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McK's Science Review > DNA and Biotechnology > Flashcards

DNA and Biotechnology Flashcards

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1
Q

nucleosides

A

five-carbon sugar, bonded to a nitrogenous base and formed by covalently linking the base of C-1’ to the sugar, carbon atoms in sugar have prime to distinguish them from nitrogenous base

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2
Q

nucleotides

A

when one or more phosphate groups are attached to C-5’ of a nucleoside, nucleotides are the building block of DNA

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3
Q

If the pentose is a ribose, the nucleic acid is…

A

RNA

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4
Q

If the pentose is a deoxyribose, the nucleic acid is …?

A

DNA

deoxyribose is a ribose with the 2’ OH group replaced by a H

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5
Q

Bond breaking is…?

A

Endothermic

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6
Q

Bond making is….?

A

Exothermic

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7
Q

What is the backbone of DNA composed of?

A

Alternating sugar and phosphate groups, it is read 5’- 3’, it is formed as nucleotides are joined by 3’-5’ phosphodiester bonds, carries a negative charge

5’ end of DNA will have an -OH or phosphate group bonded to C-5’ of the sugar while the 3’ end has a free -OH on C-3’ of the sugar

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8
Q

Purines

A

Al Gore is Pure

adenine and guanine, both found in DNA and RNA, two rings

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9
Q

Pyrimidines

A

Pyramids are CUT, only contain one ring, cytosine, uracil, and thymine

thymine is only in DNA
uracil is only found in RNA

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10
Q

What are the 4 rules for something to be aromatic?

A
  1. compound is cyclic
  2. compound is planar
  3. compound is conjugated, alternating single and multiple bonds or lone pairs, creating at least one unhybridized p-orbital for each atom in the ring
  4. follows Huckel’s rule: 4n+2

ex. benzene

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11
Q

complementary base pairing

A

A is paired with T (via two hydrogen bonds); G always pairs with C (via three hydrogen bonds), hydrogen bonds provide stability to the structure

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12
Q

Chargaff’s Rues

A

amount of A equals the amount of T; the amount of G equals the amount of C

%A=%T
%G= %C

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13
Q

B-DNA

A

double helix of most DNA is a right-handed helix, forming B-DNA, makes a turn every 3.4 nm and contains about 10 bases within that span

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14
Q

Z-DNA

A

zigzag appearance; it is a left-handed helix that has a turn every 4.6 nm and contains 12 bases in each turn, unstable and hard to research

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15
Q

denatured

A

will melt DNA into two single strands that have separated from each other…heat, alkaline (basic) pH, and chemicals like formaldehyde and urea are all able to denature DNA

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16
Q

reannealed

A

when denatured, single-stranded DNA is brought back together (can occur if the denaturing condition is slowly removed)

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17
Q

probe DNA

A

DNA with known sequence, can be used to provide evidence of a gene of interest

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18
Q

how many chromosomes are in humans?

A

46 chromosomes

DNA is divided up among the 46 chromosomes found in the nucleus of the cell

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19
Q

histones

A

a group of small basic proteins

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20
Q

When DNA is wound around histones it forms…?

A

chromatin

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21
Q

DNA wrapped around a protein complex forms a ….?

A

Nucleosome –> create a much more organized and compacted DNA

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22
Q

Nucleoproteins

A

proteins that associate with DNA, example histones, others stimulate processes like transcription

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23
Q

What is compacted chromatin called? (Occurs during interphase)

A

heterochromatin

dark, dense, silent

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24
Q

What is dispersed chromatin called?

A

euchromatin, appears lights under light microscopy

light, uncondensed, expressed

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25
Q

telomere

A

a simple repeating unit (TTAGGG) at the end of the DNA, forms a telomere

have high GC content, makes them notably strong

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26
Q

What enzyme helps rebuild telomeres?

A

telomerase, more expressed in rapidly dividing cells

27
Q

Centromeres

A

a region of DNA found in the center of chromosomes, often referred to as the site of constriction, because they form noticeable indentations

28
Q

repliosome/replication complex

A

a set of specialized proteins that assist the DNA polymerases

DNA unwinds at points called the origins of replication, the generation of new DNA proceeds in both directions, creating replication forks on both sides of the origin

29
Q

sister chromatids

A

two identical copies of the same chromosome formed by DNA replication, attached to each other by a structure called the centromere

30
Q

helicase

A

the enzyme responsible for unwinding the DNA, generating two single-stranded template strands ahead of the polymerase

single-stranded DNA binding proteins will bind to the unraveled strand, preventing both the re-association of the DNA strands and the degradation o fDNA by nucleases

31
Q

supercoiling

A

a wrapping of DNA on itself as its helical structure is pushed even further toward the telomeres during replication (like a telephone cord that’s all wrapped up)

32
Q

parental strands

A

serve as a template for the generation of the new daughter strands

replication is semiconservative

33
Q

DNA polymerases

A

responsible for reading the DNA template, or parental strand, and synthesizing the new daughter strand

reads 3’ to 5’; synthesizes the complementary strand 5’ to 3’

34
Q

lagging strand

A

strand that is copied in a direction opposite the direction of the replication fork

35
Q

Okazaki fragments

A

small strands that are produced on the lagging strand during replication

36
Q

primase

A

synthesizes a short primer in the 5’ to 3’ direction to start replication on each strand

37
Q

DNA polymerase III (prokaryotes)

DNA polymerase alpha, delta, epsilon

A

will begin synthesizing the daughter strand of DNA in the 5’ to 3’ manner

38
Q

DNA polymerase I

DNA polymerase delta

A

replacement of RNA with DNA (gets rid of spot where the RNA primer had been)

39
Q

DNA ligase

A

seals the ends of the DNA molecules together, creating one continuous strand of DNA

40
Q

DNA topoisomerases/DNA gyrase

A

removal of positive supercoils ahead of advancing replication forks

41
Q

cancer

A

cell proliferate excessively bc they are able to divide when they shouldn’t

42
Q

metastasis

A

migration to distant tissues by the bloodstream or lymphatic system

43
Q

oncogenes

A

mutated genes that cause cancer

proto-oncogenes before they are mutated

44
Q

tumor suppressor genes/ antioncogenes

A

p53, Rb…encode proteins that inhibit the cell cycle or participate in DNA repair processes; normally function to stop tumor progression

45
Q

mismatch repair

A

cells have machinery in the G2 phase of the cell cycle, enzymes are encoded by genes, detect and remove errors introduced in replication that were missed during the S phase of the cell cycle

46
Q

nucleotide excision repair (NER)

A

thymine dimers are eliminated from DNA NER mechanism, excision endonuclease makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligonucleotide

47
Q

base excision repair

A

first, the affected base is recognized and removed by a glycosylase enzyme, leaving behind an apurinic/apyrimidinic (AP) site, also called an abasic site…AP site is recognized by an AP endonuclease that removes the damaged sequence from the DNA…DNA polymerase and DNA ligase can then fill in the gap and seal the strand, as described above

48
Q

recombinant DNA technology

A

allows a DNA fragment from any source to be multiplied by either gene cloning or polymerase chain reaction (PCR), provides the reagents necessary for genetic testing, such as carrier detection and prenatal diagnosis of genetic disease, also useful for gene therapy

49
Q

DNA cloning

A

a technique that can produce large amounts of a desired sequence; requires that the investigator ligate the DNA of interest into a piece of nucleic acid referred to as a vector, forming a recombinant vector

vectors are usually bacterial or viral plasmids

50
Q

vectors

A

usually bacterial or viral plasmids that can be transferred to a host bacterium after insertion of the DNA of interest

51
Q

restriction enzymes (restriction endonucleases)

A

enzymes that recognize specific double-stranded DNA sequences, sequences are palindromic, can cut through the backbones of the double helix

52
Q

DNA libraries

A

large collections of known DNA sequences

53
Q

genomic libraries

A

contain large fragments of DNA and include both coding (exon) and noncoding (introns) regions of the genome

54
Q

cDNA

A

complementary DNA, constructed by reverse transcribing processed mRNA, shorter, lacks introns, sometimes called expression libraries

55
Q

hybridization

A

the joining of complementary base pair sequences

DNA-DNA recognition or DNA-RNA recognition

56
Q

polymerase chain reaction (PCR)

A

automated process that can produce millions of copies of a DNA sequence without amplifying the DNA in bacteria; requires primers that are complementary to the DNA that flanks the region of interest, nucleotides (dATP, dTTP, dCTP, and dGTP) and DNA polymerase

57
Q

gel electrophoresis

A

technique to separate macromolecules, like DNA and proteins, by size and charge, uses agarose gel, long the DNA strand, the slower it moves

58
Q

Southern Blot

A

gel electrophoresis is often used, used to detect the presence and quantity of various DNA strands in a sample; DNA is cut by restriction enzymes and then separated by gel electrophoresis

probe will bind to its complementary sequence and form double-stranded DNA

59
Q

DNA sequencing

A

template DNA, primers, an appropriate DNA polymerase, and all four deoxyribonucleotide triphosphates; fragments are separated by gel electrophoresis

60
Q

gene therapy

A

offers potential cures for individuals with inherited diseases, intended for diseases in which a given gene is mutated or inactive, giving rise to a pathology; vectors are used to transfer the cloned gene into the target cells’ DNA

61
Q

transgenic mice

A

mice that are altered at their germ line by introducing a cloned gene into fertilized ova or into embryonic stem cells; cloned gene is known as the “transgene”

better for studying dominant genes

62
Q

knockout mice

A

a gene has been intentionally deleted (knocked out) in a mouse, provide valuable models in which to study human disease

63
Q

chimera

A

offspring have patches of cells, including germ cells, derived from each of the two lineages

McK's Science Review (24 decks)

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