k bio e3

fredrick griffin experiment

found that DNA can transform bacteria by transferring genetic material between them (transformation), had 2 strains of which one was harmless and one was pathogenic, he had heat kill the pathogenic strain and mixed it with the harmless strain resulting in the transformation of harmless to pathogenic killing the mice

hershey & chase experiment

found that DNA is genetic material of a phage (T2), one out of two components of T2 enters e.coli cell during infection, injected DNA of phage provides genetic information

chargaff experiment

discovered that amounts of A:T and G:C bases are equal

crick & watson experiment

studied protein structure with x-ray crystallography that they copied, showed that DNA was a double helix, they created the DNA model with the antiparallel helix and nitrogenous backbones with backbones, structure suggest that DNA replication forms two daughter cells

semiconservative model

crick and watson modeled replication of a double helix where each daughter molecule will have one old and one new strand

DNA structure

5’ P to 3’ OH, need energy, uses thymine

bactrophage/phage

protein device that carries DNA , helped scientists determine if genetic material was DNA or proteins

Origin of Replication (def & 6 parts)

where 2 DNA stands are separated and replication begins (helicase, single stranded DNA protein, topoismerase, primase, DNA polymerase, DNA ligase)

Helicase

turns double stranded DNA into single stranded DNA, unwinds

Single Stranded DNA Protein

keeps DNA single stranded and open

Topoisomerase

corrects super coiling upstream of replication fork

Primase

makes short RNA primer, starts RNA chain from scratch and adds nucleotides one at a time using parental DNA as a template

DNA Polymerase

reads template and makes new DNA on 3’

DNA Ligase

joins DNA fragments together

Mechanisms for regulating gene expression in eukaryotes

control points where gene expression can be turned on or off, sped up or slowed down, only a few are important for particular proteins

Genetic Prokaryote & Eukaryote Facts

both can alter gene expression in response to a changing environment, multicellular eukaryotes gene expression regulates development and is responsible for different cell types, RNA molecules play roles in eukaryote gene expression

Bacteria Response to Environmental Changes

natural selection is favored so only products that are needed at produced by that cell, a cell can regulate the production by gene regulation of feedback inhibition, controlled by the operon model

Operator

regulatory switch positioned within the promoted in a segment of DNA

Operon

the entire stretch of DNA that includes the operator, promoter, and the genes that they control

Tryptophan

repressible operon

Repressor

switches off the operon, prevents gene transcription by binding to the operator and blocking RNA polymerase, product of a separate regulatory gene

Tryptophan Absent

repressor inactive, operon on

Tryptophan Present

repressor active, operon off

Repressible Operon

usually on, binding of a repressor to the operator shuts off transcription (ex- trp)

Inducible Operon

usually off, a molecule called an inducer inactivates the repressor and turns on transcription (ex- lac operon), if lactose is absent then the repressor is active, in prokaryotic cells

Lac Operon

inducible operon, contains genes that code for enzymes used in the hydrolysis and metabolism of lactose

Lac Repressor

active and switches the lac operon off

Inducer

inactivates the repressor to turn the lac operon on

Eukaryote Gene Expression Regulation

all organisms must regulate which genes are expressed at any given time, in multicellular organisms regulation of gene expression is essential for cell specialization

Differential Gene Expression

almost all the cells in an organism are genetically identical but the expression of different genes by cells with the same genome, abnormalities can lead to issues and disease

Regulation of Chromatin Structure

genes within highly packed heterochromatin are usually not expressed, chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression

Histone Acetylation

Acetyl groups are attacked to positively charged lysines in histone tails, they loosen chromatin structure and promote the initiation of transcription

DNA Methylation

the addition of methyl groups to certain bases in DNA, can cause inactivation of genes

Epigenetic Influence

the inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence, passing on to future generation of cells

Control Elements

associated with most eukaryotic genes, segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription, critical for regulation of gene expression

Transcription Factors

initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins, essential for all protein coding regions,

Enhancers

where transcription factors bind to enhance the gene, distal control elements, may be far away from a gene

Alternative RNA Splicing

produced different mRNA from the same transcript and results in the production of more than one polypeptide form the same gene

micro/small RNA

bind to complementary sequences on mRNA molecules, either degrade the target mRNA or block translation

RNA Interference

the use of microRNA to artificially control gene expression by injecting microRNAs into a cell to turn off a specific gene sequence/protein synthesis

Later Stages

after eukaryotic mRNA is fully processed and transported to the cytoplasm, gene expression can still be regulated by breakdown of mRNA, initiation of translation, protein activation, and protein breakdown

RNA Primer

can only add onto 3’ ends, gets things started on short initial nucleotide strand, starting point for new DNA strand

1 Parental Strand

5’ end facing into fork

2 Parental Strand

3’ end facing into fork

Leading Strand

copied into the fork

Lagging strand

copied away from the fork in sections (okazaki fragments)

Mismatch Repair

repair and correct error in base pairing, low error rate, could result in a mutation

Nucleotide Excision Repair

nucleotides cut out and replace damaged stretches of DNA

Transcription (where in prokaryotes & eukaryotes)

DNA to RNA, produces mRNA, first stage of gene expression, starts when RNA polymerase binds to promoter and ends when it encounters terminator

Prokaryote - Cytoplasm

Eukaryote - Nucleus

Translation

mRNA to protein, contains ribosomes and tRNA, starts when ribosome is at start codon and stops at stop codon, synthesis of polypeptide from mRNA

Gene Expression

DNA directs protein synthesis (transcription & translation)

Primary Transcript

initial RNA transcript from any gene prior to processing

Triplet Code

non-overlapping 3 nucleotide information, transcribed mRNA then translated to protein

Template Strand

template for ordering the sequence of complementary nucleotides in RNA transcript

Codons

mRNA base triplets read 5’ to 3’, each specifies/codes for an amino acid

RNA Polymerase

catalyzes RNA synthesis, pries DNA stands apart and hooks together RNA nucleotides

Promotor

DNA sequence where RNA polymerase attaches and signal starts

Terminator

sequence signaling the end of transcription

Transcription Unit

stretch of DNA that is transcribed

3 Steps of Transcription

initiation, elongation, termination

Initiation

starts with methyanine, transcription factors help bind RNA polymerase

Methynine

promotor AT rich, look for TATA box for transcription start point (critical for eukaryotes initiation)

Transcription Factors

help bind RNA polymerase and initiation of transcription

Transcription Initiation Complex

completed machine of transcription factors and RNA polymerase bound to promotor

Elongation

RNA polymerase moves along DNA and untwists double helix, transcription progresses, gene transcribes by several RNA polymerase, nucleotides are added to 3’ end growing/elongating the molecule

Termination - Prokaryotes

polymerase strops transcription at the end of the terminator and mRNA translates

Termination - Eukaryotes

RNA polymerase transcribes polydenylation signal sequence, RNA transcript is released 10-35 nucleotides past the sequence

RNA Processing

after transcription enzymes in eukaryotic nucleus modify pre-mRNA before the genetic messages are dispatched to the cytoplasm, both ends are altered and some parts are cut

mRNA Modification

5’ end receives nucleotide 5’ cap, 3’ end gets poly-A tail, they facilitate the export of mRNA, protect mRNA from hydrolytic enzymes, help ribosomes attach to 5’ end

Introns

non-coding regions

Exons

regions that are eventually expressed/translated into amino acid sequences

RNA Splicing

removes introns and joins exons, creating mRNA with a continuous coding sequence

Splicosomes

variety of proteins and small nuclear riboproteins that recognize sites

Alternative RNA Splicing

some introns may regulate gene expression, some genes can encode more than one kind of polypeptide (more proteins are produced than genes)

tRNA

molecules are not identical, each carries a specific amino acid on one end and anticodon on the other end paired with complementary codon on mRNA, single strand 80 nucleotides long and flat

Aminoacyl tRNA Synthase

charge tRNA, add amino acids to match tRNA

Wobble Effect

flexible pairing at 3rd codon base and allows tRNA to bind to more than one codon

Ribosomes

facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis, subunits are made of proteins and rRNA

E-Site

exit

P-Site

process, grow, carry

A-Site

holds tRNA

3 Steps of Translation

require protein factors

Methylated DNA

tightly coiled DNA, decreases gene expression

Acetylated Histones

unwound DNA, increases gene expression

Initiation - Translation

brings together mRNA, tRNA with the first amino acid, and two ribosomal subunits

Elongation - Translation

amino acids are added one by one to proceeding amino acid, 3 steps (codon recognition, peptide bond formation, translocation), along mRNA in 5’ to 3’ direction

Termination - Translation

occurs when stop codon in the mRNA reaches the A site of ribosome, A site accepts a protein called release factor, water is added, reaction releases polypeptide and assembly comes apart

Completion of Functional Protein

polypeptide chains are modified after translation, it coils into 3D shape, some are activated by enzymes and others form subunits

Targeting Polypeptides to Specific Locations

free ribosomes synthesize proteins (in cytosol), bound ribosomes make proteins of endomembrane system that are secreted from cell (attached to er), identical and can switch