AP Biology Unit 6

Eukaryotic chromosomes

Multiple, linear DNA molecules that are wrapped around histone proteins to form chromatin

• In the nucleus

Prokaryotic chromosomes

Single, large circular, and double stranded DNA molecule

• In the nucleoid region.

• Carry essential genes for survival

Plasmid

Small, circular, and double stranded DNA molecules that are seperate from the main bacterial chromosome.

• Carry non essential accessory genes

• Replicate independently of the bacterial chromosome

How is DNA able to be used to hereditary information?

Linear sequence of nucleotide bases act as a code that stores genetic information.

Bases are grouped to form genes

Importance of complementary base pairing in DNA

Important for accurate replication of DNA: each DNA strand can serve as a template for a new strand which allows for the creation of two new, identical DNA molecules.

• Preserves genetic information and minimizes mutations.

Semiconservative

Each new DNA strand formed consists of one new strand and one old strand.

Direction of DNA synthesis

5’ to 3’

• DNA polymerase adds new nucleotides to the 3’ hydroxyl end

Reads the strands 3’ to 5’

Replication fork

Y-shaped structure formed when the double helix is unwound.

• Replication bubble: Open region of DNA where replication occurs, each bubble contains 2 replication forks.

Steps of DNA replication

1) DNA replication begins at sites called origins of replication (eukaryotic cells have many while prokaryotic cells have 1)

2) Helicase unwinds the DNA strands

3) Single stranded binding proteins bind to each strand of DNA to prevent them from joining again

4) Topoisomerase relaxes supercoiling ahead of the fork

5) Primase adds primers to each of the strands (DNA polymerase can only add nucleotides to an existing strand.

6) DNAP III adds nucleotides, synthesizing new strands of DNA. Proofreads as it goes.

7) Ligase joins Okazaki fragments

Leading strand

Synthesized by DNAP III continuously because its template strand runs 3’ to 5’ toward the replication fork, so DNAP III follows helicase

• One primer

Lagging strand

Synthesized by DNAP III discontinuously because its template strand runs 3’ to 5’ away from the replication fork, so DNAP III has to keep jumping back.

• Synthesized in short Okazaki fragments

• Multiple primers

DNAP I

Replaces RNA nucleotides with DNA nucleotides

Telomerase

Enzyme that adds telomeres (repeating nucleotide sequences) to the 3’ end of the aging strand template, so lagging strand synthesis can finish.

• Form a protective cap at the end of DNA

mRNA

Carries genetic information from DNA to ribosomes

tRNA

Carries amino acids to the ribosome during translation.

• Have an anticodon that matches an mRNA codon.

rRNA

Along with various proteins it helps form the ribosome.

• Helps link amino acids together: acts as a ribozyme, forming peptide bonds.

Promoter

A DNA sequence upstream of a gene that serves as a binding site for RNAP

• In prokaryotes, RNAP binds directly to the promoter.

• In eukaryotes, the promoter region is called the TATA box.

• regulatory sequence

Template and coding strand

Template strand is read by RNAP

• Antisense

Coding strand contains the sequence of nucleotide bases that will match the bases (With the exception of T, which gets replaced by U) on the mRNA.

• Sense

Steps of transcription

Initiation: RNAP binds to the promoter. The two DNA strands separate.

Elongation: RNA polymerase moves along the template strand, reading it 3’ to 5’.

• Complementary RNA nucleotides re added in the 5’ to 3’ direction.

• As enzyme moves forward, the helix rezips behind it.

Termination: Termination sequence on the DNA is reached, RNAP lets go of DNA and releases mRNA.

Transcription in prokaryotes vs eukaryotes

Prokaryotes: occurs in cytoplasm, mRNA transcript can be immediately translated by ribosomes

• Sometimes transcription and translation occur simultaneously

Eukaryotes: occurs in the nucleus, the pre-mRNA needs to be modified

mRNA modifications

5’cap: modified guanine cap at the 5’ end which helps with ribosomal recognition

3’ cap: 50-250 adenine nucleotides at the 3’ end which makes mRNA more stable

Splicing: non-coding regions (introns) are removed and coding regions (exons) are joined together.

• Alternative splicing: different exon combinations are joined, allowing one gene to code for multiple proteins.

Translation

Process by which an mRNA is read and a polypeptide sequence is generated

• Ribosomes in the cytoplasm/those on the RER.

Initiation in Translation

Small ribosomal subunit binds to the mRNA, and a tRNA carrying methionine, binds to the start codon.

Large subunit joins (has the A, P, and E sites).

The first tRNA goes to the P site, but every other tRNA will go to the A site.

Ribosome reads mRNA from 5’ to 3’.

Elongation in Translation

Codon recognition: A new tRNA brings the corresponding amino acid to the next codon, and binds in the A site.

Peptide bond formation: A peptide bond is formed which transfers the polypeptide chain on the tRNA in the P site to the amino acid on the tRNA in the A site.

Translocation: Ribosome moves one codon over. tRNA that was in the A site moves to P, tRNA that was in the P site moves to E and leaves. A site is open for the next tRNA.

Universal genetic code

With minor exceptions, codons code for the same amino acids among all organisms.

• Evidence of common ancestry.

Termination in Translation

A stop codon in the mRNA reaches the A site.

• Codes for a release factor which hydrolyzes the bond that holds polypeptide to the P site, which makes the polypeptide release.

Retroviruses

Information flows from RNA to DNA

• Reverse transcriptase synthesizes DNA from an RNA template.

• This viral DNA is integrated into the host cells genome, and the host cells machinery is used to transcribe and translate the foreign DNA.

Regulatory sequences

Regulate transcription and gene expression by binding regulatory proteins.

• Non-coding sequences of DNA

Promoters, enhancers, silencers, operators

Regulatory switches

The mechanism of regulatory sequences and regulatory proteins that turn genes on or off.

Enhancers

Increase likelihood and rate of transcription by binding activators

Silencers

Reduce/turn off transcription by binding silencers

Regulatory genes

Genes that control the expression of other genes through its product (protein or RNA molecules)

Transcription factors

Proteins that bind to specific DNA sequences to control gene expression

• Activators and repressors

• Different cells have different TF’S

Activators

Regulatory proteins that increase transcription by binding to promoters or enhancers

Repressors

Regulatory proteins that decrease or block transcription by binding to silencers (eukaryotes) or operators (prokaryotes)

Inducers

Molecules that bind to regulatory proteins (activators or repressors) and cause a conformational change that enables or disables their ability to bind to DNA.

Operons

A group of genes under the same promoter

composed of: promoter (where RNA P attaches), operator (binds repressors), and the genes.

Repressible operon

Transcription is on, but can be repressed (turned off)

Inducible operon

Transcription is usually off, but can be induced (turned on)

Trp operon

Repressible operon, controls the synthesis of tryptophan.

When tryptophan (co-repressor) is abundant, it is more likely to bind to the repressor which activates it and causes it to bind to the operator, stopping transcription.

• Tryptophan is an allosteric activator

Lac operon

Inducible operon, controls synthesis of lactase.

Lac repressor is bound to the operator (allosterically active)

The inducer allolactose (converted lactose) will bind to the repressor, making it change shape and turning it off (allosterically inactive)

When glucose levels are low cAMP levels rise and they(hunger signal) bind to CAP protein which binds to DNA and helps RNAP attach.

When there is glucose and lactose, there is low level transcription (repressor released but CAP inactive)

When there is no glucose but is lactose, there is high level transcription (lac repressor released, cAMP levels high so CAP is active.

Phenotype of cell/organism

Determined by the combination of genes that are expressed and the levels at which they are expressed.

• Function and amount of gene products influences phenotype

Histone acetylation

Adds acetylene groups to histones, which loosens the DNA

• Eukaryotic gene expression regulation

• Activates gene expression

DNA methylation

Adds methyl groups to DNA, which causes chromatin structure to condense.

• Eukaryotic gene expression

• Inhibits gene expression

Micro RNA and siRNA

Bind to mRNA to degrade it/block translation

• Eukaryotic gene expression

Induction

Cell to cell signals that cause a change in gene expression.

Gene regulation

Results in differential gene expression: formation of different cells: different genes expressed in different cells

Point mutation

One nucleotide is substituted for another

Frameshift mutation

Nucleotides are inserted or deleted which causes a shift in the codon reading frame

Nonsense mutation

A point mutation causes a premature stop codon

Missense mutation

A point mutation leads to a codon that codes for a different amino acid

Silent mutation

A point mutation that leads to a codon that codes for the same amino acid as the original codon

Aneuploidy

An abnormal number of chromosomes in a cell which can cause new phenotypes (disorders)

A result of errors during mitosis or meiosis such as nondisjunction

Deletion

A segment of a chromosome is lost, leading to missing genetic material

Duplication

A segment of a chromosome is duplicated, resulting in extra genetic material

Inversion

A segment of a chromosome flips (turns upside down) and inserts itself back into the chromosome

Translocation

A segment of one chromosome is transferred to another chromosome, or two chromosomes exchange segments

Horizontal gene transfer

Movement of genetic information between organisms other than by descent

In prokaryotes

Conjugation

A donor cell extends a pilus to a receiver cell, through the pilus plasmids or other genetic information is transferred

Transformation

Uptake of naked DNA fragments by a bacterial cell

Transduction

Transfer of genetic information via a bacteriophage

Phage infects a host cell inserting its genetic information. This DNA replicates and when new phages are assembled, host DNA is packaged instead of the viral DNA. The phage infects a new host and transfers the non viral DNA.

Transposition

Movement of DNA segments within and between DNA molecules

Gel electrophoresis

Separates DNA molecules by size, smaller ones travel farther.

Fragments form bands: horizontal lines on the gel, representing DNA fragments of the same size and molecular weight.

Polymerase chain reaction

Technique used to make millions of copies of specific DNA segments.

Denaturation separates the strands, in annealing primers bind, in extension DNAP builds new strands.

DNA sequencing

Determines the order of bases in a DNA molecule.

Allows for a DNA fingerprint that can be compared to DNA sequences in other samples.