Bio 171 Exam 1

What are some characteristics that separate living organisms from non-living entities?

What are some characteristics that separate living organisms from non-living entities?

• Made cells

• Respond to the environment

• Have genetic material (DNA)

• Carbon + water-based

• Populations evolve

• Need energy + matter from their surroundings

• Can reproduce

Are viruses alive? Why or why not?

No, viruses do not have cells, don’t acquire energy, and cannot respond to the environment. However, it can be argued that they are because viruses can reproduce and adapt to their environment.

What are the three domains in life? Which domains are prokaryotes? What is an important difference between a eukaryote and a prokaryote?

• Three domains of life: Archaea, Bacteria, and Eukarya

• Archaea and Bacteria are prokaryotes

• Eukaryotes cells have membrane-bound organelles like a nucleus

• Prokaryotes are unicellular with no nucleus

What does the tree showing the three domains of life tell us about how Eukarya, Archea, and Bacteria are related to each other? Which other domain are Archea more closely related to? Which domain do animals belong to?

• Archaea and Bacteria are related, but Archea are more closely related to Eukarya than it is to bacteria because it splits higher up the tree meaning it is more recent

• Animals and plants belong in the Eukarya domain

Where do archaea and bacteria live? What roles do they play ecologically?

• Archea and bacteria live in virtually every habitat, including extreme environments (they are extremophiles) and extreme thermophiles (thrive in very hot environments)

• They are both important for

  • oxygen in atmosphere

  • Nitrogen fixation

  • Decomposition

  • Cycling of nutrients (critical for soil fertility)

  • Important for mutualisms

What is the genetic material of all living organisms? What are the four key characteristics of it?

• All living organisms have DNA

• Characteristics:

  • Diversity of structure

  • Ability to replicate

  • Mutuability

  • Gene Expression - “the central dogma”

What allows for a diversity of structure in DNA?

• There are different combinations of nucleotides that create different DNA molecules.

  • Nucleotide pairing in DNA forms a structure known as a double helix

  • A-T

  • G-C

Why is it important to be able to replicate DNA? What needs to happen in order for DNA to replicate? What is the end product of DNA replication?

• Replicating DNA helps with the process of making proteins.

• DNA is replicated by separating the two strands and using each one as a template to make a new strand by creating new A: T and G: C pairs

• The end product is turning one double helix into two double helix’s that has one old and one new DNA strand

What does it mean to say there was a mutation? What do mutations lead too? Are they all bad?

Mutuability: Errors during DNA replication introduce mutations and create genetic variation

• they are not all bad

• they can be repaired by cellular machinery

• Frequency is increased by chemical mutagen, UV exposure, and smoking

What does it mean to say mutations are spontaneous and random?

We do not control them

What are proteins and what do they do?

Proteins are polymers of amino acids

• make enzymes

• DNA replication

• structure

• signaling

• Movement

What is a gene?

A section of DNA that contains information for building a protein (or RNA molecule)

What is meant by the phrase “The central dogma”

Gene expression

What is transcription? What regulates it? What is a key enzyme that is a part of this process? What is different about base pairing in transcription as opposed to DNA replication?

• Genes are transcribed into mRNA strands by pairing A:U and G:C (DNA to RNA)

• key Enzyme: RNA Polymerase

• Regulated by a non-coding DNA

What is translation? How does the ribosome do translation and what is a ribosome made of? What is an anticodon? What is the end product of translation?

• Translation: RNA to proteins, complementary base pairing and the genetic code are used to translate mRNA into protein

• Ribosomes are made of proteins and rRNA

• mRNA contains 3 base sequences known as codons that pair with anticodons on tRNA molecules

  • tRNA carries an amino acid

  • once the amino acids fold the proteins are made

What is the genetic code? How do you use the table that contains the genetic code?

The relationship between codons in an mRNA sequence and the amino acid added by the matching tRNA

Three kinds of RNA play roles in the central dogma: what are their names and roles?

mRNA(messeneger)- carrier instructions for making proteins from DNA to the ribosome

rRNA(ribosomal)- Makes up the ribosomes (with protein) which are protein factories

tRNA (transfer)- Transfer amino acids to growing polypeptide chain at ribosome during translation, and complementary base pairing between codon on mRNA and anti-codon on tRNA

What process produced the diversity of life that we see all around us?

Natural selection

Why are rRNA genes used to build the tree of life?

Because all living things have ribosomes and rRNA has ribosomes

How do you know if a person is doing science? What types of activities can be classified as science? What are some activities that cannot be classified as science?

A person is doing science when they seek to explain the natural world by testing and explaining using evidence is science.

Why is peer review a valuable part of the scientific process

It determines wether or not the experiments get published

How do scientists ensure that their work can be replicated? We use the term replication in two different ways in this course. What is the second definition

Replication:

• if we replicate a whole study and get some results, it is really confident (reproducibility)

• Replicates within a study are multiple subjects or samples treated the same way

Describe the different ways biologists investigate how nature works

They ask questions

propose hypothesises ( potential explanations)

Test and evaluate hypotheses, using evdience from:

• Observational studiies

• experiments

• computer simulations/mathematical models

Compare and contrast observational studies with experimental studies

Observational study:

• can have or lead to hypothesis

• always have dependent variablels

• sometimes have independent variables

• can tell us is 2 variables are correlated

• include predictions

Experiment

• Can have or lead to hypothesis

• often has pos/neg controls

• independent and dependent variable

• manipulate independent vairbales

• can tell us if there is a cause and effect relationship

• need replicates

• include predictions for each test +control group

Hypothesis

A testable, possible explanation for some natural phenomenon (for tightly focused question)

Prediction

A description of an expected outcome in the test (experimental) group an in each control group

Theory

An explanation for broad pattern(s) in nature that has been tested many times and is well-substained

Negative control group

A control group that has no expected outcome (the variable is not changed)

Positive control group

A control group that has a specific outcome (the variable is manipulated)

+_2SE error bars

• If the bars overlap we can conclude no difference between 2 means or 2 groups

• of the bars don’t overlaps we can conclude no statistacally significant difference

r

per capita population growth rate

rmax

maximum possible growth rate per capita, often called “intrusic rate of increase”

Density-dependent factor

Affects a population differently depending on its size

EX: When predator pops are high, they eat more prey

Fewer predators eat less pray

Density-independent factor:

Affects a population the same regardless of its size

EX: a tornado destroys 80% nests in the forest

Describe the basic structure of a virus and explain how virals replication occurs?

Nondeveloped virus- has genome and capsid (protein)

Enveloped virus- (phospholipid bilayer comes from host cell) It has a genome, capsid (protein), and envelope

they have gnetetic mateiral (DNA or RNA) that can be single-stranded or double-stranded

Replication: Requires a host cell to highjack and get into its genetic material

Explain the factors that allow an infectious disease to (re)emerge and the factors that affect
the spread of an EID

• High rates of travel

• Increases in human population size and risky behaviors

• Increased urbanization

• encroachment on wilderness areas (contact with animal resoviours)

• Evolution of pathogens (drug ressistence)

• Enciormental change

• Reduced vaccination rates

• health inequities

Explain why R0 is important and how it can be used to inform vaccination programs

The expected number of secondary cases one case produces on average in a completely susceptible population.

Describe how mRNA vaccines produce protein antigens

The vaccines code for the antigen, the host cell translates the vaccine mRNA.

Compare and contrast zoonotic diseases with vector-borne diseases

Zoonotic-

• spread between humans and non-humans

• non-human animals is NOT the vector

Vector Borne

• mode of transmission is via an insect or other arthropod EX: Malaria

Describe the structure of HIV’s genome, explain how HIV enters its host cell, how it
converts its RNA into DNA and inserts its DNA into the host cell’s genome, the types of
cells it infects and how it attacks the immune system

HIV is a retrovirus

• has a genome made up of single stranded RNA

• Has an enzyme called reverse transcripentise that alow it to convert its RNA into DNA

• it attacks the immune system directly; infects helper T cells & macrophages (cells with CD4 receptors and coreceptors

• currently no cure)

Explain the evolutionary origins of HIV; be able to state the organisms in which HIV
originated

Chimpanzees and sooty mangabees

Explain how evolutionary processes can help us explain why HIV is so hard to treat/cure as
well as inform treatment strategies; describe the purpose of PrEP

• HIV has high genetic variablility (high mutation rate)

• it integrates its genome into hosts DNA

• HIV attacks the immune system directly and destorys helper t-cells

• PREP helps prevent HIV if you have been exposed to it

Describe the processes by which viral DNA can become part of the human genome

For measles, understand what has allowed it to reemerge in recent years, its effects on other
infectious diseases, and the benefits of vaccination.

Reduced vaccination, it has came back into society

if not vaccinated it makes them vulnerable to other diseases

Vaccination/immunization

One groups of white blood cells called b cells make antibodies, which are proteins that are specific to a particular species of a pathogen and which tag the pathogen for destruction by other immune cells. Antigens are parts of disease agents, often protiens that cause an immune response,

COVID:

• MRNA vaccines consist oof a piece of mRNA that codes for an antigen, a COVID spike protein.

• The COVID spike protein is made by the host cell translating the vaccine mRNA, and is involved in attachment and fusion of the COVID virus particle into a host cell