BSCI222 exam 3 vocab

semiconservative replication

replication in which the two nucleotide strands of DNA separate, and each serves as a template for the synthesis of a new strand. all DNA replication is semiconservative

equiibrium density gradient centrifugation

method used to separate molecules or organelles of differen density by centrifugation

replicon

unit of replication consisting of DNA from the origin of replication to the point at which replication on either side of the origin ends

origin of replication

site where DNA replication is initiated

theta replication

replication of circular DNA that is initiated by the unwinding of the two nucleotide strands, producing a replication bubble.Unwinding continues at one or both ends of the bubble, making it progressivey larger. DNA replication on both of the template strands is simultaneous with unwinding until the two replication forks meet;

replication bubble

segment of a DNA molecule that is unwinding and undergoing replication

replication fork

point at which a double-stranded DNA molecule separates into two single strands that serve as templates for replication

bidirectional replication

replication at both ends of a replication bubble

rolling-circle replication

replication of circular DNA that is initiated by a break in one of the nucleotide strands, producing a double-stranded circular DNA molecule and a single-stranded linear DNA molecule, the latter of which may circularize and serve as a template for the synthesis of a complementary strand

DNA polymerase

enzyme that synthesizes DNA

continuous replication

replication of the leading strand of DNA in the same direction as that of unwinding, allowing new nucleotides to be added continuously to the 3’ end of the new strand as the template is exposed

leading strand

DNA strand that is replicated continuously

discontinuous replication

replication of the lagging strand of DNA in the direction opposite that of unwinding, which means that DNA must be synthesized in short stretches (Okazaki fragments)

lagging strand

DNA strand that is replicated discontinuously

okazaki fragments

short length of newly synthesized DNA produced by discontinuous replication on the lagging strand; these fragments are eventually joined togetherini

initiator protein

protein that binds to an origin of replication and causes a short section of DNA to unwind, allowing helicase and other single-strand-binding proteins to attach to the polynucleotide strand

DNA helicase

enzyme that unwinds double-stranded DNA by breaking hydrogen bonds that exist between the bases of the two nucleotide strands of a DNA molecule

single-strand-binding protein (SSB)

protein that attaches tightly to the exposed single-stranded DNA during replication and prevents the formation of secondary structures that would interfere with replication

DNA gyrase

topoisomerase enzyme in E. coli that relieves the torsional strain that builds up ahead of the replication fork

primase

enzyme that synthesizes a short stretch of RNA on a DNA template; functions in replication to provide a 3’-OH group for the attachment of a DNA nucleotide

primer

short stretch of RNA on a DNA template; provides a 3’-OH group for the attachment of a DNA nucleotide at the initiation of replication

DNA polymerase III

bacterial DNA polymerase that synthesizes new nucleotide strands by adding new nucleotides to the 3’-OH group provided by the primer

B sliding clamp

a ring-shaped polypeptide component of DNA polymerase III that encircles DNA and allows the polymerase to slide easily along the DNA template strand during replication

DNA polymerase I

bacterial DNA polymerase that removes RNA nucleotides of the primers and replaces them with DNA nucleotides

DNA ligase

enzyme that catalyzes the formation of a phosphodiester bond between adjacent 3’-OH and 5’-phosphate groups in a DNA molecule without adding another nucleotide to the strand

proofreading

process by which DNA polymerases remove and replace incorrectly paired nucleotides in the course of replication

mismatch repair

process that corrects mismatched nucleotides in DNA after replication has been completed. Enzymes excise incorrectly paired nucleotides from the newly synthesized strand and use the original nucleotide as a template for replacing them

autonomously replicating sequence (ARS)

DNA sequence that confers the ability to replicate; contains an origin of replication

origin-recognition complex (ORC)

multiprotein complex that binds to an origin of replication and unwinds around it to initiate DNA replication

replication licensing factor

protein that ensures that replication takes place only once at each origin of replication; required at the origin before replication can be initiated and removed after the DNA has been replicated

DNA polymerase a

eukaryotic DNA polymerase that initiates nuclear DNA synthesis

DNA polymerase δ

eukaryotic DNA polymerase that replicates the lagging strand during DNA synthesis; also carries out DNA repair and translesion DNA synthesis

DNA polymerase E

eukaryotic DNA polymerase that replicates the leading strad during DNA synthesis

translesion DNA polymerase

specialized DNA polymerase that is able to replicate DNA through distorted structures and bulky lesions that halt other DNA polymerases; often makes more errors during DNA synthesis than other DNA polymerases

g-rich 3’ overhang

a guanine-rich sequence of nucleotides that protrudes beyond the complementary c-rich strand at the end of a chromosome

telomerase

ribonucleoprotein enzyme that replicates the ends (telomeres) of eukaryotic chromosomes. the RNA part of the enzyme has a template that is complementary to repeated sequences in the telomere and pairs with them, providing a template for the synthesis of additional copies of the repeats

homologous recombination

exchange of genetic information between homologous DNA molecules

heteroduplex DNA

DNA consisting of two strands, each of which is from a different chromosome

holliday unction

special structure resulting from homologous recombination that is initiated by single-strand breaks in a DNA molecule

ribozyme

RNA molecule that can act as a biological catalyst

ribosomal RNA (rRNA)

RNA molecule that is a structural component of the ribosome

messenger RNA (mRNA)

RNA molecule that carries the coding instructions for a polypeptide chain from DNA to a ribosome

pre-messenger RNA (pre-mRNA)

the immediate products of transcription in eukaryotic cells. modified after transcription to become mRNA

transfer RNA (tRNA)

RNA molecule that carries an amino acid to the ribosome and transfers it to a growing polypeptide chain in translation

small nuclear RNA (snRNA)

small RNA molecule found in the nuclei of eukaryotic cells; functions in the processing of pre-mRNA

small nuclear ribonucleoprotein (snRNP)

structure found in the nuclei of eukaryotic cells that consists of small nuclear RNA (snRNA) and protein; functions in the processing of pre-mRNA

small nucleolar RNA (snoRNA)

small RNA molecule found in the nuclei of eukaryotic cells; functions in the processing of rRNA and in the assembly of ribosomes

microRNA (miRNA)

small RNA molecules, typically 21 or 22 bp in length, produced by cleavage of double-stranded RNA arising from small hairpins within RNA that is mostly single stranded. the miRNAs combine with proteins to form a complex that binds (imperfectly) to mRNA molecules and inhibits their translation

small interfering RNA (siRNA)

single-stranded RNA molecule (usually 21 to 25 nucleotides in length) produced by the cleavage and processing of double-stranded RNA that binds to complementary sequences in mRNA and brings about the cleavage and degradation of the mRNA. some siRNAs bring about changes in chromatin structure

piwi-interacting RNA (piRNA)

small RNA molecule belonging to a class named after Piwi proteins, with which these molecules interact; similar to microRNA and small interfering RNA, has a role in suppressing the expression of transposable elements in reproductive cells

long noncoding RNA (lncRNA)

a class of relatively long RNA molecules found in eukaryotes that do not code for proteins; they provide a variety of functions, including regulation of gene expression

CRISPR RNA (crRNA)

small RNA molecules found in prokaryotes that assist in the destruction of foreign DNA molecules

template strand

the nucleotide strand that is used as a template during transcription. the RNA synthesized during transcription is complementary and antiparallel to the DNA template strand

nontemplate strand

the DNA strand that is complementary to the template strand; not ordinarily used as a template during transcription

transcription unit

sequence of nucleotides in DNA that encodes a single RNA molecule and the sequences necessary for its transcription; normally contains a promoter, an RNA-coding sequence, and a terminator

promoter

DNA sequence that the transcription apparatus recognizes and binds so as to initiate transcription; indicates the direction of transcription, which of the two DNA strands is to be read as the template, and the starting point of transcription

RNA-coding region

sequence of DNA nucleotides that is copied into an RNA molecule

terminator

sequence of DNA nucleotides that brings about the termination of transcription

ribonucleoside triphosphate (rNTP)

substrate of RNA synthesis; consists of a ribose sugar and a base (a nuceloside) attached to three phosphate groups. in transcription, two of the phosphates are cleaved, producing an RNA nucelotide

RNA polymerase

enzyme that synthesizes RNA from a DNA template during transcription

core enzyme

five subunits at the heart of most bacterial RNA polymerases that, during transcription, catalyze the elongation of the RNA molecule by the addition of RNA nucleotides; consists of two copies of a subunit called alpha (a) and single copies of subunits beta (B), beta prime (B’), and omega (w)

sigma factor

subunit of bacterial RNA polymerase that allows the RNA polymerase to recognize a promoter and initiate transcription

holoenzyme

complex of an enzyme and other protein factors necessary for its complete function

RNA polymerase I

eukaryotic RNA polymerase that transcribed large ribosomal RNA molecule

RNA polymerase II

eukaryotic RNA polymerase that transcribed pre-mRNA, snoRNAs, some miRNAs, and some smRNAs

RNA polymerase III

eukaryotic RNA polymerase that transcribed small sibosomal molecules- tRNAs, small rRNAs, some mrRNAs, and some snRNAs

RNA polymerase IV

RNA polymerase that transcribed RNAs that play a role in chromatin structure in plants

RNA polymerase V

RNA polymerase that transcribes RNAs that play a role in heterochromatin formation in plants

consensus sequence

sequence that comprises the most commonly encountered nucleotides found at a specific location in DNA or RNA

-10 consensus sequence (pribnow box)

consensus sequence (TATAAT) found in most bacterial promoters approximately 10 bp upstream of the transcription start site

-35 consensus sequence

consensus sequence (TTGACA) found in many bacterial promoters approximately 35 bp upstream of the transcription start site

upstream element

consensus sequence found in some bacterial promoters that contains a number of A-T pairs and is located about 40 to 60 bp upstream of the transcription start site

abortive initiation

process during initiation of transcription in which RNA polymerase repeatedly generates and releases short transcripts, from 2 to 6 nucleotides in length, while still bound to the promoter. occurs in both prokaryotes and eukaryotes

rho-dependent terminator

sequence in bacterial DNA that requires the presence of the rho factor to terminate transcription

rho factor

a protein that binds to bacterial RNA polymerase and facilitates the termination of transcription of some genes

rho-independent terminators

sequence in bacterial DNA that does not require the presence of the rho factor to terminate transcription

polycistronic mRNA

single RNA molecule transcribed from a group of several genes; uncommon in eukaryotes

transcription factor

protein that binds to DNA sequences in eukaryotic cells and affects levels of transcription

general transcription factor

protein that binds to a eukaryotic promoter near the transcription start site; part of the basal transcription apparatus that initiates transcription

basal transcription apparatus

complex of transcription factors, RNA polymerase, and other proteins that assemble on the promoter and are capable of initiating minimal levels of transcription

core promoter

the DNA sequence located immediately upstream of a eukaryotic gene, and the site to which the basal transcription apparatus binds

TATA box

consensus sequence (TATAAA) commonly found in eukaryotic RNA polymerase II promoters; usually located -25 to -30 bp upstream of the transcription start site. the TATA box determines the start point for transcription

regulatory promoter

DNA sequence located immediately upstream of the eukaryotic core promoter; contains consensus sequences to which transcription factors bind

enhancer

sequence that stimulates maximal transcription of distant genes; affect only genes on the same DNA molecule (is cis acting), contains short consensus sequences, is not fixed in relation to the transcription start site, can stimulate promoters in its vicinity, and may be upstream or downstream of the gene. the function of an enhancer is independent of sequence orientation

internal promoter

promoter located within the sequences of DNA that are transcribed into RNA

TATA-binding protein (TBP)

polypeptide chain found in several different transcription factors that recognizes and binds to the TATA box