module 1 Flashcards
homeostasis
the tendency toward a relatively stable equilibrium between interdependent elements, especially as maintained by physiological processes
gene speciation
gene that contributes to the splitting of two lineages by reducing the amount of gene flow between them.
HeLa cells
derived from human tumor cells
kept alive through nutrients (growth media)
provide method to experiment in in-vitro system that contains human cells
Genetic program
genetic information is used to
encode nucleic acids
used based on needs of cell or organism as a whole
conserved across life forms: different species carry similar genes
Blast
determines closeness in genetic code
first entry should be the sequence entered
max score value gives positive value of homology, higher the value, the more closely related
E-value gives probability result was random and not homologous, lower the number the greater the homology
ion channel
protein molecules that span across the cell membrane allowing the passage of ions from one side of the membrane to the other
bacteria
circular plasmid hold genetic makeup
“loss of function mutation”
A type of mutation in which the altered gene product lacks the molecular function of the wild-type gene
receptor
A molecule inside or on the surface of a cell that binds to a specific substance and causes a specific effect in the cell.
paralog
genes related by duplication within a genome, may evolve to produce new functions, usually related to the original one
genome
complete set of genes or genetic material present in a cell or organism.
dna
contains code prescribing rna codon, code is arranged in genes
deoxyribose sugar (has H at 2’ position)
rna
ribose sugar (has OH group at 2’ spot)
rna codon prescribes order of synthesis for amino acids in protein
differentiation
the normal process by which a less specialized cell undergoes maturation to become more distinct in form and function.
NCBI
data base managed by national center for biotechnology information
basic local alignment search tool used to search homology of protein of nucleotide sequences
vesicle transport
responsible for molecular traffic between a variety of specific membrane-enclosed compartments
virus
Submicroscopic particles which can not replicate without a host. Viruses consists of genetic material (RNA or DNA) and an encapsulating protein envelop (caspid).
ligand
substance that forms a complex with a biomolecule to serve a biological purpose
could be used as a signal when binds to protein
signal transduction
process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, which ultimately results in a cellular response.
DNA replication
process by which the genome’s DNA is copied in cells.
nucleic acid
purine (2 ring) or pyrimidine (1 ring), ring structure contains N and C
makes up DNA and RNA
integrase
allows integration of viral DNA into the genome of the T-cell
ex: raltegravir
HIV
infects helper t-cells by gp120 protein
high mutation rate since reverse transcriptase is error prone
single strand RNA requires reverse transcriptase for making the DNA copy of the virus.
alpha-complementation
positive selection for gene introduction
used to determine success of cloning
homology
two genes derived from the same gene in a common ancestor
orthologue
genes in different species that evolved from a common ancestral gene by speciation, normally retain same function in the course of evolution
genetic material
passed from parent cells and helps determine characteristics
enzymes
used to achieve the activation energy to enable chemical reactions to occur rapidly
metabolism
total of cell’s chemical reactions
prokaryotes
cells without defined nuclear envelope
eukaryote
cells with defined nucleus separated from the cytoplasm by a membrane structure
bacteriophage
virus that can infect bacteria
genome is replicated by bacteria
can clone gene into the viral DNA, infect the bacteria, recover the DNA
can have selectable markers such as antibiotic resistance
During the lytic cycle of infection will release progeny DNA
reverse transcriptase
DNA polymerase enzyme that transcribes single-stranded RNA into DNA. This enzyme is able to synthesize a double helix DNA once the RNA has been reverse transcribed in a first step into a single-strand DNA.
hybrid
new species that has acquired a barrier to genetic exchange form parent species and are unable to produce fertile offspring
peptide bonds
covalent linkages of one amino acid to another
strong bonds
require energy to break
give protein a primary structure
glycosidic bonds
covalent oxygen bonds between sugars
phosphodiester bonds
bond that joins two RNA or DNA linkages
the 3’ end of one joins with the 5’ end of another
hydrogen bonding
Bonds C,G, A,T base pairs
helix stabilized by these bonds
ionic bonding
attraction between oppositely charged atoms where electrons are donated and accepted
covalent bonding
chemical reactions formed when these are formed or broken
sharing of electrons
hydrophobic interactions
interacts with nonpolar amino acids, side chains, and other lipid moieties
has these reactions with stacking bases that aid in helix stability
motif
defined arrangements between conformations
domain
distinct modules that fold individually of other portions of the proteins
coiled-coiled motif
two or more alpha helices that wrap around each other
helix loop helix motif
found in transcription factors which have DNA binding and protein interaction domains
zinc finger motif
small protein structural motif that is characterized by the coordination of one or more zinc ions in order to stabilize the fold
transcription factor
protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.
channel
special arrangement of amino acids which embeds in the cell membrane, providing a hydrophilic passageway for water and small, polar ions
transformation
term for putting plasmid into the bacteria
transfection
term for putting plasmid into a eukaryotic cell
fusion protein
have same dynamics as WT protein, is florescent and can be seen with florescent microscope
least two domains that are encoded by separate genes that have been joined so that they are transcribed and translated as a single unit, producing a single polypeptide
probe and target
radioactive
blot membrane with probe of complementary sequence to DNA of interest
RFLP
pattern of DNA after endonucleases cleave DNA restriction sites through out the genome of an individual
each person has unique pattern of fragments
Bradford analysis
proteins quantitated by Coomassie blue conjugation and spectrometry at abs=595 nm
accurate at 1.0 microgram/ ml
prepare standard curve
Palindromic
nucleic acid sequence in a double-stranded DNA or RNA molecule whereby reading in a certain direction on one strand is identical to the sequence in the same direction on the complementary strand.
southern blot
use to know whether DNA sample contains homolog of gene of interest
SDS
detergent that will denature proteins to rod shapes and cover them with uniform negative charges, will help spread on gel be determined my mw
immunoprecipitaion
prepare cell/tissue
add primary antibody targeting protein of interest, to supernate
add secondary antibody conjugated with agarose resin
wash precipitated complexes and apply on SDS-PAGE
cross-linking
process of forming covalent bonds or relatively short sequences of chemical bonds to join two polymer chains together.
GFP
green fluorescent protein
fusion protein created containing this, should cause the protein to exhibit fluorescence
site-directed mutagenesis
put mismatch on primer designed from inserted gene
use pcr to perform
method to create specific, targeted changes in double stranded plasmid DNA
chimera
ingle organism that’s made up of cells from two or more individuals, contains two sets of DNA with code to make two separate organisms
ie: fetus absorbing twin
gel filtration
used to separate proteins
high molecular weight macromolecules elute first
determine proteins in eluate using suitable assay
estimate approximate molecular weight of unknown proteins/ complexes using calibration curve with pre-run standard proteins of known mw
restriction endonuclease
restriction enzymes cut at specific protein sequences, producing smaller pieces of DNA with specific ends
bacteria derived form enzyme that recognizes palindromic sequence of nucleotides and cleaves DNA backbone in a particular manner through the palindrome
DNA denature
electrophoresis to separate DNA fragments and denature them, creates single stranded DNA
EMSA
construct radioactive probe
mix hot DNA with protein mixture
separate non-denaturing gel by PAGE
dry gel on membrane
Use autoradiography to detect the bands from radiation on the DNA probe
use control to show specific DNA binding
Use a control to demonstrate specific protein
blocking
prevents others from binding
PCR
tool used to amplify DNA from genes for assays
makes possible to increase the amount of dna from small sample
uses principles of replication and melting/annealing cycles
knock in/knock-out trangenic mouse
create a loss of function mutation of gene of interest in mouse and observe the phenotype
knockout= gene targeted and inactivated
knockin= alter mouse genetic sequence to add foreign genetic material
analytical centrifugation
uses special centrifuge with detection optics to measure the moving speeds of components in a solution
output numbers are in Svedberg units
PAGE
type of denaturing or nondenaturing gel
used to separate proteins by charge
Primary and secondary antibodies
add to protein of interest to supernate
yeast-2 hybrid
involves cloning of 2 plasmids to make fusion proteins
primers
short stretches of DNA that target unique sequences and help identify a unique part of genome
native gel/ non-denatured gel
uses non-denatured gels for the separation of proteins. Unlike SDS PAGE, no denaturing agent is added in the preparation of gels
hydrophilic
water loving
hydrophobic
water fearing
acidic COO-
carboxyl group
amino acids contain
basic NH3+
amino acid group
in amino acid structure
OH Hydroxyl
serine
threonine
Tyrosine
amphipathic
molecules that have polar and nonpolar ends
allows for interaction between aqueous cytosol and hydrophobic interactions with non-polar amino acids, side chains, and other lipid monities
sulfhydrol
Sulfur and hydrogen bonded
mostly found in the oxidized form as disulfide linkages. The disulfide linkages contribute to the tertiary and quaternary structures of proteins.
major groove
where the backbones are far apart
minor groove
occurs where they are close together
consensus sequence
sequence of DNA, RNA, or protein that represents aligned, related sequences
Leeuwenhoek
used the microscope to observe unicellular organisms
Hooke
sent by Royal Society to investigate early microscopy and described his observations as cells
Schleiden
studied plant cells and yeast. Renowned for ability to study cell structure and organization from the microscope
Schwann
Documented that tissues were comprised of nucleated cells
Virchow
first doctor to describe leukemia, studied cellular pathology and encouraged the use of the microscope by doctors trying to understand the disease
canine ditempter etiology
paramyxovirus
cantine distempter
highly contagious virla disease
labile in environment, dies easily
“hard pad disease” hairy paws patches on nose
canine distemper transmission
aerosol droplets
carriers shed for 2 months
canine distemper incubation
3-7 days
canine distemper diagnosis
fever w neurologic disease
canine distemper treatment
fluids
caloric maintence
control pyrexia
control seizures with tranquilizers
antibiotics to prevent secondary infection
