Bio 110 - Final Exam (UWSP)

Virus

Need a host cell to be able to replicate and hijack cellular processes

Why are viruses not considered alive?

not made of cells, can’t stabilize, can’t make their own energy, don’t grow

What are viruses made of?

protein capsid with a nucleic acid genome

Capsid

the protein shell that surrounds a virus genome / nucleic acid

Host Range

The certain specific species that a virus can infect by recognizing surface proteins

Examples of a wide host range

West nile virus that infect humans, birds and other mammals

Examples of a narrow host range

Measles that only infects humans

Retrovirus

uses RNA as it’s genetic material instead of DNA (RNA to DNA - going backwards)

Example of a retrovirus

HIV / AIDS

What are the different virus types?

Helical, icosahedral, viral envelopes, and bacteriophages

Helical virus genome

cylinder shaped, single stranded RNA genome

• Tobacco mosaic virus

Icosahedral Virus genome

proteins hang off, double stranded DNA genome

• Adenovirus (cold symptoms)

Viral Envelope genome

Circular shape, RNA mixed with protein, membrane has proteins hanging off. single stranded RNA genome

• influenza

Bacteriophage Virus genome

Infect only bacteria by injecting it’s genome into host bacterial cell. genome usually made of DNA

Lytic Cycle

Bacteriophage injects DNA into chromosome, process is deadly and kills host cell, causing it to explode which infects new cells

Lysogenic Cycle

Bacteriophage inserted into bacterial genome for replication

Why do our cells not recognize a viral envelope easily? (flu type viruses)

it has a phospholipid bilayer that allows the virus to easily pass through, making it harder for immune cells to recognize

Prion

a misfolded protein that forms chains and causes plaques, causes neurodegenerative disease and eventually death

Can prions be killed?

no, denaturing does not affect them and you cannot remove them

Vaccine

a harmless derivative of a pathogen that can be used for viruses and bacterial infections

T or F: viruses respond to antibiotics

False

T or F: viruses can mutate as a response to environmental changes

True (malaria is a good example)

Biotechnology

The manipulation of organisms / parts of organisms and their components to make useful products

Common examples of biotechnology

Biofuels like ethanol and genetically modified crops

Genetic Engineering

Direct manipulation of the genome / genetic components to make useful products

Gene cloning

Many copies of a particular gene are created for sequencing or gene expression

How is gene cloning done?

by using plasmids from bacteria

Plasmid

a circular molecule made of extra-chromosomal DNA that we use to insert a gene of interest for cloning in bacteria by using restriction enzymes

Restriction Enzymes

cut plasmid DNA at certain spots on DNA strands to insert the gene onto the plasmid

Where is the cut made on DNA with a restriction enzyme?

at the palindrome

Palindrome

where the sequence is complementary and anti-parallel forwards and backwards (same forwards and backwards) and creates sticky-ends due to the uneven cut

When sticky ends are recombined onto DNA, they can create:

Recombinant plasmid DNA that has an inserted gene and can be used to treat/fight diseases

Polymerase Chain Reactions

a laboratory technique that is used to denature and renature segments of DNA using DNA polymerase I and Taq polymerase + bacteria from Yellowstone NP

How many cycles does PCR go through?

30-35 to make billions of copies of DNA

How does it make these copies of DNA? (PCR)

Denaturing, Annealing and Extension

Denaturing

Done at 95 degrees C, splits the DNA and straightens it

Annealing

Done at 45-55 degrees C, when primers bond to the now single stranded DNA

Extension

Done at 75 degrees C, DNA polymerase and Taq polymerase extend primers along complementary strand

Electrophoresis

Uses a porous matrix of agarose gel and electricity to separate DNA by size

Do short molecules move faster than larger molecules during electrophoresis?

Yes (True)

How is DNA cut during electrophoresis?

using various enzymes

What direction does DNA move during electrophoresis?

towards positive electric charge

DNA Ladder

DNA fragments of known lengths that are used to estimate sizes of DNA fragments of unknown lengths

DNA sequencing

determines complementary base pairing and can help determine if you found a new species. If you know the DNA sequence, you can find the protein sequence

Gene Cloning

Making multiple copies of a gene

Organismal Cloning

Creating an entirely new organism by somatic cell transfer or embryo splitting

Totipotent Cell

Can give rise to any cell in an organism, less differentiated

Pluripotent Cell

Can give rise to some cells in an organism, fully differentiated (it is one type of cell usually - ex: blood cell, sperm, bone marrow)

Induced Pluripotent Cells

Deprogrammed and then reprogrammed into whatever type of cell you desire. Dedifferentiated but still pluripotent.

CRISPR CAS9

CAS9 protein with RNA complex that is complementary to DNA, cuts DNA when bound. Direct removal of bad genes, can insert good genes

Genomics

The study of genes and their interactions

Bioformatics

Using computers to understand and analyze biological data

Do eukaryotes have more nucleotides and genes than prokaryotes?

On average, yes.

How many genomes does a human have?

Approximately 20,000

How many proteins can each gene make in a human?

Anywhere from 2-over 100 through alternative splicing of introns and exons

Structural Genes

Genes that directly code for mRNA and proteins

Prokaryotes and number of genes to proteins

1 gene = 1 protein

Eukaryotes and number of genes to proteins

1 gene = many proteins

Pseudogene

Genes that have become nonfunctional or mutated (15% of genome)

Repetitive Sequences of DNA

includes “junk DNA” that do not have a known function

Transposons

pieces of DNA that jump from a piece of chromosome to another

Retrotransposons

use RNA to put themselves in a different place on a chromosome

What are the differences in gene expression between humans and animals?

when genes are expressed during development and the increased transcription in humans (we have 5x more RNA)

FOXP2 is the gene that gives us vocalization, its expressed differently in humans than it is animals

Charles Darwin’s main points about Evolution

Living things are connected by common ancestry and descendants have radiated from a common ancestor and have accumulated adaptations over time

Adaptation

Inherited characteristics that enhances survival or reproduction

Adaptation Rules

traits are results of natural selection, makes things less vulnerable to predation and disease, and some adaptations have improved reproduction

Natural Selection

Individuals have inherited traits because the traits survived through generations which increases overall survivability of the trait or gene

Natural Selection Laws

Individuals do not evolve, traits must already exist, advantages depend on environment, and evolution is not goal oriented

Fitness

Organisms ability to reproduce

Artificial Selection

Selective breeding done by humans for traits that we deem desirable in other organisms

How do descent with modification and natural selection relate to changes in species over time?

Organisms that are more adapted to environmental changes or have had to adapt over time will be more likely to survive long term and pass on favorable genes or traits that enabled their success

Microevolution

How species make small changes over time

Macroevolution

New species arising from different species

Four Postulates of Natural Selection

Individuals vary within populations

Variations are passed from parents to offspring

Individuals differ in their capacity to survive and reproduce

Survival and Reproduction is correlated to individual variations

Morphology

Shape and structure

Homology

Similarity in anatomical structure, differences in function

Analogy

Similar function, but different structure

Gene Pool

All copies of every type of allele, at every locus, in all members of the population

Population

A group of individuals of the same species that live in the same area and interbreed

How is variation introduced into populations?

Crossing over during meiosis, Random assortment during meiosis, random fertilization, and mutations.

In organisms that reproduce sexually:

most genetic variation comes from the unique combination of alleles that are inherited

Genetic Drift

Unpredictable changes in allele frequencies from natural disasters, new predators, etc.

Bottleneck Effect

Leads to a loss of genetic diversity when a population is greatly reduced. Even if a population recovers, genetic diversity might not be the same as it was prior

Founder Effect

Genetic drift that is caused by organisms colonizing a remote area such as an island

Gene flow

transmission of genes across populations that can maintain genetic diversity

Sexual Dimorphism

A physical distinction in the appearance between males and females

Sexual Selection

individuals with certain characteristics are more likely than other individuals to obtain mates

Primary sex characteristics

Directly related to gamete production such as hormone production and ovulation

Secondary sex characteristics

mating rituals, songs, courtship behaviors

Speciation

When a population changes enough that it diverges from its parent population and results in an entirely new species

Extinction

Decreases diversity

New species

Increases diversity

Species

organisms that are capable of interbreeding and have ancestor-dependent relationships among individuals

Biological Species Concept

populations where members can interbreed and produce fertile offspring with each other but not with members of other species

What does the biological species concept emphasize?

reproductive isolation

What does the biological species concept not work with?

asexual reproduction

Reproductive Isolation

Biological barriers against formation of hybrids such as prezygotic isolating mechanisms and postzygotic isolating mechanisms

Pre-zygotic Isolating Mechanism

Happens before fertilization, usually due to habitat isolation, temporal isolation (timing), behavioral isolation, mechanical isolation (reproductive parts incompatible), and gamete isolation.

Example of a species with pre-zygotic isolating mechanisms

Sea Urchins

Post-Zygotic Isolating Mechanisms

Happens after fertilization and lowers fitness after the embryo has formed. Leads to reduced hybrid life span and reduced fertility (hybrid is sterile)