What is the relationship between Gene Expression and Trait?

Genes are expressed at the molecular level to produce functional proteins. The functioning of proteins within living cells ultimately affects an organism's traits.

What is the relationship between Mutation and Allele?

Alleles are alternative forms of the same gene. The difference between alleles is caused by a mutation.

In diploid species that carry out sexual reproduction, how are genes passed from generation to generation?

When a diploid individual makes haploid cells for sexual reproduction, the cells contain half the number of chromosomes. WHen two haploid cells combine, a zygote is formed that begins the life of a new individual. THe zygote has inherited half of its chromosomes, and therefore, half of its genes from each parent.

What is a trait?

The characteristics of an organism?

What are the four important categories of larger cellular molecules?

Nucleic Acids (DNA & RNA)
Proteins
Carbohydrates
Lipids

What are macromolecules?

Comprised of many repeating units of smaller building blocks made by nucleic acids, proteins, or carbohydrates. DNA is the largest macromolecule found in living cells.

What is a proteome?

All of the proteins that a cell makes at a given time

What is an enzyme?

Proteins that accelerate chemical reactions.

What is DNA?

Deoxyribonucleic acid, composes the genetic material of living organisms. Stores the information needed for the synthesis of all cellular proteins.

What experiment did Griffith conduct?

He conducted an experiment that involved the injection of live and/or heat-killed bacteria (Smooth and Rough Pneumococcus). Smooth bacteria has a capsule that kill mice. Inject Smooth bacteria, mice died. Inject rough bacteria, mouse lived. Inject heat-killed type smooth bacteria, mouse lived. Inject living type rough and heat-killed smooth, mouse dies and living type smooth bateria was found. TRANSFORMATION caused the smooth type to transform the rough type.

What did Avery discover with DNase, RNase, and protease?

Using rough and smooth Pneumococcus, he found that rough cells did not transform to smooth cells when DNase was added, but still did when RNase and protease was added. This concluded that DNA was the genetic material that has the transform principle.

Explain Hershey & Chase's experiment with T2 Phage

T2 phage is a bacteriophage and infects e.coli. The phage coat or capsid is composed entirely of protein. DNA is found inside the head of the T2 capsid. The phage is only composed on DNA and proteins. A virus cannot synthesize new viruses, so it must introduce its genetic material into the cytoplasm of a living cell. The cytoplasm then grows more viruses and released (lysis). Hershey and CHase separate the phage coat from the genetic material that is released into the cytoplasm by using a kitchen blender. They then used radioisotpes to distiguish proteins from DNA. (Sulfur for protein, Phosphorous for DNA) More sulfur was found in the supernatant, so not in the cell. DNA is the genetic material injected.

How is information carried in a cell? Characteristics needed of the carrier?

-Highly accurate replication
-storage
-transmission
-Large carrying capacity
-Capable of variation

Nucleotide composition?

Phosphate, pentose sugar (deoxy ribose and ribose), and nitrogenous base

What are the five different nitrogenous bases that make up nucleotides?

Purines: adenine and guanine
Pyrimidines: Thymine, Cytosine, and Uracil

What is the linkage in DNA or RNA strands called?

Phosphodiester linkage

Discovery of the Double-Helix Structure?

Watson & Crick, Linus Pauling helix of proteins, and Franklin and Wilkins x-ray of double helix

Chargraff found out what about DNA?

That amount of A equals T and amount of G equals C. Extracted chromosomal material, remove protein, and hydrolyze the DNA to release the bases.

What does complementary mean?

Two strands connect perfectly, so they are complementary to each other.

What is the opposite orientation of two DNA strands referred to?

Antiparallel

How are the bases connected?

Hydrogen bonds
A - T: 2 hydrogen bonds
G - C: 3 hydrogen bonds

What is a right handed double helix?

- 2 nm diameter
- 10 bases/ turn
- bases perpendicular in relationship to axis
- known as 'b' DNA
- Access to base sequence through the major groove

What is 'A' DNA?

- Right handed helix
- 2.3 nm diameter
- 11 bases/turn
- base pairs tilted in relationship to axis

What is 'Z' DNA?

- Left handed helix
- 1.8 nm diameter
- 12 bases/turn
- base pairs not parallel
- no real major grooves

What information does denaturation/renaturation give?

Slow heating and slow cooling of DNA can give information on the base composition and the level of unique base sequences of DNA

What happens during denaturation?

Slowly heating double-stranded DNA will break the hydrogen bonds holding the strands together resulting in two single strands. The higher the number of hydrogen bonds, the higher the temperature needed to denature DNA.

What happens during renaturation?

Slow cooling of the denatured DNA allows the double-stranded DNA to reform. The rate of reannealing is related to the amount of DNA and the percentage of unique sequences. The greater the amount of DNA and/or the higher percentage of unique sequences the slower the rate of reannealing .

What is the COT plot?

Renaturation is graphed using the COT plot. Co=initial concentration
C= concentration of single-stranded DNA after time has elapsed
t= time of the reaction

What are the three different DNA replication models? What is the correct one?

Conservative model, semiconservative model, dispersive model.
Semiconservative model was proved correct after Meselson and Stahl completed a density experiment.
15N = heavy dna
14N = light dna

Crick came up with the Central Dogma of Genetics

Replication:
DNA(transcription)-RNA(translation)-Protein

Kornberg discovered the first enzyme that catalyzed the reaction for adding a nucleotide to another nucleotide was what?

DNA Polymerase I

What are the features of DNA Polymerase I?

-Could remove nucleotides in a 5'-3' direction and/or 3'-5' direction from the end of DNA strand
-Could add bases in only one direction (5'-3')So an open 3' end needed to be present
-Could remove RNA (RNA nuclease)

What are the problems of DNA Polymerase I?

-Only adds bases in one direction
-Needs a nucleotide with an open 3' end to be present to start adding bases
-DNA Polymerase is too slow (did not add bases fast enough)

What is the principal enzyme for prokaryotic replication?

DNA Polymerase III

What happens in the initiation of DNA replication?

Opening of DNA strands by the initiator protein, helicase, topoisomerase, and single strand binding proteins.
Synthesis of RNA primer by primase

The site on the bacterial chromosome where DNA synthesis begins is known as the

Origin of Replication

The synthesis of daughter DNA strands is initiated within the origin and proceeds in both directions or ______ around the bacterial chromosome

bidirectionally

Two ________ move in opposite directions outward from the origin. This is where the parental DNA strands have separated and new daughter strands are being made.

Replication forks

DNA replication is initiated by the binding of ______ to sequences within the origin known as DNaA box sequences

DNaA proteins

In a eukaryotic cell what DNA sequences are needed to ensure proper transcription.

1. promoter sequence (binds the mRNA for the initiation of transcription. It is the starter.)
2. Leader sequence (follows
3. Gene sequence
4. Terminator Sequence

Complete each phrase to best describe the typical structure of genomic DNA found in a cell (prokaryotic or eukaryotic)
a) Two strands of DNA form a (Left/Right) handed double helix.
b)The two strands are (Anti-parallel/Parallel) with regard to their 5' - 3' directionality.
c) Complementary bases in opposite strands form (h-bonds/covalent bonds)
d) Chargraff's rule indicates DNA composition (A-G,T-C/A-T,G-C)
e) Purines have _ rings
f) Pyrimidine bases have _ rings
g) AT pairing forms _ hydrogen bonds
h) GC pairing forms _ hydrogen bonds

a) Right handed
b) anti-parallel
c) H-bonds
d) A-T, G-C
e) 2 rings
f) 1 ring
g) 2 bonds
h) 3 bonds

What keeps parental DNA strands seperate?

Single Strand Bonding Proteins

What alleviates positive supercoiling (also called DNA gyrase)

Topoisomerase

What makes a RNA primer?

Primase

What covalently joins ends of DNA fragments?

Ligase

What synthesizes a daughter strand of DNA?

DNA polymerase III

What unwinds DNA double helix?

Helicase

What excites RNA primers and fills in with DNA?

DNA polymerase I

Is sigma factor prokaryotic or eukaroyotic?
Is rho dependent termination prokaryotic or eukaryotic?
Are Telomeres prokaryotic or eukaryotic?

Sigma factor is prokaryotic
Rho dependent termination is prokaryotic
Telomeres are eukaryotic

Are CAAT box and GC box prokaryotic or eukaryotic?
Is flap endonuclease prokaryotic or eukaryotic?
Are priboow box(-10 sequences) prokaryotic or eukaryotic?

CAAT box & GC box are eukaryotic
Flap endonuclease is eukaryotic
Priboow box is prokaryotic

Are exons/introns prokaryotic or eukaryotic?
Are ARS elements prokaryotic or eukaryotic?
Are oriC (origin of chromosomal replication) prokaryotic or eukaryotic?

Exons/Introns are eukaryotic
ARS elements are eukaryotic
OriC is prokaryotic

What is responsible for RNA synthesis?

Core enzyme

What recognizes promoter sequence?

Sigma factor

What is a DNA strand from which RNA transcribed?

Template strand

What is a DNA strand similar to RNA transpript?

Coding strand

What provides a site for RNA polymerase to bind and form an open complex?

Promoter

What sequence causes transcription to end?

Terminator

What interacts with RNA transcript to cause RNA polymerase to release

Rho protein

What does topoisomerase do?

Allows DNA to move from a supercoiled state to a relaxes state. Enzyme is also called gyrase

What does helicase do?

Unwinds the double DNA helix

SSBps (destabilizing enzymes) Single stranded binding proteins. What do they do?

Keeps strands separated

What does the initator protein do?

Binds to the DNA at the origin of replication

What does primase do?

Make a RNA primer

What does DNA Polymerase I do?

Removes RNA primer and repairs any errors (proofreads)

What does ligase do?

Joins ends of DNA fragments (Ozaki fragments)

Which direction does a leading strand go?

3'-5' and the lagging strand follows

What does DNA Polymerase III do?

attaches to 3' end of RNA primers and starts to attach complementary nucleotides in the 5' to 3' direction

What are the differences between prokaryotic and eukaryotic replicatin?

-Different DNA polymerases
-Multiple origins of replication (eukaryotic)
-RNA primer removal
-replication of the 3' end of the linear eukaryotic DNA

What is the origin of replication for eukaryotes?

ARS (Autonomously Replicating Sequence)
-Many ARS elements per chromosome
-~50 bp in length
-AT rich
-

How do eukaryotic cells remove RNA primer?

Using a flap endonuclease to remove flaps

How is chromosome shortening prevented in eukaryotes?

Each chromosome has telomerase
Telomerase contains protein subunits and RNA
It can synthesize repeats to end of a strand using an internal RNA sequence as a template

What is transcription?

The formation of a RNA molecule upon a DNA template by complementary base pairing, mediated by RNA polymerase

What are the three basic components of transcription?

1. RNA Polymerase
2. DNA template
3. Nucleotides: ATP, UTP, GTP, CTP

Prokaryotic RNA Polymerase contains what two units?

1. sigma factor
2. core enzyme

How does prokaryotic transcription work?

1. Initation: The promoter acts as a recognition site for transcription factors. The transcription factors allow for RNA polymerase to bind to the promoter. The DNA is then denatured into a bubble called the open complex.
2. Elongation/Synthesis: RNA polymerase slides along the DNA in the open complex to synthesize RNA
3. Termination: A terminator is reached that causes RNA polymerase and the RNA transcript to disassociate from the DNA

What happens in the iniation sequence of prokaryotic transcription?

-Binding of the sigma factor to the core enzyme
-Binding of the RNA polymerase to the DNA template
-Slide along DNA until promoter is recognized
-Release of the sigma factor

What occurs at the prinbow box?

Tighter binding. 10 base pairs from the iniation site for transcription. This is the site where the DNA opens

What is the template strand?

The one strand of DNA that is transcribed. It is read 3'-5'

What are the two types of termination?

Rho-dependent
Rho-independent

What happens during intrinsic (rho-independent) termination?

After the synthesis of the two fold symmetry, the RNA polymerase transcribes a uracil rich sequence. When the hairpin loop forms, it interferes with the RNA polymerase causing release

What happens during rho-dependent termination?

A seperate protein factor (rho) with the RNA transcript and RNA polymerase causing the RNA polymerase to release

What are the two factors required for rho-dependent termination?

1) rut site occurs upstream of terminator, recognition site for binding rho
2)termination sequence, RNA sequence containing several GC base pairs forming a hairpin

What can block a rho protein from binding?

Ribosomes

What are the three RNA polymerases in eukaryotic transcription?

1. Ribosomal RNA (rRNA)
2. Messenger RNA's (mRNA)
3. Transfer RNA's (tRNA)

What does RNA Polymerase I do in eukaryotic transcription?

Transcribes rRNA's
Promoter found in the 3' flanking region of the DNA
Single upstream regulatory elements helps to bind RNA polymerase I to promoter
Not highly conserved across species

What does RNA Polymerase III do in eukaryotic transcription?

Transcribes tRNA's
Two regulatory elements, called A and B boxes, facilitate binding of RNA polymerase III to promoter

What does RNA Polymerase II do in eukaryotic transcription?

a) Core promoter: TATA box (Goldberg-Hogress box)
-25 bps
b) Regulatory Elements: CAAT box, GC box
c) Conserved across species

What are regulatory elements (enhancers and silencers)?

Proteins (factors) bind to these sequence sites upstream or downstream from the gene stimulation/inhibiting transcription

What are the two types of proteins that facilitate or modulate initiation of transcription in eukaryotes?

1.Transcription factors
2.Mediator

What do transcription factors do?

Proteins that facilitate initiation of transcription

What does a mediator do?

Mediates interactions between RNA polymerase II and regulatory transcription factors that bind to enhancers or silencers

What is endogenous transcriptional control?

Binding of proteins to DNA to block transcription is a common form of gene regulation

What is exogenous transcriptional control?

Pharmaceuticals are available that can bind to DNA or RNA polymerase

What is messenger RNA?

Intermediate carrier of the genetic code
Large molecular weight
Relatively short lived, will vary among genes
May be translated many times
2 to 10% of cellular RNA

Difference in mRNA between eukaryotes and prokaryotes is the processing required after transcription.

Eukaryotes:
DNA(transcription)-pre mRNA(RNA processing modification) - mRNA - Ready for translation
Prokaryotes:
DNA(transcription)- mRNA(RNA processing modification - Ready for translation

What is RNA modification?

-Processing(cleavage of a large RNA into smaller pieces)
-Splicing(cleavage and joining of RNA molecules)
-5' capping (attachment of 7-methylguanosine cap to the 5' end of mRNA)
-3' polyA tailing (attachment of a string of adenine nucleotides to the 3' end of mRNA)
-RNA editing (change of the base sequence of RNA after it has been transcribed)

Why the need for splicing?

Remove the RNA that does not code for the specific peptide

What is processing and what does it involve?

Processing happens in the eukaryotic nucleus to process pre-mRNA to produce mRNA.
Involves:
Removing introns
Adding a guanine cap on the 5' end
Adding a poly-adenine tail on the 3' end

What is an extron?

Region that codes for part of the gene product

What is an inton?

Region that does not code for part of the gene product

What are spliceosomes?

Combination of proteins and small nuclear RNA called small ribonucleoproteins
1. Bind to the intron and identify intron-extron boundary
2. Hold the pre-mRNA in the correct configuration for splicing
3. Remove the intron and covalently link the exons

What is the function of 5' cap?

Cap structure is recognized by cap binding proteins, provide exit from nucleus
Cap structure is recognized by initation factors required for translation
Important in efficient splicing of introns, especially the first intron

What is the function of 3' polyA tail?

May act as an attachment site for proteins that protect or assist in the transport of the mRNA through the cytoplasm

How many nucleotides are there? How many amino acids?

4 nucleotides, 20 amino acids

What is a codon?

A 3 base sequence for one amino acid

What is the wobble hypothesis?

Crick hypothesized that the specificity of the code is more in the first two bases allowing for variation in pairing at the third base without changing the amino acid
Would increase speed of protein synthesis and decrease errors

What are the classes of proteins?

-Enzymes
-Receptor Proteins
-Transport Proteins
-Structural Proteins
-Nucleic acid binding proteins
-Ribosomal proteins
-Storage proteins

What is the primary structure of a protein?

Linear sequence of amino acids

What is the secondary structure of a protein?

Interaction of amino acids in the polypeptide in the form of hydrogen bonds that result in the folding of the polypeptide into various shapes/structures

What is the tertiary structure of a protein?

Additional folding of the polypeptide, arranging secondary structure into a thermodynamically stable state.

What is the quaternary structure of a protein?

Interaction between polypeptides

What dictates the function of a protein?

It's structure
changing the amino acids may change the structure

What is translation?

The formation of a polypeptide with the amino acid sequence directed by the nucleotide sequence of a specific RNA molecule

What are the three primary types of RNA needed for translation?

1. rRNA
2. mRNA
3. tRNA

What is transfer RNA (tRNA)?

Low molecular weight
70 to 90 nucleotides in length
Contains modified bases
Modification of the bases occurs post-transcription
Some tRNA requires processing
10 to 15% of cellular RNA
Has regions of double stranded RNA
Each tRNA is specific for one amino acid
There may be more than one tRNA for an amino acid

What is an anticodon loop?

Has three bases complementary to the 3 base codon on the mRNA

What is ribosomal RNA (rRNA)?

Found in ribosomes
Variable molecular weights/number of nucleotides
70 to 80 percent of the cellular RNA

What does translation require?

-tRNAs for 20 amino acids
-20 types of tRNA synthetases
-Large ribosomal unit
-Small ribosomal unit
-mRNA
-modified met-tRNA
-Initiation, Elongation, Termination factors

What are characteristics of translation?

-3 stages (initation, elongation, termination)
-mRNA is translated 5'-3'
-protein synthesis occurs(N-terminal to C-terminal)
-leader section of mRNA is not translated

What is the rate of translation for prokaryotes?
Eukaryotes?

15-20 amino acids/sec (prokaryotes)
2-6 amino acids/sec (eukaryotes)

What are the steps in the intiation of translation?

1) small subunit attaches to 5' end of mRNA
2) fmet-tRNA attaches to peptidyl site of the small ribosomal subunit
3) large subunit attaches to the small subunit

What are the steps in elongation of translation?

1) Next amino acid- tRNA enters the site assited by elongation factor
2)Peptide bond formation occurs
3) Translocation of the ribosome to the next codon assisted by elongation factor
4)Uncharge tRNA is released from the E site and the next amino acid-tRNA enters
5) Process continues with amino acids being added based on the base sequence of the mRNA until a stop codon is reached

What are the steps in termination of translation?

1)The ribosome reaches one of the three terminaton codons(UAG, UAA, UGA).
2)Release factor binds to site
3)Polypeptide is cleaved from tRNA and the tRNA is released
4)Disassociation occurs

Describe Eukaryotic translation:

Very similar to prokaryotic translation
Differences:
-5' cap is the attachment site for the small subunit of the ribosome
-Formylmethionine is not required to start translation, instead a tRNAmet is required. The start codon is still AUG.
-A greater number of initiation, elongation, and temination factors are required