Unit 6 - Gene Expression and Regulation

An individual's genotype is physically expressed through their phenotype.

Purines

Double Ring Structure

Adenin and Guanine

Pyrimidines

Single Ring Structure

Cytosine, Thymine, and Uracil

Nucleotide Pairing

2 hydrogen bonds for Adenine and Thymine/Uracil

3 hydrogen bonds for Guinine and Cytosyin

DNA

double stranded helix, sugar-phosphate backbone, antiparallel strands, and the primary source of heritable information

Plasmids

small, circular DNA molecules that are seperate from chromosomes

replicate independently from chromosomal DNA and primarily found in ptokaryotes

Conservation DNA Replication

the parental strands are fully conserved and an entirely new double stranded molecule is formed

Semi-Conservation DNA Replication

the parental strands make a copy of itselves so the two daughter molecules have one parental and one new strand

Disperse DNA Replication

the parental strands material is dispersed randomly between two daughter molecules so there is a random mix of parental and new DNA

Step 1 of DNA Replication

begins at the origin of replication where various proteins attach and begin replication on multiple sites of one strand

Step 2 of DNA Replication

Helicase unwinds the DNA strands while single stranded binding proteins (SSBPs) keep the DNA open and Topoisomerase prevent the strain ahead from relaxing/supercoiling

Step 3 of DNA Replication

Primase initiates replication by adding short RNA primer segments to be the foundation of DNA synthesis

Step 4 of DNA Replication

Antiparallel Elongation - DNAP III attaches to each primer and move in the 3’ to 5’ direction adding nucleotides in the 5’ to 3’ direction.

Leading Strand

requires one primer; in the 5’ to 3’ direction

Lagging Strand

requires many primers; in the 3’ to 5’ direction

Step 5 of DNA Replication

The leading strand is synthesized in one continuous segment and the lagging strand moves away from the replication fork and is synthesized in chunks

Okazaki Fragments

segments of lagging strand replicated in the 3’ to 5’ direction

Step 6 of DNA Replication

After DNAP III forms an okazaki fragment, DNAP I replaced RNA nucleotides with DNA molecules

Transcription

synthesis of RNA using info from DNA; allows for message of DNA to be transcribed and occurs in the nucleus

Translation

synthesis of polypeptide using information from RNA; occurs in the ribosomes and the nucleotide sequence turns in the amino acid sequence

mRNA

synthesized during transcription using a DNA template; carries information from the DNA to the ribosomes in the cytoplasm

tRNA

each carry a specific amino acid and attach to mRNA via their anticodon to allow information to be translated into a peptide sequence

rRNA

helps form ribosomes and helps link amino acids together

codons

the mRNA nucleotide triplets

64 combinations in total but only 61 code for amino acids as 3 are stop ___

Redudancy

more than one codon codes for each amino acid

reading frame

codons on the mRNA must be read in the correct groupings during translation to synthesize the correct protiens

Transcription Initiation

RNA polymerase molecules attach to a promoter region of the DNA but it doesn’t need a primer and the promoter is walways upstream of the gene of Intrest to be transcribed

EUKARYOTES - promoter region is called the TATA box transcription factors help RNA polymerase bind

PROKARYOTES - RNA polymerase can bind directly to the promoter

Transcription Elongation

RNA Polymerase opens the DNA and reads the triplet code of the template strand so that the growing mRNA strand peels away and the DNA double helix can reform

Transcription Termination

EUKARYOTES - RNA Polymerase transcribes the polyadenylation signal which releases the pre-mRNA from the DNA and undergo modifications before Translation

PROKARYOTES - a termination sequence cause RNA polymerase to detach, the mRNA reanscript is released and can proceed to Translation without modifications

5’ Cap

one pre-mRNA modification where the 5’ end recieves a modified guanine nucleotide “cap”

Poly-A Tail

one pre-mRNA modification where the 3’ end recieves 50 to 250 adenine nucleotides

RNA Splicing

one pre-mRNA modification where intron sections (intervening sequences not coding for amino acids) are removed and extron sections (expressed section coding for amino acids) are joined together

A site

one of the three sites of a large ribosomal subunit which is specifically the amino acid site and holds the next tRNA carrying an amino acid

P site

one of the three sites of a large ribosomal subunit which is specifically the polypeptide site and holds the tRNA carrying the growing polypeptide chain

E site

one of the three sites of a large ribosomal subunit which is specifically the exit site

Translation Initiation

when the small ribosomal subunit binds to the mRNA and a charged tRNa binds to the start codon (Met) on the mRNA on the P site while the rest will attach to the A site first

Translation Elongation

the next tRNA comes and attaches to the A site where it will wait and attach the carrying amino acid to the growing chain

Codon Recognition

Step 1 of Translation Elongation where the appropriate anticodon of the next tRNA goes to the A site

Peptide Bond Formation

Step 2 of Translation Elongation where the polypeptide transfers from the A site to the one on the P site

Translocation

Step 3 of Translation Elongation where the tRNA in the A site moves to the P site and the one at the P site moves to the E site so that the A site is open for the next tRNA and the cycle repeats till a stop codon appears

Translation Termination

when a stop codon in the mRNA reaches the A site of the ribosome and signals for a release factor to stop Translation

Gene Expression

Organisms must be able to regulate which genes are expressed at any given time

Operon

groups of genes that can be turned on or off and contain three parts: promoters, operators, and genes

Promoter

where RNA polymerase can attach

Operator

the on/off switch

Genes

code for related enzymes in pathways

regulatory gene

prodices a repressor protein that binds to the operator to block RNA polymerase from transcribing the gene

Point Mutations

change a single nucleotide pair of a gene

Substitution

replacement of one nucleotide

Silent

the change still codes for the same amino acid due to redundancy

Missense

the change results in a different amino acid

Nonsense

the change results in a stop codon

Frameshift Mutation

when reading frame of the genetic code is alterned

Insertion

nucleotide is inserted

Deletion

nucleotide is removed

Nondisjunction

chromosomes don’t seperate properly in meiosis and results in the wrong number of chromosomes like in Down Syndrom

Translocation

a segment of one chromosome moves to another

Inversions

a segment is reversed

Duplications

a segment is repreated

Deletions

a segment is lost

Transformation

uptaking of DNA from a nearby cell

Transduction

viral transmission of genetic material

Conjunction

cell to cell transfer of DNA

Transposition

movement of DNA segments within and between DNA molecules

Gel Electrophoresis

technique used to seperate DNA fragments by size since DNA is negatively charged so the smaller fragments more to the positive pole

Polymerase Chain Reaction (PCR)

a method used to moke several copies of a specific DNA segment by amplifying and analysing them through gel electrophoresis

DNA sequencing

process of determining the order of nucleotides in DNA

Restriction Map

the fragments of DNA created from restriction enzymes are amplified by PCR and can be analyzed based on the results of a gel electrophoresis test

Helicase

unzips DNA

Topoisomerase

loosens the DNA coil

SSBPs

proteins that relax the DNA coil

DNAP I

DNA editor

DNAP III

DNA copier

RNA Primase

adds RNA primer to begin replication

Ligase

“glues” nucleotides and joins the okazaki fragments to form a continuous DNA strand

Repressible Operon

on to off

ex. transcription is usually on, but can be repressed or stopped; the end product of the metabolic pathway

Inducible Operon

off to on

ex. transcription is usually off, but can be induced or started; the E. coli lac operon

Allosteric Operon

a model system that uses effector molecules to regulate transcription and allosteric transitions

Regulatory Operon

a genetic regulatory system that controls the expression of genes in bacteria and viruses