Molecular Genetics (11)

DNA Polymerase I

Replaces RNA primers with DNA; especially important on lagging strand because Okazaki fragments need a lot of Okazaki fragments

DNA Polymerase II

Moves slower than DNA polymerase III and makes less mistakes; used for proofreading

What are the characteristics of DNA replication in prokaryotes?

Chromosomes are circular and small; two replication forks, one replication bubble

Replisome

The molecular machinery at the replication fork working in unison

Where does transcription take place?

Nucleus

Where does translation take place?

Ribosomes

Messenger RNA (mRNA)

Carries the genetic signal from the nucleus to the ribosomes

Ribosomal RNA (rRNA)

Makes a large part of the physical structure of the ribosome

Why doesn't transcription need a topoisomerase to unwind the DNA?

It only needs genes at portions of the DNA, not the entire chromosome

Initiation (Transcription)

RNA polymerase binds to a sequence of DNA called the promoter and separates the DNA

Which strands form in initiation?

Template strand from 3' to 5' and coding strand from 5' to 3'

Promoter

A region of a gene that contains recognition sites called TATA boxes in eukaryotes and archaebacteria

Termination (Transcription)

RNA polymerase transcribes the terminator signal that causes pre-mRNA to separate from the template strand and RNA polymerase

What nucleotide is the 5' cap?

Guanine

Can multiple ribosomes translate the same mRNA?

Yes

What are the parts of a ribosome?

Large subunit, small subunit, APE sites for tRNA

E Site (Exit)

Where the empty codon leaves the ribosome complex

Which side of the tRNA does the amino acid bind to?

The 3' end, or the amino acid attachment site

How does initiation of translation work in prokaryotes?

Small subunit and first tRNA assemble to form the initiation complex around the start codon with a Shine-Dalgarno sequence before it; the large subunit assembles on top of the first tRNA in the P site

How does initiation of translation work in eukaryotes?

Small subunit and first tRNA assemble to form the initiation complex, which attaches to the 5' cap of the mRNA and moves in the 3' direction until it reaches the first start codon; the large subunit assembles on top of the first tRNA in the P site

What can happen to a released polypeptide after it is translated?

It can pass through the endomembrane system, or it could fold and form proteins

How might regulation be different in multicellular organisms than unicellular organisms?

Multicellular organisms may have specialized cells

Why does DNA synthesis occur?

For mitosis and meiosis

DNA Replication

A semi-conservative process in which an original strand provides a template to create a new strand; each duplicated DNA consists of one old strand and one new strand

Topoisomerase

Relaxes DNA supercoiling in front of the replication fork

Helicase

Breaks the hydrogen bonds between the two template strands; single-stranded DNA binding proteins bind to the strands to prevent reannealing

In what direction is DNA synthesized?

5' to 3'

Leading Strand

The strand that grows continuously in the 5' to 3' direction

Lagging Strand

The strand that grows discontinuously in the 3' to 5' direction in 5' to 3' chunks; creates Okazaki fragments

DNA Ligase

Connects disjointed ends of the DNA backbone in the new strands, such as between Okazaki fragments

Why do we need ligase?

DNA Polymerase I only adds phosphodiester bonds behind each nucleotide, leaving a gap between the last nucleotide is places down and the first nucleotide of the next fragment

What are the characteristics of DNA replication in eukaryotes?

Chromosomes are linear and large; many replication forks, many replication bubbles

Plasmids

Small segments of circular DNA that are separate from the chromosomes and replicate independently

What are the two major groups of prokaryotes?

Archaebacteria and Eubacteria

Transfer RNA (tRNA)

Pulls amino acids into the ribosome to be synthesized as prescribed by the mRNA

Micro RNA (microRNA)

Regulates mRNA translation and breakdown; takes place in post-transcriptional regulation

RNA Polymerase

The multipurpose enzyme that makes pre-mRNA; unzips, primes, and copies DNA in transcription

Elongation (Transcription)

RNA polymerase reads the template strand 3' to 5' and creates pre-mRNA in the 5' to 3' direction

Rho-Independent Termination

Transcription that is terminated by a hairpin loop in the mRNA; used by eukaryotes and some prokaryotes

Rho-Dependent Termination

Transcription that is terminated by a Rho factor; used by some prokaryotes

What kind of pattern in the genetic code would create a rho-independent termination signal?

The nitrogen bases in the DNA and, consequently, the pre-mRNA are complementary, with a section of non-complementary bases in the middle, allowing the hairpin loop to form

5' Cap and 3' Poly-A Tail

Helps protect the mRNA for exonucleases in the cytoplasm; in eukaryotes only

RNA Splicing

Pre-mRNA develops into mature-mRNA by removing the introns in the transcribed RNA; occurs in eukaryotes and archaebacteria only

Introns

Segments of DNA or RNA that do not code for a protein; removed in RNA splicing

Exons

Segments of DNA or RNA that code for a protein; become part of the mRNA that leaves the nucleus

Alternate Splicing

Occurs when one region of DNA can code for multiple proteins by using different exons

Translation

Process of polypeptide chain from mRNA sequence at a ribosome

What is translation like in prokaryotes?

Occurs simultaneously with transcription; no post-transcriptional modifications

What is translation like in eukaryotes?

Must exit the nucleus first; post-transcriptional modifications

Why don't prokaryotes need a 5' cap or a poly-A tail on their mRNA?

The mRNA doesn't travel very far between transcription and translation in prokaryotes; eukaryotes are much bigger, so the mRNA must be protected from exonucleases

Codon

A set of three nucleotides that codes for an amino acid

Start Codon

Methionine (AUG)

Stop Codon

UAA, UAG, UGA

A Site (Aminoacyl)

The attachment site for one tRNA with an amino acid

P Site (Peptidyl)

Binds the incoming tRNA to the peptide chain

Anticodon

Three nucleotides on the tRNA that are complementary to the codon on the mRNA

Wobble Pairing

When the last nucleotide in an anticodon doesn't match up to the codon but still works

Initiation (Translation)

Ribosome assembles around the start codon

Elongation (Translation)

Amino acids are added to the polypeptide chain

Termination (Translation)

Release factor binds to the stop codon

How does elongation of translation work?

A new tRNA enters the A site, and a peptide bond is formed between the amino acids in the A and P sites, causing the tRNA in the P site to release the peptide chain; the ribosome shifts over one codon, and the empty tRNA in the E site leaves

How does termination of translation work?

The ribosome shifts until there is a stop codon in the A site; a release factor enters the A site and binds to the stop codon, causing the ribosome complex to completely break apart, releasing the polypeptide

Do stop codons have tRNA that are complementary to them?

No; they can only be recognized by a protein called the release factor

Regulatory Sequence

A non-coding region of DNA that can influence gene expression; promoters, operators, enhancers, and silencers

Regulatory Gene

A coding gene that produces a product that can influence gene expression

Transcription Factor

A protein that can influence gene expression by binding regulatory sequences

Activator

A transcription factor that turns on or promotes transcription

Repressor

A transcription factor that turns off or decreases transcription

Prokaryotic Operon

A series of related genes where transcription is initiated by one promoter; creates one mRNA and multiple proteins

How are operons regulated?

A repressor attaches downstream of the promoter in the operator region; the repressor physically blocks RNA polymerase

What are the differences between prokaryote and eukaryote genetic code?

Eukaryotes have linear DNA in the nucleus, and prokaryotes have circular DNA in the nucleoid

Primase

Adds an RNA primer from which replication can start from

DNA Polymerase III

Creates a new DNA strand that is complementary to the template strand, starting from the RNA primer

Inducible Operon

Transcription is turned off until an inducer binds to the repressor, releasing the repressor from the operator

How does lactose work in the Lac Operon?

It is an inducer that triggers the transcription of genes responsible for the breakdown of lactose

How do activators work?

They bind to enhancers (regulatory sequences) and guide polymerase onto the promoter

How does cAMP work in the Lac Operon?

It is a coactivator that is produced in the absense of glucose; it turns on CAP (activator) and triggers transcription of genes responsible for the breakdown of lactose

If both glucose and lactose are present, is the Lac Operon turned on or off?

Off

If both glucose and lactose are absent, is the Lac Operon turned on or off?

Off

If glucose is present and lactose is absent, is the Lac Operon turned on or off?

Off

If glucose is absent and lactose is present, is the Lac Operon turned on or off?

On

Repressible Operon

Transcription is turned on until a corepressor binds to the repressor, enabling the repressor to bind to the operator

How does tryptophan work?

It is a corepressor that stops the transcription of genes responsible for the synthesis of tryptophan

Basal/General Transcription Factors

All eukaryotic genes require basal transcription factors for the RNA polymerase to bind to the promoter

Why don't prokaryotes need basal transcription factors?

RNA polymerases in prokaryotes can often bind on their own

Upstream Regulatory Sequences (E)

Eukaryotic regulator sequences can be very far upstream from the promoter, so one regulator sequence can affect multiple promoters/genes

Upstream Regulatory Sequences (P)

Prokaryotic regulator sequences are always proximal to the promoter, so one regulator sequence only affects one promoter

Histones (Eukaryotes & Archaebacteria)

Proteins that DNA wraps around, determining chromatin density

Can RNA polymerase access DNA when wrapped around a histone?

No; for example, no transcription occurs during mitosis

DNA Methylation

A methyl group can be added to the nitrogen bases (C or A, usually C)

How does DNA methylation affect promoters?

It turns off gene expression

How does DNA methylation affect histones?

It turns off or on gene expression

What type of patterns does DNA methylation often lead to?

More long-term patterns in gene expression

What is a likely common application of DNA methylation in multicellular organisms?

Cell specialization

Mutation

Change in DNA; can be good, bad, or neutral

How can a mutation affect a phenotype without affecting coding DNA?

Regulatory sequences can be mutated, but it may have no effect on the translated DNA

Where will mutations have no effect?

Non-coding DNA, introns, or the third nucleotide in the codon

Where will mutations affect amino acid sequence?

Coding DNA

Where will mutations affect protein output?

Regulatory sequences and genes

Missense Mutation

One nucleotide changes to another, resulting in a change in amino acid