Chapter 3- From Genes to Proteins Flashcards

1
Q

what was Griffith’s experiment?

A

worked with two forms Pneumococcus, one was an encapsulated bacterium that forms smooth colonies and causes death when injected into mice, the other is a mutant strain that lacks the enzymes needed to synthesize a capsule and forms rough colonies and does not cause death when injected into mice; found that when he heat-treated wild-type did not cause death in mice because it destroyed the capsule; found that when he combined heat-treated wild type and mutant type, the mouse died and he found encapsulated bacteria in the mouse tissue, indicated that the mutant strain had incorporated the virulent element from the heat-treated wild type; concept of “transformation”

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2
Q

what was the Avery , Macleod, and Mccarty experiment?

A

determined that DNA was the transforming principle, found that transformation still occurred if other bio molecules were destroyed by enzymes, but that transformation would not occur if the sample was given enzymes that destroyed DNA

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3
Q

what was the Hershey and Chase experiment?

A

When bacteriophages containing 32P (radioactive), were allowed to infect nonradioactive bacteria, all the infected cells became radioactive and, in fact, much of the radioactivity was passed on to the next generation of bacteriophages.
However, when the bacteria were infected with bacteriophages labeled with 35S, and then the virus coats removed (by whirling them in an electric blender), practically no radioactivity could be detected in the infected cells.
because P is in DNA and S is in proteins, indicated that DNA was the molecule of heredity

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4
Q

what was the model developed by Pauling and Corey?

A

DNA adopts a triple-helical structure, three chains tightly packed together, phosphate on the inside of the triple helix, nitrogenous bases on the outside, stabalized by hydrogen bonds between the interior phosphate groups

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5
Q

which bases are purines?

A

adenine and guanine

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6
Q

which bases are pyrimidines?

A

cytosine, thymine, and uracil

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7
Q

which bases does DNA contain?

A

A,C,T, and G

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8
Q

which bases does RNA contain

A

A,C,U and G

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9
Q

what forms a nucleoside?

A

linking atom N9 in a purine or atom N1 in a pyrimadine to a five-carbon sugar at C 1’

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10
Q

what is the sugar in DNA

A

2’-deoxyribose (2’ C contains a H attached to it instead of an OH

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11
Q

what is the sugar in RNA

A

ribose

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12
Q

what is a nucloeotide?

A

nucleoside to which one or more phosphate groups are linked, typically at C5’ of the sugar

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13
Q

what are the functions of nucleotides?

A

building blocks for DNA and RNA, involved in energy transduction, intracellular signaling, and regulation of enzyme activity

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14
Q

what is the linkage between nucleotides?

A

phosphodiester bond (single phosphate group forms ester bonds to both C5’ and C3’)

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15
Q

what happens when a nucleoside triphosphate is added to the polynucleotide chain?

A

a diphosphate group is eliminated

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16
Q

what is a residue?

A

what a nucleotide is formally known as once incorporated into a polynucleotide

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17
Q

what does the nucleic acid structure look like?

A

nucleotides consecutively linked by phosphodiester bonds in which the bases project out from a backbone of repeating sugar-phosphate groups

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18
Q

what is the 5’ end?

A

the end of the polymer that bears a phosphate group attached to a C5’

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19
Q

what is a 3’ end?

A

the end of the polymer that bears a free OH group

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20
Q

how are base sequences in a polynucleotide read?

A

from 5’ end to 3’ end

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21
Q

how are the two strands of DNA connected

A

hydrogen bonds between base pairs

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22
Q

what are Chargaff’s rules?

A

A=T, C=G; A+C=G=T

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23
Q

how many hydrogen bonds like adenine and thymine?

A

two

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24
Q

how many hydrogen bonds link guanine and cytosine?

A

three

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25
Q

why is the sugar-phosphate backbone of the two strands of DNA separated by a constant distance?

A

all base pairs, consist of a purine and pyrimidine, have same molecular dimensions ( about 11 A wide)

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26
Q

what is the shape of DNA?

A

double helix, the two strands twist around each other

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27
Q

what does it mean that the two polynucleotide strands are antiparallel?

A

their phosphodiester bonds run in opposite directions, one strand has 5’ to 3’ orientation, the other has 3’ to 5’ orientation

28
Q

which was is the DNA latter twisted

A

in a right hand fashion (if you climbed the ladder, railing would be help with right hand)

29
Q

what are the major and minor grooves?

A

the twisting of the DNA helix creates two grooves of unequal width

30
Q

what defines the exterior of the helix?

A

sugar-phosphate backbone

31
Q

what defines the interior of the helix?

A

base pairs, stack on top of one another

32
Q

are the base pairs accessible to the solvent?

A

the planar faces of the base pairs are not accessible, but their edges are exposed in the major and minor grooves, which allows for certain DNA binding proteins to recognize specific bases

33
Q

what is an oligonucleotide?

A

a short single-stranded polymer of nucleotides

34
Q

what are the function of polymerases?

A

polymerize nucleotides

35
Q

what are the function of nucleases?

A

hydrolyze the phosphodiester bonds linking nucleotide residues

36
Q

what is the function of an exonucleas?

A

removes a residue from the end of a polynucleotide chain

37
Q

what is the function of an endonucleuase?

A

cleaves a reside from some point along the chain not at the end

38
Q

what is the structure of RNA?

A

single-stranded, greater conformational freedom, can fold back on itself so that base pairs can form between complementary segments of the same strand, assume intricate 3D shapes

39
Q

what is an RNA-DNA hybrid double helix?

A

residues of RNA capable of base-pairing with a complementary single strand of DNA, wider and flatter than typical double stranded DNA, inclined to the helix axis by 20 degrees

40
Q

what is A-DNA?

A

DNA helix adopting same structure as the RNA-DNA hybrid double helix

41
Q

what is B-DNA?

A

standard DNA double helix

42
Q

what does the structural stability of a double helix depend upon?

A

stacking interactions, a from of van der Waals interaction between adjacent base pairs, weak but additive along the length of DNA; doesn’t depend as much on hydrogen bonds between base pairs because the bases could satisfy their hydrogen-bonding requirements by forming hydrogen bonds with water

43
Q

what stacking interactions are the strongest?

A

between neighboring GC pairs; double helix rich in GC harder to disrupt

44
Q

what is the melting temperature of DNA?

A

temperature at which half the DNA has separated into single strands, midpoint of the melting curve

45
Q

what is denaturation (melting)?

A

slowly increasing the temperature, at a high temp the base pairs begin to unstack, hydrogen bonds break, and the strands begin to separate

46
Q

what is renaturation?

A

separated strands can reform a double helix by reestablishing hydrogen bonds between complementary strands and by restacking base pairs, occurs when temperature is lowered slowly

47
Q

what happens is separated DNA is cooled too rapidly?

A

it may not fully renature becuae base pairs may form randomly between short complementary segments, at low temps the improperly paired segments are frozen in place since they do not have enough thermal energy to melt apart and find their correct complements

48
Q

what determines the rate of renaturation?

A

the length of the DNA strand, short sequences come together faster because bases in each strand must locate their partners along the length of the complementary strand

49
Q

what is the purpose of an oligonucleotide probe?

A

can be used to detect the presence of a complementary nucleic acid sequence in a complex mixture

50
Q

what is the central dogma of molecular biology?

A

a portion of the DNA , a gene, is transcribed to produce a complementary strand of RNA, the RNA is then translated into a protein

51
Q

what is a genome?

A

an organism’s complete set of genetic info

52
Q

what are the other names for the template strand?

A

the noncoding strand, the antisense strand, the negative strand

53
Q

what are the other names for the nontemplate strand?

A

the coding strand, the sense strand, the positive strand

54
Q

what is the orientation of the template strand?

A

3’ to 5’

55
Q

what is the orientation of the nontemplate strand

A

5’ to 3’

56
Q

what does the RNA look like that gets transcribed from the template strand?

A

has same sequence as (except for the substitution of U for T) and the same 5’ to 3’ orientation as the nontemplate strand of DNA

57
Q

what is the transcribed RNA called?

A

messanger RNA (mRNA)

58
Q

what translates the mRNA?

A

a ribosome

59
Q

what occurs during translation?

A

small molecules called transfer RNA (tRNA) which carry amine acids, recognize sequential sets of three bases (called codons) in the mRNA through complementary base-pairing (the tRNA has anticodons), the ribosome covalently links the amino acids carried by successive tRNAs to form a protein

60
Q

how many codons are there in total?

A

64

61
Q

what direction does RNA polymerase read?

A

3’ to 5’

62
Q

what does it mean when diseases are polygenic?

A

many genes contribute to the disease

63
Q

what does it mean when diseases are monogenic?

A

only one gene causes the disease

64
Q

what types of organisms have the least amount of DNA and the fewest genes?

A

organisms with the simplest lifestyles

65
Q

how does the proportion of noncoding DNA relate to the complexity of the organism?

A

in general, the proportion of noncoding DNA generally increases with the complexity of the organism

66
Q

what are transposable elements?

A

short segments of DNA that are copied many times and inserted randomly into the chromosome, make up a good portion of the noncoding DNA

67
Q

what is an open reading frame (ORF)

A

a stretch of nucleotides that can potentially be transcribed and translated, begins with a start codon: AUG which specifies methionine, ends with stop codon: AUU, AUC, or ACU