bio exam 4 - Sheet1 Flashcards
1
Q
Host range
A
number of species that can be infected
2
Q
Host cell
A
- The number/types of cells infected by a virus
- A living cell that serves as a shelter and a food source to the foreign organism
- example; what type of cell is this viruses host cell?
3
Q
Capsid
A
protein coat; encloses the nucleic acid; composed of one or more protein subunits called CAPSOMERS
4
Q
viral envolope
A
Encloses the capsid; lipid bilayer (derived from plasma membrane of the host cell); may have spike glycoproteins; not all have an envelope
5
Q
genome
A
DNA versus RNA, single stranded (ss) versus double stranded (ds), linear versus circular; some have several copies; vary in size (6400 bp (TMV) vs thousands)
6
Q
1 Virus process: attachment
A
phage binds to proteins in outer bacterial wall
7
Q
2 Entry
A
some mechanism to inject nucleic acid into the cell (example-degrade a small part of the cell wall with lysozyme)
8
Q
3 viral integration
A
DNA enters cell and can integrate with the host chromosome(doesn’t have to)
9
Q
4 synthesis of viral components
A
phage DNA directs synthesis of cellular components, DNA circulates, host chromosome DNA is degraded.
10
Q
5 viral assembly
A
Some viruses self-assemble
11
Q
6 release
A
virus-derived protein dissolves cell wall, causes lysis, and allows virus to be released and infect new cells
12
Q
why r viruses not alive
A
only have RNA, don’t maintain hemeostasis, does not need energy, not made of cells.
13
Q
lysogenic cycle includes
A
integration, replication, and excision
14
Q
lytic cycle
A
synthesis, assembly, and release
15
Q
temperature phages have a
A
lysogenic cycle
16
Q
virulent phages have a
A
lytic cycle
17
Q
latency in human viruses (1)
A
Virus integrates into host genome and may remain dormant for longperiods of time
18
Q
episomes (type of latency)
A
- genetic elements that replicate independently of host DNA (can be in nucleus,nerve cell)
- An episome is a special type of plasmid, which remains as a part of the eukaryotic genome without integration.
19
Q
viroids
A
RNA that affect plants,Some replicate in host cell nucleus, others in chloroplast
20
Q
RNA genome does not code for
A
proteins
21
Q
Prions
A
proteins that affect animals
22
Q
Prions induce
A
abnormal protein folding
23
Q
Genetic properites of bacteria
A
single type of circulur chromosome,may have more then one copy of chromosome
24
Q
Nucleid
A
region where tightly packed bacterial chromosome found
25
proteins important
for loops and supercoiling the DNA
26
vertical gene transfer
genes are passed from one generation to the next among individuals of the same species
27
horizontal gene transfer
when genes are passed to non-offspring, possibly of different species
28
17% of genes havbe been acquired from
horizontal transfer
29
antiboitic resistence from
horizontal transfer
30
bacterial strain
A lineage that has genetic differences from another lineage(same species, but with different genetics)
31
conjugation(gene transfer)
Plasmid transferred from the donor to the recipient through "appendage"; both cells now have the plasmid; could be to same or different species of bacteria
32
transformation(gene transfer)
DNA fragment from a dead, degraded bacterium enters a competent recipient bacterium and is exchanged for a piece of DNA of the recipient.
33
transduction
Bacteriophage infects donor and "picks up" some donor DNA. Then phage infects new cell and transfers the DNA to recipient
34
Bacterial transformation does not require
direct contact between cells
35
Only competent cells with competence factors are capable of
transformation
36
Recombinant DNA technology
Use of laboratory techniques to bring together fragments of DNA from multiple sources
37
genomics
is the molecular analysis of the entire genome of a species
38
DNA cloning, why useful
makes lots of DNA, allows to study, large amount of DNA product
39
3 steps to gene cloning
1. isolate DNA,
40
resistance plasmoids
defend against poisons/toxins (like antibiotics)
41
degradative plasmoids
help remove unusual substances/pollutants
42
virulence plasmoids
carries genes for pathogenesis
43
fertility plasmoids
promote gene transfer
44
Only competent cells with competence factors
are capable of transformation
45
common vectors
* Plasmids, Have special sequences to make cloning easier*,
* Carry a selectable marker (like antibiotic resistance gene)*
46
plasmids
small, self-replicating, circular pieces of DNA found naturally in many strains of bacteria
47
viral vectors(step 1 in gene cloning)
viruses which infect living cells and propagate themselves using the host cell's machinery
48
How can you get the DNA of interest?
PCR
49
polyamerase chain reaction (PCR)
-a method for amplifying DNA from a small amount so a sufficient amount is available for analysis
50
How to do PCR
Mix all reagents/components in a tube., 2. Put in a PCR machine. Machine essentially doesall the work! 1. Repeated rounds of denature, anneal, andextend will amplify your DNA of interest.
51
primers in PCR
designed to flank the exact region you want to amplify by complementation, comparison of DNA replication to PCR
52
Step 1: Part 1 Denature(PCR)
temp is raised very high (usually around 95 °C - 98°C); this causes the 2 strands of the dsDNA to separate from each other.
53
Step 1: Part 2 Anneal (PCR)
temp is dropped to a chosen temperature that will allow your designed primers to bind by complementation
54
Step 1: part 3 extend (PCR)
temp is raised to the optimal temp for the polymerase to be used
55
Step 2 insert DNA of interest into the vector(plasmid) (PCR)
Use commercially available restriction enzymes to cut the vector and DNA of interest, 1. The enzyme will make these pieces complementary/share an affinity for each other
Add a ligase (similar to the one we discussed during DNAreplication) that will combine these two pieces of DNA together to create 1 new piece
this makes the recombinant plasmid
56
Step 2: part 2 After cutting the DNAs, combine them.(PCR)
1. After restriction enzyme digests, the vector and DNA of interest share complementary sequences where the enzyme had cut.,
2. Combine two pieces of DNA, they will associate with each other by complementation.
3. add a ligase, will enzymatically permanently combine two pieces of DNA together to create 1 new vector (plasmid).
4. end result is new plasmid that carries your DNA of interest= RECOMBINANT VECTOR or PLASMID
57
Step 3 of PCR
transform a host strain to make copies of your DNA of interest (or translate the encoded protein)
58
How do restriction enzymes work?
* Made naturally by bacteria as protection against bacteriophages*,
* Cut at specific known restriction sites in the DNA*
* Most restriction sites are palindromic(complementery)
* May produce sticky ends
59
Restrction enzymes
can cut DNA at specific sequences
60
When certain restriction enzymes cut,
they leave a tiny bit of an overhang; not a blunt cut; this can allow complementary base pairing between fragments
61
Restriction enzyme leaves a short, complementary sequence between the two pieces so that
they will be able to bind each other; then ligase combines/joins the pieces
62
to screen for your successful cloning you can -
1. Isolate the plasmid DNA and do PCR on it
2. Isolate the plasmid DNA, use restriction enzymes to cut out inserted DNA, then analyze on agar gel thru gel electrophoresis.
63
Agarose gel electrophoresis
* used to separate macromolecules on a gel, based on their charge, size/length, and mass
* evaluate the results of a cloning experiment
64
applications of genomics
mapping of genome --> Could involve sequencing the genome of organisms, functional genomics -->whole courses taught on this subject
65
If a ddNTP is incorporated into a growing DNA strand, it ___
terminates the strand; no more nucleotides can be added because of the missing 3' OH
66
how does sequencing work?
it simultaneously identifies DNA bases(A,T,G,C) while incorporating them into a nucleic acid chain.
67
expression analysis
which genes turn on or off in particular cells
68
why is genomics important?
* Bacteria cause disease*,
* Can apply knowledge to more complex organisms*,
* Origin of first eukaryotic cell involved union of archaeal and bacterial cell*,
* Bacteria often used as tools in research,
69
why r Archaeal and bacterial genomes less complex than eukaryote
Lack centromeres and telomeres
70
Reasons to sequence eukaryotic genomes:
* -Great benefit from identifying and characterizing genes in model organisms,
* -More information to identify and treat human diseases,
* -Improved strains of agricultural species,
* -Way to establish evolutionary relationships
71
evolution
heritable change in one or more characteristics of a population or species from one generation to the next
72
microevolution
Change in allele frequencies in a population over generations.
73
macroevolution
large-scale evolutionary changes that take place over long periods of time
74
species
group of related organisms; capable of interbreeding
75
theory of evolution, how did it come about?
relies on observation rather then life from a spiritual point of view, believe forms are changed over time
76
darwins influence on evolution
Formulated theory of evolution by mid-1840s
77
variation, within a given species
Traits heritable - passed from parent to offspring•, Genetic basis was not yet known
78
natrual selection
individual with better traits flourish and reproduce• Competition for limited resources, More offspring produced than can survive•
79
evidence of evolution: fossil record
Can see change in fossils when looking directly at oldest to youngest fossils
80
transitional form
a species that is intermediate between two different species
81
evidence of evolution:biogeography
* The study of the geographic distribution of extinct and living species;
* Example: islands may have unique species compared to mainland due to isolation
82
endemic
* native species, only found in one place
83
convergant evolution
When 2 species from different lineages have independently evolved similar characteristics (because they occupy similar environments)
84
homoligies
Fundamental similarity due to descent from a common ancestor
85
anatomical(type of homology)
Example: homologous structures
86
developmental(type of homology)
Example: embryonic structures
87
molecular(type of homology)
Example: similarities in gene sequences
88
vestigial structures
A structure that is present in an organism but no longer serves its original purpose
| exe- earlobes, tailbone
89
homologous structures
* two genes, in different species, derived from the same ancestral gene;
* similar but not identical
90
paralogeous genes (single celled)
homologous genes within a single species; frequently arise due to duplication event
91
gene pool
Combined genetic information of all the members of a particular population
92
population
Group of individuals of the same species that occupy the same environment and can interbreed with one another
93
microevolution
looks at changes in a population's gene pool from generation to generation
94
reproductive success
Likelihood of an individual contributing fertile offspring to the next generation
95
reproductive success reason 1
Certain characteristics make organisms better adapted and more likely to survive to reproductive age
96
reproductive success reason 2
ability to find a mate and ability to produce viable gametes and offspring
97
fitness
* likelihood that genotype will contribute to gene pool of next generation compared to other genotypes;
* quantitative measure of reproductive success;
98
directional selection
Individuals at one extreme of a phenotypic range have greater reproductive success in a particular environment
99
stabilizing selection
* Favors the survival of individuals with intermediate phenotypes(and against both of the extremes)
Example involves clutch size of birds: Too many eggs and offspring - die due to lack of care and food,
Too few eggs - does not contribute enough to next generation
100
Diversifying/Disruptive selection
Favors the survival of two or more different genotypes that produce different phenotypes
101
balancing selection
Two or more alleles are kept in balance, and therefore are maintained in a population over the course of many generations
102
selective breeding
Procedures used to modify traits in domesticated animals/plants (aka: artificial selection)--traits chosen by breeders to make more desirable offspring (from human perspective)
103
sexual selection
Directed at certain traits of sexually reproducing species that make it more likely forindividuals to find or choose a mate and/or engage in successful mating how members ofone sex choose who to mate with; reproductive success influenced by specific traits
104
Sexual dimorphism
significant difference between the morphologies of the two sexes within a species (could be male or female is bigger than the other)
105
Intrasexual selection
Males directly compete for mating opportunities or territories
106
Intersexual selection 2
one chooses its mate from the other sex based on desirable characteristics
107
Less common type of intersexual selection: Cryptic female choice
females can use chemical or physical mechanisms to control mating success
108
genetic drift
changes allelic frequencies due to random chance (affects gene pool)
109
Random events
are unrelated to fitness
110
Genetic Drift rapidly alters allele frequencies when the population size
dramatically decreases
111
bottleneck affect (genetic drift)
reduced population size rebuilds, Randomly eliminates members without regard togenotype
112
founder effect (genetic drift)
small group starts a new colony,less genetic variation
113
Gene flow
occurs when individuals migrate between populations having different allele frequencies (genes move between populations)
114
Migration tends to
reduce differences in allele frequencies between the two populations
115
nonrandom mating - Assortative mating
* Individuals with similar phenotypes or genotypes are more likely to mate, Increases the proportion of homozygotes(similaroffspring)
* * Like breeds with like
116
nonrandom mating - Disassortative mating
Dissimilar phenotypes mate preferentially, Favors heterozygosity(differentness in offspring)
117
inbreeding
choice of mate based on genetic history
118
integration lysogenic cycle
integration of the bacteriophage nucleic acid into the genome of the host bacterium
119
replication lysogenic cycle
involves the virus assimilating its genome with the host cell's genome to achieve replication without killing the host.
120
excision lysogenic cycle
121
lytic cycle
