AP Bio Unit 6

The primary source of hereditary material

is DNA and in some cases RNA

Genetic information is stored as

the sequence of bases in DNA and RNA

Before genetic information is passed from parent to daughter cells

DNA is packaged into chromosomes

Many viruses use

RNA molecules to encode genetic information

DNA and sometimes RNA

exhibits specific nucleotide base pairing

How are DNA and RNA structurally similar

* Both are polymers containing nucleotides
* Both are chain-like molecules
* Both follow base pairing rules

Specific nucleotide base pairing is conserved through

evolution

DNA and RNA both follow conserved base pairing rules in which

pyrimidines pair only with specific purines

Pyrimidines (def and identify the bases)

have a single ring structure (includes uracil, cytosine, thymine)

Purines (def and identify the bases)

have a double ring structure (includes adenine and guanine)

Prokaryotic organisms typically have which kind of chromosomes

circular chromosomes

Eukaryotic organisms have which type of chromosomes

multiple, linear chromosomes

Prokaryotic genomes are typically ------- then eukaryotic genomes

Prokaryotic genomes are typically smaller than eukaryotic genomes

Plasmids

small extra-chromosomal, double stranded, circular DNA molecules

Prokaryotic plasmids are found

in the cytosol

Eukaryotic plasmids are found

in the nucleus

Genetic information is transmitted from one generation to the next via

DNA or RNA

Most of the time genetic information is transmitted via

DNA

Heritable information provides for

continuity in life

(Historical experiment that proves DNA is the carrier of information) Griffith

* Mice injected with live cells of harmless strain R do not die. Live R cells are in their blood.
* Mice injected with live cells of killer strain S die. Live S cells are in their blood.
* Mice injected with heat-killed S cells do not die. No live S cells are in their blood.
* Mice injected with live R cells plus heat-killed S cells die. Live S cells are in their blood.

\

Plasmids are

small-extra chromosomal, DNA molecules (mainly in prokaryotes)

DNA replication ensures

continuity of hereditary information

Semiconservative replication

the process by which DNA makes copies of itself, each strand, as it separates, synthesizing a complementary strand.

Central Dogma (main flow of genetic information)

DNA ^^→^^ RNA %%→%% Protein

^^Transcription^^

%%Translation%%

Flow of genetic information in some viruses

RNA → DNA → RNA → Protein

Structure of DNA

double helix made of nucleotides

The backbone of DNA is

covalent bonds (do not break apart easily)

The bonds formed in between nucleotides in DNA are

hydrogen bonds that break apart easily to use or replicate strand

How many hydrogen bonds are between Adenine and Thymine

two

How many hydrogen bonds are between Cytosine and Guanine

three

Nucleotides are

subunits of DNA

Chargaff’s Rules

* A to T 2 hydrogen bonds
* G to C 3 hydrogen bonds
* A purine binds with a pyrimidine

DNA strands run in an

ANTIPARALLEL WAY

Example of antiparallel

Structure of Eukaryotic Chromosome

* DNA wraps around histones (protein) to form spools or nucleosomes
* Spools of wrapped histones then wrap/coil to form chromatin fiber
* Chromatin fiber then bundles/coils to form chromosome

Visual of the structure of Eukaryotic Chromosomes

RNA molecules are used to

facilitate protein synthesis using DNA information

Ribosomes

contain RNA and assemble protein

Transcription is the process in which

an enzyme directs the formation of an mRNA molecule

DNA Replication

* Two strands of double helix unwind
* Each strand serves as template for the new strands
* DNA polymerase adds new nucleotide subunits
* Additional enzymes and other proteins required to unwind and stabilize DNA helix

DNA Helicases

Open the double helix by disrupting the hydrogen bonds that hold the two strands together.

Topoisomerases

Break one or both DNA strands, preventing excessive coiling during replication, and rejoin them.

DNA Polymerases

Link nucleotide subunits together.

DNA Primase

Synthesizes short RNA primers on the lagging strand. Begins replication of the leading strand.

DNA ligase

Links Okazaki fragments by joining the 3’ end of the new DNA fragment to the 5’ end of the adjoining DNA.

Telomerase

Lengthens telomeric DNA.

Bidirectional

starting at the origin of replication, strands replicate at the replication fork

From what direction can new nucleotides only be added to the old strand

New nucleotides can only be added to the old strand from the 3’ to 5’ direction

Telomeres

short, non-coding repetitive DNA sequences

Telomeres shorten slightly

with each cell cycle

Telomeres can be extended by

telomerase

Absence of telomerase activity may be the cause of

cell aging

Most cancer cells have ---------- to maintain…

Most cancer cells have telomerase to maintain telomere length and resist apoptosis

Humans have 46 chromosomes and thus

46 DNA molecules

DNA Polymerase proofreads

DNA polymerase proofreads each nucleotide that it adds against the template

If an error is made, DNA Polymerase

deletes the nucleotide and continues synthesizing DNA

DNA Repair/Excision Repair

* Nucleases cut out (incise) the incorrect nucleotide
* DNA Polymerase adds the correct nucleotide
* Ligase connects the new nucleotide to the strand

DNA Repair mechanisms

DNA polymerases proofread DNA sequences during DNA replication and repair damaged DNA

When proofreading and repair mechanisms fail, an error becomes

a mutation- a permanent change in the DNA sequence

Structure of RNA

* Formed from nucleotide subunits
* Each nucleotide subunit contains ribose, a base, and three phosphates
* Like DNA, RNA subunits are covalently joined by a 5’--3’ linkage to form alternating sugar phosphate backbone

Function of DNA

It permanently stores a cell’s genetic information, which is passed to offspring

Functions of RNA

Some serve as disposable copies of DNA’s genetic message; others are catalytic

mRNA

Messenger RNA, contains information transcribed from DNA

rRNA

Ribosomal RNA, main component of ribosomes, where polypeptide chains are built

tRNA

Transfer RNA, delivers amino acids to ribosomes

Sequences of the RNA bases, together with the structure of the RNA molecule, determine

RNA function

The Central Dogma

Transcription Translation

DNA %%→%% RNA → Protein

%%RNA Polymerase%% Ribosomes

The three basic steps of TRANSCRIPTION

1. %%Initiation%%
2. Elongation
3. @@Termination@@

The process of TRANSCRIPTION

* DNA opens at the appropriate site
* RNA Polymerase attaches to the DNA (%%Initiation%%) and adds RNA nucleotides (Elongation). The sequence is read from the 3’ to the 5’ end of the DNA strand. Either DNA strand may be used.
* When RNA Polymerase reaches the appropriate sequence, it stops adding nucleotides and detaches from the newly formed mRNA (@@Termination@@).

DNA replication and transcription both

synthesize new molecules by base-pairing

In TRANSCRIPTION…

a strand of mRNA is assembled on a DNA template using RNA nucleotides

* Uracil (U) nucleotides pair with Adenine (A) nucleotides
* RNA Polymerase adds nucleotides to the transcript

TRANSLATION occurs in

the cytoplasms

In TRANSLATION…

a polypeptide chain (aka protein) specified by the mRNA is synthesized

Three steps in TRANSLATION

* Initiation
* Repeating cycles of elongation
* Termination

Each sequence of three nucleotide bases in the mRNA constitutes

a codon

TRANSLATION requires

tRNA’s and cell machinery, including ribosomes

tRNA structure

tRNA has the anticodon on one end and the amino acid that corresponds to the codon on the mRNA

Universal start codon

AUG

Three stop codons

UAA, UAG, UGA

TRANSLATION in a nutshell

1. mRNA interacts with the rRNA to INITIATE translation at the start codon (AUG)
2. The sequence of nucleotides is read in triplets (codons), each codon encodes for a specific amino acid
3. tRNA brings the anticodon and amino acid to the mRNA
4. Amino acids are added until the stop codon is reached
5. The newly formed amino acid is released

Proteins have 4 levels of structure

Primary: the sequence of amino acids bonded by peptide bonds

Secondary: Alpha helix or Beta pleated by hydrogen bonds

Tertiary: Folding due to interactions from side chains

Quaternary: Peptide chains interact with different chains to form protein

In eukaryotic cells enzyme-regulated modifications occur to the mRNA transcript

* Addition of poly-A tail, which is made of adenine nucleotides and protects from enzymes and is added at the 3’ end
* Addition of GTP cap, which is made of modified guanine nucleotides, helps ribosomes attach to the mRNA, and stabilizes and is added at the 5’ end
* introns
* exons
* splicing

Introns

sequences of an mRNA transcript that do NOT code for amino acids and are excised during RNA processing

Exons

sequences of an mRNA transcript that DO code for amino acids and are retained during RNA processing

Alternative splicing

the process of splicing introns and connecting retained exons

Coupled transcription and translation in bacteria

Unlike eukaryotes, translation of the bacterial mRNA molecule usually begins before the 3’ end of the transcript is even finished

Retroviruses

flow of genetic information is reversed by reverse transcriptase, ex of retroviruses, HIV and AIDS

Reversetranscriptase

Enzyme that turns RNA into DNA

Phenotypes are determined through

protein activities

Example of how phenotypes are determined

Melanin Synthesis

• At least 8 different genes are involved in melanin production (main determinant of skin color) \n • These genes are co-dominant \n • Sexual reproduction allows for different proteins to be synthesized, therefore, producing many different melanin shades

Genetic Engineering techniques

can manipulate the heritable information of DNA, and in special cases RNA

Electrophoresis

Identifies length of DNA fragments

Process of Electrophoresis

1. Cut DNA with restriction enzymes
2. Place fragments on a gel and a solution and apply a current
3. The smaller pieces will travel further than the larger ones, DNA travels from negative to position

Bacterial Transformation

Bacteria can import bits of DNA and express genes from it

Bacterial Transformation can be used to make

recombinant DNA: Mix of DNA from 2 species

Plasmids can be used to express human genes in bacteria

1. Make DNA copy from human mRNA
2. Use restriction enzyme to paste DNA onto a plasmid
3. Introduce plasmid into bacteria
4. Bacteria now expresses new gene

This is how insulin is made!

Restriction Enzymes

Cuts DNA at specific locations, allows 2 pieces of DNA to join together

Genetically Modifies Organisms (GMO)

allows plants to produce new proteins/express different (resistant typically) genes