator on the trp operon to prevent tryptophan production

Eukaryotic Transcription location

replication in the nucleus → transcription → mRNA → modification→ cystol → translation

Transcription Factors

needed in eukaryotes to help RNA polymerase bind to promoters (TATA) and enhancers

TATA box

found inn the promoter region of eukaryotic RNA strands, AT rich sequence that transcription factors recognize and bind to

Enhancers

eukaryotic DNA sites that activator proteins can bind to, increase transcription found upstream and downstream

Silencers

eukaryotic DNA sites that repressor proteins can bind to, decrease transcription of a gene, found upstream and downstream

poly- A- signal

terminator sequence in eukaryotes that ends transcriptions.

DNA bending protein

allows for colocalization, bringing the enhancers and silencers closer to the promoter regions so transcription factors can bind to promote transcription

post transcriptional modifications

conversion of pre mRNA into processed mRNA which leaves the nucleus, three main types

5’ capping

guanine cap is added to the 5’ end of the mRNA during elongation, protecting the mRNA from degradation and aiding in translation

3’ polyadenylation

addition of a poly a tail on the 3’ end to prevent degradation, signals for end of transcription

Splicing

introns are removed from pre mRNA leaving behing exons that encode functional RNA

spliceosomes

remove the introns from pre mRNA

20,000

human genome contains approximately ___ protein coding genes and contains more non coding introns than exons

Alternative splicing

single pre mRNA has multiple possible spliced mRNA products, increasing diversity of proteins and functions

miRNA

microRNA, small RNA molecules that silence mRNA expression as a post transcription regulation mechanism by base pairing with mRNA

DNA binding motifs

recognize and bind to the major groove of regulatory sequences in eukaryotes and prokaryotes twithought unwinding the double helix, zinc finger, helix turn helix, homeodomain, leucine zipper

Translation

process of converting mRNA into protein products, relying on Ribosomes and tRNA

Ribosomes

made up of one small sub unit and one large subunit, composed of rRNA and proteins

Eukaryotes

40s small and 60s large, 80s ribosome

Prokaryotes

30s small and 50s large, 70s ribosome

codon

group of 3 mRNA bases that code for an amino acid

Codon Degeneracy

there are more codons than amino acids, so several codons can translate into the same amino acid

Start codons

AUG (methionine amino acid)

Stop codon

UAG, UGA, and UAA (do not code for an amino acid)

open reading frame

stretch of DNA between start and stop codons that will be translated

anticodon

group of three tRNA bases that base pairs with a codon, each tRNA carries an amino acid to be added to the growing protein

Aminoacyl tRNA

tRNA bound to an amino acid, functional in translation

Ribosomal binding sites

A- aminoacyl trna, first site

P- peptidyl trna, second site, elongation of peptide bonds

E- exit site, third site, lets go of tRNA

Initiation of Translation

AUG (start codon) pairs with methionine tRNA at the P site

Elongation of Translation

aminoacyl trnas enter the a site, peptide bond formation between polypeptide in p site to the a site trna, translocation (A→P→E)

Termination of translation

stop codon releases factors and polypeptide releases from the ribosome

chaperonin

protein that encompasses peptide chains after they have been translated to ensure they fold correctly to become functional proteins

DNA Mutation

occurs in the germ cell (genetic) somatic (all other cells), Frameshift or Point/Base mutations

Point mutations or Base substitution

one nucleotide is replaced by another, silent, missense (c or nc), or nonsense

Silent mutation

type of point mutation, no change in the amino acid due to the wobble of base three in a codon, relies on codon degeneracy

Missense mutation

type of point mutation, single change in amino acid sequence can have little effect in function (conservative) or large effect in protein function (nonconservative)

Nonsense mutation

type of point mutation, one base change creates a stop codon, early termination