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417 terms

Genomics

STUDY
PLAY
why cells divide
1. reproduction
2. repair/replacement
3. growth
growth factor
A growth factor is a naturally occurring substance capable of stimulating cellular growth, proliferation and cellular differentiation. Usually it is a protein or a steroid hormone. Growth factors typically act as signaling molecules between cells.
two things a cell needs in order to survive
1. space - contact inhibition
2. good grip - anchorage dependence
cells that break survival rules
cancer cells (overgrowth of cells, breaks rule #1, how cancer spreads, breaks rule #2)
telomere
protective cap at the end of each chromosome, cell dies when it starts to eat away at genes
telomerase
enzyme that rebuilds telomeres, makes cell immortal
cells that telomeres is "on" in
stem cells
gamete cell lines
malignant tumors
grow into organs and disrupt functions
benign tumors
just a tumor, no impact on the body
radiation
cause mutation in DNA, break DNA cancer cell dies
side effect of radiation
cancer
chemotherapy
depending on drug, different cells and mechanisms are targeted
cells targeted by chemo
white blood cells
hair cells
lining of gut
red blood cells
side effects of chemo
hair loss, nausea, suppressed immune system, fatigue
plants crucial to treatment of cancer
rosy periwinkle
vincristine
rinblastine
mitosis
makes new cells that are identical in genetic makeup to the original cell
meiosis
make new cells that have half the chromosomes of the original cell, contain half of genetic information
diploid
two copies of each chromosome
haploid
one copy of each chromosome
genetic variation
1. crossing over
2. independent assortment of chromosomes
3. random fertilization
4. mutation
genome
a cells complement DNA
prokaryotes
eukaryotes
chromosome
discrete molecule of DNA
gene
a portion of a chromosome that codes for a specific trait
locus (plural loci)
the location of a gene on a chromosome
chromatin
the complex of DNA and proteins that makes up a eukaryotic chromosome
sister chromatids
identical copies on a chromosome, joined together by the centromere and eventually separating during mitosis or meiosis 2, until they divide they are considered a single chromosome
chromatids
a single member of a pair of sister chromatids, only called chromatids when joined, called chromosome when they take place in mitosis or meiosis 2
centromere
the narrow "waist" where sister chromatids are joined together
centrioles
"organizing center" in the cell, aids in mitosis
homologous pair
chromosome pairs of the same length, centromere position and staining pattern that possess genes for the same characters/traits at corresponding loci, one pair paternal, or maternal
gametes
egg and sperm, sex cells
somatic
body cells, any cell except gametes
gene deletion
losing a piece of chromosome
gene relocation
portion of gene relocated to a different chromosome, non-homologus
why inheritance is important
1. allows life to give rise to similar life
2. allows good traits to be passed on (evolution, adaptation)
inheritance
ability to pass on characteristics/traits/genes
alleles
alternate version of a gene
mendels law of segregation
only one of two alleles for a gene is put into a gamete
dominant allele
will be expresses in a heterozygous individual
recessive allele
will only be expressed in a homozygous recessive individual
phenotype
how an organism looks; how the gene is expressed
genotype
the alleles that an organism has
mendels law of independent assortment
dominant and recessive don't always sort together, equal probability
incomplete dominance
occurs when a heterozygote exhibits an intermediate phenotype between two homozygotes
sickle - cell disease
homozygous disease, incomplete dominance
why is sickle - cell still here?
1. malaria - parasite
2. heterozygous, get resistance to malaria
blood type
case of co-dominance, alleles are both fully expressed in heterozygote
polygenic traits
lots of different genes contributing to one trait
pleiotrophy
one gene effecting many traits
1. disrupts red blood cells
2. causes cells to be inhospitable to material parasites
linkage
the closer the genes are on a chromosome the more likely they will be inherited together
epistasis
one gene controlling the expression of another
huntingtons disease
fatal dominant autosomal disease, onset 30s and 40s, late onset (after reproduction)
most disorders are autosomal recessive diseases
DD - not affected
dd - affected
Dd carriers (not affected, but can pass it on)
autosomal recessive diseases
likely polygentic
1. schizophrenia and bipolar disease
2. autism
color blindness, hemophilia
sex linked recessive disorder carried on X chromosome
to be colorblind
female must inherit from both parents
male must inherit from your old hen
to have normal vision
female can inherit normal vision from mom or dad
male must inherit normal vision from mom
aneuploidy
Aneuploidy is an abnormal number of chromosomes, and is a type of chromosome abnormality. An extra or missing chromosome is a common cause of genetic disorders (birth defects).
x chromosome
turner syndrome
short
learning disabilities
webbed skin between neck and shoulders
underdeveloped ovaries
trisomy
A trisomy is a type of polysomy in which there are three copies, instead of the normal two, of a particular chromosome. A trisomy is a type of aneuploidy (an abnormal number of chromosomes).
xyx chromosome
klinefelter syndrome
overweight
tall
intellectually normal
infertile
development of some female features
xyy chromosome
"super males"
taller than average
moderate to severe acne
lower intelligence
xxx chromosome
"meta females"
sterile
no obvious physical or mental problems
polyploidy
having additional sets of chromosomes
promoter
sequence of DNA that signals the beginning of transcription
players in transcription
promoter
RNA polymerase
terminator
sequence of DNA that signals the end of transcription
RNA polymerase
enzyme that builds the RNA polymer (unwinds DNA reading one side of DNA strand)
splicing
taking/cutting out (introns spliced out)
intron
intervening region
exon
expressed region (exits nucleus)
ribosomes
site of protein synthesis
2 pieces
nucleolus makes subunits
amino acids
20 of them
if you read nucleotides 1 at a time you can code for four amino acids
codon
words of three
transfer RNA (tRNA)
two attached sites
has anti codon, complementary to AUG
ribosome
site of translation
tRNA
translator, amino acid, attachment site, anti-codon (complementary to mRNA codon)
steps in translation
initiation
elongation
termination
initiation
ribosomal subunits, first tRNA join with mRNA
elongation
ribosome moves down mRNA and tRNA's add new amino acids according to the order of codons
termination
when ribosome reaches a stop codon, the ribosome releases the mRNA and the proteins, translation ends.
players in translation
stop codon
start codon
stop codon
ends translation, sequence of mRNA
start codon
begins translation, sequence of mRNA
point mutations
base pair substitution, one nucleotide change can have no effect or great effect
three substitutions of point mutation
silent mutation
missense mutation
nonsense mutation
silent mutation
amino acids sequence remains same
missense mutation
amino acid sequence is changed
nonsense mutation
mutation that changes an amino acid to a stop, polypeptide production stops
frame shift mutation
changes the reading frame, everything after will be different
base pair insertion
insert one or more
base pair deletion
take out one or more
single base pair substitution
cause disease, evolution
translation
process by which info from mRNA is use to synthesize a polypeptide change
transformation
change in a genotype and phenotype to the assimilation of external DNA
central dogma
Taking DNA and making it into a protein

DNA
-transcription
RNA
-translation
protein
Genetic engineering
The process of altering an organism′s DNA. This is usually by design.
Restriction Enzymes
DNA-cutting proteins found primarily in bacteria. Enzymes cleave (cut) the phosphodiester backbone of double-stranded DNA at specific nucleotide sequences (restriction sites). Commercially available restriction enzymes are essential for molecular biology experiments.
Plasmid DNA
Small, circular, self-replicating double-stranded DNA molecules found primarily in bacterial cells. Plasmids often contain genes coding for antibiotic resistance proteins and are routinely used for DNA-cloning experiments.
Substrates
Molecule or molecules on which an enzyme performs a reaction.
Palindromes
A word or phrase that reads the same forward and backward (for example, "a toyota"). In the context of biotechnology, a DNA sequence with complementary strands that reads the same forward and backward. Most restriction enzyme recognition sequences are palindromes.
Recognition sequence
Specific sequence of DNA nucleotides recognized and cut by a restriction enzyme.
Restriction Site
Specific sequence of DNA nucleotides recognized and cut by a restriction enzyme.
Cohesive ends
Overhanging single-stranded ends of a DNA molecule created by the action of certain restriction enzymes.
Blunt ends
Double-stranded ends of a DNA molecule created by the action of certain restriction enzymes.
Vectors
DNA (or viruses) that can be used to carry and replicate other pieces of DNA in molecular biology experiments; for example, plasmid DNA, viruses used for gene therapy; also refers to organisms that carry disease.
Transformation
The process by which bacteria take in DNA from the surroundings. Term also is used to define changes that cause a normal cell to become a cancer cell.
Electroporation
A process for transforming bacteria with DNA that uses electrical shock to move DNA into cells; can also be used to introduce DNA into animal and plant cells.
Antibiotic selection
Laboratory technique used to identify bacteria containing recombinant DNA of interest; involves growing bacteria on media with antibiotic or other selection molecules.
Origin of replication
Specific locations in a DNA molecule where DNA replication begins.
RNA polymerase promoter
Copies RNA from a DNA template; different forms of RNA polymerase synthesize different types of RNA.
Copy number
The number of copies of a particular DNA molecule or gene sequence such as a plasmid in a bacterial cell.
Insulin
Protein hormone produced by cells of the pancreas; involved in glucose metabolism by cells; deficiencies in insulin production or insulin-receptor production can cause different forms of diabetes.
Humulin
The recombinant form of human insulin, became the first recombinant DNA product to be approved for human applications by the U.S. Food and Drug Administration.
Lytic cycle
A process of bacteriophage replication that involves phages infecting bacterial cells and then replicating and rupturing (lysing) the bacterial host cells.
Plaques
Small clear spots of dead bacteria appearing on a culture plate, caused by bacterial cell lysis by bacteriophage.
Expression vectors
DNA vector such as a plasmid that can be used to produce (express) proteins in a cell.
Cosmid vectors
Large circular double-stranded DNA vector that is used for gene-cloning experiment in bacteriophages.
BAC
Large circular vectors that can replicate very large pieces of DNA; used to clone pieces of human chromosomes for the Human Genome Project.
YAC
Plasmid vectors grown in yeast cells that can replicate very large pieces of DNA; used to clone pieces of human chromosomes for the Human Genome Project.
Ti vectors
Plasmid DNA vector derived from soil bacterium that can be used to clone genes in plant cells and deliver genes into plants.
Complementary DNA libraries
DNA copies of all mRNA molecules expressed in an organism′s cells; can be "screened" to isolate genes of interest.
Reverse transcriptase
Viral polymerase enzyme that copies RNA into single-stranded DNA. This commercially available enzyme is used for many molecular biology experiments, such as creating cDNA.
Retroviruses
Viruses that contain an RNA genome and use reverse transcriptase to copy RNA into DNA during the replication cycle in host cells.
DNA probe
A single-stranded radioactive or nonradioactive DNA fragment that is complementary to the gene of interest
Oligonucleotide
Short, single-stranded synthetic DNA sequences; used in PCR reactions and as DNA probes.
PCR
Laboratory technique for amplifying and cloning DNA; involves multiple cycles of denaturation, primer hybridization, and DNA polymerase synthesis of new strands.
Taq DNA polymerase
DNA-synthesizing enzyme isolated from Thermus aquaticus, a thermophilic Archae that lives in hot springs; its ability to withstand high temperatures (thermostable) without denaturation makes it valuable for use in PCR experiments.
Restriction map
An arrangement or "map" of the number, order, and types of restriction-enzyme cutting sites in a DNA molecule.
Agarose gel electrophoresis
Laboratory procedure that involves using an electrical charge to move and separate biomolecules of different sizes, such as DNA, RNA, and proteins, through a semisolid separating gel matrix. Examples include agarose gel electrophoresis and polyacrylamide gel electrophoresis (PAGE).
Ethidium bromide
Tracking dye that penetrates (intercalates) between the base pairs of DNA. Commonly used to stain DNA in gels because ethidium bromide fluoresces when exposed to ultraviolet light.
DNA sequencing
Laboratory technique for determining the nucleotide "sequence" or arrangement of A, G, T, and C nucleotides in a segment of DNA.
Dideoxyribonucleotide
modified nucleotide. A ddNTP differs from a normal deoxyribonucleotide (dNTP) because it has a hydrogen group attached to the 3′ carbon of the deoxyribose sugar instead of a hydroxyl group-OH.
Fluorescence in situ hybridization
Laboratory technique that uses single-stranded DNA or RNA probes labeled with fluorescent nucleotides to identify gene sequences in a chromosome or cell in situ (Latin for "in its original place").
Southern blotting
Laboratory technique invented by Ed Southern that involves transferring (blotting) DNA fragments onto a filter-paper blot for use in probe hybridization studies.
Northern blotting
Laboratory technique for separating RNA molecules by gel electrophoresis and transferring (blotting) RNA onto a filter paper blot for use in hybridization studies.
Western blotting
Laboratory technique for separating protein molecules by gel electrophoresis and transferring (blotting) proteins onto a filter paper blot that is usually probed with antibodies to study protein structure and function.
DNA microarray
A chip consisting of a glass microscope slide containing thousands of pieces of single-stranded DNA molecules attached to specific spots on the slide; each spot of DNA is a unique sequence.
Quantitative PCR
Uses primers made with fluorescent dyes and specialized thermal cyclers that enable researchers to quantify amplification reactions as they occur
Site-directed mutagenesis
With this technique, mutations can be created in specific nucleotides of a cloned gene contained in a vector. The gene can then be expressed in cells, which results in translation of a mutated protein. This allows researchers to study the effects of particular mutations on protein structure and functions as a way to determine what nucleotides are important for specific functions of the protein.
siRNA
Small (21 or 22 nt) double-stranded pieces of nonprotein coding RNA, so named because they were shown to bind to mRNA and subsequently block or interfere with translation of bound mRNAs.
genomics
The study of genomes.
bioinformatics
Interdisciplinary science that involves developing and applying information technology (computer hardware and software) for analyzing biological data such as DNA and protein sequences; also includes the use of computers for the analysis of molecular structures and creating databases for storing and sharing biological data.
national center for biotechnology information
formed the RAC which was charged with evaluating risks of recombinant DNA technology
GenBank
Renowned public database of DNA sequences provided by researchers throughout the world; resources for sharing and analyzing DNA sequence information.
Semiconservative replication
Process by which DNA is copied; one original (parent) DNA molecule gives rise to two molecules, each of which has one original strand and one new strand.
Helicase
Enzyme that separates two strands of a DNA molecule during DNA replication.
Single-stranded binding protein
Proteins that bind to unraveled single strands of parental DNA during DNA replication to prevent DNA from reforming double strands before being copied.
Origin of replication
Specific locations in a DNA molecule where DNA replication begins.
Primase
Oligonucleotides complementary to specific sequences of interest; used in PCR reactions to amplify DNA and DNA-sequencing reactions.
DNA polymerase
Key enzyme that copies strands of DNA during DNA replication to create new strands of nucleotides; has important applications for synthesizing DNA in molecular biology experiments.
Leading Strand
During DNA replication, the strand of newly synthesized DNA that is copied by DNA polymerase in a continuous fashion, 5′ to 3′ into the replication fork.
Lagging Strand
During DNA replication, the strand of newly synthesized DNA that is copied by DNA polymerase in a discontinuous (interrupted) fashion, 5′ to 3′ away from the replication fork as a series of short DNA pieces called Okazaki fragments.
DNA ligase
Enzyme that forms covalent bonds between incomplete (Okazaki) fragments of DNA during DNA replication; routinely used for joining DNA fragments in recombinant DNA experiments.
What is Genomics?
Study of molecular organization, genomes, information content, and gene products they encode.
Who discovered the Synthetic method in determining DNA Sequence?
Frederick Sanger.
What is the purpose of the Sanger DNA Sequencing?
To terminate a DNA Sequence.
What is another name of the Sanger DNA Sequencing?
The Chain-Termination DNA Sequencing Method. (it terminates the chain at some point)
What is the sugar the Chain-Termination DNA Sequencing Method uses?
Dideoxynucleoside triphosphates (ddNTP).
What is in the pentose sugar in ddNTP that's different from DNA? What is the purpose?
An H atom is inserted instead of the hydroxyl group present in DNA and it terminates the chain.
What is the first step in the Sanger Method?
Single strands of DNA are mixed with DNA Polymerase I, 4 deoxynucleotides, and a small amount of one ddNTP.
What is the second step?
DNA Synthesis, and RANDOM insertion of ddNTP's creat DNA fragments of varying lengths.
How many reactions are carried out in the Sanger Method?
Four (think of four nucleotides), and each with a different dNTP/ddNTP.
How are the reactions in each mixture separated?
Electrophoretically.
How is the sequence read in the Sanger Method?
Through gel autoradiographication.
What is the difference between the traditional Sanger Sequencing with the Automated Sequencing?
It uses four different fluorescent dyes instead of radiolabeled ddNTP.
How is the order determined in automated sequencing?
Through electrophoresis and laser beam.
How many nucleotides are able to appear in one lane of automated sequencing?
Up to 600 Nucleotides.
What are 3 types of more rapid, less cumbersome, and less expensive methods as an alternative to the Sanger DNA Sequencing?
Pyrosequencing, SOLEXA Sequencing, SOLiD Technology.
Who developed the Whole Genome Shotgun Sequencing?
J. Craig Venter and Hamilton Smith.
How many stages are in the Whole Genome Shotgun?
Four Stages.
(1st Stage) Library Process
Colnes portions of the genome.
(2nd Stage) Random Sequencing
Determines the order of the clone sequencing.
(3rd Stage)
Fragment alignment and gap closure.
(4th Stage)
Editing.
What does Bioinformatics provide?
Structure, arrangement, protein structure and function, and location of genes on newly sequenced genome.
What is Genome Annotation?
Process that locates genes in the genome map.
What is the kind of reading frame that the Genome Annotation identifies?
One with more than 100 Codons and is not interrupted by a stop codon.
What are ORF's presumed to encode?
Protein.
What does the BLAST provide?
Base by base comparison of two or more gene sequences, function of gene, and protein structure.
What is functional genomics?
Determination how genome works, usus maps for location of genes.
What information does Functional Genomics Provide?
Metabolic Pathways, transport mechanisms, regulatory and signal transduction mechanisms.
What does DNA Microarray Analysis?
Determines which genes are expressed at a specific time.
What are arrays?
Solid supports to which DNA is attached.
What is another name for a DNA Spot?
Probe.
What does a probe represent in DNA Microarray Analysis?
Represents a single gene or ORF.
How are spotted arrays prepared?
By a robotic application of DNA Probe.
What are some examples of Probes?
PCR Product, cDNA, or oligonucleotide.
What are oligonucleotides probes for eukaryotes called?
Expressed Sequence Tags (EST).
How does Microarray analysis work?
Based on the hybridization of DNA probe and targets, which are the nucleic acids, are analyzed.
How are the target (nucleic acids) prepared for microarray analysis?
They are labeled with fluorescent dyes, and then incubated with gene chip.
How is hybridization detected in microarray analysis?
By the scanning of chip with laser beams to detect fluoresence--indicates hybridization has occurred.
What is the purpoe of the microarray analysis?
to see which genes have changed their expression.
What is the hierarchical cluster analysis?
Groups of genes with similar function or patterns of regulation.
What is analysis of transcription?
When all mRNA's are present.
What is proteomics?
Study of the proteome, entire collection of proteins an organism produces. (This is not available in mRNA studies)
How is proteome analyzed?
Through a two dimensional gel electrophoresis.
How is the first dimension arranged?
It is in isoelectric focusing--makes a pH gradient which determines the isolectricpoint.
How is the second dimension arranged?
It is electrophoresis (SDS PAGE) and separates by size.
What happens in Tandem Mass Spectrometry?
Unknown spot from 2-D gel is cut and cleaved.
How is Tandem Mass Spectrometry analyzed?
By mass spectrometer, the mas of fragments is then plottedn amd protein is accurately described from probable amino acid composition.
What is Genetics
Science of heredity; refers to single gene function
What is Genomics
Study of entire genome; how a set of genes interact with each other and the environment
What is Pharmacogenetics (PGx)
Study of how specific genes cause variability in drug response & toxicity
What is Pharmacogenomics
Sutyd of how a person's genetic make up influences response to drugs
What is Sir Archibald Garrod famous for
Alkaptonuria, inborn errors of metabolism (Homogentisic acid oxidase deficiency in Alkaptonuria)
What is Favism
A range of symptoms due to hemolytic anemia (G6PD deficiency)
Pyrimidines are
Single ring (Cytosine, Thymine, Uracil)
Purines are
Double ring (Adenine, and Guanine)
DNA mehtylation CpG results in
Transcriptional silencing
DNA Histone Acetylation makes
DNA more accessible to TFs
Ferritin is needed to
Store iron, in presence of Iron its IRE-BP is bound to iron and unable to inhibit its translation
Transferrin is needed to
Import Iron into the cell, Low levels of iron will leave the IRE-BP free to bind and stabilize the mRNA
Name the post-translational modifications
Folding, Degradation, Proteolytic cleavage, and Phosphorylation, Glycosylation
Trisomy21
Down's Syndrome
Trisomy13
Severe retardation
Trisomy18
Microcephaly
Mendel's laws of genetics
Law of segregation, and Law of independent assortment
An example of genetic imprinting is
X-inactivation
What is Genetic anticipation
Caused by trinucleotide repeat expansion, found in exons, introns, as well as 5' or 3' UTRs
What is Genetic imprinting
Imprinted genes are expressed from only one chromosome, if this chromosome is absent or has a defect there will be a defect
Prader-Willi Syndrome (PWS) is caused by
Genetic imprinting, Obesity, short-stature, hypogonadism, mental retardation
Angleman Syndrome
Sister syndrome of Prader-willi, due to maternal deletion instead of pateranal on chromo 15
Restriction enzymes do what
Carry out double-stranded DNA cuts (staggered or blunt)
Southern blotting involves and is used for
Involves Restriction enzymes on DNA and can be used to determine the presence of specific DNA sequences
Restriction Fragment Length polymorphisms (RFLP) involves and is used for
Involves restriction sites and determining whether a gene has a restriction site mutation
Northern blot involves and is used for
involves isolating RNA and using specific DNA or RNA probes and is used to study gene expression
PCR involves and is used for
Involves amplifying a region of DNA by using set primers in both the 5' and 3' direction, and then amplifying them over and over; it is used to examine DNA
RT-PCR involves and is used for
Involves mRNA making DNA and then amplifying DNA using gene-specific primer; can be used to help determine gene expression (need only a small sample size)
DNA microarrays involves and is used for
Involves comparing two single stranded DNA (antisense) strands to figure out whether DNA will overexpress or downregulate specific genes
2D Gel electrophoresis involves and is used to
Involves mass spectrometry and allows you to predict which proteins are present or upgregulated
A SNP site will have at least
two alleles
Synonymous
No Change
Non-Synonymous
Change
A Haplotype is
A set of neighboring SNPs within a gene that tend to be inherited together (More than 3 SNPs)
BAC (Bacterial artificial chromosome)
An artificial version of a bacterial chromosome that can carry inserts of 100,000 to 500,000 base pairs.
Biotechnology
The manipulation of living organisms or their components to produce useful products.
cDNA library
A limited gene library using complementary DNA. The library includes only the genes that were transcribed in the cells examined.
Cloning vector
An agent used to transfer DNA in genetic engineering. A plasmid that moves recombinant DNA from a test tube back into a cell is an example, as is a virus that transfers recombinant DNA by infection.
cDNA (complementary DNA)
A DNA molecule made in vitro using mRNA as a template and the enzyme reverse transcriptase. A cDNA molecule therefore corresponds to a gene, but lacks the introns present in the DNA of the genome.
Denaturation
In DNA, the separation of the 2 strands of the double helix. Denaturation occurs under extreme conditions of pH, salt concentration, and temperature.
DNA fingerprint
An individual's unique collection of DNA restriction fragments, detected by electrophoresis and nucleic acid probes.
DNA microarray assay
A method to detect and measure the expression of thousands of genes at one time. Tiny amounts of a large number of singe-stranded DNA fragments representing different genes are fixed to a glass slide. These fragments, ideally representing all the genes of an organism, are tested for hybridization with various samples of cDNA molecules.
Electroporation
A technique to introduce recombinant DNA into cells by applying a brief electrical pulse to a solution containing cells. The electricity creates temporary holes in the cells' plasma membranes, through which DNA can enter.
Expression vector
A cloning vector that contains the requisite prokaryotic promoter just upstream of a restriction site where a eukaryotic gene can be inserted.
Gel electrophoresis
The separation of nucleic acids or proteins, on the basis of their size and electrical charge, by measuring their rate of movement through an electrical field in a gel.
Gene therapy
The alteration of the genes of a person afflicted with a genetic disease.
Genetic engineering
The direct manipulation of genes for practical purposes.
Genetically modified organism
An organism that has acquired one or more genes by artificial means; also known as a transgenic organism.
Genomic library
A set of thousands of DNA segments from a genome, each carried by a plasmid, phage, or other cloning vector.
Genomics
The study of whole sets of genes and their interactions.
Human Genome Project
An international collaborative effort to map and sequence the DNA of the entire human genome.
In vitro mutagenesis
A technique to discover the function of a gene by introducing specific changes into the sequence of a cloned gene, reinserting the mutated gene into a cell, and studying the phenotype of the mutant.
Nucleic acid hybridization
Base pairing between a gene and a complementary sequence on another nucleic acid molecule.
Nucleic acid probe
In DNA technology, a labeled single-stranded nucleic acid molecule used to tag a specific nucleotide sequence in a nucleic acid sample. Molecules of the probe hydrogen-bond to the complementary sequence wherever it occurs; radioactive or other labeling of the probe allows its location to be detected.
Physical map
A genetic map in which the actual physical distances between genes or other genetic markers are expressed, usually as the number of base pairs along the DNA.
Polymerase chain reaction (PCR)
A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides.
Proteomics
The systematic study of the full protein sets (proteomes) encoded by genomes.
Recombinant DNA
A DNA molecule made in vitro with segments from different sources.
Restriction enzyme
A degradative enzyme that recognizes and cuts up DNA (including that of certain phages) that is foreign to a bacterium.
Restriction fragment
DNA segment resulting from cutting of DNA by a restriction enzyme.
(Restriction fragment length polymorphisms) RFLPs
Differences in DNA sequence on homologous chromosomes that can result in different patterns of restriction fragment lengths (DNA segments resulting from treatment with restriction enzymes); useful as genetic markers for making linkage maps.
Restriction site
A specific sequence on a DNA strand that is recognized as a cut site by a restriction enzyme.
SNPs (Single nucleotide polymorphisms)
One base-pair variation in the genome sequence.
Southern blotting
A hybridization technique that enables researchers to determine the presence of certain nucleotides sequences in a sample DNA.
Sticky end
A single-stranded end of a double-stranded DNA restriction fragment.
Ti plasmid
A plasmid of a tumor-inducing bacterium that integrates a segment of its DNA into the host chromosome of a plant; frequently used as a carrier for genetic engineering plants.
YAC (yeast artificial chromosome)
A vector that combines the essentials of a eukaryotic chromosome-an origin for DNA replication, a centromere, and two telomeres- with foreign DNA.
functional genomics
the study of the roles of genetic sequences-DNA,RNA, and amino acid sequences- in a given species
proteome
the entire collection of proteins a given cell or organism can make.
proteomics
the study of the function and interaction of proteins in a cell or organism
bioinformatics
the use of computers, mathematical tools, and statistical techniques to record, store and analyze biological information.
DNA microarray
a small silica or plastic slide that is dotted with many different sequences of DNA, corresponding to short sequences within known genes.
cluster analysis
the statistical technique to identify genes whose patterns of expression seem to strongly correlate with one another.
chromatin immunoprecipitation
a method to determine whether proteins can bind to a particular region of DNA.
ChIP-chip assay
a form of chromatin immunoprecipitation that utilizes a microarray to determine where in the genome a particular protein binds.
gene knockout
the altering of a gene in a way that inactivates its function.
alternative splicing
the phenomenon in which a pre-mRNA can be spliced into more than one version.
RNA editing
a change in the base sequence of RNA after it has been transcribed.
postranslational covalent modification
modification in the covalent structure of a protein after it has been translated.
two-dimensional gel electrophoresis
a technique that can separate up to thousands of different proteins within a cell.
isoelectric focusing
the migration of a protein to a point in the gel where its net charge is zero.
mass spectrometry
the measurement of the mass of a molecule
tandem mass spectrometry
the use of two mass spectrometers, the first to analyze the full protein, and the second to analyze the protein after it has been broken down into smaller fragments. used to determine the amino acid sequence of a polypeptide.
protein microarrays
a collection of protein molecules blotted onto a silica or plastic slide.
sequence recognition
the identification of a sequence of symbols with a specialized meaning.
pattern recognition
the identification of a pattern that can occur within any sequence arrangements
search-by-signal
an approach of searching for genes by using known promoters, start or stop codons to predict whether or not a DNA sequence contains a gene.
search-by-content
an approach of searching for genes by identifying regions in a sequence that differ significantly from what would be expected in a random distribution.
open reading frame
a region of a nucleotide sequence that does not contain any stop codons
homologous
two sequences derived from the same ancestral gene
orthologs
two or more homologous genes found in different species
paralogs
two or more homologous genes found in the same species
gene family
two or more paralogs within the genome of a single organism.
homology
implied common ancestry
similarity
two sequences are similar to each other
multiple sequence alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties.
basic local alignment search tool
a computer program that starts with a particular sequence and then locates homologous sequences within a large database. Easier among proteins than DNA
E-value
the number of times that a match with a particular sequence would be expected to occur purely by random chance.
homology based modeling
the modeling of a three-dimensional structure of a molecule based on its homology to another molecule whose structure is already known.
reverse transcriptase
An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis.
transcription
the synthesis of RNA using a DNA template
translation
The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of "language" from nucleotides to amino acids.
transduction
the process of transfering genetic material from one cell to another by a plasmid or bacteriophage
conjugation
In prokaryotes, the direct trasfer of DNA between two cells (of the same or different species) that are temporarily joined.
RNA polymerase
an enzyme that links ribonucleotides into a growing RNA chain during transcription
transposon
a segment of DNA that can become integrated at many different sites along a chromosome (especially a segment of bacterial DNA that can be translocated as a whole)
methylation
the addition of groups to DNA that disables genes
nucleosome
The basic, beadlike unit of DNA packing in eukaryotes, consisting of a segment of DNA wound around a protein core composed of two copies of each of four types of histone.
histone
A small protein with a high proportion of positively charged amino acids that binds to the negatively charged DNA and plays a key role in its chromatin structure.
euchromatin
The less condensed form of eukaryotic chromatin that is available for transcription.
heterochromatin
Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.
looped domain
the 30-nm fiber forms loops atached to a chromosome scaffold made of proteins, thus making up a 300-nm fiber.
RFLP (Restriction Fragment Length Polymorphism)
A single nucleotide polymorphism (SNP) that exists in the restriction site for a particular enzyme, thus making the site unrecognizable by that enzyme and changing the lengths of the restriction fragments formed by digestion with that enzyme. This can be in coding or noncoding DNA.
PCR (polymerase chain reaction)
technique for amplifying DNA sequences in vitro by incubating it with specific primer, a heat resistant DNA polymerase, and nucleotides.
cDNA
single-stranded DNA that is complementary to messenger RNA or DNA that has been synthesized from messenger RNA by reverse transcriptase
restriction enzyme
any of the enzymes that cut nucleic acid at specific restriction sites and produce restriction fragments
ligase
An enzyme that connects two fragments of DNA to make a single fragment. Combines foreign DNA fragment with plasmid through phosodiester linkages thus making a recombinant plasmid.
plasmid
a small, circular, double-stranded DNA molecule that carries accessory genes separate from those of a bacterial chromosome.
retrovirus
An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.
promoter
A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA.
structural gene
a gene that controls the production of a specific protein or peptide
proto oncogenes
normal cellular genes that are important regulators of normal cellular processes, they promote growth. alterations in the expression of these cells resulr in oncogenes
oncogenes
a gene found in viruses or as part of the normal genome that is involved in triggering cancerous characteristics
tumor suppressor genes
A gene whose protein products inhibit cell division, thereby preventing uncontrolled cell growth that contributes to cancer.
recombinant DNA
A DNA molecule made in vitro with segments from different sources.
clone
(1) A lineage of genetically identical individuals or cells. (2) In popular usage, a single individual organism that is genetically identical to another individual. (3) As a verb, to make one or more genetic replicas of an individual or cell. See also gene cloning.
restriction site
A specific sequence on a DNA strand that is recognized as a "cut site" by a restriction enzyme.
restriction fragments
DNA segment resulting from cutting of DNA by a restriction enzyme
sticky ends
a single stranded end of a double-stranded restriction fragment. (formed by restriction enzymes)
cloning vector
In genetic engineering, a DNA molecule that can carry foreign DNA into a host cell and replicate there. _________ _________s include plasmids that move recombinant DNA from a test tube back into a cell and viruses that transfer recombinant DNA by infection.
nucleic acid hybridization
The process of base pairing between a gene and a complementary sequence on another nucleic acid molecule.
denaturation
For proteins, a process in which a protein unravels and loses its native conformation, thereby becoming biologically inactive. For DNA, the separation of the two strands of the double helix. _______ occurs under extreme conditions of pH, salt concentration, and temperature.
expression vector
A cloning vector that contains the requisite bacterial promoter just upstream of a restriction site where a eukaryotic gene can be inserted, allowing the gene to be expressed in a bacterial cell.
YAC (yeast artificial chromosome)
a vector that combines the essentals of a eukaryotic chromosome (an origin for DNA replication, a centromere, and two telomeres) with foreign DNA
heat shock
1.exposing DNA to high temperatures to force them to separate 2.cools DNA, allowing primers to bind (anneal) to target DNA 3.temperature is raised again so that polymerase can attach to primers and make complementary strand
genomic library
a set of cell clones containing all the DNA segments from a genome, each within a plasmid, phage, or other cloning vector
gel eletrophoresis
procedure used to separate and analyze DNA fragments by placing a mixture of DNA fragments at one end of a porous gel and applying an electrical voltage to the gel
DNA microarray
a method to detect and measure the expression of thousands of genes at one time.
RNA interference (RNAi)
a technique used to silence the expression of selected genes; uses synthetic double-stranded RNA molecules that match the sequence of a particular gene to trigger the breakdown of the gene's mRNA
single nucleotide polymorphisms
a single base-pair in a genome where nucleotide variation is found in at least 1% of the population
gene therapy
the introduction of genes into an afflicted individual for therapeutic purposes
transgenic organism
and organism whose genome contains a gene introduced from another organism of the same or a different species.
operon
A unit of genetic function common in bacteria and phages, consisting of coordinately regulated clusters of genes with related functions.
operator
In prokaryotic 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.
repressor
a protein that inhibits gene transcription. In prokaryotes, these bind to the DNA in or near the promoter. In eukaryotes, these 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 controls the transcription of another gene or group of genes
corepressor
a small molecule that binds to a bacterial repressor protein and changes its shape, allowing it to switch an operon off
tryptophan
This molecule is the corepressor in the trp operon; it binds to the repressor which then binds to the operator
B-galactosidase
the enzyme reponsible for the breakdown of lactose into its component sugars, glucose and galactose. LacZ codes for this (idk what other definition to use.. help?!)
inducible
off operon; inducer inactivates the repressor and turns on transcription
repressible
on operon; co repressor/protein binds to the operator shutting off transcription
negative gene regulation
the operons are switched off by the active form of the repressor protein (examples lac operon and trp operon)
positive gene regulation
cAMP & Catabolite Activator Protein (CAP)- activator of transcription (what else can be said about this?!)
codon
Group of three nitrogenous bases - code for an amino acid
anti-codon
Group of 3 bases found on tRNA
tRNA
Transfers amino acids
rRNA
Makes up ribosomes
mRNA
Single stranded version of a gene; recipe for a protein
ribosome
Makes polypeptides
amino acid
Monomer of a polypeptide
DNA polymerase III
Adds new DNA nucleotides to a replicating DNA molecule
Helicase
Unizips DNA
telomere
Protects the ends of the chromosomes, when they degrade, the cell dies.
Lac 1 protein
The protein that binds to the operator in the lac operon to prevent transcription
tryptophan
This molecule is the corepressor in the trp operon; it binds to the repressor which then binds to the operator
transcription
The process where mRNA is produced
translation
The process where a protein is produced from an mRNA recipe
spliceosome
A protein that removes introns from mRNA
exon
Section of DNA that codes for proteins
template strand
The DNA strand that is used to produce mRNA
Okazaki
Name of fragments formed on the lagging strand in DNA replication
Primase
The enzyme that builds RNA primers
Ligase
The enzyme that glues fragment backbones together
Semiconservative
Theory of DNA replication where each new strand is built on an old strand after DNA is unzipped.
antiparallel
Parallel, but running in opposite directions.
Gyrase
Relieves tension in an unwinding DNA strand
Anneal
The pairing of complementary strands of DNA
Nonsense
A type of mutation where a stop codon is added prematurely
Silent
A type of mutation where there is no change in the resulting polypeptide.
Inversion
A type of mutation where the two strands of DNA switch positions, or flip
Translocation
Type of mutation where a section of DNA moves to another location.
Restriction enzyme
Used to cut DNA into fragments
Plasmid
A DNA donut found in bacteria cells that can be transferred between cells
Conjugation
The process where bacteria cells transfer plasmids to each other
Electrophoresis
A process where DNA fragments are separated according to size using electrical charges
5-3
Direction that new DNA is built in (3-5 or 5-3)
purine
Double ringed nitrogenous base
nucleotide
DNA subunit
nucleic acid
DNA is this type of molecule
poly-A
Type of tail that protects mRNA
methyl guanosine
Type of cap that protects mRNA (5' cap)
ribose
Type of sugar in RNA
deoxyribose
Type of sugar in DNA
phosphate
DNA has a sugar and _____ backbone
hydrogen
Type of bond between nitrogenous bases
covalent
Type of bond between atoms in DNA backbone
2
Number of hydrogen bonds between A and T
uracil
Nitrogenous base seen only in RNA
double helix
DNA's shape; 2 strands, twisted
prokaryote
Cell that has no nucleus - general term
methionine
Start codon codes for this amino acid
AUG
start codon
lactose
This molecule bonds to the lac 1 protein, removing it from the operator
substitution
A mutation that causes a single amino acid to change in a protein
frameshift
A mutation that results from either adding or deleting one or 2 bases
centromere
Found in the middle of chromosomes
degeneracy
Refers to repetition in the genetic code
plasmid
Bacteria have these; can code for antibiotic resistance
pyrimidine
Single ringed nitrogenous base
lagging
Strand that is made slower in DNA replicaton
PCR
DNA amplification; force DNA to replicate
RFLP
Can be used to sequence DNA, using a nylon membrane
negative
DNA's charge
biotechnology
Using living things to make a useful product
prokaryotic
Type of cell where transcription and translation can happen simultaneously
mutation
Change in DNA sequence; can be from radiation, etc.