bio exam 5

Frederick Griffith

discovered transformation in bacteria

Transformation

process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria

Avery, MacLeod, McCarty

Determined that DNA was Griffith's "Transforming Factor."

Hershey and Chase

concluded that the genetic material of the bacteriophage was DNA, not protein.

Bacteriophage

A virus that infects bacteria

Friedrich Miescher

Discovered DNA

Components of nucleic acids

a nitrogenous base, a 5-carbon sugar, and a phosphate

phosphodiester bond

the type of bond that links the nucleotides in DNA or RNA. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide

Erwin Chargaff

discovered that A=T and G=C

Chargaff's Rules

A=T and G=c; the ratio of G-C to A-T varies with different species

X-ray diffraction

process used by Rosalind Franklin to make images of DNA that helped reveal the structure of DNA

Dimensions of DNA

double helix, diameter of 2nm, and a complete helical turn every 3.4nm

Tautomers

Isomers that can interconvert by exchanging the location of a proton.

Watson and Crick

Figured out structure of DNA was a double helix with two chains of nucleotides intertwined

phosphodiester backbone

repeating sugar and phosphate units joined by phosphodiester bonds

The two grooves in DNA

major and minor

base pairs

Any of the pairs formed between complimentary bases in the two nucleotide chains of DNA, such as A-T and C-G (DNA); A-U and C-G (RNA)

purine

Adenine and Guanine

Pyrimidines

Cytosine and Thymine

complementary

Describes genetic information in which each nucleotide base has a complementary partner with which it forms a base-pair.

antiparallel configuration

a single strand of DNA has an inherent polarity. 5' and 3' end.

Meselson and Stahl

Determined that DNA replication is semiconservative.

conservative model

Both parental strands stay together after DNA replication

semiconservative

method of replication that implies that each new strand of DNA is half original and half new

dispersive model

each strand of both daughter molecules contains a mixture of old and newly synthesized DNA

DNA replication requires 3 things

template, nucleotides, and polymerase enzyme

nucleoside triphosphate

a building block and energy source for replicating DNA

dna replication Initiation

protein recognizing a DNA sequence

dna replication elongation

new strands of DNA are synthesized by DNA polymerase

dna replication termination

Proteins release the replication complex

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

Replicon

DNA controlled by an origin

dna pol I

Acts on lagging strand to remove primers and replace them with DNA

dna pol II

enzyme that proofreads the daughter strand of replicated DNA and corrects any base pairing errors; does not play a role in replication

DNA poly III

adding bases to the new DNA chain; proofreading the chain for mistakes

endonuclease

an enzyme capable of cleaving phosphodiester bonds between nucleotides located internally in a DNA strand

exonuclease

an enzyme that removes successive nucleotides from the end of a polynucleotide molecule

Helicase

unwinds DNA

Supercoiling

The coiling in space of double-stranded DNA molecules due to torsional strain, such as occurs when the helix is unwound.

Topoisomersase

Any of a class of enzymes that can change the topological state of DNA to relieve torsion caused by unwinding.

dna gyrase

Enzyme that temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix

leading strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.

lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

replication fork

The Y-shaped end of a growing replication bubble in a DNA molecule undergoing replication.

primase

synthesizes RNA primer

DNA ligase

joins the ends of dna segments; dna repair

Replisome

group of proteins needed for DNA synthesis

mutagen

An agent that induces changes in DNA (mutations); includes physical agents that damage DNA and chemicals that alter DNA bases.

DNA repair

Collective term for the enzymatic processes that correct deleterious changes affecting the continuity or sequence of a DNA molecule.

specific repair

targets a single kind of lesion in DNA and repairs only that damage

nonspecific repair

use a single mechanism to repair multiple kinds of lesions in DNA

mismatch repair

The cellular process that uses special enzymes to fix incorrectly paired nucleotides.

Photorepair

Specific repair mechanism for one particular form of damage caused by UV light

excision repair

nonspecific; locates and repairs incorrect sequence by removing a segment of the DNA and then adding the correct nucleotides

Archibald Garrod

first suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions

George Beadle and Edward Tatum

showed that genes encode a cell's enzymes

nutritional mutants

mutants unable to grow without added nutrient

one gene-one enzyme hypothesis

the function of a gene is to dictate the production of a specific enzyme

Central Dogma of Molecular Biology

DNA -> RNA -> Protein

Transcription

synthesis of an RNA molecule from a DNA template

Translation

Process by which mRNA is decoded and a protein is produced

Retroviruses

use reverse transcriptase to copy their RNA genome into DNA

reverse transcriptase

An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis.

template strand

The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript.

coding strand

the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine

mMRNA

The RNA transcribed from structural genes; RNA molecules complementary to a portion of one strand of DNA, which are translated by the ribosomes to form protein.

rRNA

A class of RNA molecules found, together with characteristic proteins, in ribosomes; transcribed from the DNA of the nucleolus.

tRNA

A class of small RNAs (about 80 nucleotides) with two functional sites; at one site, an "activating enzyme" adds a specific amino acid, while the other site carries the nucleotide triplet (anticodon) specific for that amino acid.

snRNAs

In eukaryotes, a small RNA sequence that, as part of a small nuclear ribonucleoprotein complex, facilitates recognition and excision of introns by base-pairing with the 5′ end of an intron or at a branch site of the same intron.

SRP RNA

In eukaryotes, a cytoplasmic complex of proteins that recognizes and binds to the signal sequence of a polypeptide, and then docks with a receptor that forms a channel in the ER membrane. In this way the polypeptide is released into the lumen of the ER.

siRNA

A class of micro-RNAs that appear to be involved in control of gene transcription and that play a role in protecting cells from viral attack.

Codons

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

reading frame

The correct succession of nucleotides in triplet codons that specify amino acids on translation. The reading frame is established by the first codon in the sequence as there are no spaces in the genetic code.

frameshift mutation

A mutation in which a base is added to or deleted from the DNA sequence. These changes alter the reading frame downstream of the mutation.

Nirenberg

deciphered the genetic code

stop codon

UAG, UAA, or UGA; the codon that ends all RNA.

start codon

AUG; the codon that begins all RNA.

core polymerase

capable of RNA elongation but not initiation

Holoenzyme

initiate synthesis

Promoter

specific region of a gene where RNA polymerase can bind and begin transcription

transcription unit

The region of DNA between a promoter and a terminator.

transcription bubble

the region of locally unwound DNA that allows for transcription of mRNA

operon

group of genes operating together

Introns

Noncoding segments of nucleic acid that lie between coding sequences.

Exons

Coding segments of eukaryotic DNA.

spliceosome

A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

pre-mRNA splicing

In eukaryotes, the process by which introns are removed from the primary transcript to produce mature mRNA; pre-mRNA splicing occurs in the nucleus.

snRNPs

In eukaryotes, a complex composed of snRNA and protein that clusters together with other snRNPs to form the spliceosome, which removes introns from the primary transcript.

exon shuffling

The variation in the patterns by which RNA may produce diverse sets of exons from a single gene.

Transcriptome

all the RNA molecules transcribed from a genome

Proteome

the entire set of proteins expressed by a given cell or group of cells

alternative splicing

In eukaryotes, the production of different mRNAs from a single primary transcript by including different sets of exons.

aminoacyl-tRNA synthetase

An enzyme that joins each amino acid to the appropriate tRNA.

acceptor stem

the 3' end of a tRNA molecule that is the site of attachment for a particular amino acid, based on the anticodon

anticodon loop

contains 3 nucleotides complementary to mRNA codons

charging reaction

The reaction by which an aminoacyl-tRNA synthetase attaches a specific amino acid to the correct tRNA using energy from ATP.

Bacterial ribosomes 3 sites

A site, P site, and E site

A-site

(aminoacyl) binds to the tRNA carrying the next amino acid to be added

P-site

(peptidyl) binds to the tRNA attached to the growing peptide chain