Bio 309 Exam
phenotype the physical, observable expression of a characteristic or trait; "what you see"
wildtype the phenotype we expect to see in wild individuals; notated by x+ where x is the
allele for the gene and defined by having an allele frequency of greater than 1%
mendel's law of independent assortment describes how different alleles of different genes behave individually
linked genes genes that are located near each other on a chromosome and tent to travel
together during meiosis
gene cloning the process of using living cells to make exact replicas of a fragment of foreign
DNA
polymerase chain reaction (PCR) an in vitro method of detection and isolation of genomic fragments using cyclic
repetitions of DNA synthesis reactions; involves a thermostable DNA polymerase
that catalyzes multiple rounds of DNA synthesis, beginning with two primers that
flank a region of interest within a target DNA template
forward primer the PCR primer with the same sequence as the top strand, and binds to the
bottom strand
reverse primer the PCR primer with the same sequence as the bottom strand, that binds to the
top strand
genetically modified organisms (GMO) an organism whose genome has been engineered to have a desirable phenotype
covalent bond a strong type of chemical bond in which two atoms share one or more pairs of
electrons
endonucleases an enzyme that cleaves the phosphodiester bond within a polynucleotide tail (ie.
DNA)
exonucleases an enzyme that removes successive nucleotides from the end of a
polynuncleotide (ie. DNA)
restriction endonucleases endonucleases that cut DNA at specific positions
denaturation the reversible process of unfolding a protein or DNA
renature the process of refolding unfolded protein or DNA strands
hydrophobic interactions interactions between non-polar chemical groups or molecules, and polar water
, Bio 309 Exam
supercoiling the effect on DNA where the double helix is coiled on itself
open circular form the relaxed, non-supercoiled form of a plasmid that has broken a strand of DNA
covalently closed circular form the natural, supercoiled for of plasmid
open reading frame (ORF) a continuous stretch of codons that begins with a start codon and ends at a stop
codon (ie. the part of a reading frame that has the ability to be translated)
consensus sequence a sequence of DNA in a promoter that is similar in all genes eg. TATA consensus
sequence (TATA box)
trans-acting element a factor that regulates gene expression but is not located on that gene eg.
repressor proteins
cis-acting element factors coded for within DNA that regulate gene expression for that gene eg.
binding sites for trans-acting elements
enhancer a regulatory site that increases transcription; can be located far away (can be
10,000 base pairs away) from the core promoter, or can be quite close; cis acting
exon coding sequence for the promoter product; sequences found in both a gene's
DNA and in the mature mRNA
intron non-coding sequences found in a gene's DNA but not in the mature mRNA;
removed from the primary transcript during splicing
shine-dalgarno sequence a sequence of the ribosome binding site in bacteria, generally located about 8
bases upstream of the start codon AUG; helps recruit the ribosome to the mRNA
to initiate translation by aligning the ribosome with the start codon
operon a unit of DNA composed of specific genes, plus a promoter and an operator,
which act in unison to regulate the response of the structural genes to
environmental changes
epigenetic phenomena changes in gene expression not related to sequence changes
RNA interference the action of miRNAs to alter mRNA stability and translational efficiency to
reduce protein production
alternative splicing the regulated process during gene expression that results in a single gene
coding for multiple possible proteins through different splicing patterns (ie.
removal of different segments as introns)
upstream before the transcription start site
, Bio 309 Exam
downstream after the transcription start site
fusion protein a protein created through the joining of two or more genes that originally coded
for separate proteins
translational fusion the joining of genetic information affecting the translation of a protein product, to
result in a fusion protein
transcriptional fusion fusion at the transcriptional level to produce a fusion protein product; aka.
promoter::reporter fusions; replacing the coding region of a gene with the coding
sequence for reporter gene to monitor the activity of a promoter
reporter genes genes that are easily detectable and are used to: monitor protein location,
movement, interactions (ie. translational fusions), or monitor promoter activity
(eg. transcriptional fusions) eg. luciferase, green fluorescent protein, Lac Z
induction the process by which a tissue or cell directs neighbouring tissues or cells to
develop in a specific way
genetic approach an in vivo approach to studying molecular biology in which we study organisms
with mutations in specific genes to learn about the function of corresponding
gene products (ie. requires functional organisms)
forward genetics a type of genetic approach in which we find a mutant first, then identify what
caused the phenotype, genetically; ie. analyze phenotype --> analyse gene eg.
Mendel and his peas
reverse genetucs a type of genetic approach in which we start with a gene of interest, then create
an organism that expressed that gene abnormally (ie. mutant) due to the
introduction of additional sequences (transgenes); includes gene silencing; ie.
analyze the gene --> analyze phenotype
biochemical approach an in vitro approach to studying molecular biology in which we study proteins or
metabolites (ie. activity, structures, etc.)(ie. does not require a functional
organism)
bioinformatic approach an in silico approach to studying molecular biology in which we create databases
of large data sets and develop query algorithms to mine data to make
experimental predictions and biological models (ie. requires computers)
screen the act of analyzing every member of a population to identify which are abnormal
for the trait in question
select isolation of the mutant in question, after screening
transgene a gene that has been introduced into the genome artificially
biochemistry the study of proteins and enzyme activities
homogenate a component of a biochemical approach that maintains the functionality of the
protein of interest using a pH buffer, salts, cofactors, and protease inhibitorsl;
aka. extract
phenotype the physical, observable expression of a characteristic or trait; "what you see"
wildtype the phenotype we expect to see in wild individuals; notated by x+ where x is the
allele for the gene and defined by having an allele frequency of greater than 1%
mendel's law of independent assortment describes how different alleles of different genes behave individually
linked genes genes that are located near each other on a chromosome and tent to travel
together during meiosis
gene cloning the process of using living cells to make exact replicas of a fragment of foreign
DNA
polymerase chain reaction (PCR) an in vitro method of detection and isolation of genomic fragments using cyclic
repetitions of DNA synthesis reactions; involves a thermostable DNA polymerase
that catalyzes multiple rounds of DNA synthesis, beginning with two primers that
flank a region of interest within a target DNA template
forward primer the PCR primer with the same sequence as the top strand, and binds to the
bottom strand
reverse primer the PCR primer with the same sequence as the bottom strand, that binds to the
top strand
genetically modified organisms (GMO) an organism whose genome has been engineered to have a desirable phenotype
covalent bond a strong type of chemical bond in which two atoms share one or more pairs of
electrons
endonucleases an enzyme that cleaves the phosphodiester bond within a polynucleotide tail (ie.
DNA)
exonucleases an enzyme that removes successive nucleotides from the end of a
polynuncleotide (ie. DNA)
restriction endonucleases endonucleases that cut DNA at specific positions
denaturation the reversible process of unfolding a protein or DNA
renature the process of refolding unfolded protein or DNA strands
hydrophobic interactions interactions between non-polar chemical groups or molecules, and polar water
, Bio 309 Exam
supercoiling the effect on DNA where the double helix is coiled on itself
open circular form the relaxed, non-supercoiled form of a plasmid that has broken a strand of DNA
covalently closed circular form the natural, supercoiled for of plasmid
open reading frame (ORF) a continuous stretch of codons that begins with a start codon and ends at a stop
codon (ie. the part of a reading frame that has the ability to be translated)
consensus sequence a sequence of DNA in a promoter that is similar in all genes eg. TATA consensus
sequence (TATA box)
trans-acting element a factor that regulates gene expression but is not located on that gene eg.
repressor proteins
cis-acting element factors coded for within DNA that regulate gene expression for that gene eg.
binding sites for trans-acting elements
enhancer a regulatory site that increases transcription; can be located far away (can be
10,000 base pairs away) from the core promoter, or can be quite close; cis acting
exon coding sequence for the promoter product; sequences found in both a gene's
DNA and in the mature mRNA
intron non-coding sequences found in a gene's DNA but not in the mature mRNA;
removed from the primary transcript during splicing
shine-dalgarno sequence a sequence of the ribosome binding site in bacteria, generally located about 8
bases upstream of the start codon AUG; helps recruit the ribosome to the mRNA
to initiate translation by aligning the ribosome with the start codon
operon a unit of DNA composed of specific genes, plus a promoter and an operator,
which act in unison to regulate the response of the structural genes to
environmental changes
epigenetic phenomena changes in gene expression not related to sequence changes
RNA interference the action of miRNAs to alter mRNA stability and translational efficiency to
reduce protein production
alternative splicing the regulated process during gene expression that results in a single gene
coding for multiple possible proteins through different splicing patterns (ie.
removal of different segments as introns)
upstream before the transcription start site
, Bio 309 Exam
downstream after the transcription start site
fusion protein a protein created through the joining of two or more genes that originally coded
for separate proteins
translational fusion the joining of genetic information affecting the translation of a protein product, to
result in a fusion protein
transcriptional fusion fusion at the transcriptional level to produce a fusion protein product; aka.
promoter::reporter fusions; replacing the coding region of a gene with the coding
sequence for reporter gene to monitor the activity of a promoter
reporter genes genes that are easily detectable and are used to: monitor protein location,
movement, interactions (ie. translational fusions), or monitor promoter activity
(eg. transcriptional fusions) eg. luciferase, green fluorescent protein, Lac Z
induction the process by which a tissue or cell directs neighbouring tissues or cells to
develop in a specific way
genetic approach an in vivo approach to studying molecular biology in which we study organisms
with mutations in specific genes to learn about the function of corresponding
gene products (ie. requires functional organisms)
forward genetics a type of genetic approach in which we find a mutant first, then identify what
caused the phenotype, genetically; ie. analyze phenotype --> analyse gene eg.
Mendel and his peas
reverse genetucs a type of genetic approach in which we start with a gene of interest, then create
an organism that expressed that gene abnormally (ie. mutant) due to the
introduction of additional sequences (transgenes); includes gene silencing; ie.
analyze the gene --> analyze phenotype
biochemical approach an in vitro approach to studying molecular biology in which we study proteins or
metabolites (ie. activity, structures, etc.)(ie. does not require a functional
organism)
bioinformatic approach an in silico approach to studying molecular biology in which we create databases
of large data sets and develop query algorithms to mine data to make
experimental predictions and biological models (ie. requires computers)
screen the act of analyzing every member of a population to identify which are abnormal
for the trait in question
select isolation of the mutant in question, after screening
transgene a gene that has been introduced into the genome artificially
biochemistry the study of proteins and enzyme activities
homogenate a component of a biochemical approach that maintains the functionality of the
protein of interest using a pH buffer, salts, cofactors, and protease inhibitorsl;
aka. extract
