BIO EXAM 4 (LEARNING OUTCOMES)

2 main types of Nucleic acids

DNA & RNA

DNA structure

Deoxyribose

Double Helix (Double Stranded

Sugar-Phosphate backbone

A pairs with T

RNA structure

Ribose

Single Stranded

Uracil over Thymine

A pairs with U

2 Nitrogenous Bases

Purines and Pyrimidines

Purine

Adenine and Guanine

Pyrimidines

Thymine, Cytosine, and Uracil

Three Main types of RNA

Messenger RNA, Transfer RNA, and Ribosomal RNA

Messenger RNA (mRNA)

carries code from DNA to ribosome for protein synthesis

Transfer RNA (tRNA)

transport specific amino acid to ribosome for protein synthesis

Ribosomal RNA (rRNA)

assembles amino acids brought by tRNA in a specific order from mRNA to make proteins

made of RNA by nucleotides

Nucleic Acid Structure

Phosphate group

phosphodiester Bonds

5-carbon Sugar

5’ to 3’ orientation

Avery, Macleod, and McCarty experiments

removed protein from purified cell extracts

added RNA to purified cell extracts

Added DNA to purified cell extracts

Put into mouses to test

Hershey Chase experiment

studied viruses that infect bacteria that are composed of only nucleic acids and proteins

the protein sample labeled with 35S and 32P is found in bacteria and was labeled on DNA

Meselson-Stahl experiment

three different models of DNA replication {conservative, semiconservative, and dispersive} was tested

Outcome of Avery, Macleod, and McCarty experiment

protein-transformed bacteria- Mouse died

RNA-digesting enzymes DIDN'T destroy transforming ability (Mice still died)

DNA-digesting enzymes destroyed all transforming ability (Mice didn't die)

Outcome of Hershey Chase experiment

In the protein, the 35S was found in the supernatant

in the bacteria, the 32P was found in a bacterial pellet

Outcome of Meselson-Stahl experiment conservative model

after one round of replication, two densities should have been observed: DNA strands would either be all-heavy (parental) or all-light (daughter): the model was rejected,

Outcome of Meselson-Stahl experiment semi-conservative model

after one round of replication, a single density would be predicted because all DNA molecules would have half light strand and a heavy strand- so two densities would be observed: the model was supported

Outcome of Meselson-Stahl experiment dispersive model

after two round of replication the dispersive model would still yield only single density; DNA strands would be composed of 3/4 light and 1/4 heavy molecules instead two densities were observed: the model was rejected

Conclusion of Avery, Macleod, McCarty experiment

Supported DNA as the genetic material, at least in bacteria

Conclusion of Hershey Chase experiment

the DNA was radioactive while the protein was not meaning that genetic material was carried in DNA not protein

Conclusion of Meselson-Stahl experiment

DNA replicated semi-conservatively

Proteins of Leading Strand replication

helicase, single strand binding proteins, primase, and DNA poly III

Helicase

unwinds double helix

Single stranded binding protein

prevents reannealing of separated strands

Primase

synthesizes RNA primers

Polymerase III

synthesizes DNA

leading strand

serves as the template of DNA replication

DNA ligase

joins DNA segments

Polymerase 1

removes and replaces RNA primer with DNA

DNA topoisomerase

relaxes supercoiling

LAGGING strand

strand of daughter DNA that is synthesized discontinuously in DNA replication

molecular process of transcription.

- DNA-directed synthesis of RNA
- T (thymine) in DNA replaced by U (uracil) in RNA
- mRNA used to direct the synthesis of polypeptides
-RNA chain grows in the 5′-to-3′ direction as ribonucleotides are added

Transcription bubble

contains RNA polymerase, DNA template, and growing RNA transcript

RNA Chain grows in a

5′-to-3′ direction as ribonucleotides are added

DNA to RNA

transcription

RNA to Protein

Translation

Start Codon

Always AUG

Stop Codons

UAG

UGA

UAA

3 types of mRNA processing in EUKARYOTES

5’ cap

3’ Poly-A tail

Alternative Splicing

5’ Cap

GTP is added to the 5' end, the GTP gets modified by addition of methyl group (methyl-G cap)

Associated with translation initiation, RNA stability & further processing

3’ Poly-A tail

Created by poly-A polymerase

Other termination mechanisms exist using other factors

Alternative splicing

removal of introns

may be the cause of many human genetic disorders

Introns (intervening sequences)

non coding sequences

Eukaryotic Cell

Post-translation regulation
Chromatin structure
Initiation Complex
Transcription factors

General transcription factors (Eukaryotic cell)

Mediate the binding of RNA polymerase 1 to the promoter (enhancers, promoters)

Specific transcription factors (Eukaryotic cell)

have specific promoters recognized by specific TFs

Major differences of Eukaryotes

DNA organized into chromatin complicating protein-DNA interactions

Transcription occurs in nucleus while translation occurs in cytoplasm (more regulatory DNA)

Translation (Beginning)

Occurs in ribosomes
Several RNA and proteins work together to achieve translation (mRNA & tRNA)

Elongation (Middle)

Amino acids are brought to the ribosome by tRNAs and linked together to form a chain

Helicase is not used, but instead holoenzyme

Termination (End)

The finished polypeptide is released and does its job in the cell.

Uses a hairpin loop to end the transcription process

Prokaryotic Positive control by activators

Activators enhance the binding of RNA polymerase to promoter

Prokaryotic Negative control by repressors

Repressors bind to operators (DNA sequence) that prevent or decrease initiation frequency

Effector molecules

alter binding/activity of repressors or activators

RNA polymerase in prokaryotes exist in 2 forms

core polymerase

Holoenzyme

Core polymerase

synthesizes RNA using a DNA template core subunits besides the sigma

Holoenzyme

initiates synthesis because Core polymerase can’t

4 core subunits plus Sigma factor

Template strand

Only one strand of DNA copied as RNA

Coding strand

The strand of DNA not used as a template

Exon

Expressed sequence

Promoters

forms a recognition and binding site for the RNA polymerase

Sigma Factor

Recognizes signals for the holoenzyme

Operon

a cluster of genes that are transcribed together to give a single messenger RNA

Eukaryotic RNA polymerase 1

transcribes rRNA

Eukaryotic RNA polymerase 2

transcribes mRNA

Eukaryotic RNA polymerase 3

transcribes tRNA

Three main mutations

silent mutation

missense mutation

nonsense mutations

Silent Mutation

same amino acid inserted, no net effect

Missense mutation

changes amino acid inserted

Nonsense mutation

changed to stop codon

Mature mRNA

made by splicing

Has 5’ cap

Has 3’ poly-A tail

No introns only EXONS

Large subunit of Ribosome

makes the protein

Small subunit of Ribosome

reads the mRNA and pushes it along

Release Factors

protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence

Beta clamp

Holds DNA pol 3 onto the thing

Inherited mutation

mutation is passed from parent to offspring

Acquired Mutation

environmental agents (mutagens) damage DNA, or errors during DNA replication and recombination

Insertion/Deletion nutation

Gain or loss of 1 to 50 bp

Framshift mutation

addition or deletion of base

Alter reading frame downstream

Trinucleotide repeat (TNR) or triplet repear mutation

transition mutation

purine to purine or pyrimidine to pyrimidine

transversion

purine to pyrimidine or pyrimidine to purine

lac operon

encodes proteins necessary for the use of lactose as an energy source

Lac Repressor gene

lacL

Linked to the rest of the lac operon

In the absence of lactose

lac repressor binds to operator to block transcription

In the presence of lactose

lac repressor can no longer bind to operator

Transcription proceeds

Low Glucose =

promoter to be activated

High Glucose =

promoter not activated

trp operon

encodes genes for the biosynthesis of tryptophan

high tryptophan levels =

trp repressor binds to block transcription

low tryptophan levels =

trp repressor cant bind to operator

so transcription occurs

DNA viruses

double-stranded, Replicated in the nucleus of eukaryotic host cell

RNA viruses

single-stranded, Replicate in the host's cytoplasm

(Replication is error−prone, so high rates of mutation =difficult targets for the immune system and vaccines/drugs)

Virus hijacks the cell's transcription and translation machinery to

expresses Early genes, Intermediate genes, Late genes

Virus Early genes

allows transcription and translation

takes over host cell machinery

Virus intermediate

capsid protein production

Virus Late genes

releasing viral particles

Lytic cycle

1. Attachment

2. Penetration or injection: T4 pierces cell wall to inject viral genome,

3. Synthesis: Cell makes viral components,

4. Assembly: Put together new pages,

5. Release: Mature virus particles are released by an enzyme that lyses the host or buds through a host cell wall

lysogenic cycle

1. Integration: leads to prophage,

2. Propagation: reproduction of lysogenic bacteria, 3. Induction: prophage exits the bacterial chromosome, and viral genes are expressed

Capsid

Protein Shell

2 shapes of Viruses

Helical

Icosahedral