micro midterm Flashcards
single molecules(monomers) that make up proteins(polymers) called?
AMINO ACIDS
R group present on glycine?
Hydrogen(H) grp
R group present on Alaine?
Methyl(CH3)
R group present on Cysteine
Sulfhydryl(CH2SH)
Covalent bond btw two amino acids?
peptide bond
Two amino acids joined by a peptide bond through a process of dehydration synthesis is?
Dipeptide
4-9 amino acids joined by peptide bonds
peptide
10-2,000 or more amino acids joined by peptide bonds are?
polypeptides(proteins)
primary structure
the number and sequence of amino acids(AA’s) in a single polypeptide chain
secondary structure
H-bond interactions btw AAs of a single polypeptide chain forms a coiled structure: an a-helix or b pleated sheet
tertiary structure
the helix of a single polypeptide chain folds irregularly on itself due to R group interactions btw AA forming DISULFIDE bonds or other bonds. a supercoiled structure formed
- 2 degree and 3 degree structure determine proteins 3D shape and function
Quaternary Structure
2 or more polypeptide chains are joined together, usually by disulfide bonds
disulfide bonds
bond formed when two cyteines( types of amino acids) are joined
proteins attached to organic compound are called?
conjugated proteins
ex: glycoprotein. lipoprotein, nucleoprotein, hemoglobin
which organic compounds are classified as nucleic acids?
DNA and RNA
what are the building blocks(monomers) of nucleic acids called?
nucleotides
3 components that make up each nucleotide?
- pentose sugar
- phosphate group
- nitrogen base(A,G,T, or C)
which component distinguishes the 4 types of nucleotides from each other?
nitrogen base(N-base)
which N bases are purines?
Adenine(A)
Guanine(G)
which N bases are Pyrimidines?
Cystosine(C)
Thymine(T)
or Uracil(U) in RNA
who discovered the structure of the DNA molecule?
James watson & francis crick
James and Crick findings?
1) two chains of nucleotides joined at nitrogen bases by H-bonds
2)Complementary base pairing between nitrogen bases
A w/ T(2h bonds)
C w/ G(3h bonds)
3) two chains of nucleotides(base pairs) from a double helix(twisted ladder configration)
- sugar-phosphate backbone forms sides of ladder
- nitrogen bases from rungs of ladder
4) the two chains are oppositely orientated, anti parallel
- 1st nucleotide chain begins at C #5 and ends at C #3 on deoxyribose.
- 2nd nucleotide chain begins at C #3 and ends at C #5 on deoxyribose)
DNA
5’ AAA TTT CCC CAC 3’
3’ TTT AAA GGG GTG 5’
DNA
- double stranded
- nitrogen base: A<G
- A bonds with T
- C bonds with G
- deoxyribose sugar is missing oxygen on carbon 2
- longer molecule containing thousands of genes
RNA
-single stranded
-nitrogen bases: A<u><G
-A bonds w/ U
C bonds w/ G
-ribose sugar has oxygen on carbon number 2
-shorter molecule decoded from one gene</u>
genetics
the study of the structure, function, and transfer of genes from one generation to the nexy
chromosome
structure containing the hereditary information(genes) of the cell
gene
segment of DNA that codes for(give instructions or recipe for) trait/characteristics/protein/phenotype in an organism
genotype
genetic make up of an individual, eukaryotes have paired genes;
prokaryote have single genes
phenotype
- trait or protein
- physical or physiological expression of a gene resulting from a genotype
Genome
sum of all genes in cells of organisms
- include plasmids if present
- e coli=5,000-10,000
DNA replication
- duplication of chromosomes prior to cell division
- identical genes passed to next generation(daughter cells)
protein synthesis
- gene expression at the ribosome
- making of proteins from copied genes
- 2 process
- transcription: a gene in a DNA is copied into an mRNA transcript, a copied gene
-recombination: a piece of DNA containing several genes is passed from donor to recipient bacterial cells in same generation
3 steps in DNA replication
1) unzipping: helicase unwinds DNA and breaks hydrogen bonds holding the two chains together, exposing nitrogen bases on each template strand of DNA
2) complementary copying of each template strand inDNA:
DNA polymerase complementary base pairs free DNA nucleotides in the cytoplasm with each nitrogen base on each template strand in a 5’ to 3’ direction
3) Termination of replication: the two new molecules of DNA rewind and separate
which enzyme proofreads for errors during DNA replication?
DNA polymerase
what would happen if the enzyme that proofreads for error during replication misses the error?
MUTATION
define SEMIconservative replication
-produces 2 new molecules of DNA each with one original strand and one newly synth strand
what direction is the template stand on DNA copied?
5 to 3
protein synthesis
gene expression at the ribosome making protein from copied gene
components invovled in protein synthesis
1) DNA gene: segment of DNA that codes for a trait/protein/phenotype/characteristic of an organism
2) 3 types of RNA
- mRNA: carries copied gene(RNA transcript) to ribosome during translation.
- rRNA: Unkown
- tRNA: carries amino acids to ribosomes during translation
3) genetic code: rules that determine how a nucleotide sequence in a gene encodes an amino acids sequence in a protein.
why is the genetic code called a degenerate(redundant code)
more than one mRNA codon can encode the same AA
mRNA codons encode for?
AMINO ACIDS
nonsense mRNA codons(UGA,UAG,UAA)
do not code for amino acids
start mRNA codon
AUG founds at the beginning of mRNA transcript and codes for the AA methionine
-it initiates translation of AA in protein
stop/terminator mRNA codons
- UGA, UAG, UAA(nonsense codon)
- always found at the end of an mRNA transcript and terminates translation
Transcription
-a gene in DNA is copied into a mRNA transcript, a copied gene
3 steps:
A) initiation: RNA polymerase binds promoter sequence prior to DNA gene, it complementary copies 1st triplet nucleotide–> AUG
B) Elongation: RNA polymerase moves along the template strand in DNA gene and complementary base pairs free RNA nucleotides w/ each DNA nucleotide in a 5’ to 3’ direction, producing an mRNA transcript.
C) termination: mRNA transcript encodes a specific sequence of amino acids in a protein at the ribosome
introns
non-coding portion of DNA that do not code for AA in proteins
exons
coding portions of DNA that code for AA in protein, are transcribed by RNA polymerase into a pre-mRNA transcript
splicing
ribozymes in nucleus remove(cut out) intron-deived RNA and splice together exon-derived RNA into a mature mRNA, which is further modified and passes thru pores of the nuclear membrane into the cytoplasm, where it directs protein synthesis at the ribosome
mutation
- alteration of gene
- change in base sequence of DNA in a gene
frequency of mutation
-the probability that a gene will mutate when the cel divides or replicate
spontaneous mutation
arise as a result of errors in replication at a rate of 1 in 10(9) replicated base pairs or 1 in 10(6) replicate genes
induced mutation
mutagenic agents(mutagens) in the environment that increase the mutation rate to 1 in 10(5)(1/100,000) or 1 in 10(3) (1/1000) replicated genes during DNA replication. -mutagenic agents damage DNA and interfere with its functioning
mutagen(mutagenic agent)
-a chemical agent or physical agent in the environment that indirectly or directly causes mutations in DNA, cause base substitution or frameshift mutations
neutral(silent)
-mutation is a gene that results in the same AA, produces the same protein
harmful(disadvantageous)
a mutation in a gene that results in a different or unfinished protein in its environment.
ex: lac-,pen-s
beneficial mutation
mutation in a gene that results in a different protein thats advantageous to survival
ex: lac+, pen-R(good for bacteria)
silent
a mutation that results in the same AA produces the same protein
misense
a mutation that results in a different AA frequently produces a different protein which can be beneficial or harmful to the organisms survival in its environment
nonsense
a mutation that results in a nonsense(STOP) codon in the middle of an mRNA transcript produces a non-functional(unfinished) protein, a protein that is always harmful and is disadvantageous to microbes survival in its environment
-frameshift becomes nonsense unfinished proteins
UV rays produce thymine dymers
x ray cause breaks in DNA backbone
AMES test
-used to identify the effects of potential carcinogens on DNA in bacterial systems in order to identify carcinogens(cancer causing agents) in humans and other animals
genetic recombination
gene transfer, gene exchange, horizontal gene transfer occurs when a piece of DNA containing several genes is passed from donor to recipient bacterial cells in the SAME generation and usually incorporates into recipients chromosomes. the recipient is now called recombinant cell can express new traits(new proteins)
*vertical gene transfer is passage of genes from parent cell to offspring in next generation via replication
3 different mechanisms of genetic transfer(genetic recombination)
- transformation
- transduction
- congregation/mating
transformation
a naked piece of DNA in environment is passed from donor lysed to recent bacterial cell
transduction
mistakenly packaged piece of bacterial DNA is transferred from donor to recipient bacterial cell via a bacteriophage
congregation/mating
DNA, usu. plasmids is transferred form donor(F+) to recipient (F-) bacterial cell via sex pilus
plasmid
small, extra-chromosomal circular strands of DNAm found in many bacterial species, contain genes usu. not crucial to the organisms survival in its environment, but confer selective/adaptive traits such as antibiotic resistance
transposans
jumping genes or transposable elements are special segments of DNA that can move from one part of a chromosome and insert into another part of the same chromosome, a different chromosome, or a plasmid and back
transposition
process by which transposons jump btw chromosomes
transposase gene code for
transposase enzyme and enzyme which cuts out the transposons from one location in a chromosome and inserts it into another location(target DNA)
results of transpositions
1- genetic diversity
2- harmful mutation
3- genetic transfer
viruses
non-living infectious particles
-viruses are inactive particles outside host cells and active particles inside host cells they infect.
viruses are described as obligate intracellular parasites b/c
- non-living, inactive infectious particles outside host cells or active particles inside host cells they invade
- completely dependent on host cells for their survival as they have few or no enzymes to carry out protein synthesis, replication or form ATP.
- Rely on synthetic (genetic) machinery (ribosomes,RNA,AAs) on on metabolic macherinery(enzymes,tap) or host cells to multiple into virons–> fully formed infectious particles that are virulent
what type of organisms do viruses infect?(hint domains)
- ARCAEA
- BACTERIA
- EUKARYA
what are bacteriophages aka phages?
-virus that infect bacterial cells
viral specificity(host range)
- refers to the fact that viruses have a limited number and kind of host cells they infect. host range for a particular virus is determined by specific host attachment sites(receptors)
- phages attach to CW receptors and animal viruses attach to CM receptors
restrictive animal viruses
- infect very specific cells w/ in their host range
- ex. HIV viruses infect human T helper cells w/ CD4 receptors
intermediate
infect species w/ in a moderate host range
-ex. polio virus infect intestinal and nerve cells of primates
broad
- infect species w/ in a wider host range
ex. rabies virus infects all mammalian nerve cells, such as rodent, bats, dogs, etc..
structure found in a typical virus
Outer coat.
- capsid
- envelope
Inner core:
- nucleic acid
- proteins
capsid
outer protein layer around viruses, composed of protein molecules, subunits called capsomeres
two types of capsids
Helical capsid: capsomers arranged in a helical formation that form rigid or flexible rods
Icosahedral capsid: aka polyhedral or crystalline capsid: capsids w/ 20 triangular sides that form a geometric polyhedron
envelope
the envelope, a lipid layer surrounding the capsid only found around certain animal viruses
how do certain animal viruses obtain their envelope
-modified piece of animals host cells membrane obtained as animals virus “bud off” animal host cell by the process of exocytosis, process called budding
glycoprotein that protrude from most enveloped viruses, which function in attachment to host cell membranes
spikes
a virus w/o an envelope
1- nukes virus
2-nucleocapsid
3-non-enveloped viruses
nucleic acid(inner core)
viruses contain either DNA or RNA type of nucleic acid, BUT NEVER BOTH
-genome contains between a few and a thousand genes
proteins(inner core)
-encoded by viral genes include protein capsid, protein spikes, lysozyme or reverse transcriptease(produce by hiv to convert RNA to DNA
two groups of complex(atypical) viruses)
-viruses that exhibit a morphology or structure that is not typical
pox virus and bacteriophages
pox virus
bricked shaped viruses w/ several layers of lipoproteins and coarse fibrils(envelope) enclosing nucleoproteins
bacteriophages
phages consist of an icosahedral head(capsid) that encloses DNA. phages also possess a collar sheath, central tube, base plate, tail pins and tail fibers for attachment to host bacterial CW.
-types of bacteriophages are t-even(ex T4) or temperate phages
4 taxa into which viruses are categorized
- superfamily
- family
- general genus
- species/strain
super family
-7 DNA super families and 14 RNA super families, classified by type of nucleic acid they possess
family(latin name and viridae)
classified by morphology, presence of an envelope or where the virus replicates in the host
-ex: herpesviridae
general genus(latin and virus)
- classified by host target tissue
ex. herpesvirus
species/strain
- classified by shared genes, host range(ecologic niche) or geographic location where 1st discovered
- ex HSV-1 or HSV-2
Herpes simplex virus type 1
-cause fever blisters(cold sores) on MM or skin
Herpes simplex virus type 2
-genital herpers(blisters on genitals)
cytomegalovirus
- cells swell
- cause mono(w/ fever and rash)
- reactivation in weakened host
epstein barr virus
- cause mono
- burkitts lymphoma or nasopharyngeal carcinoma
varicella zoster
- cause initial disease
- chicken pox
- and then reactivation disease later in life
- herpes zoster aka shingles
- VZV can also cause reyes syndrome(brain and liver dysfunction=death)
why are in vivo or in vitro methods used to grow, isolate and ID viruses in lab?
since viruses are obligate intracellular parasites they can be grown outside live host cells on nutrient media such as BAP(blood agar plate)
BAP
blood agar plate
4 techniques to grow, isolate, and ID viruses(bacteriophages and animal virus)
- plaque method
- Tissue(cell) culture technique
- animal virus grown in live lab animal host
- animal virius grown in bind embryos
plaque method
-to detect and count bacteriophages
bacteriophages are mixed w/ host bacterial cells in melted agar and poured over a nutrient medium.
-after 24-48hr incubation period the petri dishes are examined for plaques(plaque forming units or pfu’s). plaques are clear spaces where bacterial cells have been lysed, seen against a “lawn” of bacterial growth. each plaque corresponds w/ a single virus particle in the initial incoculum sample
Tissue(cell) culture technique
- most common and economical techniques
- used to grow certain animal viruses
- animal tissue is treated w/ enzymes to separate cells and placed in glass chamber w/ nutrient medium to support growth
- two types animal tissue cels lines are used
- primary cell lines: normal animal cell derived from kidney heart bone marrow
- continuous(immortal cell line)- cancerous/mutated/transformed animal cells that divide for an infintie no of generations
- cytopathic effects(CPEs): cytopathic effects, abnormalities in host tissue, viewed under microscope include
1. deterioration(plaques) in host tissue
2. multiple nuclei(synctia)
3. inclusion bodies
animal viruses grown in live lab animal hosts
a viral suspension is injected into the brain, blood, muscle or skin of a live lab animal to
a) study the animals immune response to viral infection
b) observe signs and symptoms in the animal
c) to microscopically observe cytopathic effects in the lab animal
animal viruses grown in bind embryos
- this method id used to grow animal viruses for vaccine preparations
- method: a hole is drilled in the egg shell, the viral suspension is injected into extra-embryonic membranes or bird embryo(egg) itself
- viral growth is exhibited as death of chick embryo
- developmental defects or pocks
- lesions or opaque spots in egg embryo indicative of host cell lysis by virus
diagnosis of animal viral disease in humans is based on signs and symptoms as well diagnostic test
- cytopathic effects(seen under a microscope
2. serological(immunolgy) test or modern molecualar method using nucleic acids/ DNA fingerprinting
how are animal virus treated and prevented?
- antiviral drugs: interfere with certain stage of viral multiplication
ex: AZT, drug used to treat aids, target nucleic acid synthesis stage
ex. protease inhibtors=newer class of hiv drugs, disrupt final assembly stage of viral life cycle - interferon: naturally occurring human cell products that are used to treat certain viral infections ex. HBV,SSPE
- Vaccines: altered forms of foreign agent, designed to induce a specific immune(Ab) response in the host
T even bacteriophages carry out lytic cycle
the lytic cycle is carried out by t even bacteriophages
5 stages of the lytic cycle(attachment/absorption)
- occurs after chance collision between phage and host bacterial cell.
- viral specific proteins at end tail fibers attach to specific receptors proteins on bacterial host cell wall
5 stages of the lytic cycle(generation)
- entry of phage into bacterial host cell
- virus(phage) uses lysozyme to digest a hole in bacterial cell wall
- phages DNA is then injected into bacterial host cells cytoplasm
- capsids remain outside as “ghosts” (empty capsids)
5 stages of the lytic cycle(biosynthesis)
- replication and protein synthesis
- viral replication and protein synthesis occur in bacterial host cells cytoplasm
- virus particles or viral enzymes(nuclease) inhibit or fragment bacterial chromosomes(inhibit replication and protein synthesis
- phage take over genetic and metabolic machinery of host bacterial cells
- viral DNA is replicated ad proteins are synthesized, using bacterial hosts enzymes–> early and late proteins
5 stages of the lytic cycle(Maturation/ assembly)
-spontaneous assembly of viral components into fully formed infectious vial particles that are virulent/virons(fully formed virus particles)
5 stages of the lytic cycle(release/lysis)
phage uses lysozyme to a digest a hole in bacterial cell wall,
- resulting in host cell lysis or burst
- phages escape and bacterial host cells are killed/destroyed in the process
- after release, visions infect.invade neighboring bacterial cells
lysogenic cycle as seen in bacteriophages
90 percent of bacteriophages that infect bacterial host cells are temperate phages
prophage
latent viral DNA that integrates into bacterial chromosomes, replicates and daughter cells express new traits
reactivation
-host bacterial cell containing the prophage in the lysogenic cycle is stimulated by some stress factor causing the latent viral DNA(prophage) to pop out of bacterial chromosome and resume the lytic cycle where host bacteria cells are destroyed
lysogenic conversion
bacterium carrying prophage can express new phage proteins
-ex. s pyogens(strep throat) carrying erythrogenic toxin–>scarlet fever
4 type of animal virus infections(acute viral infection)
- produce life long immunity
- short-lived viral infections
- flu measles
- gradually eliminated by host immune system over days or months
4 type of animal virus infections(latent virus infection)
- initially virus HSV induces a lytic infection in host
- then viral NA becomes inactive and enters a latent phase inside host for long periods without disease, but may become reactivated later by some stress factor and produce disease symptoms
4 type of animal virus infections(slow viral infection/persistent viral infection)
- initial viral infection
- measles followed by a slow viral infection in which viral particles multiply and gradually increase in number over a long period of time w.o elicting apparent symptoms in the patient. Then a slow, progressive lethal disease(SSPE) develops
4 type of animal virus infections(chronic)
- in long term infections
- virus particles can be detected in tissue samples at alt me because they are continually multiplying at a slow rate with or w.o symptoms, or disease develops later
- ex. congenital rubella syndrome and serum hepatitis
latent, persistant, chronic viral infections
establish a carrier state in their animal host in which disease may or may not develop
- the carrier state ranges from a few weeks to a life-long relationship with the animal host
- ex: latter HSV infections
prions
proteinaceous infections particles
prions
infectious, misfolded proteings
-cause spongiform encephalopathies(fatal, wasting disease, produce holes in the brain
prions diseases
- sheep scraple
- crutzfiend jacob diseas
- bovine spongyform encephalitlts(mad cow disease)
animal viruses
effect cell membrane
hiv comes equip with w/ own enzyme = reverse transcriptease copies RNA-DNA
bacteriophages effect bacteria
lytic cycle
cause host cells to lyse(burst) killing host cell
lysogenic or latent cycle
-viral dan remains dormant or integrates into host cell chromosome as latent DNA=> latter replication w/ host chromosome=> host cells are not killed
