Bio Ch. 11

DNA

Deoxyribonucleic acid

Genes occur on chromosomes Mutations in genes cause metabolic errors It is composed of nucleotides

Chargaff's Rule

1. The amount of A, C, G, and T varies from species to species

2. In each species, the amount of A is equal to T and the amount of G is equal to C

A nucleotide from DNA contains one base, one phosphate group and the sugar deoxyribose.

DNA contains 4 types of nucleotides: Adenine and Guanine (Purines) Cytosine and Thymine (Pyrimidines)

Nucleotide

a compound consisting of a nucleoside linked to a phosphate group.

In DNA, contains one base, one phosphate group and the sugar deoxyribose.

Purine

Adenine and Guanine--- will look like two rings fused together.

Pryimidine

Cytosine and Thymine--- will look like a single ring

DNA Replication

Requires several steps: initiation, elongation, termination

The process of copying a DNA molecule.

The original strands serve as templates of the new DNA.

Considered semiconservative because one original strand is present in each new DNA helix.

Helicase

Enzyme Breaks the hydrogen bonds between the nucleotides. Think of a zipper on a pair of jeans

DNA polymerase

A type of enzyme that is responsible for forming new copies of DNA, in the form of nucleic acid molecules.

RNA primase lays down a primer first so ___ "knows" where to start.

DNA Ligase

Utilized to fix any breakage.

If two pieces of DNA have matching ends, ligase can link them to form a single, unbroken molecule of DNA.

Codon

A sequence of three consecutive nucleotides in a DNA or RNA molecule that codes for a specific amino acid.

AUG (Start) UAA (Stop) UAG (Stop) UGA (Stop)

Promoter Region

Transcription begins here.

Region of DNA with a special nucleotide sequence that marks the beginning of a gene.

RNA polymerase

Binds to promoter region. Moves down the DNA strand, the DNA strand is opened a little at a time.

Stop Codon

Triplet code that tells transcription to stop. Once it is reached, mRNA is released.

UAA UAG UGA

Primary mRNA

A primary transcript is the single-stranded ribonucleic acid product synthesized by transcription of DNA, and processed to yield various mature RNA products.

Goes through 3 stages: capping and tailing, splicing

Mature mRNA

Is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation.

Anticodon (tRNA)

Binds to the codon of the mRNA.

Acceptor arm (tRNA)

Part of the tRNA that binds to the appropriate amino acid.

A site (mRNA)

Newly arrived tRNA carrying an amino acid.

P site (mRNA)

tRNA attached to peptide.

E site (mRNA)

tRNA exits the ribosome.

Regulatory Proteins

Cells regulate gene expression using___

Repressor Proteins

Prevent transcription by covering up promoter region of gene.

Activator Proteins

Facilitate transcription by assisting in unwinding of double helix.

Operon

Cluster of bacterial genes along with DNA control sequence.

Erwin Chargaff

Equal proportions between two bases indicated that the bases were paired in the structure of DNA.

The order in which these nucleotides occur differ, producing great variability in the DNA.

Rosalind Franklin

Used X-ray crystallography to study the structure of DNA.

The X-ray diffraction pattern suggested that DNA had a helical shape.

The Watson and Crick Model

Developed the definitive model of DNA structure.

1. The sugar and phosphate groupds are bonded in alternation sequences to form the sides of a twisted ladder.

2. Bases are joined by hydrogen bonds to form the rungs of the ladder.

3. Complementary base pairing occurs, meaning A only bonds with T and G only bonds with C.

Central Dogma of genetics

Genetic information flows from DNA to RNA to protein

DNA replication --> transcription --> RNA --> translation --> protein

Must carry out these processes to maintain homeostasis Cell growth cycle DNA replication Protein synthesis

Semiconservative

DNA replication is considered this because one original strand is present in each new DNA helix.

DNA Replication: Initiation

DNA double helix must unwind and separate.

Utilizes helicase.

Helicase breaks the hydrogen bonds between the nucleotides.

DNA Replication: Elongation

New nucleotides need to be added to the strands (always grows 5' to 3').

Nucleotides are added using DNA polymerase.

Leading strand is elongated continuously.

Lagging strand is in Okazaki fragments.

DNA Replication: Termination

Once all nucleotides are added, DNA replication needs to be terminated.

DNA replication is not perfect.

Utilizes DNA ligase to fix any breakage.

Stages of DNA Replication

Initiation, Elongation, Termination

DNA and RNA Differences

DNA- found in nucleus, genetic material, sugar is deoxyribose, bases are A T C G, double-stranded, is transcribed

RNA- found in nucleus and cytoplasm, helper to DNA, sugar is ribose, bases are A U C G, single-stranded, mRNA is translated

Overall DNA

Found in nucleus Genetic Material Sugar is deoxyribose Bases are A, T, C, G Double-stranded Is transcribed (to give mRNA, tRNA, and rRNA)

Overall RNA

Found in nucleus and cytoplasm Helper to DNA Sugar is ribose Bases are A, U, C, G Single-stranded mRNA is translated (to give proteins)

Types of RNA

Messenger (m), Transfer (t), Ribosomal (r)

Messenger RNA

Is produced by a process called transcription.

Carries genetic information from DNA to the cytosol.

Transfer RNA

Is a carrier molecule for amino acids, delivering them to the site of protein synthesis.

There are 20 different types; one for each type of amino acid.

Ribosomal RNA

The two subunits joined with proteins in the cytosol to form the subunits ribosomes.

The free ribosomes, polyribosomes, and ribosomes attached to the ER all synthesize proteins.

Protein Synthesis

Two stages :Transcription and translation

The genes in DNA contain the instructions for the amino acid sequence of a protein.

In order to synthesize a protein, the genetic information in the DNA must be converted to an amino acid.

Protein synthesis: Transcription

DNA is in the nucleus but protein synthesis occurs in the cytoplasm.

Must create RNA "transcript"- mRNA.

3 stages- initiation, elongation, and termination

Transcription: Initiation

Begins in the promoter region.

RNA polymerase binds to promoter region.

As RNA polymerase moves down the DNA strand, the DNA strand is opened a little at a time.

Transcriptions: Elongation

RNA polymerase adds new nucleotides.

This continues until RNA polymerase reaches a stop codon.

Transcriptions: Termination

RNA polymerase reaches a stop codon.

Once stop codon is reached, mRNA is released.

Doesn't leave nucleus (yet)

mRNA (at this point) is call primary mRNA.

mRNA Processing for protein synthesis

In order to function properly, the primary mRNA strand must be processed. It goes through three stages capping, tailing and splicing.

Capping and Tailing

Add additional nucleotides to both ends of mRNA strand. 5' cap and poly-A tail

Splicing

The removal of introns and the fusion of exons.

Introns: junk DNA; must be removed to have functional mRNA strand.

Exons: protein-coding regions of mRNA

Protein synthesis: Translation

The process of translating the mRNA to proteins.

Must have: Enzymes, rRNA, tRNA, and mRNA to proceed.

3 stages; initiation, elongation, and termination

Translation: Initiation

mRNA, rRNA, and tRNA come together

Translation: Elongation

Polypeptide chain increases in length one amino acid at a time.

Steps: tRNA at the P site contains the growing peptide chain. This tRNA passes its peptide to tRNA-amino acid at the A site. tRNA (original, now empty) moves from the P site to the E site. The tRNA-holding the peptide chain moves to the P site

Translation: Termination

Occurs when a stop codon appears in the "A" site.

Formed polypeptide and translation components separate. release factor binds to stop codon and cleaves the polypeptide from the last tRNA.

Gene expression is prokaryotes

E. coli lives in our intestines and can quickly adjust its enzymes according to what we eat.

If we drink milk, E. coli immediately begins to make 3 enzymes to metabolize lactose.

Chromatin Condensation

Used to keep genes turned off.

Heterochromatin- darkened region of DNA (staining). Inactive region of chromatin.

Euchromatin- Loosely packed form of chromatin. Contains active genes.

DNA transcription

Many regulatory proteins per gene.

Transcription factors: binds to promoter region.

Transcription activators: speed up transcription.

mRNA processing for genetic expression

Alternative mRNA processing. The same primary-mRNA can produce different protein products.

Achieved by splicing certain exons.

mRNA translation

Cytoplasm contains proteins that control whether translation takes place.

Initiation factor- inhibit the start of protein synthesis.

Tails and caps- determine how long mRNA can survive in the cytoplasm.

Protein activity

Some proteins are not active immediately after synthesis.

Signaling between cells in eurokaryotes

3 phases:

Reception- chemical signal binds to receptor protein. Tranduction- Signal causes the receptor protein to initiate the signal tranduction pathway. Response- the end product of the pathway directly affects the metabolism of the cell.