BIO 20A Midterm 2

Frederick Griffith

Showed that a heat-killed S strain of Streptococcus bacteria can "transform" a living R strain of into a virulent strain that causes pneumonia

Transformation

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

Alfred Hershey and Martha Chase

Conducted the "Waring blender experiment" that showed that bacteria inject DNA, not protein, into bacteria

Bacteriophage

viruses that infect bacteria

James Watson and Francis Crick

discovered the structure of DNA

Semi-conservative

in each new DNA double helix, one strand is from the original molecule, and one strand is new

Origin of replication

Site where DNA replication begins.

DNA helicase

An enzyme that unwinds the DNA double helix during DNA replication

Replication fork

A Y-shaped region on a replicating DNA molecule where new strands are growing.

Single-stranded DNA-binding proteins

keep, helix from reforming

Topoisomerase

keep DNA from getting tangled up as it is unwound

Primer

nucleic acid containing a 3" OH to which net nucleotide can be added

Template strand

The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript. Always has the promoter and termination site and is read 3' to 5' by RNA polymerase.

Complementary strand

the sequence of DNA that corresponds to the template strand of DNA (A-T, G-C)

Primase

An enzyme that makes a short RNA primer to start DNA synthesis.

Leading strand

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

Lagging strand

A synthesized DNA strand that elongates by Okazaki fragments(short pieces of DNA that need additional primers), 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.

DNA polymerase III

adds nucleotides to 3'OH of RNA primer

DNA polymerase I

replaces the RNA primers with DNA

DNA ligase

joins the Okazaki fragments to form a continuous DNA strand.

Deoxynucleoside triphosphates

Free nucleotides with three phosphate groups

Breaking covalent bond to release pyrophosphate (two phosphates) provides energy to connect nucleotides

Mismatch repair

repair enzymes correct errors in base pairing

Transcription

synthesis of an RNA molecule from a DNA template

RNA polymerase

The enzyme that synthesizes RNA from DNA template. Adds nucleotides to the 3' end of the growing RNA as it moves to the 5' end of the template strand.

Translation

Process by which mRNA is decoded and a protein is produced

Codon

three-nucleotide sequence on messenger RNA that codes for a single amino acid

Kilobase (kb)

1000 base pairs

Megabase (Mb)

1,000,000 base pairs

Start (initiation) codon

"AUG" Beginning of every mRNA

Stop (termination) codon

UAA, UAG, and UGA; in protein synthesis, these codons signal the termination of a polypeptide chain

Reading frame

specific way a sequence of nucleotides is divided into groups of three, called codons

Open-reading frame (ORF)

a stretch of bases uninterrupted by termination codons

Coding sequence

determines the sequence of amino acids in the protein

Untranslated region (UTR)

The region of mRNA before the start codon AUG, it allows the ribosome to bind to mRNA

Promoter

specifies where RNA polymerase will initiate transcription. Also "tells RNA polymerase which DNA strand to use as the template

TRANSCRIPTION initiation, elongation & termination

1) initiation: RNA Pol binds promoter, unwinds short region of DNA to expose template strand and then begins synthesizing RNA complementary to template strand (at the 5' end of the RNA

2)RNA Pol adds nucleotides complementary to the template strand to teh 3'OH of RNA one at a time, RNA transcript is released as it is made; DNA double helix immediately reforms 3)Transcription stops when RNA Pol reaches the termination site

Primary transcript

The initial mRNA transcript that is transcribed from a protein coding gene. Also called pre-mRNA.

Mature mRNA

Processed mRNA ready for translation.

Transcription unit

region of DNA that encodes an RNA

Regulatory element

binding sites (specific DNA sequences) for regulatory proteins that activate or repress transcription

Nuclear envelope

A double membrane that surrounds the nucleus in the cell

Inner and outer nuclear membranes

-inner: contains specific proteins used for anchoring chromatin and the nuclear lamina

-outer: continuous with the membrane of the ER; studded with ribosomes

Nuclear pore

hole in nuclear membrane

RNA processing

Modification of RNA primary transcripts, including splicing out of introns, joining together of exons, and alteration of the 5' and 3' ends before translated.

Capping

addition of a modified guanine nucleotide to 5' end of the pre-mRNA

Polyadenylation

post-transcriptional addition of 200-300 adenine nucleotides to 3' end of the pre-mRNA

What RNA processing (capping and polyadenylation) do

Alter the stability and translation of eukaryotic mRNAs

Poly A tail

Modified end of the 3' end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides.

RNA splicing

removal of specific, internal segments of the pre-mRNA. Removes introns and keeps the regions that remain in the RNA called exons.

Intron

sequence of RNA that is spliced out

Exon

a segment of RNA molecule that is NOT spliced out

5' and 3' splice sites

Mark the beginning and end of an intron, introns are flanked by the 5' and 3' splice sites

Alternative splicing

Splicing of introns in a pre-mRNA that jumps/skips certain exons that increases the diversity of proteins that can be produced from a single gene

Spliceosome

A complex of small nuclear RNAs and associated proteins (snRNPS) that removes introns and joins exons back together

codon

three-nucleotide sequence on messenger RNA that codes for a single amino acid

Transfer RNA (tRNA)

recognizes codons in the mRNA and link them to specific amino acid mRNA and link them to specific amino acids

Anticodon

group of three bases on a tRNA molecule that are complementary to an mRNA codon

Aminoacyl tRNA synthetase

Enzyme that makes sure that the correct amino acid attaches to tRNA ("charging")

tRNA charging

the attachment of a tRNA to its appropriate amino acid

Ribosome

the site of protein synthesis and the "workbench" where aminoacyl tRNAs and mRNA are brough together during translation. Catalyzes formation of the peptide bond between amino acids. Contains large and small subunits; each subunit contains both ribosomal proteins and RNAs (rRNAs)

ribosomal RNA (rRNA)

type of RNA that combines with proteins to form ribosomes

ribosomal protein

Any protein that makes up a ribosomal subunit.

small and large ribosomal subunits

the small subunit is responsible for decoding the mRNA and binding to the ribosome. the large subunit catalyzes peptide bond formation, which links amino acids together to form proteins

aminoacyl tRNA

tRNA linked to its corresponding amino acid.

peptidyl tRNA

tRNA holding the growing polypeptide chain.

E, P and A sites

Order of amino acids go from A->P->E. A-site: aminoacyl tRNA binding site that binds the tRNA bearing the next amino acid to be added. P-site: peptidyl tRNA binding site that binds the tRNA bearing growing polypeptide chain. E-site where tRNA exits the ribosome

TRANSLATION initiation, elongation and termination

initiation: small subunit attaches to mRNA, met amino acid attaches to P site, large attaches

elongation: amino acids added one at a time in three step process as polypeptide grows. 1) codon recognition: incoming aminoacyl tRNA binds to codon at the A site. 2) peptide bond formation: polypeptide is transferred from tRNA in P site to the tRNA in the A site. 3) translocation: ribosome advances by one codon as the tRNA bearing the nascent polypeptide is transferred from the A site to the P site

termination: when the A site encounters stop codon, release factor binds to A site. Completed polypeptide chain is released, ribosomal subunits dissociate

Peptidyl transferase

An enzyme in the ribosome responsible for catalyzing peptide bond formation during translation.

Release factor

when a stop codon is encountered in the A-site, a release factor enters the A-site and translation is terminated and newly formed protein is released.

insertion Mutation

a mutation in which one or more nucleotides are added to a gene

Deletion Mutation

a mutation in which one or more pairs of nucleotides are removed from a gene

Silent mutation

change nucleotide sequence, by not protein sequence. (AAG lysine to AAA lysine)

Missense mutation

change base sequence and amino acid sequence (AAG lysine to GAG glutamic acid)

Nonsense mutation

change codon to termination codon (AAG lysine to UAG stop codon)

Frameshift mutation

effect of insertions and deletions if not divisible by 3 that changes how DNA sequence is read

Transcriptional regulation

Control of gene expression at transcription level. Usually yields slower, longer lasting effects. (Example: Regulation of amino acid biosynthesis in E.coli)

Regulation of Tryptophan Biosynthesis in E.Coli

Classic example of transcriptional regulation. Trp operon controls expression of polycistronic mRNA and trp repressor is a regulatory proteins that binds the trp operator tryptophan that blocks transcription of operon by RNA polymerase. Low trp levels=repressor doesn't bind, transcription occurs. High trp=repressor binds, transcription repressed.

translational regulation

Control of gene expression at translational level. Usually yields allows much more rapid regulation. (Example: regulation of cellular iron levels in humans)

Regulation of Cellular Iron levels

If irons level are high, cells increase the level of ferritin an iron storage protein. Iron-regulatory proteins are RNA-binding proteins that bind to iron-response elements when iron levels are low. Low iron: IRPs bind IREs and translation of ferritin mRNA is blocked. Ferritin levels drop and iron is not stored. High iron: iron binds IRP. IRPs do not bind IREs and ferritin is translated. Ferritin levels increase and iron is stored.

Operon

group of genes operating together

Polycistronic

multiple proteins are encoded on a single molecule of mRNA

Trp operon

repressible operon

Operator

25 base pair DNA sequence downstream of promoter that binds trp repressor protein

Trp repressor

a protein that binds to the operator site of the trp operon and inhibits transcription

Ferritin

iron storage protein

IRPs

Iron regulatory proteins that binds that is the sensor in regulation of iron

IREs

Iron-response elements that is target in regulation of iron (RNA sequence)