AP Biology Unit 6 Study Guide

transformation

transformation

a change in genotype and phenotype due to the assimilation of external DNA by a cell. When the external DNA is a member of a different species, this results in horizontal gene transfer

bacteriophages

a virus that infects bacteria; AKA phage

virus

an infectious particle incapable of replicating outside of a cell, consisting of a DNA or RNA genome surrounded by a protein coat (capsid) and for some viruses, a membraneous envelope

double helix

the form of native DNA, referring to its 2 adjacent antiparallel polynucleotide strands wound around an imaginary axis into a spiral shape

antiparallel

referring to the arrangement of the sugar-phosphate backbones in a DNA double helix (they run opposite 5’-3’ directions)

semiconservative model

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

origin of replication

short stretches of DNA that have a specific sequence of nucleotides

replication fork

a y-shaped region on a replicating DNA molecule where the parental strands are being unwound and new strands are being synthesized

helicases

an enzyme that untwists the double helix of DNA at replication forks, separating 2 strands and making them available as template strands

single stranded binding proteins

a protein that binds to the unpaired DNA strands during DNA replication, stabilizing them and holding them apart while they serve as templates for the synthesis of complementary strands of DNA

Topoisomerase

a protein that breaks, swivels, and rejoins DNA strands. During replication, topoisomerase helps to relive strain in the double helix ahead of he replication fork

primer

a short polynucleotide with a free 3’ end, bound by complementary base pairing to the template strand and elongated with DNA nucleotides during DNA replication

primase

an enzyme that joins RNA nucleotides to make a primer during DNA replication using the parental dna strand as a template

dna polymerase

an enzyme that catalyzes the elongation of new dna by the addition of nucleotides to the 3’ end of an existing chain. there are several different dna polymerases; III and I

leading strand

the new complementary dna strand synthesized continuously along the template strand toward the replication fork in the mandatory 5’-3’ direction

lagging strand

a discontinuously synthesized dna strand that elongates by means of Okazaki fragments, each synthesized in a 5’-5’ direction away from the replication fork

Okazaki fragments

a short segment of dna synthesized from the replication fork on a template strand during dna replication. many suck segments are joined together to make up the lagging strand of newly synthesized dna

dna ligase

a linking enzyme essential for dna replication

mismatch repair

the cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides

nuclease

an enzyme that cuts dna or RNA, either removing 1 or a few bases or hydrolyzing dna or rna completely into its component nucleotides

nucleotide excision repair

a repaire system that removes and then correctly replaces a damaged segment of dna using the undamaged strand as a guide

telomeres

the randomly repetitive dna at the end of a eukaryotic chromosome dna molecule. telomeres protect the organs genes from being eroded during successive rounds of replication

nucleoid

a non membrane enclosed region in a prokaryotic cell where its chromosome is located

euchromatin

the less condensed form of eukaryote chromatin that is available for transcription

heterochromatin

eukaryote chromatin that remains highly compacted during interphase and is generally not transcribes

nucleic acid hybridization

the process of base pairing between a fine and a complementary sequence on another nucleic acid model

genetic engineering

the direct manipulation of genes for practical purposes

dna cloning

the production of multiple copies of a specific dna segment

plasmid

a small, circular, double-stranded dna molecule that carries accessory genes separate from those of a bacterial chromosome; in dna, cloning can be used as a vector carrying up to about 10,000 base pairs

recombinant dna molecule

a dna molecule made in vitro with segments from different sources

gene cloning

the production of multiple copies of a gene

cloning vector

in genetic engineering, a dna molecule that can carry foreign dna into a host cell and replicate there

restriction enzymes

an endonuclease enzyme that recognizes and cuts dna molecules foreign to a bacterium. cuts at specific nucleotide sequence

restriction site

a specific sequence on a dna strand that is recognized and cut by a restriction enzyme

restriction fragments

a dna segment that results from the cutting of dna by a restriction enzyme

sticky ends

a single stranded end of a double stranded restriction fragment

gel electrophoresis

a technique for seperating nucleic acids or proteins on the basis of their size and electrical charge, both of which affect their rate of movement through an electric field in a gel made of agarose or other polymers

polymerase chain reaction

a technique for amplifying dna in vitro by incubating it with specific primers, a heat resistant polymerase, and nucleotides

dna sequencing

determining the order of nucleotide bases in a gene or dna fragments

one-gene one-enzyme hypothesis

that the function of a gene is to dictate the production of a specific enzyme

transcriotion

the synthesis of rna using a dna template

messanger rna

a type of rna, synthesized using a dna template that attaches to the ribosomes in the cytoplasm and specifies the primary structure of a protein (in eukaryotes the primary rna transcript must undergo rna processing to become mrna)

translation

the synthesis of a polypeptide using the genetic info encoded in a mrna molecule. there is a change of language from nucleotides to amino acids

ribosomes

a complex of rrna and protein molecules that functions as a site of protein synthesis in the cytoplasm; consists of a large subunit and a small subunit. in eukaryotic cells, each subunit is assembled in the nucleolus

primary transcript

an initial rna transcript from any gene; aka pre-mana when transcribed from a protein-encoding gene

triplet code

a genetic information system in which a series of 3-nucleotide long words specifies a sequence of amino acids for a polypeptide chain

template strand

the dna strand that provides the pattern, or temperature for ordering, by complementary base pairing, the sequence of nucleotides in an rna transcript

codons

a 3 nucleotide sequence of dna or mrna that specifies a particular amino acid or termination signal; the base unit of genetic code

reading frame

on an mrna, the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis

rna polymerase

an enzyme that links ribonucleotides into a growing rna chain during transcription

elongation

the polymerase moves downstream unwinding the dna and elongating the rna transcript 5’-3’. after transcription has occurred the dna strands form a double helix

initiation

after rna polymerase binds to the promoter, the polymerase unwinds the dna strands and initiates rna synthesis at the start point on the template strand

termination

eventually the rna transcript is released and the polymerase detaches from the dna

promoter

a specific nucleotide sequence in the dna of a gene that binds rna polymerase, positioning it to start transcribing rna at the appropriate place

terminater

in BACTERIA a sequence of nucleotides in dna that marks the end of a gene and signals rna polymerase to release the newly made rna molecule and detach from the dna

transcription unit

a region of dna that is transcribed into an rna molecule

prokaryotes

only have 1 type of rna polymerase; eukaryotes have 3 rna polymerase II Is the one used for pre-mrna

start point

in transcription, the nucleotide position on the promoter where rna polymerase begins synthesis of rna

transcription factors

a regulatory protein that binds to dna and affects transcription of a specific gene (only after this binds to promoter does the rna polymerase II bind to it)

transcription initiation complex

the completed assembly of transcription factors and rna polymerase bound to a promoter

TATA box

a dna sequence in eukaryotic promoters crucial in forming the transcription initiation complex (one transcription factor must bind to this before rna polymerase II can bind in the correct position and orientation)

rna processing

modification of rna primary transcripts, including splicing our of introns, joining together of exons ,a dn alteration of the 5’ and 3’ ends

5’ cap

a modified form of guanine nucleotide added onto the end of a pre-mrna molecule

poly-a-tail

a sequence of 50-250 adenine molecules added onto the 3’ end of a pre-mrna molecule before exiting nucleus

what is the purpose of the 5’ cap and the poly-a-tail

1. they facilitate the export of mature mrna from nucleus

2. they protect mrna from degration by hydrolytic enzymes

   1. they help ribosomes attach to 5’ end of the mrna once it reaches the cytoplasm

untranslated regions

at the ends of the mrna. part of mrna that won’t be translated into proteins, but have other functions such as ribosomes binding

rna splicing

after synthesis of eukaryotic primary rna transcript, the removal of the portions of the transcript (introns) that will not be included in the mrna and the joining together of the remaining portions (exons)

introns

a noncoding INTerving sequence with in a primary transcript that is removed from the transcript during rna processing; also refers to the region to dna from which the sequence was transcribed

exons

a sequence with in a primary transcript that remains in the rna after rna processing; also refers to the region of dna from which this sequence was transcribed

alternative rna splicing

a type of eukaryotic gene regulation at the rna processing level in which different mrna molecules are produced from the same primary transcript, depending on which rna segments are treated as exons and introns

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 jining the 2 adjacent introns

ribozyme

an rna molecule that functions as an enzyme, such as an intron that catalyzes its own removal during rna splicing

transfer rna

an rna molecule that functions as a translator between nucleic acid and protein languages by picking up a specific amino acid and carrying it to the ribosome, where the trna recognized the appropriate codon in the mrna

anticodon

a nucleotide triplet at one end of a trna molecule that base pairs with a particular complementary codon on an mrna

aminoacyl-trna synthetases

an enzyme that joins each amino acid to the appropriate trna

wobble

flexibility in the base pairing rules in which the nucleotide at the 5’ end of a trna anticodon can form hydrogen bonds with molecules other than one kind of base in the 3’ end of a codon

ribosomal rna

rna molecules that, together with proteins make ip ribbons the most abundant type of rna

p site

one of a ribosomes 3 binding sites for trna during translation. p site holds the trna carrying the growing polypeptide chain

a site

holds the trna carrying the next amino acid to be added to the polypeptide chain

e site

where discharged trnas leave the ribosome

translation initiation complex

union of mrna, initiator trna, and ribosomes brought together by initiative factors

signal peptide

a sequence of about 20 amino acids at or near the leading end of a polypeptide that targets ut too the er or other organelles in eukaryotes

signal recognition particle

a protein rna complex that recognized a signal peptide as it emerges from a ribosome and helps direct the ribosome to the er by binding to a receptor protein on the er

mutations

a change in the nucleotide sequence of an organisms dna or in the dna or rna of a virus

point mutations

a change in a single nucleotide pair of a gene

nucleotide pair substitution

a type of point mutations in which one nucleotide in a dna strand and its partner in the complementary strand are replaces by another pair of nucleotides

silent mutations

a nucleotide pair substitution that has no observable effect on the phenotype

missense mutations

a nucleotide pair substitution that results in a codon that codes for a different amino acid

nonsense mutation

a mutation that changes an amino acid codon to one of the 3 stop codons, resulting in a shorter and usually non functional protein

insertions and deletions

additions or losses of nucleotide pairs in a gene

frameshift mutations

a mutation occurring when nucleotides are inserted in or deleted from a gene and the number inserted or deleted isn’t a multiple of 3, resulting in the improper grouping of the subsequent nucleotides into codons

mutagens

a chemical or physical agent that interacts without dna and can cause a mutation

gene regulation

how we make a protein or not and how we express a gene or not

regulation

produces a regulation protein which promotes the expression of a gene; this usually happens during transcription; and TATA proteins allow DNA Polymerase to attach

coordinately controlled

a single “on-off” switch can control the whole cluster of functionally related genes

operator

in bacterial and phage dna, a sequence of nucleotides near the start of an operon to which an active repressor can attach. the binding of the repressor prevents rna polymerase from attaching to the promoter and transcribing the genes of the operon

operon

a unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway

repressor

a protein that inhibits gene transcription. in prokaryotes, repressors bind to the Dna within or near the promoter. in eukaryotes, repressors may bind to control elements within enhancers, to activators, or to other proteins in a way that blocks activators from binding to dna

regulatory gene

a gene that codes for a protein, such as a repressor, that contains the transcription of another gene or group of genes

corepressor

a small molecule that binds to a bacterial repressor protein and changes the proteins shape, allowing It to bind to the operator and switch off