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BIOL-2301 Final Exam > Chapter 1-3 > Flashcards

Chapter 1-3 Flashcards

1
Q

What are chromosomes made of?

A

DNA and proteins

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2
Q

What did Frederick Griffith do?

A

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

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3
Q

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

A

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.

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4
Q

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

A

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.

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5
Q

What did Oswald Avery et. al. do?

A

discovered that transformation was caused by DNA

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6
Q

Describe Oswald Avery’s experiments

A

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

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7
Q

Who conducted the blender experiment?

A

Hershey and Chase

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8
Q

What did Hershey and Chase conclude

A

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

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9
Q

Describe Hershey and Chase experiments

A

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.

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10
Q

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

A
  • proposed the first correct 3D structure of DNA

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

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11
Q

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

A

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

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12
Q

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

A

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.

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13
Q

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

A

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.

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14
Q

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

In vivo?

A

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.

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15
Q

Characteristics of Purines

A

2 rings, adenine and guanine

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16
Q

Characteristics of Pyramidine

A

1 ring, thiamine, uracil and cytosine

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17
Q

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

A

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)

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18
Q

What did Archibald Garrod propose

A

Inborn Errors of Metabolism, studied alkaptonuria

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19
Q

What is the proposal of Inborn Errors of Metabolism?

A

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

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20
Q

Characteristics of Alkaptonuria

A

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

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21
Q

Characteristics of Phenyl Ketonuria

A

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.

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22
Q

What did Beadle and Tatum do?

A

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.

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23
Q

What is a mutant screen?

A

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

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24
Q

Complementation Test

A

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

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25
Q

Complementation vs non complementation

A

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.

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26
Q

Define central dogma

A

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’

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27
Q

RNA vs DNA

A
  • 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
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28
Q

Which enzyme makes transfer Rna

A

aminoacyl-tRNA synthetase

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29
Q

Start codon?

A

Methionine, AUG

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30
Q

Define Wobble Hypothesis

A

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

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31
Q

Exons vs Introns

A

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

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32
Q

Reasons why a mutation could be silent

A

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)

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33
Q

Define Pleiotrophy

A

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.

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34
Q

How many chromosomes does a human have

A

46

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35
Q

How many chromosomes are in a human reproductive cell?

A

23

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36
Q

Are exons more populous that introns in the human body?

A

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

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37
Q

Define Genetic Markers

A

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

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38
Q

Define DNA markers

A

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

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39
Q

Define Genomic Data

A

the total DNA extracted from cells of an organism

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40
Q

Characteristics of Purines

Characteristics of Pyrimadines

A

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

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41
Q

Comment on general carbon numbering in a nucleotide

A

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

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42
Q

Define nucleoside

A

sugar+base

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43
Q

Define nucleotide

A

sugar+base+phosphate group

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44
Q

What bonds hold up a polynucleotide chain?

A

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

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45
Q

Elaborate on Chargaffs rules

A

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

46
Q

Define Base composition and it’s main feature

A

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

47
Q

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

A

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

48
Q

Define B form DNA

A

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

49
Q

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

A

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

50
Q

Define Base Pairing. What bonds hold the bases together?

A

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

51
Q

Define nucleic Acid Hybridization and its requirements

A

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
52
Q

Define PCR and its requirements

A

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
53
Q

How are restriction enzymes made and how do they work?

A

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.

54
Q

characteristic of restriction site

A

palindrome

55
Q

Main characteristic of restriction enzyme

A

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.

56
Q

What chemical allows for UV visualization of a gel electrophoresis plate

A

Ethidium Bromide

57
Q

Factors that affect separation/visualization in Gel electrophoresis

A

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.

58
Q

Process involving nucleic acid hybridization

A

southern blot

59
Q

Define denaturation in terms of nucleic acid hybridization

A

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

60
Q

How does alkali treatment aid in denaturation?

A

disrupts Hbonds

61
Q

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

A

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

62
Q

What does southern blot do?

A

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.

63
Q

Steps of southern blot

A

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.

64
Q

Requirements for DNA Amplification

A

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

65
Q

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

A

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.

66
Q

What is PCR? What does it use? Characteristics?

A

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

67
Q

Define DNA Polymorphisms.

A

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.

68
Q

Define SNP

A

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

69
Q

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

A

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.

70
Q

Define RFLPs. How can RFLP’s be found?

A

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.

71
Q

At a molecular level, DNA behaves in a _____ manner

A

Codominant

72
Q

Define Tandem Repeat Polymorphisms. How can they be found?

A

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.

73
Q

Define SSRP and VNTR, how are they similar?

A

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

74
Q

Define Wild type

A

non mutant allele of a trait

75
Q

Difference between round seeds and wrinkled seeds

A

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.

76
Q

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

A

T

77
Q

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

A

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.

78
Q

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

A

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

79
Q

Why did mendel use peas?

A

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

80
Q

Define Outcrossing

Define Hybrid

A

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.

81
Q

Define reciprocal cross:

A

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

82
Q

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

A

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

83
Q

Define mendel’s first law:

A

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.

84
Q

Define Test Cross

A

Hetero dominant phenotype x homo-recessive

85
Q

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

A

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

86
Q

What makes a seen green vs. yellow?

A 
yellow= dominant 
green= recessive, has stay green gene, cannot break down chlorophyll.
87
Q

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

A

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

88
Q

Mendels Second Law

A

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

89
Q

How can you test for independent assortment?

A

test cross with heterdom and homo recessive

90
Q

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

A

Phen: 27”9’9’9’3’3’3’1
Geno: 3^3= 27

91
Q

Product rule

A

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

92
Q

Sum rule

A

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

93
Q

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

A 
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
94
Q

Define penetrance

A

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

95
Q

Complete penetrance

A

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

96
Q

Characteristics of fully penetrant dominant traits

A

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

97
Q

Examples of dominant traits

A

huntingtons, marfan syndrome, hypercholesterolemia

98
Q

Define Variable Expressivity

A

differences in severity of the expression of a particular genotype.

99
Q

Characteristics of fully penetrant recessive alleles

A

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

100
Q

Examplmes of Recessive human conditions

A

tay sachs
cystic fibrosis
alkaptonuria

101
Q

Why is the co dominant behavior of DNA useful?

A

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

102
Q

Define Epistasis

A

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

103
Q

Define Incomplete Dominance

A

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

104
Q

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

A

F

105
Q

Co dominance

A

heterozygote phenotype is DISTINCT from both homo phenotypes

106
Q

Example of multiple alleles

A

Blood types

107
Q

9:7 phenotypic ratio of dihybrid cross

A

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

108
Q

12:3:1 phenotypic ratio of dihybrid cross

A

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.

109
Q

9:4:3

A

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.

110
Q

9:6:1

A

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.

BIOL-2301 Final Exam (6 decks)

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