Chapter 1-3

Question 1

What are chromosomes made of?

Answer 1

DNA and proteins

Question 2

What did Frederick Griffith do?

Answer 2

Discovered process of transformation using S and R strains of pneumonia on mice.

Question 3

Describe Frederick Griffith’s experiment, what is the difference between s and r strains?

Answer 3

S strain has a protective and SMOOTH polysaccharide capsule that can cause illness in rats.
R Strain has ROUGH capsule and does not cause illness.
Both strains are true-breeding.

Frederick injected a mouse with live R cells and DEAD S cells, but the mouse still died. Realized that in order for R bacteria can undergo transformation into S bacteria, there was some sort of substance that enabled R Cells to begin to synthesize smooth capsule coats.

Question 4

Using knowledge of the concentration of base pairs, how could you determine whether the DNA of an organism is single stranded or double stranded?

Answer 4

An organism would have the same concentrations of complimentary base pairs (A)=(T) etc. A single stranded organism would have differing concentrations of bases because the bases on a single strand are not complimentary to each other.

Question 5

What did Oswald Avery et. al. do?

Answer 5

discovered that transformation was caused by DNA

Question 6

Describe Oswald Avery’s experiments

Answer 6

If mouse was injected with mixture of destroyed SRNA and protein in live R cells, transformation from R to S still occurred and mouse died.

If mouse was injected with mixture of destroyed SDNA in live R cells, transformation from R to S did not occur and mouse still lived.

Concluded that dna of s needed to be present in order for R to transform into S

Question 7

Who conducted the blender experiment?

Answer 7

Hershey and Chase

Question 8

What did Hershey and Chase conclude

Answer 8

demonstrated that DNA and not protein directed the production of progeny T2 Phages

Question 9

Describe Hershey and Chase experiments

Answer 9

tagged either phage DNA with 32P or phage protein with 35S in separate trials, and injected them into e.coli cells.
Ecoli was swirled into a blender to remove phage material from the cell surfaces

When analyzed, they noticed that 32P was integrated into the ecoli, whereas 35S was mainly outside of the cells.
Therefore, the T2 phage transfers most of its DNA into the bacteria in order to replicate, but very little protein.

Question 10

What is the general structure of DNA that Watson and Crick Proposed?

Answer 10

• proposed the first correct 3D structure of DNA

- 2 Long chains of nucleotide subunits, running antiparallel in a polarized fashion

Question 11

What did Watson and Crick infer about the probable mechanisms of replication, coding, and mutation from their proposed structure?

Answer 11

Replication: one strand can act as a template in order to form a complimentary strand. One DNA duplex can produce two identical duplexes.

Coding: genetic information could be coded by the sequence of bases along the DNA molecule

Mutation: changes in genetic information could results from errors in replication

Question 12

Why did Hershey and Chase choose to study a bacteria phage?

Answer 12

DNA was stored in the head while the rest of the phage was mostly protein. This compartmentalization allowed for easy tagging because the head contents were transfeered into the bacteria, while majority of the protein would be left outside the cell.

Question 13

What can you conclude about the equal percentages of A,T,G, and C in an organism

Answer 13

The amount of A=T, and the amount of G=C. Therefore, adenine and thiamine must pair together, and guanine and cytosine must pair together. In order for the bases to pair with each other, the DNA is most likely double stranded.

Question 14

In vitro, how many reading strands can a DUPLEX of DNA make?

In vivo?

Answer 14

In vitro: 6 reading strands per duplex; 3 reading per single strand. This is because in vitro, hybridization can occur at any point without the need for a start codon.

In Vivo: 2 reading strand; one reading strand per single strand. In vivo/cell, DNA polymerase needs a start methionine codon in order to begin synthesis of the other chain.

Question 15

Characteristics of Purines

Answer 15

2 rings, adenine and guanine

Question 16

Characteristics of Pyramidine

Answer 16

1 ring, thiamine, uracil and cytosine

Question 17

What direction does DNA synthesis occur in? How is the template strand read?

Answer 17

Synthesis in 5’-3’. Therefor, the template strand is read in 3’-5’ direction. One strand is therefor made continuously (the one using 3’-5’ template), and the other strand is synthesized in fragments (5’-3’ template)

Question 18

What did Archibald Garrod propose

Answer 18

Inborn Errors of Metabolism, studied alkaptonuria

Question 19

What is the proposal of Inborn Errors of Metabolism?

Answer 19

Any hereditary disease resulting in abnormal cellular metabolism is a result of an INHERITED deficient/defective enzyme

Question 20

Characteristics of Alkaptonuria

Answer 20

black urine disease caused by excretion of accumulated homogentistic acid. HA cannot be broken down because of defective 1,2, dioxygenase enzyme.

Question 21

Characteristics of Phenyl Ketonuria

Answer 21

Disease that results in mental retardation because of the accumulation of phenylalanine. Phenylalanine cannot be broken down into tyrosine, due to defective phenylalanine hydroxylase (PAH) enzyme. Phenylalanine then crosses the blood brain barrier and then affects an individuals myelin in neurons.

Question 22

What did Beadle and Tatum do?

Answer 22

found the connection between genes and enzymes by studying N.Crassa fungus. Each set of mutation, and therefore each individual gene, corresponds to one enzymatic step in a metabolic pathway

Concluded: each block corresponded to a defective enzyme and prevents the metabolic pathway from running to completion. A defective enzyme is a result from a defective gene.

Question 23

What is a mutant screen?

Answer 23

the isolation of a set of mutants affecting any biological process.

Question 24

Complementation Test

Answer 24

Process where 2 mutations are mated in order to identify mutations that have defects in the same gene.
HELPS TO DETERMINE MUTANT FORMS SHOWING THE SAME PHENOTYPE

Question 25

Complementation vs non complementation

Answer 25

Complementation (+)= normal offspring from two mutants are produced, and mutations were thus on different genes. Usually produces a 9:7 phenotypic ratio is F2 non Complementation (-)= mutant offspring from two mutants are produced, and thus the mutations from both parents were on the SAME gene.

Question 26

Define central dogma

Answer 26

the idea that information flows from DNA to the phenotypic effect via DNA--> RNA-->Protein. The sequence of nucleotides in a DNA Gene specifies the sequence of nucleotides in RNA, which specifies the sequence of amino acids in a polypeptide chain The genetic code for a protein is contained in ONE STRAND, and it is decoded in a linear order 5'-3'

Question 27

RNA vs DNA

Answer 27

- RNA is single stranded, DNA is double - In RNA, thiamine is replaced with uracil - RNA incorporates ribose sugar instead of deoxyribose - 3 different types of RNA; mRNA, tRNA and rRNA

Question 28

Which enzyme makes transfer Rna

Answer 28

aminoacyl-tRNA synthetase

Question 29

Start codon?

Answer 29

Methionine, AUG

Question 30

Define Wobble Hypothesis

Answer 30

anti-codon of a specific tRNA may recognize 2 or more codons. Base pairing must be between a purine and a pyrimidine

Question 31

Exons vs Introns

Answer 31

Exons are protein-coding regions, introns are non-coding/pseudogene regions

Question 32

Reasons why a mutation could be silent

Answer 32

1) mutation occurred in a non-coding intron region 2) a base pair substitution still coded for the same amino acid 3) the amino acid changed to a similar one. Ex/ leucine and valine)

Question 33

Define Pleiotrophy

Answer 33

when one defective gene affects multiple phenotypes. Example: mutation in PAH gene results in PKU but also affects melanin production because tyrosine cannot be made from the phenylalanine, which is building up. Thus, most individuals with PKU also have blonde hair, blue eyes.

Question 34

How many chromosomes does a human have

Answer 34

46

Question 35

How many chromosomes are in a human reproductive cell?

Answer 35

23

Question 36

Are exons more populous that introns in the human body?

Answer 36

No. Exons only make up 1.3% of the entire genome, of that, only 0.1% differs from one human to the next

Question 37

Define Genetic Markers

Answer 37

Any difference in genotype whose patterns can be traced through generations. NEEDS PHENOTYPIC DIFFERENCE

Question 38

Define DNA markers

Answer 38

Any difference in DNA sequence. DOES NOT require phenotypic difference to be seen, but DOES NEEDS DNA sequencing

Question 39

Define Genomic Data

Answer 39

the total DNA extracted from cells of an organism

Question 40

Characteristics of Purines | Characteristics of Pyrimadines

Answer 40

Purine: 2 Rings, A and G Pyrimidine: 1 Ring, T,U,C

Question 41

Comment on general carbon numbering in a nucleotide

Answer 41

1' is the carbon where the base attaches to the sugar 2' carbon of the sugar, it will have 2 hydrogens in DNA, and 1 H+1OH in RNA 5' is where the phosphate attaches to the sugar

Question 42

Define nucleoside

Answer 42

sugar+base

Question 43

Define nucleotide

Answer 43

sugar+base+phosphate group

Question 44

What bonds hold up a polynucleotide chain?

Answer 44

phosphodiester bonds by the 5'phosphate and 3'OH group

Question 45

Elaborate on Chargaffs rules

Answer 45

1) amount of A=amount of T 2) amount of C=amount of G 3) (A+G)=(T+C) 4) base composition is different among species but is constant in all cells of an organism within a species

Question 46

Define Base composition and it's main feature

Answer 46

Base comp= % of (G+C), the higher the base comp, the more energy required to break the DNA molecule because C and G pairs have 3 HBS where as AT pairs have 2 HBS

Question 47

In terms of Hydrogen bonding, what are the differences between AT pairs and GC pairs

Answer 47

C and G pairs have 3 HBS where as AT pairs have 2 HBS

Question 48

Define B form DNA

Answer 48

Typical DNA Structure: DNA Duplex consisting of 2 polynucleotide chains, with around 10.4 bases per helical turn. Strands run antiparallel to one another and they turn clockwise. B form DNA participate in Base STACKING

Question 49

Define Base Stacking. What kind of DNA molecule does this create?

Answer 49

nitrogen bases stack on top of each other in order to minimize their overall contact with aqueous environment. Due to the fact that upper and lower faces of the nitrogenous bases are flat and nonpolar. Creates and AMPHIPATHIC DNA molcule

Question 50

Define Base Pairing. What bonds hold the bases together?

Answer 50

Each base in a polynucleotide chain is paired to a complimentary baes in the other strand via hydrogen bonds.

Question 51

Define nucleic Acid Hybridization and its requirements

Answer 51

Recognizing the presence of a specific DNA fragments in a sample of genomic data - identifies original data itself, needs a larger amount of genomic DNA, - you do not need to know the particular sequence - requires restriction enzymes to cut the genomic DNA into smaller fragments

Question 52

Define PCR and its requirements

Answer 52

Replicates a specific fragments of interest - requires only a small amount of original data, identifies sequences in MANUFACTURED DATA - you need to know the sequence you are looking for in order to replicate the right fragments

Question 53

How are restriction enzymes made and how do they work?

Answer 53

Made from prokaryotic organisms, binds to DNA strand at a specific sequence (Restriction site) and cleaves the phsophodiester bond, usually leaving a base overhanging on each side, called stickey ends. Produces free 5'-P and 3'-OH.

Question 54

characteristic of restriction site

Answer 54

palindrome

Question 55

Main characteristic of restriction enzyme

Answer 55

1) most RES recognize a single site 2) a restriction site is recognized without regard of the source of DNA 3) the # of DNA cuts is determined by the number of restriction sites present.

Question 56

What chemical allows for UV visualization of a gel electrophoresis plate

Answer 56

Ethidium Bromide

Question 57

Factors that affect separation/visualization in Gel electrophoresis

Answer 57

1) concentration of agar: higher conc allows better spread of large molecules, lower conc allows better spread for small chains. 2) smaller fragments move up the plate faster than longer fragments 3) to see a band, you must have at lease 5.0x10^9 molecules. If you dont have enough, you need to amplify the DNA.

Question 58

Process involving nucleic acid hybridization

Answer 58

southern blot

Question 59

Define denaturation in terms of nucleic acid hybridization

Answer 59

the process of making a dna duplex single stranded via heat or treatment with alkali to disrupt H bonds

Question 60

How does alkali treatment aid in denaturation?

Answer 60

disrupts Hbonds

Question 61

Define renaturation/hybridization, what're the conditions in which it occurs at

Answer 61

the coming together of complimentary strands at midrange temp and high salt content

Question 62

What does southern blot do?

Answer 62

a process involving nucleic acid hybridization and tag probes that allow tagged and denatured DNA to be added to a mixture of other dna fragments. Under proper condtions, the probe tags any molecules in the mixture that it can hybridize with, allowing one to see (IDENTIFY) whether or not the mixture contains any desirable fragments.

Question 63

Steps of southern blot

Answer 63

1) DNA is denatured with alkali 2) denatured DNA is immobilized and transffered onto nitro paper film. 3) probe dna (SINGLE STRAND) (the strand you want to see in the mixture) added to paper film 4) Hybridization allowed to occur under moderate heat and high salt content. 6) film is washed to get rid of any unbound dna 7) XRAY exposes film and reveals the location of desired fragments.

Question 64

Requirements for DNA Amplification

Answer 64

1) single stranded GENOMIC DNA 2) DNA polymerase 3) oligonucleotide primers 4) all 4 nucleotides

Question 65

Why is DNA synthesized in a 5'-3' direction?

Answer 65

the rxn catalyzed by DNA polymerase results in the FORMATION OF A PHOSPHODIESTER bond between free 3'-OH group of the chain being extended, and the innermost 5' P atom of the nucleoside triphosphate being incorporated at the 3'end.

Question 66

What is PCR? What does it use? Characteristics?

Answer 66

amplifies dna, need to know sequence before hand, very sensitive. Uses Taq Polymerase (DNA polymerase) because it is head resistant, and primers.

Question 67

Define DNA Polymorphisms.

Answer 67

DNA Markers. Genetic difference between individuals. Different alleles/ Different DNA sequences for any location along a chromosome, does not necessarily need to show a phenotypic difference because it is not a genetic marker.

Question 68

Define SNP

Answer 68

Single nucleotide polymorphism. a single nucleotide sequence difference at a single position. Most do not result in phenotypic change, BUT PKU is caused by SNP

Question 69

Do SNPS require DNA sequencing to be found? Why or why not

Answer 69

DNA sequencing vie SNPCHIPS/Microarrays is required for analysis because SNPs are randomly located- you cannot tell what is a snp or what isn't until you sequence the entire genome.

Question 70

Define RFLPs. How can RFLP's be found?

Answer 70

a SNP that is in a restriction site. The SNP interferes and destroys the site, yielding a larger restriction fragments than normal. Can be determined using southern blot bc it uses restriction enzymes.

Question 71

At a molecular level, DNA behaves in a _____ manner

Answer 71

Codominant

Question 72

Define Tandem Repeat Polymorphisms. How can they be found?

Answer 72

TRP's are the difference in number of copies of a DNA sequence that may repeat multiple times at a particular site of a chromosome. Repeats a NONCODING region. Can be determined via southern blot or gel electrophoresis because the more repeats, the heavier it will be and won't migrate up the plate. can also be determined via PCR using primers.

Question 73

Define SSRP and VNTR, how are they similar?

Answer 73

single sequence repeat polymorphism. small repeats of sequence 2-9 nucleotides long. ex/ ACACACACACAC variable sequence repeat polymorphism. larger repeats of sequence around 10-60 nucleotides long. Both forms of tandem repeats polymorphisms, both are highly polymorphic and can result in multiple different genotypes

Question 74

Define Wild type

Answer 74

non mutant allele of a trait

Question 75

Difference between round seeds and wrinkled seeds

Answer 75

round seeds contained amylopectin and is the dominant trait. Wrinkled seeds do not contain amylopectin because it has a defective SBE1 gene that makes it difficult to make glycosidic linkages.

Question 76

True or False: the phenotype of a heterozygous organism determines which allele is dominant

Answer 76

T

Question 77

In the wrinkled pea seed, how is the SBE1 gene affected?

Answer 77

there is a transposable element that was inserted into the gene that usually codes for SBE1. Transposable element: a DNA sequence capable of moving from gene to gene.

Question 78

Molecularly, what is the relationship between the round and wrinkled alleles of the pea plant?

Answer 78

they are RFLPs, the transposable element results in possible restriction site destruction, yielding different fragment sizes if using southern blot visualization.

Question 79

Why did mendel use peas?

Answer 79

1) they were self pollinating and thus true breeding (homozygous) 2) multiple variations and traits of study in one plant 3) Fast germination

Question 80

Define Outcrossing | Define Hybrid

Answer 80

Outcrossing: the process of producing hybrids from normally true-breeding plants via cross pollination Hybrid: progeny resulting from the outcrossing of plants that differ by one or more trait. Hybrids are not true breeding.

Question 81

Define reciprocal cross:

Answer 81

2 methods of crossing Sexual organisms :affected female x normal male, or normal female x affected male.

Question 82

What are the phenotypic/genotypic ratios of the F2 generation in a monohybrid cross?

Answer 82

Phenotypic: 3:1 Genotypic: 1:2:1

Question 83

Define mendel's first law:

Answer 83

Law of segregation: in the formation of gametes, paired alleles segregate in such a way that they have each gamete is equally likely to contain either member of the pair.

Question 84

Define Test Cross

Answer 84

Hetero dominant phenotype x homo-recessive

Question 85

How can WW round seeds and Ww round seeds be distinguished?

Answer 85

Either by letting F2 progeny self fertilize, or by conducting a test cross.

Question 86

What makes a seen green vs. yellow?

Answer 86

``` yellow= dominant green= recessive, has stay green gene, cannot break down chlorophyll. ```

Question 87

What are the phenotypic/genotypic ratios for a mendelian dihybrid cross?

Answer 87

phenotypic: 9:3:3:1 Genotypic: 1:2:1:2:4:2:1:2:1

Question 88

Mendels Second Law

Answer 88

Law of Independent Assortment: Segregation of the members of any pair of alleles is independed of the segregation of other pairs in the formation of reproductive cells. Applicable in dihybrid + crosses

Question 89

How can you test for independent assortment?

Answer 89

test cross with heterdom and homo recessive

Question 90

What are the phenotypic/genotypic ratios for a mendelian trihybrid cross?

Answer 90

Phen: 27"9'9'9'3'3'3'1 Geno: 3^3= 27

Question 91

Product rule

Answer 91

probability of independent events occurring together is the product of the probabilities of the individual events

Question 92

Sum rule

Answer 92

probability of either of the two mutually exclusive events occurring is the sum of their individual probabilities

Question 93

How many progeny do you need in order to obtain a 95% confidence level if your probability of interested is 1/256?

Answer 93

``` P of success= 1/256 P of fail= 255/256 Product rule for sample size= (255/256)^n therefor P success= 1-(255/256)^n 95% confident= 1-(255/256)^n 0.05=(255/256)^n n=765 ```

Question 94

Define penetrance

Answer 94

the proportion of individuals with the "affected" genotype that actually express the physical trait.

Question 95

Complete penetrance

Answer 95

when 100% of the individuals with the affected genotype express the physical trait

Question 96

Characteristics of fully penetrant dominant traits

Answer 96

1) affected progeny need affected parent 2) trait is present in every generation 3) trait affects males and females equally 4) generally, half of the progeny are affected 6) normal progeny need to be homozygous for normal (recessive) allele

Question 97

Examples of dominant traits

Answer 97

huntingtons, marfan syndrome, hypercholesterolemia

Question 98

Define Variable Expressivity

Answer 98

differences in severity of the expression of a particular genotype.

Question 99

Characteristics of fully penetrant recessive alleles

Answer 99

1) affected progeny probs don't have affected parents 2) parents are probs carriers 3) parents are probs related (consangeous relationship) 4) Affected progeny probs have affected siblings 5) male and females are equally likely to have disease 6) affected PARENTS usually have normal offspring because they usually mate with a homo normal individual

Question 100

Examplmes of Recessive human conditions

Answer 100

tay sachs cystic fibrosis alkaptonuria

Question 101

Why is the co dominant behavior of DNA useful?

Answer 101

1) Heterozygous genotypes are disinguishable from homo genotypes 2) high levels of heterozygosity=most matings are informative in regards to segregation

Question 102

Define Epistasis

Answer 102

When more than one gene affects one phenotype, gene interactions perturbs expected mendelian ratios for PHENOTYPES. GENOTYPE RATIOS ARE CONSTANT

Question 103

Define Incomplete Dominance

Answer 103

When the phenotype of a heterozygous individual looks like a combination/VARIATION of the homozygous genotypes.

Question 104

T/F: a phenotype resulting from incomplete dominance or codominance can be made into a truebreeding plant

Answer 104

F

Question 105

Co dominance

Answer 105

heterozygote phenotype is DISTINCT from both homo phenotypes

Question 106

Example of multiple alleles

Answer 106

Blood types

Question 107

9:7 phenotypic ratio of dihybrid cross

Answer 107

When homozygous recessive of either or both traits results in ONE mutant phenotype. At least one dominant allele is required in both genes of the dihybrid cross in order to produce the wildtype phenotype

Question 108

12:3:1 phenotypic ratio of dihybrid cross

Answer 108

When homo/hetero dominant (WW or Ww) allele of the first loci masks the expression of all genotypes in the second loci. As long as there is one dominant allele in the first gene, the second gene's trait will not be expressed.

Question 109

9:4:3

Answer 109

When the homozygous recessive (ww) allele of the first loci masks the expression of the phenotype at locus 2, regardless if the allele at locus 2 is dominant. Ex, coat colors or flower pigments.

Question 110

9:6:1

Answer 110

homozygosity for either of the 2 recessive alleles produces the same distinct phenotypes; double homo reccesive or double homo dominant genotypes have their own phenotypes.