AP BIO Unit 6 (Part 1)

exonuclease

enzymes that cleave nucleotides one at a time from the end of a polynucleotide chain

helicase

during replication

induced mutation

mutation that results from exposure to chemicals or environmental agents

lagging strand

during replication

leading strand

strand that is synthesized continuously in the 5'-3' direction which is synthesized in the direction of the replication fork

ligase

enzyme that catalyzes the formation of a phosphodiester linkage between the 3' OH and 5' phosphate ends of the DNA

mismatch repair

type of repair mechanism in which mismatched bases are removed after replication

mutation

variation in the nucleotide sequence of a genome

nucleotide excision repair

type of DNA repair mechanism in which the wrong base

Okazaki fragment

DNA fragment that is synthesized in short stretches on the lagging strand

point mutation

mutation that affects a single base

primase

enzyme that synthesizes the RNA primer; the primer is needed for DNA pol to start synthesis of a new DNA strand

primer

short stretch of nucleotides that is required to initiate replication; in the case of replication

proofreading

function of DNA pol in which it reads the newly added base before adding the next one

replication fork

Y-shaped structure formed during initiation of replication

silent mutation

mutation that is not expressed

single-strand binding protein

during replication

sliding clamp

ring-shaped protein that holds the DNA pol on the DNA strand

spontaneous mutation

mutation that takes place in the cells as a result of chemical reactions taking place naturally without exposure to any external agent

telomerase

enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends

telomere

DNA at the end of linear chromosomes

topoisomerase

enzyme that prevents overwinding of DNA when DNA replication is taking place

transformation

process in which external DNA is taken up by a cell

transition substitution

when a purine is replaced with a purine or a pyrimidine is replaced with another pyrimidine

transversion substitution

when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine

7-methylguanosine cap

modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist translation

aminoacyl tRNA synthetase

enzyme that “charges” tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid

anticodon

three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon

CAAT box

(GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors

Central Dogma

states that genes specify the sequence of mRNAs

codon

three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation

colinear

in terms of RNA and protein

consensus

DNA sequence that is used by many species to perform the same or similar functions

core enzyme

prokaryotic RNA polymerase consisting of α

degeneracy

(of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate

downstream

nucleotides following the initiation site in the direction of mRNA transcription; in general

exon

sequence present in protein-coding mRNA after completion of pre-mRNA splicing

FACT

complex that “facilitates chromatin transcription” by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by

GC-rich box

(GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter

hairpin

structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides

holoenzyme

prokaryotic RNA polymerase consisting of α

initiation site

nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a “+1”

initiator tRNA

in prokaryotes

; in eukaryotes

called tRNAi; a tRNA that interacts with a start codon

intron

non–protein-coding intervening sequences that are spliced from mRNA during processing

Kozak’s rules

determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5’-GCC(purine)CCAUGG-3’; the bolded bases are most important

nonsense codon

one of the three mRNA codons that specifies termination of translation

nontemplate strand

strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA

Octamer box

(ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter

peptidyl transferase

RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds

plasmid

extrachromosomal

poly-A tail

modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus

polysome

mRNA molecule simultaneously being translated by many ribosomes all going in the same direction

preinitiation complex

cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template

promoter

DNA sequence to which RNA polymerase and associated factors bind and initiate transcription

reading frame

sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein

Rho-dependent termination

in prokaryotes

Rho-independent

termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase

RNA editing

direct alteration of one or more nucleotides in an mRNA that has already been synthesized

Shine-Dalgarno sequence

(AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30S ribosome

signal sequence

short tail of amino acids that directs a protein to a specific cellular compartment

small nuclear RNA

molecules synthesized by RNA polymerase III that have a variety of functions

splicing

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

start codon

AUG (or rarely

TATA box

conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription

template strand

strand of DNA that specifies the complementary mRNA molecule

transcription bubble

region of locally unwound DNA that allows for transcription of mRNA

upstream

nucleotides preceding the initiation site; in general

Watson & Crick

Double Helix Model

Franklin

DNA structure, “Photo 51”

Griffith

studied streptococcus pnrumoniea (rough strain and smooth strain)

transforming agent

Hershey & Chase

studied bacteriphages using phosphorus and sulfur to prove that DNA carries genetic information

Chargaff

discovered the base pairing rules and that the amount of nucleotides variers between species but not within organisms of the same species

A-T

G-C

DNA is replicated in the

5’ to 3’ direction

DNA is read in the

3’ to 5’ direction

5’ end of DNA/RNA has a

phosphate group

3’ end of DNA/RNA has a

hydroxyl group

missense mutation

change in a nucleotide base that results in a different amino acid being incorporated into the protein sequence

nonsense mutation

change in a nucleotide base that converts a codon into a stop codon (premature termination)

frameshift mutation

causes mRNA to be read incorrectly on each remaining codon

insertion

addition of nucleotide pairs in a gene

deletion

removal of nucleotide pairs in a gene