Module 3 Genetics Vocab

Conservative model of DNA replication

Daughter strands and parental strands are separate in the final product 

Semiconservative model of DNA replication

Each daughter strand goes with a parent strand in the final product; the correct model

Dispersive model of DNA replication

Each parent and daughter strand is broken up into pieces and put back together with parts of a different strand

Unwinding (de-annealing)

the step in DNA replication where the parent strands are separated

Complementary base pairing

The step in DNA replication where each parental strand serves as a template for a new strand

Joining

The step in DNA replication where the nucleotides are connected

Origin of replication 

Where DNA replication begins, an A/T rich sequence site 

Replication bubble

Forms as the two parent strands are separated

Replication forks

The junction where the replication bubble meets double-stranded DNA; Y-shaped; two are present in the replication of prokaryotic DNA

Replicon 

The DNA produced from a single origin of replication 

Helicase

AN enzyme that unwinds the original DNA chromosome and begins separating the two strands of the double helix

Topoisomerase

An enzyme that corrects overwinding in the strands before the helicase arrives by breaking, swiveling, and rejoining cut DNA

Single-stranded binding proteins (SSBPs)

Bind to the separated strands to prevent re-annealing of the strands back into the double helix before they are used as a template 

Primase (RNA polymerase)

An enzyme that attaches a small piece of RNA (primer) to the 5’ end of the leading strand and at the 5’ end of each Okazaki fragment; serves as a start site to initiate DNA polymerization 

DNA polymerase III (DNA pol III)

Requires a single template strand and a primer, starts the synthesis of DNA; builds a second complementary DNA strand in the 5’ to 3’ direction (attaches a new nucleotide to the 3’ end) (prokaryotic)

Tsuneko and Reiji Okazaki

The husband and wife duo that discovered leading and lagging strands/fragments

Leading strand

Continuous daughter strand that is made in the same direction as the replication fork movement

Lagging strand 

Discontinuous daughter strand made in opposite direction of fork movement; also called Okazaki fragments

DNA polymerase I (DNA pol I)

Replaces primers with DNA in prokaryotic DNA replication (prokaryotic)

DNA ligase

Seals the small gaps between fragments (prokaryotic)

Gyrase

Another term for topoisomerase

DNA polymerase II (DNA pol II)

Works in DNA repair, assists DNA pol III (prokaryotic)

DNA polymerase a (alpha)

Starts polymerization directly off of primer (eukaryotic)

DNA polymerase b (beta)

Works in DNA repair, proofreading; key for maintaining error-free copying

DNA polymerase d (delta)

Works on lagging strand synthesis and primer substitution (eukaryotic)

DNA polymerase E (epsilon)

Works on leading strand synthesis (eukaryotic)

Ribonuclease H

Removes RNA primers from Okazaki fragments (eukaryotic)

DNA ligase I

Closes up the new DNA of the lagging strand afterwards (eukaryotic)

FEN1 (flap endonuclease I)

A protein that processes the 5’ end of Okazaki fragments in lagging strand, also involved in DNA repair

End replication problem 

Primers at the ends of eukaryotic chromosomes cannot be replaced, leaving a gap; this is solved by placing telomeres on the ends of chromosomes

Telomeres

“Caps” of repetitive nucleotides which are present at the ends of linear chromosomes and are non-coding (not involved in genes) and are dispensable

Hayflick limit (HL)

The limit on cell replication imposed by the shortening of telomeres with each division; it depends on the length of telomeric regions at the ends of chromosomes

Telomerase 

An enzyme that helps cells “rebuild back” their telomeres and not reach Hayflick limit 

Senescence

When the telomeres disappear and the cells stop dividing

Gene expression

The process by which DNA directs protein synthesis

Transcription/translation in prokaryotes

No nucleus, transcription and translation are coupled, no time to proofread/modify RNA

Transcription/translation in eukaryotes

Transcription and translation happen in different places, immature RNA is first processed before translation

Messenger RNA (mRNA)

The type of RNA that contains the genetic information for the amino acid sequence of a protein; is the final product which is used as a template for translation

Ribosomal RNA (rRNA)

The type of RNA which is made in the nucleolus and is part of the structure of ribosomes

Transfer RNA (tRNA)

The type of RNA which transports an amino acid to a ribosome and transfers it to a growing polypeptide chain during translation 

Transcription

The first step of gene expression, involves the synthesis of RNA from a DNA gene template (callled the template strand), messenger RNA (mRNA) is the resulting product

Transcription unit

A stretch of DNA that encodes an RNA molecule; normally contains a promoter, an RNA-coding sequence, and a terminator

Coding strand 

The DNA strand used directly for transcription 

Non-coding strand

The DNA strand that is not used directly for transcription

Upstream

The regions of RNA near the beginning of a gene sequence

Downstream

The regions of RNA near the end of a gene sequence

The 3 steps of transcription

Initiation, elongation, and termination

Initiation

The first step of transcription; the process where an RNA polymerase binds to a region of the DNA ahead of the promoter and becomes activated

Promoter

A region of DNA which defines the beginning and start site of the gene

Consensus sequence

The calculated order of most frequent residues (like nucleotides or amino acids) found at each position in a sequence alignment

Holoenzyme

A biochemically active compound formed by the combination of an enzyme with a coenzyme

TATA box

A special promoter site consisting of many A and T nucleotides used by eukaryotes during transcription

Transcription initiation complex 

The RNA polymerase II complex that unzips DNA and prepares to pair RNA nucleotides with the complementary DNA strand (in eukaryotes)

Elements of the transcription initiation complex

Enhancer and silencer sequences, activator and repressor proteins, promoter-proximal elements, architectural (DNA-bending) proteins, DNA loop

Transcription factors

Additional proteins and subunits that also direct binding of RNA polymerase to specific promoters for gene expression

Enhancer

A short DNA sequence upstream of the coding sequence that promotes more gene expression 

Silencer

A short DNA sequence upstream of the coding sequence that promotes less gene expression

Activator

A DNA binding protein that serves as a mediator between enhancers and promoter-proximal elements

Repressor 

A DNA binding protein that serves as a mediator between silencers and promoter-proximal elements

The 3 steps of initiation

Eukaryotic promoter → several transcription factors bind to DNA → transcription initiation complex forms

Elongation

The second step of transcription; involves the addition of RNA nucleotides in a 5’ to 3’ direction along the coding strand

RNA polymerase I (RNA pol I)

The eukaryotic RNA polymerase that makes ribosomal RNA 

RNA polymerase II (RNA pol II)

The eukaryotic RNA polymerase that makes mostly pre-messenger RNA

RNA polymerase III (RNA pol III)

The eukaryotic RNA polymerase that makes mostly transfer RNA

Termination

The third step of transcription; the RNA polymerase stops polymerization and releases the RNA transcript

Rho-independent (intrinsic)

Disruption of mRNA-DNA-RNA polymerase complex is triggered by the creation of a self-annealing hairpin structure and a poly-uracil residue 

Rho-dependent

Disruption of mRNA-DNA-RNA polymerase complex is performed by a Rho-factor with DNA/RNA helicase activity

Processing/modification (in eukaryotes only)

The fourth step of translation; chemical additions are made to the 5’ and 3’ ends of the RNA transcript and in eukaryotes, there is editing of regions of the transcript that are not needed (splicing)

Shine-Dalgerno sequence

Where ribosomes begin translation in prokaryotes; is a ribosomal binding site located right before (upstream of) the start codon

Untranslated regions 

The nucleotides on both sides of the coding region

5’ capping

A modified guanine (G) nucleotide structure is added, this structure also serves as a ribosomal binding site to initiate translation

3’ poly-A tail (polyadenylation)

During termination of eukaryotic transcription, a long stretch (50-200 nucleotides) of adenine (A) is added

Splicing 

Non-coding regions are removed from the primary mRNA transcript and regions which encode the eventual protein are attached together 

Introns

Intervening sequences which are not expressed

Exons

Sequence regions which are expressed

Spliceosome

A large ribonucleoprotein complex within the nucleus of eukaryotic cells; facilitates mRNA splicing in eukaryotes

Ribozymes 

RNA molecules that are capable of acting as enzymes 

Alternative RNA splicing

Genes encoding more than one kind of polypeptide depending on which exons are used; different exons will be cut out to make different proteins

Translation

The process of gene expression where mRNA transcripts are used by the ribosome to synthesize proteins using amino acids

The key players of translation

mRNA (the template), tRNA (the interpreter), and the ribosome (the site of protein synthesis)

tRNA (the interpreter)

80 nt that folds on itself to give 3D structure, physically transports the correct amino acids to the ribosome, pairs with mRNA codon to interpret the genetic code

Aminoacyl-tRNA synthetase 

Matches the cognate RNA and its amino acid, found in the cytoplasm, uses ATP as an energy source

Wobble

The third base of the codon that doesn’t pair perfectly, due to redundancy, this is usually not an issue

Ribosome (site of protein synthesis)

Made up of a large subunit (has the E, P, and A sites) and the small subunit that binds mRNA

Ribosome (function)

Protein-RNA complexes that facilitate the specific coupling of tRNA anticodons with mRNA codons in protein synthesis

Large subunit 

Has peptidyl transferase activity (it will connect amino acids and produce a polypeptide chain)

Small subunit

Binds mRNA and helps direct tRNA-codon pairings

A site (aminoacyl-tRNA binding site)

Holds the tRNA that carries the next amino acid to be added to the chain

P site (peptidyl-tRNA binding site)

Holds the tRNA that allows for peptide bond formation between the amino acid on the tRNA and the growing polypeptide chain

E site (exit site)

Where discharged tRNAs leave the ribosome