DNA Structure, Replication, Transcription, and Translation

Flashcards covering DNA structure, replication, transcription, and translation processes.

Transformation (Griffith's experiment)

The process where non-lethal bacteria acquire a factor from heat-killed lethal bacteria and turn into a lethal strain.

Avery, McLeod, and McCarty Experiment

Experiment demonstrating that DNA is the transforming factor, as transformation is disrupted by DNase.

Hershey-Chase experiment

Confirmed that DNA is heritable genetic info and showed that bacteriophage T4 DNA hereditary molecule used during infection.

Chargaff's Rules

In DNA, the % of adenine is equal to the % of thymine, and the % of guanine is equal to the % of cytosine; %A=%T and %G=%C.

Major and Minor Grooves (DNA)

Expose nucleotides, and are the result of unequal glycosidic bond angles.

Antiparallel Strands (DNA)

DNA strands that run in opposite directions, with one strand having a 5' to 3' orientation and the other having a 3' to 5' orientation.

Rosalind Franklin

Her work on DNA structure revealed DNA is a double helix structure, which is why the X formed in photo.

Purines

Nitrogenous bases with a two-ring structure; adenine (A) and guanine (G).

Pyrimidines

Nitrogenous bases with a single six-atom ring; thymine (T) and cytosine (C).

B-form DNA

Predominant form of DNA in cells; the hydrated form.

Semi-conservative Replication

Each new DNA helix consists of one parental strand and one newly synthesized strand.

Origin of Replication (ORI)

Specific site on DNA where replication begins and proceeds bidirectionally.

Topoisomerases

Enzymes that cut and religate DNA strands to resolve torsion produced by the progression of replication forks.

Helicase

Enzyme that unwinds the double helix at the replication fork by breaking hydrogen bonds.

Single-Stranded Binding (SSB) Protein

Protein that prevents reannealing of separated DNA strands during replication.

Primase

Enzyme that synthesizes RNA primers to provide a free 3' OH group for DNA polymerase to initiate synthesis.

DNA Polymerase III

Enzyme that synthesizes DNA by adding nucleotides to the 3' ends of existing strands.

DNA Polymerase I

Enzyme that removes RNA primers and replaces them with DNA nucleotides.

Ligase

Enzyme that joins DNA segments by catalyzing the formation of phosphodiester bonds b/w 5’ and 3’ ends.

Leading Strand

Strand synthesized continuously in the 5' to 3' direction towards the replication fork.

Lagging Strand

Strand synthesized discontinuously in short fragments (Okazaki fragments) in the 5' to 3' direction away from the replication fork.

Okazaki Fragments

Short DNA fragments synthesized on the lagging strand during DNA replication.

Replisome

Enzymatic complex that coordinates DNA replication.

DnaA

Initiator protein that recognizes and binds to the 9-mer tandem repeats at the origin of replication in E. coli.

DnaB

Helicase in E. coli, delivered by DnaC to open the DNA complex and unwind the strands.

Sliding Clamp

Processivity factor that keeps DNA polymerase bound to the DNA, allowing for continuous synthesis.

Proofreading

Exonuclease activity of DNA polymerases to correct mismatched base pairs.

Telomerase

Holoenzyme, reverse transcriptase, to add telomeric repeats to chromosome ends; Prevents telomere shortening.

Telomeres

Protective caps at the end of chromosomes consisting of TTAGGG repeats.

Shelterin

Protein complex that associates with telomeres and protects them against degradation.

Polymerase Chain Reaction (PCR)

Method for amplifying DNA segments through repeated cycles of denaturation, annealing, and extension.

DNA sequencing

Use of dideoxynucleotide NTP to synthesis DNA and chain termination by ddNTPs at each position they are incorporated.

Transcription

Process of RNA synthesis from a DNA template.

RNA Polymerase I

Transcribes rRNA.

RNA Polymerase II

Transcribes mRNA.

RNA Polymerase III

Transcribes tRNA and miRNA.

mRNA processing

Capping, splicing, and polyadenylation.

Promoter

Region of DNA that recruits RNA polymerase to initiate transcription.

RNA processing

Transcription + mRNA processing occurs in the nucleus.

Introns

Non-coding sequences that are part of DNA that interrupt the coding sequence.

snRNA

Important for splicing.

Types of RNA

mRNA-protein coding; used by ribosome for translation and polypeptide synthesis, rRNA, tRNA-amino acid carriers, anticodon that are reverse complement to each codon present on mRNA, snRNA, siRNA-eukaryotic gene expression.

Alternative Splicing

The same mRNA can be spliced in different ways, so there are a few different 5' splice sites or a few different 3' splice sites.

5' Capping

Addition of guanine monophosphate to the 5' end of mRNA; phosphate hydrolysis.

Polyadenylation

Post-transcriptional event, mRNA cleavage and a poly A polymerase adds 20-200 A’s to the 3’ end.

AAUAA

The Polyadenylation signal sequence.

Splicing

Removal of introns.

Spliceosome

Used for eukaryotic nuclear genes; targeting the pre-mRNA introns where ribonucleoproteins form.

Lariat

Imp intermediate; formed by cleaving just upstream of the G in 5’ splice site and forming a covalent bond b/w the G and the branch point adenine.

Translation

Process of protein production carried out by ribosomes where MRNA contains the coding sequence, a process carried out by ribosomes.

Start Codon

AUG is recognized as and defines the reading frame.

Amino Acids

The order and sequence of AAs is critical to folding, structure, and function of polypeptide.

A Site

Incoming aminoacyl tRNA charged w/ relevant AA comes in, hybridizes to codon by base pairing, and then AA is added to the chain.

P Site

Peptidyl site at which growing polypeptide is attached to a tRNA that still hybridizes to codon there.

E Site

Exit site; previous tRNA that contained chain that is now empty bc peptidic bond transferred the AA; the tRNA is released and uncharged.

tRNA

Carry the cognate amino acid to the A site where base pairing occurs b/w tRNA and codon on the mRNA.

Shine-Dalgarno Sequence

in mRNA sequence recognized by 16S rRNA; that will base pair allows for small subunit to land on molecule at right position during initiation in E.Coli.

Elongation Factors

Essential for control of translation elongation.

Release Factors

Recognize stop codons during translation termination to release polypeptide after they recognize the stop codons; UAA, UAG, or UGA.

Kozak Sequence

Consensus sequence ACCAUGG that EIF4 recognizes cap of mRNA to scan for starting AUG initiating translation in eukaryotes

Codon Degeneracy

Amino acid can be defined by more than one codon where tRNA can Wobble.

tRNA Synthetase

Recognizes anticodon and promotes binding of amino acid on the 3’ OH of the ribose to 3’ CCA of the tRNA by loading of tRNA w/ cognate amino acid