BIOLOGY 1001A

Final Exam 2022

Why aren't viruses considered to be alive?

-they cannot produce on their own

-they lack the metabolic system for energy for life cycles

-they depend on host cells that they infect for life functions

Why are viral infections difficult to treat with drugs?

-because they are "hidden" in the host cell and use their machinery to replicate

-they are unaffected by antibiotics

-viruses with tiny genomes like HIV are vey challenging to treat because the virus uses host enzymes almost exclusively

-for these reasons the focus for deadly viruses is prevention by vaccine

What are the hypothesis for the evolutionary origin of viruses?

1) they evolved after cells, they exceed from fragments of DNA/RNA and became surrounded by a protective layer of protein with recognition functions, as they evolved genes became reduced to only code for more viral particles

2) the viruses predate cells and originate from the "primordial gene pool" which is a pool of RNA thought to be the first genetic material

Why is the effectiveness of antiviral drugs like to decrease overtime?

-random mutations in RNA genome add variations to make previous antibodies ineffective

-they can become immune due to natural selection, once one virus is mutated to become resistant it is now more likely to reproduce

What are the principles underlying evolution by natural selection?

1) heritable variation is the difference in genetic code that can be passed on to offspring

2) non-random reproduction/survival causing helpful traits to survive and reproduce which causes change in the genotype population over time

Why should we use "drug cocktails"?

-we should use a combination of drugs to treat viral infections because resistance is inevitable but it is unlikely that the verse will become resistant to multiple drugs at the same time

What is the evolutionary origin of HIV and why is eradicating viral diseases so difficult?

-spillover occurred between closely related species (SIV from a non-human primate to HIV in humans) and the virus is usually more harmful in the new host making vaccine formation difficult

-HIV is an RNA virus which uses reverse transcriptase which doesn't have a "proofreading" enzyme so mutation rate is very high making vaccine formation difficult

How does viral mutation rate affect the likelihood of developing a longterm effective vaccine, or a longterm effective antiviral drug?

-a faster mutation rate causes variations that make vaccines and previous antibodies ineffective (like the flu)

-mutating faster can allow resonate to build up much quicker

What are the characteristics of a scientific theory and what is the importance of falsifiability?

Scientific Theory- is an explanation of an aspect of the natural world that can be repeatedly tested and verified in accordance with the scientific method

Falsifiability- is the capacity for a proposition, statement, throes or hypothesis to be proven wrong, a theory is not scientific unless it is falsifiable

What are some examples of "scala natura" thinking, and why is this type of classification not compatible with modern evolutionary thinking?

-Aristotle created the ladder like classification of life called the "scala natura" where humans were on the top with all other organisms said to be created by god, could never change nor become extinct and no new species could arise

-modern evolutionary thinking knows that species change constantly and new species argue while others become extinct

What evidence from geology an the fossil record, the geographic distribution of species and comparative morphology support the idea of descent with modification from a common ancestor?

Geology and Fossil Records- Darwin's fossil study confirmed Lyell's theory that the geology of earth changes over time, the fossil record indicated that some species were extinct and showed that both living and extinct organisms showed similar morphology

Geographic Distribution of Species- biography is the study of the worldwide distribution of plants and animals, very similar looking organisms live in similar habitats but far apart and Darwin observed no terrestrial mammals on oceanic islands but flying mammals

Comparative Morphology- vestigial structures are useless parts on an organism that functioned in ancestral organisms

What are some examples of homologous traits?

-homologous structures are traits that are similar due to common ancestry

-like the bones in the human arm, bat wing, dolphin flipper and pig foreleg

How has our understanding of evolution changed since Darwin's time?

-Darwin and Wallace laid down the fundamentals of natural selection but neither had an understanding of genetics

-when the "origin of species" came out Gregor Mendel just practiced his pea plants

-Darwinian evolution and Mendelian genetics are known as the modern synthesis of evolution

Why are mutations important in evolution?

-mutation provides differences in traits among organisms which is the material natural selection works with

-they are a source of variation but do not determine the path of evolution

What are some misconceptions about evolution and natural selection and why are they incorrect?

1) Natural selection and evolution are the same thing- natural selection is one of the several mechanisms that cause evolution

2) Evolution occurs slowly- the rate of evolution is controlled by many factors, on of which is generation time

3) Favourable traits arise in réponse to environmental changes- mutations are random only the proportion of fit individuals change when environment changes

What are the phases and main characteristics of the cell cycle?

-interphase is the first and longest stage of mitosis

-the G1 phase is the growth before DNA replication

-the S phase is where the cell duplicated each chromosome and synthesizes cellular molecules

-the G2 phase is the second growth phase

-cells that are not destines to divide move from G1 to G0 which is the shunt phase

What are the stages and main characteristics of mitosis?

-prophase is where extended chromosome are condensed and at the end the nuclear membrane breaks down to start pro metaphase

-metaphase the chromosomes finish condensation and align on the metaphase plate

-anaphase the sister chromatids separate and more to the opposite spindle poles

-telophase the spindle disassembles and chromosomes decidedness, the nucleolus reappears and other cell functions resume

-cytokinesis is the division of the cytoplasm

How does the amount of DNA change throughout the cell cycle?

-the amount of DNA doubles during s phase (the coefficient of C doubles)

-but the amount of chromosomes (n) remains the same

Why do purines pair with pyrimidines?

-they pair with each other due to their structures and chargaff's rule

-the two purines are guanine and adenine they have 2 fused rings of C and N, guanine has 3 places for hydrogen bonds with adenine has only 2

What conclusions did Meselson and Stahl reach?

-they demonstrated that DNA replicated in a semi-conservative manner

-E coli was grown so that the isotope of N-15 was incorporated in bases and after every replication the density decreased

What is the direction of movement of DNA polymerase on the template strand?

-DNA polymerase moves along the template strand from 3' to 5' so that DNA can be synthesized from 5' to 3'

-it moves away from the origin

What is the meaning of bidirectional, semi-conservative, semi-discontinuous and the leading and lagging strand?

Bidirectional- 2 replication forks form at the origin, each moves away from the origin and mirror each other

Semi-conservaive- he process of DNA replication in white the two parental strands separate and easy serves as a template for the synthesis of the new strand

Semi-disontinuous- since DNA strands run antiparallel one strand can be synthesized continuous in the direction of unwinding, however the other must be synthesized in the opposite direction in short segments

Leading strand- DNA strand is synthesized continuosly

How does 3' and 5' polarity of nacelle acids chains affect replication?

-each DNA strand has two distinct ends

-the 3' has an exposed hydroxyl group attached to the 3' carbon of the sugar

-the 5' end has an exposed phosphate group attached to the 5' carbon of the sugar

What is the location of DNA in eukaryotic and prokaryotic cells?

Eukaryotic- DNA is found in the nucleus, mitochondria and chloroplasts

Prokaryotic- DNA is found as a long circular nuclei, nonessential genes are in extrachromosomal plasmids

What is the shape and basic replication strategy of prokaryotic chromosomes?

-they divide by binary fission

-the chromosomes duplicate at the origin and migrate to opposite poles of the cell, plasma membrane grows inward to separate the two daughter cells

What is the shape of nuclear vs organelles chromosomes in eukaryotic cells?

-nuclear chromosomes are linear, double stranded DNA

-mitochondrial chromosomes contain a relatively small amount of circular DNA molecules

-chloroplast chromosomes can be either linear or circular

What is the location of actively cycling cells in multicellular animals/plants?

-liver cells, adult stem cells, skin cells, the stomach lining, blood cells and the cells of the immune system

What is the function of rapid cycling cells at various stages of the life cycle?

-the purpose of cel division is growth, regeneration and replacement of lost cells

What are some examples of situations where cells would be programmed to die by apoptosis?

-apoptosis is programmed cell death

-non functioning cells undergo apoptosis which helps get rid of aged cells

What are the main features of each stage of mitosis with respect to cytoskeleton and chromatin?

chromatin- duplicates in interphase and condenses in prophase, goes through mitosis and the chromosomes relax back into chromatin in telophase

centrosome- is the site near the nucleus that organizes microtubules

What are the main features of chromosome anatomy?

-the double helix winds around histones to form nucleosomes

-they package into 30nm chromatin fibres

What is the meaning of C and N?

-C is the amount of DNA in one set of nuclear chromosomes (picograms or bps, count the sister chromatids)

-N is one copy of all organisms' nuclear chromosomes (count the centromeres)

How does the coefficients of C and N change throughout the cell cycle?

G1- 2n, 2c

S- 2n, 4c

G2- 2n, 4c

M- 2n, 2c

What is the role of cycle checkpoints?

G1/S- check that DNA is undamaged and reads the extracellular signals

G2/M- commits cell to mitosis, checks the complete replication of DNA or DNA damage

Mitotic Spindle Checkpoint- assess whether chromosomes are attached properly to the spindles for proper alignment and the correct number of chromosomes per cell

What is the composition of microtubules, intermediate filaments and microfilaments?

Microtubules- are made of a-tublin and b-tublin dimers and are 25 nm wide

Intermediate Filaments- are made of keratin and are 8-12 nm wide

Microfilaments- are made of action and are 5-7 nm wide

What is the interaction between kinetochores and spindle fibres?

-kinetochores are formed on chromatids at the centromere and this is where microtubules bind

-kinetochore microtubules connect chromosomes to spindle poles

-non kinetochore microtubules extend between poles and overlap those from opposite poles

What is the role of motor proteins in chromosome segregation?

-the chromosomes "climb" along stationary microtubules using motor proteins

-tublin subunits of microtubules disassemble as the kinetochore passes making the microtubules shorter

Why do chromosomes shorten after each replication?

-the need for RNA primer results in eukaryotic chromosomes shortening after each replication

-at the 5' end when a primer is removed from the very end DNA polymerase cannot add more nucleotides

What is the function of helices?

-unwinds and unzips the DNA double helix

What does the single stranded binding protein do?

-it stabilizes the single stranded DNA and prevents it form reforming 2 strands

What does topoisomerase do?

-avoids the twisting of DNA ahead of the replication fork in circular DNA by cutting it

What is the function of primase?

-synthesizes RAN primer in the 5' to 3' direction to initiate the new strand of DNA

What is the function of DNA polymerase 111

-it is the main replication enzyme, it extends the RNA primer by adding DNA nucleotides to it

What is the function of DNA polymerase 1

-it is an enzyme that uses the 5' to 3' exonuclease activity to remove RNA of synthesized Okazaki fragments