Bio 102: Genetics Exam 3 (Chaps 15b, 16, 17)

DNA polymerase I

in lagging-strand synthesis, removes the RNA primer and replaces it with DNA

DNA polymerase

any enzyme that catalyzes synthesis of DNA; polymerizes deoxyribonucleotide monomers into DNA

Deoxyribonucleotide triphosphates (dNTPs)

the monomers used by DNA polymerase to polymerize DNA. Consists of the sugar deoxyribose, a nitrogenous base (A,T, G, or C), and three phosphate groups

Primer

short, single-stranded RNA or DNA molecule that base-pairs with a DNA template strand and is used as a starting point for DNA synthesis by DNA polymerase

Template strand

a strand of RNA or DNA for direct synthesis of a new, complementary strand via complementary base-pairing

Polymerase activity

attaching nucleotides (monomers) together by phosphodiester bonds to make a longer nucleic acid chain (polymer)

Nuclease activity

breaking down nucleic acid chain (polymer) by breaking phosphodiester bonds that hold nucleotides together

Exonuclease

an enzyme that removes deoxyribonucleotides from the ends of DNA strands

Endonuclease

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

Origin of replication

the site on a chromosome where DNA replication begins

Replication fork

the Y-shaped site where a double-stranded molecule of DNA is separated into two single strands for replication and on which DNA synthesis occurs

DNA helicase

an enzyme that breaks hydrogen bonds between nucleotides of DNA, "unzipping" a double-stranded DNA molecule in preparation for replication

Single-strand DNA-binding proteins (SSBPs)

a protein that attaches to separated strands of DNA during replication, preventing them from re-forming a double helix

Topoisomerase

an enzyme that prevents the twisting of DNA ahead of the advancing replication fork by cutting the DNA, allowing it to unwind, and rejoining it

DNA Polymerase III

the enzyme that is primarily responsible for copy E. coli's chromosome before cell division

RNA polymerase

an enzyme that catalyzes the synthesis of RNA from ribonucleotides using a template usually consisting of DNA

Primase

an enzyme that synthesizes a short stretch of RNA complementary to a DNA templated to use as a primer during DNA replication; type of RNA polymerase

Leading strand

in DNA replication, the new strand of DNA that is synthesized in one continuous piece in a direction that follows the replication fork

Lagging strand

In DNA replication, the new strand of DNA that is synthesized discontinuously (as a series of short pieces that are later joined) in a direction moving away from the replication fork

DNA Ligase

an enzyme that joins pieces of DNA by catalyzing the formation of a phosphodiester linkage between the pieces

Okazaki Fragments

short segment of DNA produced during replication of the lagging strand template; are eventually linked together to produce the lagging strand in newly synthesized DNA

Sliding clamp

holds DNA polymerase in place during strand extension

Proofreading

a mechanism for error correction during DNA synthesis in which a DNA polymerase recognizes and removes a wrong deoxyribonucleotide added during DNA replication and then continues synthesis

Mismatch repair

a type of DNA repair used to correct mismatched base pairs in DNA that result from mistakes in DNA synthesis

Nucleotide excision repair

a type of DNA repair that removes a damaged region in one strand of DNA and replaces it with the correct sequence using the undamaged strand as a template

Null alleles

A mutation in an allele that does not produce a functional gene product; also called loss-of-function alleles

Complete medium

all nutrients (building blocks) needed for growth: carbon source, inorganic salts, all building blocks (amino acids, nucleotides, vitamins)

Minimal mediumv=

basic chemicals for growth: carbon source, inorganic salts, NO building blocks

Auxotroph

cells that couldn't grow on minimal medium; cannot make its own building blocks

Prototroph

organism capable of making its own essential macromolecules; organism that can synthesize all building blocks (wild type)

One gene, one-enyzme hypothesis

The hypothesis of gene function that proposed each gene is responsible for making one enzyme. Ideas about the function of genes have expanded to include genes that produce proteins other than enzymes, RNAs as final products, or two or more related products.

Codon

(coding unit) A sequence of three nucleotides in mRNA that codes for an amino acid or a stop signal for protein synthesis.

Genetic code

set of rules that determines how the information in the nucleotide sequence of DNA/RNA is converted to amino acid sequence of proteins

Unambiguous

each sense codon codes for one AND only one amino acid

Non-overlapping

three nucleotides that are part of one codon CANNOT be a part of any other codon

Triplet

each codon (coding unit) is read in blocks of 3 nucleotides

Continuous

this means that the ribosome reads codons of the mRNA continuously. it cannot skip bases or backtrack

Nearly universal

a particular codon specifies the same amino acids in all organisms (with a few exceptions)

Redundant/degenerate

multiple codons can code for the same amino acid/61 sense codons to make 20 amino acids

Sense codon

specify an amino acid (61/64)

Nonsense codon

do not specify an amino acid (3/64), signal termination of translation, tell ribosome to fall off

Anticodon

The sequence of three bases (a triplet) in a tRNA molecule that can bind to an mRNA codon with a complementary sequence.

Open reading frame (protein coding region)

(ORF) A sequence of DNA that, if converted into an RNA sequence and translated as a set of non-overlapping codons, would produce a polypeptide of substantial size. Discovery of an ORF provides evidence for the existence a protein-coding gene.

Mutation

a stable, heritable, non-regulatable change in the nucleotide sequence of DNA

Point mutations

one or a small number of base pair changes

Chromosome-level (chromosomal) mutations

alterations to large pieces of DNA/parts of chromosomes

Substitution

one base pair (bp) is change to another

Insertion/deletion

addition/subtraction of one or more base pairs

Missense mutations

A point mutation (change in a single base pair) that changes one amino acid for another within a protein.

Nonsense mutations

A point mutation (change in a single base pair) that converts an amino-acid-specifying codon into a stop codon.

Silent mutations

A point mutation that changes the sequence of a codon without changing the amino acid that is specified.

Frameshift mutations

The addition or deletion of one or a few base pairs in a coding sequence that shifts the reading frame of the mRNA.

Non-template/sense/coding strand

The strand of DNA that is not transcribed during synthesis of RNA. With the exception of T's instead of U's, its base sequence corresponds to that of the RNA produced from the other strand. Also, in the case of protein-coding genes

Template/antisense/non-coding

A strand of RNA or DNA for direct synthesis of a new, complementary strand via complementary base-pairing.

Inversion

A mutation in which a DNA sequence or a segment of a chromosome is flipped into the reversed orientation

Deletion

In genetics, refers to a loss of a DNA sequence or chromosome.

Duplication

In genetics, refers to an additional copy of a DNA sequence or part of a chromosome.

translocation

A type of mutation in which a piece of a chromosome moves to a nonhomologous chromosome.

Upstream

in genetics, opposite to the direction from a reference point (e.g., the start of transcription) in which RNA polymerase moves along a DNA strands

Downstream

in genetics, the direction from a reference point (e.g., the start of transcription) in which RNA polymerase moves along a DNA strand

Messenger RNAs

(mRNA) an RNA molecule that carries information (in codons) that specifies the amino acid sequence of a polypeptide

Transfer RNA

(tRNA) an L-shaped RNA molecule that has an anticodon at one end and an amino acid attachment site at the other. Each tRNA can carry a specific amino acid and binds to the corresponding codon in mRNA during translation

Ribosomal RNAs

(rRNAs) any of the RNA molecules that form part of the ribosome

Initiation

the stage during which RNA polymerase and other proteins assemble at the promoter sequence and open the strands of DNA to start transcription

Elongation

the process by which RNA lengthens during transcription

Termination

the dissociation of the RNA and RNA polymerase from DNA

Holoenzyme

a general term for any multipart enzyme consisting of a core enzyme (which contains the active site for catalysis) along with other proteins required for full function

Core enzyme

a general term for the enzyme within a multipart holoenzyme that is responsible for catalysis

Sigma

a bacterial protein that associates with the core RNA polymerase to allow recognition of promoters

Promoter

a short nucleotide sequence in DNA that binds a sigma factor (in bacteria) or general transcription factors (in eukaryotes) to enable RNA polymerase to begin transcription

Ribonucleotide triphosphates (NTPs)

Building blocks for RNA synthesis.

RNA polymerase II

transcribes protein-coding genes to pre-mRNAs

Basal (core) transcription factors

any of a class of proteins, present in all eukaryotic cells, that assemble on promoters and help RNA polymerase initiate transcription.

Core (basal) promoter

a DNA sequence in eukaryotes that binds core transcription factors to enable RNA polymerase to begin transcription

TATA box

a short DNA sequence in many eukaryotic promoters that is important for assembling general transcription factors and RNA polymerase at the core promoter; located about 30 base pairs upstream from the transcription start site

Poly (A) signal

in eukaryotes, a short sequence of nucleotides near the 3' end of the future mRNA that signals cleavage of the pre-RNA and addition of the poly(A) tail

pre-mRNA

in eukaryotes, the primary transcript of protein-coding genes; processed to form mRNA

Primary transcript

in eukaryotes, a newly transcribed RNA molecule that has not yet been processed to a mature RNA; called pre-mRNA when the processed RNA is mRNA

RNA processing

in eukaryotes, the changes that a primary RNA transcript undergoes to become a mature RNA molecule. For pre-mRNA it includes the addition of a 5' cap, a 3' poly(A) tail, and splicing to remove introns

Splicing

the process by which introns are removed from primary RNA transcripts and the remaining exons are connected together

5' cap

a modified guanine (G) nucleotide added to the 5' end of eukaryotic mRNAs. Helps protect the mRNA from being degraded and promotes initiation of translation

Poly (A) tail

in eukaryotes, a sequence of about 100-250 adenine nucleotides added to the 3' end of the newly transcribed messenger RNA molecules

Exons

the expressed regions of eukaryotic genes that will be part of the final mRNA product (present in both pre-mRNA and mRNA)

Introns

the intervening noncoding sequences that will not be in the final mRNA product (only present in pre-mRNA)

Small nuclear ribonucleoproteins

(snRNPs) any class of small RNAs associated with proteins and found in the nucleus of eukaryotic cells, where they form the spliceosome and catalyze splicing

Ribosomes

a large macromolecular machine that synthesizes proteins by using the genetic information encoded in mRNA. Consists of two subunits, each composed of rRNA and proteins

Polyribosome

an mRNA molecule that is being translated by two or more ribosomes; greatly increase the number of copies of a protein that can be produced from a single mRNA

Aminoacyl tRNA

a tRNA molecule that is covalenty bonded to an amino acid ("charge" tRNA)

unaminoacycl tRNA

a tRNA that has donated its amino acid ("uncharged tRNA")

Aminoacyl-tRNA synthetases

an enzyme that catalyzes the addition of a particular amino acid to its corresponding tRNA molecule

A site

the acceptor site for an aminoacyl tRNA; holds an aminoacyl tRNA

P site

the peptidyl site where a peptide bond forms; holds the tRNA with growing polypeptide attached

E site

where tRNAs without amino acids exit the ribosome; holds a tRNA that will exit

Ribozymes

any RNA molecule that can act as a catalyst to increase the rate of a chemical reaction

Ribosome binding site

in a bacterial mRNA molecule, the sequence just upstream of the start codon to which a ribosome binds to initiate translation; also called the shine-dalgarno sequence