Unit 6 Transcription - Translation - ALL VOCAB

RNA polymerase

Enzyme similar to DNA polymerase that binds to DNA and adds RNA nucleotides from the DNA template

RNA Polymerase Direction

synthesizes RNA in 5' to 3' direction

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

Other names for template strand

noncoding strand, minus strand, or antisense strand

Other names for coding strand

non-template strand, plus strand, or sense strand,

Promoter

region of DNA that indicates to RNA polymerase where to bind to make RNA

terminator

A special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene

Enhancer

A DNA segment containing multiple control elements that can recognize certain transcription factors that stimulate the transcription of nearby genes. (not all genes need this)

Silencer

A eukaryotic DNA sequence that functions to inhibit the start of gene transcription; may act analogously to an enhancer by binding a repressor.

mRNA (messenger RNA)

a single-stranded RNA molecule that encodes the information to make a protein

rRNA (ribosomal RNA)

catalyzes peptide bond formation at the ribosome

tRNA (transfer RNA)

type of RNA molecule that transfers amino acids to ribosomes during protein synthesis

RNA Processing

The modification of mRNA before it leaves the nucleus that is unique to eukaryotes.

5' cap

The 5' end of a pre-mRNA molecule modified by the addition of a cap of guanine nucleotide.

poly-A tail

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

Splicing

the process of removing introns and reconnecting exons in a pre-mRNA

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.

Alternative splicing

Splicing of introns in a pre-mRNA that occurs in different ways, leading to different mRNAs that code for different proteins. Increases the diversity of proteins.

Chromosome structure

DNA wrapped around histones

Methylation

A chemical modification of DNA that does not affect the nucleotide sequence of a gene but makes that gene less likely to be expressed.

Acetylation

of DNA and histones causes nucleosomes to loosen and spread apart, encourages gene expression

Transcription Factor

A regulatory protein that binds to DNA and affects transcription of specific genes.

Transcription factor effect on development

Induction of transcription factors during development results in sequential gene expression

RNA interference (RNAi)

A technique used to silence the expression of selected genes. RNAi uses synthetic double-stranded RNA molecules that match the sequence of a particular gene to trigger the breakdown of the gene's messenger RNA.

Differences between DNA and RNA

DNA has deoxyribose, thymine, and is double-stranded. RNA has ribose, uracil, and is single-stranded

Structure of a nucleotide

phosphate group, sugar, nitrogenous base

Directionality of DNA

Transcription occurs in the 5' to 3' direction

5' to 3' direction

the only direction that DNA polymerase can synthesize DNA; it does so by adding nucleotides to the 3' end of a DNA strand. (5' carbon attaches to phosphate)

Major vs minor groove

The major groove occurs where the backbones are far apart, the minor groove occurs where they are close together.

Semiconservative model

Type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand.

Meselsohn and Stahl (1958)

N15 DNA cultivated, centrifuged and density tested for control

Origin of Replication

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.

Replication fork

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

replication bubble

a region of DNA, in front of the replication fork, where helicase has unwound the double helix

Helicase

An enzyme that untwists the double helix of DNA at the replication forks. (breaks hydrogen bonds between complementary bases)

Topoisomerase

Helps relieve strain in the double helix ahead of the replication fork. PREVENTS SUPERCOILING.

single stranded DNA binding proteins (SSBPs)

stabilizes single-stranded DNA (can prevent cutting by nucleases)

Nucleases

Cuts/breaks nucleic acids

Primase

An enzyme that joins RNA nucleotides to make the primer. Places down the primer for DNA replication.

It is an RNA polymerase that is used in DNA replication.

RNA Primer

short segment of RNA used to initiate synthesis of a new strand of DNA during replication. DNA polymerase recognizes to start laying down DNA nucleotides.

DNA Polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule. Always works in the 5' to 3' direction.

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.

Ligase

An enzyme that connects two fragments of DNA to make a single fragment (USES ATP)

Nucleotide excision repair

A repair system that removes and then correctly replaces a damaged segment of DNA using the undamaged strand as a guide.

Codon

A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid

unambiguous genetic code

each codon specifies only 1 amino acid

degenerate code

multiple codons encode a single amino acid

mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome

tRNA

transfer RNA

rRNA

Catalyzes peptide bond formation

Intramolecular base pairing

Base pairing within a single RNA molecule.

aminoacyl-tRNA synthetase

An enzyme that joins each amino acid to the appropriate tRNA (REQUIRES ATP).

Protein folding

The physical process by which a polypeptide folds into its characteristic three-dimensional structure, which is essential to the protein's function.

chaperone proteins

assist in folding other proteins

Ubiquitination

targets a protein for degradation by a proteasome

Proteasome

A giant protein complex that recognizes and destroys proteins tagged for elimination by the small protein ubiquitin.

Proteases

enzymes that break down proteins

wobble hypothesis

Ability of the tRNAs to recognize more than one codon; the codons differ in their third nucleotide (wobble base).

post-translational modification

Changes to the new protein that may be critical to its final function, like folding, phosphorylating, glycosylating, or lipidating