UARK Bio for Majors Exam 4

Viruses and Bacteria

cause disease but are medically important

Viruses and Viroids

nonliving particles with nucleic acid genomes that require the assistance of living cells to reproduce

True/False

Viruses and Viroids:

>make their own energy

>reproduce

>grow and develop nucleic acid

False

Components of Viruses/Infectious Particles

compose of a nucleic acid; protein coat (capsid); can infect plants, animals, and other bacteria

Host Range

number of species that can be infected by a virus

Host Cell

number/types of cells that have been infected by a virus

Capsid

protein coat that encloses the nucleic acid and is composed of one or more protein units called capsomers

Viral Envelope

encloses the capsid in a lipid bilayer and is derived from the plasma membrane of a host cell; has spike proteins; not all viruses have an envelope

Genome

DNA/RNA

Emerging Viruses

occur due to mutations

Viroids

single stranded circular RNA molecule that doesn't have a protein coat (mainly infects plants)

Prions

entirely made of proteins that infect mainly animals (more prominent in creating brain diseases)

Viral Reproductive Cycle

leads to the production of a new virus

Attachment

phage binds to cell; can have a broad or specific host cell range

Entry

phage injects DNA into the cell's cytoplasm; integration (lysogenic cycle) and synthesis components (lytic cycle)

Integration

phage integrates into cell chromosome; enzyme cuts host chromosome and inserts viral genome

Synthesis of Viral Components

break down cell chromosomes; uses host machinery

Viral Assembly

assembles phage viral proteins

Release

viral proteins help burst cells (lysozomes help degrade cell wall)

Lysogenic Cycle

phage genome integrates into the host cell as prophage when the cell replicates; excision leads to lytic cycle

Lytic Cycle

steps that lead to synthesis, assembly, and release (lysis)

Episomes

genetic elements that replicate independently of host DNA

dsDNA

genes where bacteria are found

Nucleiod

region where tightly packed chromosomes are found

Plasmid

DNA independent of chromosomes

Vertical Gene Transfer

genes that are passed from generation to generation

Horizontal Gene Transfer

genes that are passed to non-offspring

ORI

single origin of replication

Components of Plasmids in Nature

1. Resistance Plasmids

2. Degradative Plasmids

3. Virulence Plasmids

4. Fertility Plasmids

Resistance Plasmids

defend against poisons/toxins (antibiotics)

Degradative Plasmids

removal of unusual substances/pollutants

Virulence Plasmids

carries genes for pathogenesis

Fertility Plasmids

promotes gene transfer between bacteria (horizontal)

Bacterial Strain

a lineage that has a genetic difference from another lineage but same species

Genomics

molecular analysis of a species genome

3 steps of gene cloning:

1. isolate DNA

2. insert DNA

3. transform host strain

Conjugation

sexual transfer of plasmids through an appendage

Transformation

DNA fragment released into the environment and picked up by another cell

Transduction

phage infects donor in DNA and then the DNA picks up the phage

Genetic Properties of Bacteria:

single, circular chromosome

Properties of Bacterial Replication:

>fast growing

>divides asexually or by binary fission

>simple genomes

>easily manipulated

>inexpensive for lab usage

TRUE/FALSE

Bacterial transformation DOES NOT require direct contact between cells.

TRUE

Recombinant DNA Technology

use of lab techniques to combine fragments of DNA from multiple sources

Gene Cloning

process of making multiple copies of a gene

Vector

transmits infectious pathogens

Common Vectors:

Plasmids and Viral Vectors:

>has special sequencing to make cloning easier

>carry a selectable marker (antibiotic resistant genes)

>carries useful genetic elements

Viral Vectors

derived from viruses which infect living cells and propogate themselves using host machinery

Polymerase Chain Reaction

enzymatic reactions that exponentially make copies of the DNA of interest (designed primers go from 5' to 3')

What happens during PCR:

>Denature

>Anneal

>Extend

>Repeat 30 times

Denature

raise temperature to 95-98 degrees celsius (causes DNA to split)

Anneal

temperature is dropped to a chosen temperature that will allow primers to bind

Extend

temperature is raised to optimal temperature (68-72) for the polymerase to be used (polymerase finds primers that bind to DNA)

Why is PCR useful:

>starts with a small amount of template

>easy and quick

>inexpensive

>can add sequence to primers

Restriction Enzymes

cuts DNA

>made naturally by bacteria as protection against bacteriophages

>cut at specific restriction sites

>most restrictions are palindromic

>many produce sticky ends (easier for cloning)

Successful ways to screen cloning:

1. isolate the plasmid DNA from the transforments and do PCR for the DNA

2. use restriction enzymes to cut out the inserted DNA and analyze DNA on an agar gel through gel electrophoresis

>seperates DNA after gene cloning

>seperates based on length, size, and mass

-smaller=faster

-larger=slower

Mapping of Genome

sequencing the genome of organisms

Functional Genomics

how a gene is expressed

Why is studying genomics important?:

>bacteria causes diseases

>apply knowledge to complex organisms

>eukarya = bacteria + archaea

>bacteria used for research

Archaea vs Bacteria

>lacks centromeres and telomeres

>single origin of replication

>relatively little repetitive DNA

Evolution

heritable change in one or more characteristics of a population species from one generation to the next

Microevolution

changes in a single gene of a population over time

Macroevolution

formation of new species

Species

group of related organisms capable of interbreeding

Population

members of the same species in the same area at the same time

Empirical Thought

relies on observations to form an idea rather than trying to understand something from a spiritual point of view

Darwin's Influence:

>formulated evolutionary theories around the mid-1840s

>1859, Darwin's "On the Origin of Species" is published, detailing his observations

Variation:

>heritable traits

>genetic basis was not yet known

Natural Selection

individuals with better traits will flourish and reproduce

Evidence of Evolutionary Change:

>fossil records

>biogeography

>convergent evolution

>selective breeding

>homologies

-anatomical

-developmental

-molecular

Fossil Record

can see change in fossils when looking directly at the oldest to youngest fossils

Transitional Form

shows an intermediate state between the ancestor and descendant

Biogeography

the study of geographic distribution of extinct and living species due to isolation

Endemic

naturally found in one location

Convergent Evolution

when two species from a different lineage have independently evolved similar characteristics

Selective Breeding

procedures used to modify traits in domesticated plants/animals

Vestigial Structures

anatomical features with no current functions; resembles the structure of our ancestors (ex. appendix)

Homologies

fundamental similarity due to the descent from a common ancestor

Anatomical

homologous structures

Developmental

embryonic structures

Molecular

similarities in gene sequencing

Homologous Structures

two genes in a different species derived from the same ancestral gene (similar but not identical)

Paralogous Genes

homologous genes with a single species; frequently arises due to duplication event

Population Genetics

study of genes and genotypes over time

Genes in a Population

study of genetic variation within a gene pool over generations

Gene Pool

all alleles for the genes in a population

Adaptations

changes in a population that promotes survival

Reproductive Success

likelihood of an individual contributing fertile offspring to the next generation

Fitness

likelihood that a genotype will contribute to the gene pool of the next generation compared to other genotypes (max 1.0) (higher # = more likely to contribute

Types of Fitness:

>directional selection

>stabilizing selection

>disruptive/diversifying selection

>balancing selection

Directional Selection

individuals at one extreme of a phenotypic range and have greater success in an environment

Stabilizing Selection

favors the survival of individuals with intermediate phenotypes (against both extremes)

Diversifying/Disruptive Selection

favors survival of two or more different genotypes that produce different phenotypes

Balancing Selection

two or more alleles are kept in balance and therefore are maintained in a population over the course of many generations

Sexual Selection

directed at certain traits of sexually reproducing species that make it more likely for individuals to find or choose a mate and/or engage in successful mating (affects males more than females)

Sexual Dimorphism

significant differences between the morphologies of the two sexes within a species (male or female bigger than the other)

Intrasexual Selection

males directly competing for mating opportunities or territories

Intersexual Selection

one chooses its mate from the other sex based on desirable characteristics (combo of intra and inter) (usually females choose)

Cryptic Female Choice

females can use chemical or physical mechanisms to control mating success (females can have more than one partner) (affects plants and animals)

Genetic Drift

changes allelic frequencies due to random chance (affects gene pool)

Characteristics of Genetic Drift:

>unrelated to fitness

>favors loss or fixation

>loss = 0%

>fixation = 100%

>faster in smaller populations

>decreases genetic diversity