Unit 6 Gene Expression and Regulation

Purines

double ring structure (A, G)

Pyrimidines

single ring structure (C, U, T)

Antiparallel

One DNA strand runs 5’ to 3’, other strand runs in opposite, upside-down direction 3’ to 5’

• 5’ end: free phosphate group

• 3’ end: free hydroxyl group

Eukaryotic DNA

DNA found in nucleus, linear chromosomes

Prokaryotic DNA

DNA is in nucleoid region, chromosomes are circular, can contain plasmids

Plasmids

small, circular DNA molecules that are separate from the chromosomes

RNA

Ribonucleic acid, single stranded

• A=U and C=G

DNA

Deoxyribonucleic acid, double stranded

• A=T and C=G

Conservative model

the parental strands direct synthesis of an entirely new double stranded molecule

Semi conservative model

the two parental strands each make a copy of itself

Dispersive model

the material in the two parental strands is dispersed randomly between the two daughter molecules

Origins of replication

sites where DNA replication begins

Helicase

unwinds the DNA strands at each replication fork

Topoisomerase

helps prevent strain ahead of the replication fork by relaxing supercoiling

Primase

initiates replication

Primers

short segments of RNA added to the parental DNA strand

DNA Polymerase III (DNAP III)

attaches to each primer on the parental strand and moves in the 3’ to 5’ direction, adds nucleotides to the new strand

Leading strand

the newly synthesized DNA strand that is replicated continuously in the same direction as the replication fork

Lagging strand

the newly synthesized DNA strand that is replicated discontinuously in the opposite direction of the replication fork, forming Okazaki fragments

Okazaki fragments

segments of the lagging strand

DNAP I

replaces RNA nucleotides with DNA nucleotides

DNA ligase

joins the okazaki fragments forming a continuous DNA strand

Telomeres

repeating units of short nucleotide sequences that do not code for genes

Telomerase

adds telomeres to DNA to prevent chromosome shortening during replication

Mismatch repair

enzymes remove and replace the incorrectly paired nucleotide, if segments of DNA are damaged, nuclease can remove segments of nucleotides and DNA polymerase and ligase can replace the segments

Proteins

polypeptides made up of amino acids

Peptide bonds

the bonds between amino acids

Gene expression

the process by which DNA directs the synthesis of proteins

Transcription

the synthesis of RNA using information from DNA

Translation

the synthesis of a polypeptide using information from RNA

Messenger RNA

is synthesized during transcription using a DNA template, carries information from the DNA (at the nucleus) to the ribosomes in the cytoplasm

Transfer RNA

important in the process of translation, each tRNA can carry a specific amino acid via the anticodon to the ribosome where proteins are assembled

Anticodon

a complementary codon to mRNA

Ribosomal RNA

helps form ribosomes, helps link amino acids together during protein synthesis, and plays a structural role in the ribosome

Triplet code

sequence of DNA nucleotides read in groups of three

Template strand

the DNA strand is that being transcribed to produce messenger RNA (mRNA)

Codons

The mRNA nucleotide triplets, code for amino acids

Redundancy

more than one codon code for each amino acid

Reading frame

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

Termination sequence

in prokaryotes, causes a termination signal:

RNA polymerase detaches, mRNA transcript is released and proceeds to translation

RNA polymerase

opens the DNA and reads the triplet code of the template strand, moves in the 3’ to 5’ direction, mRNA elongates 5’ to 3’

Polyadenylation signal sequence

in eukaryotes, codes for a polyadenylation signal (AAUAAA), releases the pre-mRNA from the DNA, mRNA can now undergo modifications

5’ cap (GTP)

the 5’ end of the pre-mRNA receives a modified guanine nucleotide “cap,” helps mature, protect from degradation, and facilitates ribosome binding during translation

Poly-A tail

the 3’ end of the pre-mRNA receives 50-250 adenine nucleotides, helps mature, protect from degradation, and facilitates ribosome binding during translation

RNA Splicing

sections of the pre-mRNA, called introns, are removed and then exons are joined together

Introns

intervening sequence, do not code for amino acids

Exons

expressed sections, code for amino acids

Alternative splicing

a single gene can code for more than one kind of polypeptide

Mature mRNA

mRNA after modifications have occurred

Aminoacyl-tRNA synthetase

enzyme responsible for attaching amino acids to tRNA

A site

amino acid site, holds the next tRNA carrying an amino acid

P site

polypeptide site, holds the tRNA carrying the growing polypeptide chain

E site

exit site

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. The A site is open for the next tRNA

Stop codon

signals for a release factor of the polypeptide

Primary structure

chain of amino acids

Secondary structure

coils and folds due to hydrogen bonds forming

Tertiary structure

side chain interaction

Quaternary structure

2+ polypeptide chains interacting

Chaperone proteins

help the protein to fold correctly if it requires modification before it can be functional in the cell

Reverse transcriptase

An enzyme that synthesizes DNA from an RNA template, essential for retroviruses like HIV

Operons

a group of genes that can be turned on or off, made up of three parts: promoter, operator and genes

Promoter

where RNA polymerase can attach

Operator

the on/off switch

Genes

code for related enzymes in pathway

Repressible

(on to off), transcription is usually on, but can be repressed (stopped)

Inducible

(off to on), transcription is usually off, but can be induced (started)

Regulatory gene

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

Allosteric activator

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

Allosteric inhibitor

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

Differential gene expression

differences between cell types resulting from the expression of different sets of genes, leading to varied cell functions and phenotypes

Histone acetylation

adds acetyl groups to histones, which loosens the DNA

DNA methylation

adds methyl groups to DNA, which causes the chromatin to condense

Epigenetic inheritance

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

Transcription initiation

once chromatin modifications allow the DNA to be more accessible, specific transcription factors bind to control elements

Control elements

sections of non coding DNA that serve as binding sites

RNA processing

alternative splicing of pre-mRNA

Translation Initiation

translation can be activated or repressed by initiation factors

Morphogenesis

the physical process that gives an organism its shape

Cytoplasmic determinants

substances in the maternal egg that influence cells

Induction

cell to cell signals that can cause a change in gene expression

Pattern formation

a “body plan” for the organism

Homeotic genes

map out the body structures

Apoptosis

programmed cell death

Mutations

changes in the genetic material of a cell, which can alter phenotypes

Point mutations

change a single nucleotide pair of a gene

Substitution

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

Silent

change still codes for the same amino acid (remember: redundancy in the genetic code)

Missense

change results in a different amino acid

Nonsense

change results in a stop codon

Frameshift mutation

when the reading frame of the genetic information is altered

Insertion

a nucleotide is inserted

Deletion

a nucleotide is removed

Nondisjunction

when chromosomes do not separate properly in meiosis, results in the incorrect number of chromosomes

Translocation

a segment of one chromosome moves to another

Inversions

a segment of a chromosome is reversed

Duplications

a segment of a chromosome is repeated

Deletions

a segment of a chromosome is lost