BIO104 Exam 2

Describe steps and applications of DNA EXTRACTION

1. Break open cell

2. Destroy everything that is not DNA

3. Seperate the DNA

4. Transfer DNA to a one type of cell and add ethanol

describe steps and applications of PCR

1. Copies DNA without a cell being there and marks very specific copy of DNA

2. Takes double strand of DNA, uses heat instead of helicase, then separates DNA

3. Need primer in the mixture so that DNA will synthesize in one direction and another mixture so DNA can synthesize in another direction

4. When having DNA polymerase, it can attach to the different DNA mixtures

Describe steps and applications of GEL ELECTROPHORESIS

Inject DNA in wells, apply current, pulling down DNA

1. Smaller fragments of DNA comes down quicker and large fragments take longer

describe steps and applications of Restriction Enzyme Digestion

bacterial enzymes that cut DNA at very specific locations, leaves super short piece of DNA

Describe steps of molecular cloning

1. Take piece of DNA

2. Looks like double helix but has open bases

3. Take plasmid, then incorporate plasmid to the ends of open bases to create circle structure

describe whole organism cloning using somatic nuclear transfer

1. Have a donor egg and take nucelus so it is a empty with shell with other cell stuff

2. Take donor nucleus from the animal you want to clone, give empty shell electric shock

3. Then donor nucleus ends up inside empty shell

4. Then implant the egg into the species

5. You know it worked when the animal gives birth the intended species wanted

Called SNT because you transfer nucleus to another species

explain how biotechnology can be used in GENETIC TESTING

Genetic testing: knowing what mutations cause waht type of genetic conditions (people who want to concieve naturally but want to know chances)

• DNA extraction?

  • 
    

Explain how biotechnology can be used in GENE THERAPY

knowing what issue is but use viral vector to deliver a “good” gene to cell to cure the disease (inserting HIV into SKID to cure SKID)

Explain how genetically engineered organisms can be used in the production of VACCINES

Explain how genetically engineered organisms can be used in the production of ANTIBIOTICS

Explain how genetically engineered organisms can be used in the production of HORMONES

Explain how genetic engineering can improve the health of agricultural crops

FLAVR SAVOR?

describe genetic engineering using VIRAL VECTOR

viral vector used as a delivery of soemthing - take virus and coat it with lipids

Putting virus in presence of cells that you want to engineer which the virus gets into cell and dock onto the nucleus and inject nucleus into cell??

Describe genetic engineering using AGROBACTERIUM TIMEFACIENS

similar to molecular cloning, but instead of putting plasmid into Ecoli, you put plasmid into agrivactor

• take plant, take slice of leaf, we invite AT to infect the plant - the bacterium takes TI plasmid …

  • Kills catapillar without killing the plant

Describe genetic engineering using CRISPR

1. Insert DNA into cell

2. Wait genes in DNA then insert into cell

   1. They can transcribe sequence on their own, when the resulting mRNA matches an invading virus, an enzyme finds that viral DNA and bits it to destroy virus

what is whole genome sequencing?

Taking every single piece of DNA that na organism has and finding out the order of ATGC

What are some applications of genome studies?

GWAS - identify mutations associated with disease

• track evolution by looking at how popular mutation is

Pharmacogenomics - effectiveness and safety of frugal

Agriculture - identity desirable trait

How can proteomics studies be used to complement genomic studies?

helps with research - test hypothesis about genes

Some proteins are biomarkers for cancer

Can help predict probability of disease recurrence

describe the structure of a DNA nucleotide

It is a double garlic structure - one strand goes one way and the other goes the other way

Explain the concept of complementary base pairing

A-T and G-C… explain?

What does it mean for the structure of the DNA double helix to be “anti parallel”?

one strand goes to the right direction and the other is shoots allowing it formed as a helix - this allows replication

what are the differnces between RNA and DNA

DNA - phosphate carbons bonded with lots of oxygens

RNA - deozyribose

More?

how is complementary base-pairing important to replication?

The letters have to align correctly in order for the replication to happen - we need the code to be correct so that it is not just random letters

what is meant when we say DNA replication is semi-conservative?

It means it uses one strand as a template for the other?

DNA uses DNA as a template

be able to look at the picture of replication on slide 10

1. Helicase unwinds DNA

2. Synthesizing goes on because of DNA polymerase

3. RNA primes because of limitation of DNA polymerase

   1. Leading and lagging strand at the same time because polymerase can only go in one direction

Who is Elizabeth Blackburn? What did she do and why is it important?

1. Discovered Telomerase (DNA sequence at the end of chromosome)

2. Gives insight on aging

3. How something grows quickly and not become short

what are two important proofreading and correction mechanisms for DNA replication?

mismatch pair: if G and T were together, it would fix itself so it is G and C

Nucleotide repair: if T’s were next to each other on a curve, the bridge would be cut and not perfectly aligned so it tries to match it again

Mutation is always a bad thing: #provemewrong

Mutations allow us to be taking this test right now. Mutations are not always bad because it allows for genetic variation. Not just health or diseases are created, mutations allow some of us to have blue eyes or change hair color

explain teh central dogma of biology

DNA codes for RNA codes for proteins

Describe transcription and explain the importance of complentary base pairing process

It is the process uses DNA as a template to create RNA, the base pairing need to be aligned perfectly so that DNA can properly code for RNA

described translation and explain the importance of complementary base pairing to this process

Process of cell making proteins using information given from mRNA…

The codes have to translate specific amino acid to stop

What is polysome/polyribosome?

as transcription is happening, the mRNA polymerase is transcribing RNA, a piece of DNA is leaving and RNA is getting longer. Ribosomes attach to it making a chain. The multiple pieces of ribosomes release DNA

• in prokaryotic, mRNA goes straight into translation but in Euk (because transcription is in the nucelus and translation is in the cytoplasm), RNA has to cut and splice befoer going to the ribosomes

Provide two resign why eukaryotic mRNA cannot be translated while it’s still being transcribed

It has to cut and splice because the processes happen in two different parts of the cell

Explain the concept of gene regulation

gene regulation is the rate at which genes are transcribed and translated to make final product which is protein. T and T could happen little or lot depending on what proteins are needed

Describe what would happen if all genes were expressed at the same time

more genes than necessary - pop an show

Energy would exhausted (not being able to make ATP to keep it alive)

describe basics of gene regulation in prokaryotes

the gene can turn on or off - lactase enzyme

If gene is turned on, lactase enzyme works, and vise versa

describe factors that affect gene regulation in eukaryotes

If there was more than needed, it would pop and die (multiple livers being created which is no necessary)

Explain the concept of epigenetics and how it can affect the phenotype

When outside factors alter the genes - when DNA itself has not changed but the molecules attached has changed (pregnant women smoking)

describe a monohybrid cross experiment

2 true breeding parents but has one differing characteristic to show contrast

explain why Mendel’s experiments are an excellent example of the scientific method in action

bc he was able to get different results from the pea plants and flowers which made him change his hypothesis

Describe monohybrid cross experiment outcome

when breeding two monohybrids, it is able to demonstrate different variations or characteristics of the gene

Explain how Mendel’s monohybrid cross experiment allowed him to discover the LAW OF SEGREGATION

It showed how one trait would disappear but reappear in another generation. Green and yellow peas bred together but only green peas came out

Explain how Mendel’s monohybrid cross experiment allowed him to discover the LAW OF DOMINANCE

After seeing the phenotypes that came from crossing a monohybrid, it shows what trait was more dominant than the other

explain teh relationship with genotype and phenotype

genotype is the actual gene like Gg and phenotype is the characteristic demonstrated form the gene so Green

explain how Mendel’s dihybrid cross experiments allows him to discover the law of independent assortment

alleles from different genes assort differently

2 true breeding parents solace varieties, but true breeding for separate things (yellow, round and yellow, green)

Explain Mendel’s findings in terms of modern genetics

we are able to alter our genetics depending on what we want

determine the expected outcomes of crosses where the relationship between alleles is incomplete dominance, codominance, sec-linkage

Incomplete dominance: one allele is less desmonstarted than the other

Codominance: both alleles are demonstrated

Sex-linkage: depends on sec of the parent and wether the allele is dominant or recessive

explain the theme of linkage (two genes being one eh same chromosome) and recombination (crossing over) on gamete genotypes

It is when two genes are on the same chromosomes and they stick together and pass down almost the same gene togeether

What is epistatic effect? How does epistasis affect phenotypic outcomes?

when you have a double recessive phenotype, it activates the color allele and creates a different pattern of inheritance

what is the evolutionary advantage of sexual reproduction over asexual reproduction?

variability is introduced in sexual reproduction, if everything was asexual then there would be no variability and mutliple copies of the same “gene”. If something were to happen that population would be wiped out

if an organism could do either type of reproduction, what conditions might cause it change from one to the other?

stability or adapting to the enviroment will cause it to change because it has to adapt. If tehre is no need to reproduce, it will just keep reintroducing itself

Explain the three following life cycle types:

Diploid dominant

Haploid dominant

Alternation of generations

diploid dominant: one set of chromosome from each parents (2 full sets of chromosome pairs)

haploid dominant: one set of chromosomes (no mom and dad - genetic clone) - male and female sex cell

Alternation of generation: both alternate diploid and haploid so it depending on what one organism is, it could skip a gen and be the other

describe and draw and label what happens during

Mieosis 1 and 2

Meisos 1: separate homologous pairs into two cells

Meisosis 2: splits sister chromatids into 4 cells

explain how meisosis craetes genetic variation among gametes

going through PMAT, it creates variation as the new cells are being split and created, having different genetics into each cell, DNA is being altered

Describe Nondisjunction. What is the result if it occurs

Nondisjunction: failure of separating homologous pairs into two Meiosis 1 or failure of separation of sister chromatids in Meiosis 2.

Result: too many or too few chromosomes

Define the term “genome”. What are the similarities and differences between prokaryotic and eukaryotic genomes?

Genome: all the genetic material a cell contains

Euk has nuclear DNA and mitochondria DNA

Pro - no nucleus, no pairs of chromosomes, singular circle plasmid

Both - both have plasmids sometimes

Write a few sentences that demonstrate your understanding of the following terms:

Chromosome

Gene

Trait

chromosome: is a threadlike structure that contains DNA information

Gene: the sequence of DNA that functions to create specific products

Trait: a genetic inheritance that is passed down from parents

Name and describe what happens duirng three stages of interphase:

G1

S

G2

G1: Growth! Cells are starting to get ready, getting energy and building blocks and proteins

S: synthesizing! DNA is replicating, chromosomes are getting copied

G2: more growth, cells are almost ready to get bigger

Dscribe what happens to chromosomes during mitosis - explain the importance of DNA duplication

Prophase: DNA is duplicate and comes craetes X shape

Metaphase: they line up vertically

Anaphase: cells are splitting from spindle fibers

Telophase: the chromosomes bunch up and the cell splits to two

IMPORTANT for dna duplication to create two exactly same cells

What happens during Cytokensis

Animal cell: cell membranous pinches into two cells

Plant cell: cell separates into two, has a new golgi and cell wal?

Desscribe G0

holding place for cells before they replicate

Need this phase so that they can still be alive until its ready to come out

there are three cell cycle checkpoints

When do they occur:

What do they check for?

What happens if cell does not check pass inspection at each checkpoint

when do they occur: G1, S, G2

What do they check for? to see if cell is ready to replicate

Doesn’t pass? They die. Causes cancer

cancer can be described as “unregulated cell division”. How would you explain this to someone with very little understanding of biology?

we need to divide the cell, but we don’t want crazy division int he wrong place. Bad cells that go through the cycle anyway is what causes cancer

How do proto-onco genes and tumor depressor genes relate to the cell cycle?

Proto-onco genes: promote cell cycle

• cell cycle “gas”

• Proto “before mutation”, “onco” after mutation

tumor supressor: cell cycle “brakes”

Proto-oncogenes alow bad cells to go through and the tumor supressor does not stop bad cells which cause cancer (doing opposite of what they are supposed to do)

Describe binary fission in prokaryotes. How is it different from cell division in eukaryotes?

binary fission is the splitting of prokaryotic cells - it does not need Mitosis

FtsZ is of e material spindle fibers are made of but for prokaryotic genes

Explain the concept of homology as it relates to evolution. Explain teh structural and functional evidence that animates its that Tonkin and FtsZ are homologous.

homology - organisms from same cell (apes vs humans)

Come from the same origin

• tubulin (euk) and FtzZ (pro) pull apart to same chromosomes and same structure

The enzyme DNA polymerase

Uses DNA as a template for DNA synthesis

1. Which type of RNA is paired with transfer RNA during translation?

messenger RNA

rRNA

A and B

tRNA 

Brings amino acids to the ribosome

During which process will mutation occur?

Replication

Gametes made by the same person

Exhibit extreme variability regarding allele combinations

Imagine a gene for flower color with only two alleles – red (CR), which is incompletely dominant over white (CW). What genotype do red-flowering plants have?

CR CR

Chromosomes condense prior to cell division

So that cell division can proceed in an organized fashion

Regarding plant seed texture, assume that round (R) is dominant over wrinkled (r). What are the outcome ratios when a homozygous dominant plant is crossed with a heterozygous plant?

100% round

Regarding flower color, assume that red (CR) is incompletely dominant over white (CW). Heterozygotes produce pink flowers. What are the outcome ratios when two pink-flowering plants are crossed?

1:2:1 red:pink:white (25% red; 50% pink; 25% white)

Regarding blood type, assume that A and B are codominant, while O is recessive. What are the outcome ratios when an individual with Type AB blood is crossed with a Type A heterozygote?

2:1:1 type A: type AB: type B (50% type A; 25% type AB; 25% type B)

Assume that hemophilia is an X-linked recessive trait. What are the outcome ratios when a female carrier has children with an unaffected male?

1 unaffected female (25%): 1 carrier female (25%): 1 unaffected male (25%):

1 affected male (25%

Assume that fur color (black / white) and horn texture (rough / smooth) are independent characteristics in Kraggles, and that each characteristic follows a typical dominant / recessive pattern. Black fur (B) is dominant over white fur (b), and rough horns (R) are dominant over smooth horns (r). If you start with (grand)parents (P / F0 generation) who are homozygous at both loci (for simplicity, say one is BBRR and the other is bbrr), what are the possible phenotypic outcomes and ratios for the F1 and F2 generations?

F1 generation: cross between two members of the P / F0 generation

BBRR x bbrr = 100% BbRr (heterozygous at both loci, black fur and rough horns)

F2 generation: cross between two members of the F1 generation (please use a Punnett square for this cross) BbRr x BbRr

Remember that according to segregation, each gamete must get one of each letter (B or b AND R or r). We are testing the hypothesis of independent assortment, so each member of the F1 generation can make four different gametes: BR, Br, bR, and br.

Consider the following DNA TEMPLATE sequence: ACG TTA and answer the following: (6)

a. What complementary strand of DNA will be formed during replication?

b. What complementary mRNA strand will be formed during transcription?

c. What amino acids does the mRNA code for?

d. During translation, what tRNA anticodons will “match up” with the mRNA codons?