BIO EXAM 4 (LEARNING OUTCOMES)

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106 Terms

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2 main types of Nucleic acids

DNA & RNA

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DNA structure

Deoxyribose

Double Helix (Double Stranded

Sugar-Phosphate backbone

A pairs with T

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RNA structure

Ribose

Single Stranded

Uracil over Thymine

A pairs with U

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2 Nitrogenous Bases

Purines and Pyrimidines

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Purine

Adenine and Guanine

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Pyrimidines

Thymine, Cytosine, and Uracil

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Three Main types of RNA

Messenger RNA, Transfer RNA, and Ribosomal RNA

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Messenger RNA (mRNA)

carries code from DNA to ribosome for protein synthesis

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Transfer RNA (tRNA)

transport specific amino acid to ribosome for protein synthesis

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Ribosomal RNA (rRNA)

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

made of RNA by nucleotides

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Nucleic Acid Structure

Phosphate group

phosphodiester Bonds

5-carbon Sugar

5’ to 3’ orientation

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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

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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

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Meselson-Stahl experiment

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

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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)

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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

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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,

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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

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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

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Conclusion of Avery, Macleod, McCarty experiment

Supported DNA as the genetic material, at least in bacteria

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Conclusion of Hershey Chase experiment

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

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Conclusion of Meselson-Stahl experiment

DNA replicated semi-conservatively

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Proteins of Leading Strand replication

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

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Helicase

unwinds double helix

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Single stranded binding protein

prevents reannealing of separated strands

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Primase

synthesizes RNA primers

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Polymerase III

synthesizes DNA

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leading strand

serves as the template of DNA replication

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DNA ligase

joins DNA segments

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Polymerase 1

removes and replaces RNA primer with DNA

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DNA topoisomerase

relaxes supercoiling

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LAGGING strand

strand of daughter DNA that is synthesized discontinuously in DNA replication

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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

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Transcription bubble

contains RNA polymerase, DNA template, and growing RNA transcript

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RNA Chain grows in a

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

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DNA to RNA

transcription

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RNA to Protein

Translation

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Start Codon

Always AUG

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Stop Codons

UAG

UGA

UAA

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3 types of mRNA processing in EUKARYOTES

5’ cap

3’ Poly-A tail

Alternative Splicing

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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

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3’ Poly-A tail

Created by poly-A polymerase

Other termination mechanisms exist using other factors

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Alternative splicing

removal of introns

may be the cause of many human genetic disorders

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Introns (intervening sequences)

non coding sequences

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Eukaryotic Cell

Post-translation regulation
Chromatin structure
Initiation Complex
Transcription factors

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General transcription factors (Eukaryotic cell)

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

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Specific transcription factors (Eukaryotic cell)

have specific promoters recognized by specific TFs

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Major differences of Eukaryotes

DNA organized into chromatin complicating protein-DNA interactions


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

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Translation (Beginning)

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

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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

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Termination (End)

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

Uses a hairpin loop to end the transcription process

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Prokaryotic Positive control by activators

Activators enhance the binding of RNA polymerase to promoter

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Prokaryotic Negative control by repressors

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

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Effector molecules

alter binding/activity of repressors or activators

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RNA polymerase in prokaryotes exist in 2 forms

core polymerase

Holoenzyme

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Core polymerase

synthesizes RNA using a DNA template core subunits besides the sigma

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Holoenzyme

initiates synthesis because Core polymerase can’t

4 core subunits plus Sigma factor

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Template strand

Only one strand of DNA copied as RNA

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Coding strand

The strand of DNA not used as a template

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Exon

Expressed sequence

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Promoters

forms a recognition and binding site for the RNA polymerase

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Sigma Factor

Recognizes signals for the holoenzyme

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Operon

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

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Eukaryotic RNA polymerase 1

transcribes rRNA

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Eukaryotic RNA polymerase 2

transcribes mRNA

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Eukaryotic RNA polymerase 3

transcribes tRNA

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Three main mutations

silent mutation

missense mutation

nonsense mutations

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Silent Mutation

same amino acid inserted, no net effect

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Missense mutation

changes amino acid inserted

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Nonsense mutation

changed to stop codon

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Mature mRNA

made by splicing

Has 5’ cap

Has 3’ poly-A tail

No introns only EXONS

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Large subunit of Ribosome

makes the protein

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Small subunit of Ribosome

reads the mRNA and pushes it along

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Release Factors

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

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Beta clamp

Holds DNA pol 3 onto the thing

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Inherited mutation

mutation is passed from parent to offspring

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Acquired Mutation

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

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Insertion/Deletion nutation

Gain or loss of 1 to 50 bp

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Framshift mutation

addition or deletion of base

Alter reading frame downstream

Trinucleotide repeat (TNR) or triplet repear mutation

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transition mutation

purine to purine or pyrimidine to pyrimidine

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transversion

purine to pyrimidine or pyrimidine to purine

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lac operon

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

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Lac Repressor gene

lacL

Linked to the rest of the lac operon

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In the absence of lactose

lac repressor binds to operator to block transcription

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In the presence of lactose

lac repressor can no longer bind to operator

Transcription proceeds

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Low Glucose =

promoter to be activated

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High Glucose =

promoter not activated

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trp operon

encodes genes for the biosynthesis of tryptophan

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high tryptophan levels =

trp repressor binds to block transcription

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low tryptophan levels =

trp repressor cant bind to operator

so transcription occurs

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DNA viruses

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

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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)

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Virus hijacks the cell's transcription and translation machinery to

expresses Early genes, Intermediate genes, Late genes

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Virus Early genes

allows transcription and translation

takes over host cell machinery

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Virus intermediate

capsid protein production

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Virus Late genes

releasing viral particles

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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

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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

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Capsid

Protein Shell

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2 shapes of Viruses

Helical

Icosahedral