TBR 9 - Genetic Information Flashcards

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1
Q

Pangenesis.

A

The theory that states that each part of the body produced tiny particles. Pangenes were thought to be miniature replicas of each organ or tissue by the body. These pangenes were carried to the reproductive organs by the circulatory system where they are packed to sperm or egg.

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2
Q

What made pea plants easy for Gregor Mendel to study?

A

There were many true breeding varieties. The pea plants could be distinguished by 7 different pair traits. Pea plants were rather easy to grow, have a short generation time, and they are small and wouldn’t take up space.

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3
Q

Describe Mendel’s experiment.

A

Crossed for a pair of traits (like true breed purple versus white). This F1 generation expressed one of the two parental characteristics. He then allowed F1 to self-pollinate for one generation, and then noticed in the F2 generation, each of the characteristics re-appeared.

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4
Q

When mendel crossed two pairs of true breeds and then allowed them to self-pollinate, what is the ratio of the parental trait to the other parental traits.

A

3 to 1 ratio.

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5
Q

Based on Mendel’s pure cross and subsequent hybrid cross experiment, he concluded that:

A

1) Traits are either dominant or recessive.
2) The alternative form of a hereditary factor, which leads to an alternative form of a given trait is called an allele.
3) An individual who possesses two identical alleles is said to be homozygous, while an individual who possesses two diff alleles is said to be heterozygous.
4) two alleles from each parent to an offpsring do not influence each other in any way. They don’t form intermediate alleles.
5) the presence of hereditary characters in an individual doesn’t ensure that it will be expressed/

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6
Q

Test cross.

A

Ex. Crossing purple flowers of unknown genotype (WW or Ww) from the F1 generation in order to determine its genotype. Involves crossing the purple flowers with a homozygous recessive white plant.

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7
Q

Law of segregation.

A

Alternate alleles segregate from each other in heterozygous individuals and retain their identity. Two members of a pair of a gene pair segregate from each other into gametes, so that 1/2 of the gametes carry one member and the other 1/2 of gametes carry the other member of the gene pair.

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8
Q

What phenotypic ratio does a dihybrid cross result in?

A

9:3:3:1

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9
Q

What did Mendel’s dihybrid cross show?

A

Hereditary factors for different traits like color and shape assort independently from one another.

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10
Q

Mendel’s law of independent assortment.

A

Segregation of one gene pair is independent of other gene pairs during the formation of the gametes.

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11
Q

What is the law of segregation essentially, in terms of cell division?

A

Meiosis.

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12
Q

Genes.

A

Basic units of hereditary (DNA), are located at specific locations along the chromosomes.

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13
Q

Independent assortment of genes will only occur in two instances:

A

1) genes are located on different chromosomes (because the chromosomes themselves assort independently)
2) they are very far apart on the same chromosome
3) through recombination, two genes close to one another can end up on different genes.

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14
Q

Sex-linked.

A

If a given trait is determined by a gene on the X chromosome, it is said to be sex-linked.

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15
Q

Experiment with the sex-linked gene.

A

XY male with recessive white eye gene crossed with dominant red eye XX female. F1 generation is all red-eye, but all females are XwWr. The F1 generation was allowed to mate, and the resulting F2 generation had white-eyed males again (unlike F1)

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16
Q

True or false. A given genetic locus has ONE designated allele.

A

A given locus can have many alleles. Ex. ABO blood group.

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17
Q

Many genes can control a phenotype. One example is tryptophan, an essential amino acid (an AA an organism cannot synthesize itself). Explain how this works for this for an organism.

A

The biosynthesis of may compounds within the cell there can be many sequential steps. Each step is controlled by a separate EZ which in turn is controlled by a particular gene. One example would be tryptophan.

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18
Q

Tryptophan experiment - auxotroph.

A

A mutant that will grow only when its medium is supplemented with a particular compound which is not required by the normal wild-type organism.

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19
Q

Tryptophan experiment - prototroph.

A

A wild type organism.

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20
Q

Name the important components of the trrytophan experiment. Show the general pathway.

A

Chorismate - trpE -> ANTHRANILATE> Gene2, 3, 4 > trp A-> INDOLE -> trpB > TRYPTOPHAN

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21
Q

Tryptophan experiment - with a trp E- mutant, under what conditions in the medium would the organism grow.

A

The auxotroph will grow if either anthranaliate, indole, or trytophan is added.

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22
Q

Tryptophan experiment - with a trp A- mutant, under what conditions in the medium would the organism grow.

A

The mutant will NOT grow if nothing or anthranilate is added. It will grow if eithe rindole or tryptophan is added.

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23
Q

Tryptophan experiment - with a trp B mutant, under what conditions in the medium would the organism grow.

A

The bacterium will not grow if nothing, anthranilate, or indole is added to the minimal medium. This auxotroph will only grow if tryptophan is added.

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24
Q

Epistasis.

A

Two different genes which are not alleles of one another may affect the same outcome. Ex. inability to synthesize tryptophan. For the tryptophan synthesis, the dominant allele of all the genes involved in the particular biosynthetic pathway must be present.

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25
Q

There are some genes which may act in an additive fashion. Give one example.

A

1) There are 7 genes in yeast that control the synthesis of invertase which converts sucrose > glucose + fructose. If the yeast posses the dominant allele in any of these it ferments sucrose, but if it contains more than one, it ferments sucrose at a quicker rate.
2) height are also probably controlled in an additive fashion.

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26
Q

Pleiotrophy.

A

Where an individual allele has more than one effect on the phenotype. Ex. Mouse with a yellow coat with one allele present or death if both are.

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27
Q

The chromosomes that are not sex chromosomes are called ___.

A

Autosomes.

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28
Q

The long arm is designated as this letter. The short arm of a chromosome is designated as this letter.

A

The long arm is designated as “q”. The short arm is designated as “p”.

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29
Q

How many base pairs of DNA in a human cell? Genes?

A

6*10^9; 100,000 genes per haploid set.

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30
Q

What do the circles and squares represent on a pedigree? What about a slash through a box? Colored in? Left to the right arrangement?

A

1) circles = female; square = males
2) slash = heterozygous
3) colored in = has genetic defect
4) Birth order of the offspring is arranged from oldest to youngest from left to right.

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31
Q

Monosomy and trisomy.

A

Genetic abnormalities that occur during meiosis. One copy of the chromosomes called monosomy.

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32
Q

Genetic diseases due to nondisjunction.

A

Nondisjunction of XX can lead to XX in one gamete and none in the other, resulting in XXY, Klinefelters. Or XO female can result, called Turners syndrome.

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33
Q

Sex-linked recessive disease.

A

If a given disease affects both sexes equally, then it is likely to be autosomal. If males are affected almost exclusively, then the disease is likely sex-linked. Sex-linked recessive involving the X chromosome can suck for men.

34
Q

Huntington’s is what kind of genetic disorder?

A

Autosomal dominant.

35
Q

True or false. An individual who is affected with a dominant genetic trait will have at least one parent who is also affected.

A

True.

36
Q

If an individual has a 2/3 chance of having a genetic defect and she matures to adulthood and marries, what’s the chance her children will be carriers?

A

2/3 * 3/4 = 1/2
2/3 = AA, Aa, Aa
3/4 = Aa, Aa, aa –> doesn’t know what husband will be, so it’s out of 4

37
Q

Where does protein synthesis occur?

A

Synthesis of proteins occur in the cytoplasm of the cell, via ribosomes.

38
Q

Why did scientists have trouble identifying mRNA initially? Why was rRNA postulated to be the transcript from DNA?

A

mRNA have very short half lives and thus rapid turnover. You don’t want to keep on making something if you don’t need it. rRNA has a very long half life.

39
Q

True or false. Viruses can use the same ribosomes as its host.

A

True. In a bacterium infected with a phage, you will encounter mRNA from the virus and the bacterium itself. the mRNA can be translated on the same ribosome.

40
Q

Central Dogma of molecular biology.

A

DNA (transcription ) RNA ( translation) —> PROTEIN;

DNA and RNA can be replicated

41
Q

Describe the Hershey Chase experiment that showed DNA, not protein, was the genetic material.

A

1) Bacteria were infected with a phage labeled with radioactive P and S.
2) After incubation, the infection solution was placed in a blender to separate the phage from the bacteria.
3) The solution was centrifuged, resulting in supernatant and pellet.
4) The bacteria contained a higher percentage of 32P, while the phage protein supernatant contained a high percentage of sulfur (cys).

42
Q

Purines and pyrimidines and their properties.

A
Purines = adenine and guanine - bicyclic
Pyrimidines = cytosine and thymine. 
AT = two hydrogen bonds
CG = three hydrogen bonds
43
Q

What holds DNA double helix together.

A

H bonding and stacking of the bases due to the interaction of the pi electron clouds between juxtaposed bases.

44
Q

True or false. The DNA is fairly rigid.

A

DNA is constantly denaturing then reforming hydrogen bonds - a process called breathing.

45
Q

How does one denature DNA?

A

Change the pH of the solution or via heat.

46
Q

Why does DNA rich in GC denature slower?

A

Adenine and thymine are held by only TWO hydrogen bonds, whereas GC are held by THREE. If the DNA double hexlic is rich in GC, it takes longer to denature.

47
Q

Tm = melting temp?

A

Tm is the temperature at which half of the helical structure of the DNA is lost.

48
Q

How can we detect the phenomenon of DNA with more GC pairs melting slower?

A

Plot Temperature vs. Relative Absorbance. DS DNA has more stacking character and absorbs less since if ONE base pair absorbs light, the other’s ability is diminished. So, the graph is an “S” curve, with AT right to the left and GC rich to the right.

49
Q

Hypochromicity and its relevance to DNA.

A

The absorption of the total molecule is less than the sum of its parts. Each of the base pairs has its own particular absorption spectra, and when we allow these BP to form the double helix, we don’t realize their full absorptive capability.

50
Q

Conservative vs. semiconservative model for DNA replication.

A

Conservative - the parental strands remain together after replication of two new daughter strands.
Semiconservative - the two parental strands separate and two new daughter strands are synthesized off of the respective parental template (CORRECT)

51
Q

Conservative vs. semiconservative model for DNA replication. In the Meselson exp, e.coli with pure N15 DNA is incubated with only N14 as its medium. What will appear on chromatography in either case?

A

In both cases, you will still see two bands. For conservative, you’d see a 14N, 15N band. There would be 3x more 14N than 15N. For semiconservative, you’d see a 14N and 14N/15N band.

52
Q

Comment on the structure of a nucleotide versus nucleoside.

A

Nucleoside - ribose ring bonded to a purine or pyrimidine.

Nucleotide - adding a phosphate group to the 5’ hydroxyl of the ribose ring of any nucleoside

53
Q

Another way to say deoxyribonucleoside- 5’ monophosphate?

A

Deoxyribonucleotide

54
Q

What are linkages between two phosphate groups called?

A

Phosphoandyride.

55
Q

The C1 carbon of the ribose ring is bonded to either N9 of a purine or N1 of a pyrimidine base. What kind of linkage is this called?

A

N-glycosidic linkage.

56
Q

Name the four nucleosides.

A

deoxyadenosine, deoxyguanosine, deoxythymidine, deoxycytidine

57
Q

What direction is DNA synthesized? Read?

A

5’ to 3’

DNA is read 3’ to 5’

58
Q

What is needed for DNA polymerase to function?

A

A primer and dNTPs. The incoming dNTP will h-bond with its complementary base and then there will ne a nucleophilic attack by the 3’hydroxyl of the primer on the alpha phosphate of the incoming dNTP. A phosphodiester linkage is then formed between the two. Pyrophosphate is released and subsequently hydrolyzed to help drive the reaction to completion.

59
Q

dATP?

A

deoxyadenosine triphosphate.

60
Q

Is DNA a (left/right) handed helix?

A

Right-handed.

61
Q

Differences between B and A DNA.

A

B DNA contains a major and minor groove. There are different conformations of the ribose ring. The ribose ring in DNA are not planar - they can pucker. A DNA has TINY minor groove due to “s puckering”.

62
Q

Structurally, hoes does A, B, and Z DNA compare?

A

A: right handed, shorter and more compact structural organization than B; A DNA helix is tilted away from the axis by 19 degrees; N-glycosidic bonds are ANTI
B: right-handed, the majority of DNA in cells is in the B-conformation. B DNA has its bases arranged perpendicular to the helix axis; N-glycosidic bonds are ANTI
Z: left-handed, double helix winds in a zig-zag; N-glycosidic bond is anti for pyrimidine bases but SYN for purine bases; the ribose units are closer together; this DNA is skinner

63
Q

What is DNA linking number and how to find it.

A

The linking number (L) defines the number of times a
strand of DNA winds in the right-handed direction
around the helix axis when the axis is constrained
to lie in a plane; determines the degree of supercoiling;
• If both strands are covalently intact, the
linking number cannot change;
Ex. in a circular DNA of 5400 BP, L is 5400/10=540, where 10 is the basepair per turn for type B DNA.

64
Q

Positive versus negative supercoiling. What does supercoiling result in?

A

(+): If we twist a DNA molecule around its axis in the right-handed dir, then we’d introduce a double helical structure, a phenomenon known as supercoiling.
(-): If we twist a DNA molecule around its axis in the left-handed dir. we would introduce (-) supercoiling. ‘

Supercoiling changes the overall form of DNA by making it more compact and altering the accessibility to major and minor grooves.

65
Q

Topisomers.

A

DNA molecules that differ only in their linking number.
The linking number (L) defines the number of times a
strand of DNA winds in the right-handed direction
around the helix axis when the axis is constrained
to lie in a plane

66
Q

Topoisomerases - type 1 and type 2.

A

Type 1 - Cuts one strand of a DNA double helix, relaxation occurs(relaxes negative supercoils), and then the cut strand is re-ligated;
Type 2 - cuts both strands of one DNA double helix, passes another unbroken DNA helix through it, and then re-ligates the cut strands. Adds negative superfoils.

67
Q

Topoisomerases. How do these enzymes affect linking number?

A

Enzymes that participate in the overwinding or underwinding of DNA. The degree of the linking number in DNA can be altered by these enzymes.

68
Q

Does it require energy to introduce a supercoil into a DNA double helix?

A

Yes. It costs energy. A topoisomerase 2 converts the potential energy of ATP into the torsional energy of a negatively supercoiled structure.

69
Q

What makes the polymerase used in PCR unique?

A

Taq polymerase is stable at temperatures at 90C and doesn’t denature at that temperature. These were isolated from thermophilic organisms.

70
Q

Describe the steps in PCR.

A

1) Separation of DNA strands - heat DNA to 90C
2) Anneal primers - add short chain DNA primers that are complementary to the be sequence of the portion of DNA we already know; if we cool the solution to 50C, the primers will H-bond to their complimentary base
3) Nucleotide addition - let Taq DNA polymerase do its thing and add dNTPs at about 70C
4) Repeat

71
Q

Where does DNA replication begin?

A

Replication doesn’t begin at random sites, but rather “origin sites”

72
Q

Function of DNA gyrase.

A

In order for the DNA double helix to unwind, DNA gyrase adds negative supercoils ahead of the advancing replication fork. This is because when the fork is initally unwound, positive supercoils are introduced thus making DNA separtion difficult.

73
Q

Function of helicase complex?

A

The helicase binds to the “origin” site and catalyzes the ATP driven unwinding of the duplex DNA.

74
Q

What stabilizes the unwound portion of the parental DNA during replication?

A

Single-stranded binding proteins.

75
Q

Leading versus lagging strand.

A

Leading strand - the daughter strand that is synthesized continously in the 5’ to 3’ direction.
Lagging strand - the daughter stand synthesized discontinously, still in the 5’ to 3’ direction, but in fragments.

76
Q

How is the lagging strand synthesized.

A

1) DNA cannot be made until a PRIMER is synthesized. Primase is a RNA POL that synthesizes 5 nucleotides of RNA complementary to one of the DNA templates.
2) DNA POL 3 holoenzyme catalyzes the synthesize of 1000 dNTPs before is dissociate
3) DNA POL 1 has exonuclease activity that allows it to remove the short segments of RNA primer
4) When the primer is removed DNA POL 1 adds deoxyribonucleotides to the free 3’ hydroxyl
5) DNA ligase joins the free 3’ hydroxyl group of the new daughter DNA just synthesized by DNA POL 1 with the 5’ phosphate group of an Okazaki fragment ahead of it.

77
Q

Okazaki fragments.

A

Segment of RNA primer and newly synthesized DNA.

78
Q

What is the difference between DNA polymerase 1 and 3?

A

DNA polymerase 1: slow, only add 20 dNTPS; also has exonuclease activity to remove short segments of RNA primer.
DNA polymerase 3: fast, adds 1000 dNTPS

79
Q

True or false. During replication, there is only one origin site?

A

Because DNA in eukaryotic cells is quite long compared to E.coli’s DNA, it is replicated bidirectionally from many origin sites.

Bidirectional: as the parental DNA is opened, replication will proceed at two replication forks simultaneously

80
Q

Do bacteria have bidirectional DNA replication?

A

Yes.

81
Q

During what phase does DNA replication occur?

A

During the S-phase of the cell’s life cycle.