Glossary of Molecular Genetics 2

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made up of polymers of either DNA or RNA
Nucleotide Monomer
consists of a nitrogen base, a sugar, and a phosphate
sugar-deoxyribose; adenine, thymine, guanine, cytosine, constains herditary information, double helix
ribosel; adenine, uracil, guanine, cytosine
provides the instructions for assembling amino acids into a polypeptide chain, linear
delivers amino acids to a ribosome for their addition into a growing polypeptide chain, "clover leaf" shaped
combines with proteins to form ribosomes- globular
DNA Replication
during interphase when a second chromatid containing a copy of the DNA moleucle is assembled and it involves separating (unzipping) the DNA molecule into two strands, each of which is a templace for a complementary strand
Semiconservative Replication
because each of the two double-stranded molecules of DNA consists of a single strand of old DNA (the template stand) and a single strand of new, replicated DNA (the complementary strand)
enzyme that unwinds the DNA helix
replicase fork
the y-shaped end after helicase unwinds the DNA
Single-Stranded DNA binding proteins
these attach to each strand of the uncoiled DNA to keep them separate
a group of enzymes that break and rejoin the double helix allowing the twists in front of the helicase to unravel and preventing the formation of knots
DNA polymerase
moves in the 3'-> 5' direction along each template strand and the new complement strand grows in the antiparallel 5' -> 3' direction
leading strand
the complementary strand that occurs readily as the DNA polymerase follows the replication fork assembling a 5' -> 3' stand on the 3'->5' template strand
Okazaki Segments
short segments of complementary DNA that develop along the 5'->3' template strand
DNA Ligase
connects Ozaki Segments producing a single complement strand
Lagging Strand
name for the complementary strand of the 5'->3' template strand because it requires more time to assemble than the leading strand
RNA primase
initiates the first nucleotides of the leading strand and each Okasaki fragment, it initiates each complementary segment with RNA nucleotides
RNA Primer
the RNA nucleotides on the complementary segment that append succeednig DNA nucleotides, later the RNA nucleotides are replaced with DNA nucleotides
Step 1 of DNA replication
Helicase unwinds the DNA, producing a replication fork. Single-stranded DNA binding proteins prevent the single strands of DNA from recombining. Topoisomerase removes twists and knots in the double stranded templatre as a result of the unwinding induced by helicase
Step 2 of DNA replication
RNA primase initiates DNA replication at special nucleotide sequences (called origins of replication) with short segments of RNA nucleotides (Called RNA primers)
Step 3 of DNA replication
DNA polymerase attaches to the RNA primers and begins elongation, the adding of DNA nucleotides to the complement strand
step 4 of DNA replication
the leading complementary strand is assembled continuously as the double-helix DNA uncoils
step 5 of DNA replication
the lagging complementary strand is assembled in short Okazaki fragments, which are subsequently joined by DNA ligase
step 6 of DNA replication
the RNA primers are replaced by DNA nucleotides
energy for elongation
provided by the two additional phosphates that are attached to each new nucleotide, making a total of three phosphates attached to the nitrogen base. Breaking the bonds holding the two extra phosphates provides teh chemical energy for the process
what the DNA polymerase does in bacteria
Thymine Dimer
originates when two adjacent thymine nucleotides in the same strand base-pair with eachotehr instead of with the adenine bases in the complementary strand, these can be fixed by excision repair
Excision Repair
enzymes that splice out the error and use the complementary strand as a pattern, or template, for replacing the excised nucleotides
if a DNA error is not repaired (normally caused by raditation).. it is any sequence of nucleotides in a DNA molecule that does not exactly match the original DNA molecule from which it was copied
type of mutation when there is an incorrect nucleotide
type of mutation when there is a missing nucleotide
type of mutation when there is an additional nucleotide not present in the orignal DNA molecule
frameshift mutation
when an insert mutation occurs, it causes all the subsequent nucleoties to be displaced one position
radiation or chemicals that cause mutations
mutagenst that activate uncontrolled cell growth (cancer)
end products of metabolic processes regulated by enzymes
one-gene-one-enzyme hypothesis
that the gene is defined as the segment of DNA that codes for a particular enzyme
one-gene-one-polypeptide hypthesis
Since many genes code for polypeptides that are not enzymes, genes have been redefined as the DNA segment that codes for a particular polpeptide
protein synthesis
process that describes how enzymes and other proteins are made from DNA
three steps in protein synthesis
transcription, RNA processing, and gtranslation
Messenger RNA
a single strand of RNA that provides the template used for sequencing amino acids. A codon codes for one specific amino acids.
in mRNA, a triplet group of three adjacnt nucleotides that code for one specific amino acid. There are 64 possible codons but only 20 amino acids.
Genetic Code
provides the "decoding" for each codon, and it identifies the amino acid specified y each o the possible 64 codon combinations
Transfer RNA
short RNA molecule (80 nucleotides) that is used for transporting amino acids to their proper place on the mRNA template.
portion of tRNA specified by a triplet comibination of nucletides, that pairs with the codon of the mRNA.
end of the 3' end of tRNA that attcaches to an amino acid
fact that there does not need to be an exact base-paring between the third nucleotide of the tRNA anticodon and the third nucleotide of the mRNA codn, which allows the codon of some tRNA's to base pair with more than one kind of codon, therefore about 45 different tRNA's base-pair with the 64 different codons
Ribosomal RNA
molecules that are the building blocks of ribosomes. The nucleolus is an assemblage of DNA actively being transcribed into this. These are large and small ribosome subunits which form a polypeptide chain.
when RNA molecules are created by using the DNA molecules s a template
first step of transcription in which the RNA polymerase attaches to promoter regions on the DNA and begins to unzip the DNA into two strands. A promoter region for mRNA transcriptopns contains the sequence T-A-T-A
TATA box
Promoter region for mRNA transcriptions
2nd step of transcription, occurs as the RNA polymerase unzips the DNA and assembles RNA nucleotides using one strand of the DNA as a template. As in DNA replication, elongation of the RNA molecule occurs in the 5'->3' direction. In contrase, new nucleotides are RNA nucleotides and only one DNA strand is transcribed
last step of transcription- occurs when the RNA polymerase reaches a special sequence of nucleotides that serve as a termination point. In eukaryotes it is usually AAAAAAAAA
RNA Processing
after transcription, this modifies the RNA molecule with deletions and additions
the processed RNA molecules are used to assemble amino acids into a polypeptide
steps of RNA processing
before the mRNA leaves the nucleus, a 5' cap is addedand a poly-A tail, also some mRNA segments are removed
5' Cap
GTP added to 5'end (PPPG'5') which provides stability to the mRNA and a point of attachment for the small subunit of the ribosome
poly-A tail
a sequence of 150-200 adenine nucleotides added to the 3' end to provide stability and control the movement of mRNA across the nuclear envelop, may serve to regulate gene expression
sequences of mRNA that EXpress a code for a polypeptide
INtervening sequences that are noncoding in mRNA
heterogenous nuclear RNA
original unprocessed mRNA molecule that contains both the coding and the noncoding sequences
small nuclear ribonucleoproteins
snRNPs whcih delete out the introns and splice the exons together before the RNA moves to the cytoplasm
where translation occurs
in the cytoplasm, amino acids attach to the 3'end of the tRNA's forming this, requires the energy from one ATP
actually assembles proteins, has a spot for mRNA, tRNA, and then one for a second tRNA that delivers the next amino acid
molecules that provide the energy for translation
First step of Translation
Initiation begins when the small ribosomal unit attaches to a speicl region near the 5' end of the mRNA, then a tRNA (with anticodon UAC) carrying methionnie attaches to the mRNA (at the start codon AUG) with hydrogen bonds, then a large ribosmal subunit attaches to the mRNA forming a complete ribosome with the tRNA occuping the P site
Second step of Translation
Elongation begins when the next tRNA binds to the A site of the ribosome, and then methionine is removed from the 1st tRNA and attached to the amino acid on the newly arrived tRNA. The 1st tRNA is relaeased and then binds with another amino acid (repeated deliveries), the remaining tRNA moved from the A site to the P site and a new tRNA enters the A site. then the tRNA in the P site is released and the steps repeat
last step of translation
termination occurs when the ribosome encounters one of the three "stop" codons and the completed polypeptide, the last tRNA, and the two ribosomal subunits are released. the ribosomal subunits can now attach to the same of another mRNA and repeat the process
proteins that from DNA-histone complexes called nucleosomes
DNA-histome complexes that appear like beads on a string
describes regions where DNA is loosely bound to nucleosomes. DNA in these regions is actively being transcribed
represents areas where the nucleocomes are more tightly compacted and where DNA is inactive. Because of its condensed arrangement, it stains darker than euchromatin
jumping genes that are DNA segments that can move to new locations on the same or different chromosome. Some only consist only of DNA that codes for an enzyme that enables it to be transported. Otheres contain genes that invoke replication of th transpoon. After relication, a new transposon copy is transported to the new location. Wherever they are inserted, they have the effect of a mutation. They can change the expression of a gene, turn it on or off, or have no effect
or phages, these only attack bacteria
Virus parts
nucleic acid surrounded by a protein coat
protein coat surrounding a virus
parts of some capsides that assists them in penetrating their hosts. THese incorporate phospholips and proteins obtained from the cell membrane of the host
lytic cycle
when a virus pentrates the cell membrance of the host, uses its enzymes to replicate viral DNA, transcribes viral DNA into RNA, and translates the RNA into proteins. The proteins and DNA are then assembled into new viruses which subsequently erupt from the host cell, destroying the cell in the process. The new viruses then infect other cells and the process repeats
lysogenic cycle
the viral DNA is temprarily incorporated into the DNA of the host cell and remins incactive until some trigger, usually an external enviroment stimulas, causes the virus to begin the lytic cycle
or a a prophage if it is a bacteriophahe, that is in the dormant stage of the lysogenic cycle
uses REVERSE TRANSCRIPTASE to make a DNA complement of their RNA
binary fission
reproduction of a bacterial cell- the chromsome replicates and the cell divides into two cells, each one bearing one chromosome. There are no spindle apparatus, microtubules, nor centrioles
short circular DNA molecules outside the chromosome in bacteria that carry genes which are benificial but not normally essential to the survival of the bacterium. they replicate independently of the chromosome
plasmids which become incorporated into the bacterial chromosome
the process of DNA exchange between bacteria. A donor bacterium produces a tube that connects to a recipient bacterium which sends chromosomal or plasmid DNA to teh recipient
tube that is extended in conjugation, it sends plasmid or chromosomal DNA to the recipient
F plasmid
contains the genes that enable a bacterium to produce pili, so when a recipient bacterium recieves this, it can become a donor cell
R plasmids
a group of plasmids that provide bateria with resistance against antibioticss
occurs when new DNA is introduced into bacteria by a virusm and sometimes the bacterial viral DNA can recombine with the resident DNA
occurs when bacteria absorb DNA from their surroundings. Specialized proteins on the cell membrances of some bacteria facilitate this kind of DNA uptake
gene regulation
the expression of only selected genes
sequences of SNA that direct particular biosynthetic pathways
regulatory gene
of an operon, produces a REPRESSOR protein
repressor protein
a substance produced by a regulatory gene that can prevent gene expression by blocking the action of RNA polymerase
region of an operon that is a sequence of DNA to which the RNA polymerace attaches to begin transcription
region in an operon that can block the action of the RNA polymerase if the region is occupied by a repressor protein
structural genes
operons that contain DNA sequences that code for several related enzymes that direct the production of some particular end product
lac operon
in E. Coli, controls the breakdown of lactose. The regulatory gene produces an active repressor that binds to the operatr region so RNA polymerase is unable to ranscribe several structural genes that control the uptake and breakdown of lactose. When lactose is availabel though, it combines with the repssor to make it inactive so then it is able to transcribe for genes to berak down lactose. Lactose is said to be the INDUCIBLE ENZYME
inducible enzyme
substance that is required to induce (Turn on) the operon, like lactose
trp operon
in E. Coli, produces enzymes for the synthesis of the amino acid trptophan. The regulatory gene produces an inactive repressor that does not bind to the operator so then the RNA poly. transcribes the structural genes necessary to produce enzymes that synthesize tryptophan. WHen it no longer needs to make its own tryptophan, the rising levels induce some of the trypto. to react with the inactive repressor to make it active. tryptophan acts as a COREPRESSOR, and it prevenets the transcription of more tryptophan. These are called REPRESSIBLE enzymes
when an amino acts to prevent the trasncriptopn of structual genes
Repressible enzymes
structural genes that stop producing enzymes only in the presence of an active repressor, as in the trp operon
Recombinant DNA
DNA that contains DNA segments or genes from differnt sources. It can occur through viral tranduction, bacterial conjucation, transposons, or articially through recombin. DNA tech.
restriction enzymes
in recomn. DNA tech. these cut up DNA and are obtained from bacteria and manufactor these enzymes to combat invading viruses. these are very specific and cut DNA only at specific recognition sequences of nucleotides. The cut is usually staggered producing fragments that have one strand of DNA extending beyond the complementary strand
sticky end
unpaired extension after a restriction enzyme makes a staggered cut across a DNA
tansformation in recombinant DNA tech.
matching sticky ends combine and an example of this is how the human gene for insulin has been insertied into E. coli so that it produces insulin which is isolated and used to treat diabetes
gel electrophoresis
how restriction fragments can be separated and then DNA fragments of different lengths are separated as they diffuse through a gelatinour material under the influence of an electic field. The negalitively charged (phospahte groups) moves toward the postie electrode. The shorter fragments move further. This is ofen used to compare DNA fragments of closely related species in an effort to determine evolutionary relationships
restriction fragment length polymorphisms
or RFLP's, which cause the fragments to differ in length due to slight differnces in DNA sequences. (in the same species)
DNA fingerprinting
RFLP's produced from DNA left at a crime scene are compared to RFLPs from the DNA of suspects
complementary DNA
or cDNA, it is DNA obtained by using reverse transcriptase to make a DNA molecule directly from the mRNA and lacks the introns that suppress transcription
polymerase chain reaction
or PCR, this uses gragments that can be copied millions of times using DNA polymerase directly instead of yusing bacterium to clone DNA fragments. This uses synthetic primers that initate replication at specific nucleotide sequences

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