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MCAT Biochemistry > DNA and Bioctechnology (CH6) > Flashcards

DNA and Bioctechnology (CH6) Flashcards

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MCAT flashcards
1
Q

Allows a DNA fragment from any source to be multiplied by either gene cloning or by PCR (Polymerase Chain Reaction).

A

Recombinant DNA

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2
Q

Composed of a five carbon sugar (pentose) bonded to nitrogenous base and are formed by covalently linking the base to C-1’ of the sugar.

A

Nucleoside

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3
Q

Are formed when one or more phosphate groups are attached to C-5’ of a nucleoside.

A

Nucleotides

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4
Q

What is the difference between ribose and deoxyribose?

A
  • Ribose: RNA

- Deoxyribose: DNA

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5
Q

How does ATP power our cells?

A

Energy is released when a terminal phosphate is removed.

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6
Q

What quantifies whether a ring is aromatic?

A
  1. Cyclic
  2. Planar
  3. Conjugated
  4. 4n + 2π electrons (Huckel’s Rule)
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7
Q

When DNA with a known sequence is added to a mixture of target DNA sequences (that have denatured into single strands), this is called?

A

Probe DNA

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8
Q

What are some examples of DNA denatures?

A
  • Heat, alkaline pH, formaldehyde and urea.
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9
Q

To be brought back together after DNA denaturation.

A

Reanneal

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10
Q

Explain B-DNA.

A
  • Right handed helix
  • Right turn every 3.4 nm
  • 10 bases/turn
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11
Q

Explain Z-DNA.

A
  • Left handed helix (zig zag appearance)
  • Left turn every 4.6 nm
  • 12 bases/turn
  • Occurs when [G/C] or [Salt] is too high
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12
Q

Explain “histones”.

A

The DNA that makes up a chromosome is wound around a group of small basic proteins called histones, forming chromatin.

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13
Q

To prevent DNA from unraveling, what repeating unit forms at the end of DNA (aka telomeres)?

A

TTAGGG

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14
Q

If sequencing for telomeres is lost during replication, it can be replaced by what enzyme?

A

Telomerase

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15
Q

A region of DNA found in the center of chromosomes and are composed of heterochromatin (high G-C content).

A

Centromeres

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16
Q

To begin the process of replication, DNA unwinds at points called?

A

Origins of Replication

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17
Q

The enzyme responsible for unwinding DNA, generating two single stranded template strands ahead of polymerase.

A

Helicase

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18
Q

Unwound strands are kept from reannealing or being degraded by?

A

Single-Stranded DNA-Binding Proteins

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19
Q

How can DNA be degraded?

A

Nucleases

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20
Q

Supercoiling causes torsional strain on the DNA molecule, which can be released by what (hint: creates nicks in the DNA molecule to create negative supercoils)?

A

DNA Topoisomerases (Sometimes DNA gyrase for prokaryotes)

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21
Q

Why is DNA termed semiconservative?

A

Because one parental strand is retained in each of the two resulting identical double stranded DNA molecules.

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22
Q

What is responsible for reading the DNA template (or parental strand) and synthesizing the new daughter strand?

A

DNA polymerases

23
Q

How do DNA polymerases read and synthesize?

A

Read: 3’ to 5’
Synthesize: 5’ to 3’ (just like DNA repair, RNA transcription and RNA translation)

24
Q

DNA cannot be synthesized without an adjacent nucleotide to hook onto, so a small RNA primer is put down by?

A

Primase

25
Q

After a primer is added to DNA, what happens next?

A
  • Eukaryotes: DNA polymerases alpha, delta and epsilon
  • Prokaryotes: DNA polymerase III

(BOTH synthesize daughter strands of DNA in the 5’ to 3’ manner.)

26
Q

The RNA primer must be removed to maintain the sanctity of the genome and this is accomplished by the enzymes?

A

Prokaryotes: DNA polymerase I
Eukaryotes: RNase H

27
Q

These enzymes add DNA nucleotides where the RNA primer had been.

A

Prokaryotes: DNA polymerase I
Eukaryotes: DNA polymerase delta

28
Q

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

A

DNA ligase

29
Q

What eukaryotic DNA polymerases are important to the process of DNA repair?

A

DNA polymerases beta and epsilon

30
Q

What eukaryotic DNA polymerase replicates mitochondrial DNA?

A

DNA polymerase gamma

31
Q

These eukaryotic polymerases are assisted by the PCNA protein, which assembles into a trimer to form the sliding clamp. The clamp helps to strengthen the interaction between these DNA polymerases and the template strand.

A

DNA polymerases delta and epsilon

32
Q

Cancer cell migration to distant tissues by the blood stream or lymphatic system.

A

Metastasis

33
Q

Tumor surpressor genes (p53 or Rb) that encode proteins that inhibit the cell cycle or participate in DNA repair processes. These genes normally function to stop tumor progression.

A

Antioncogenes

34
Q

During synthesis, the two double-stranded DNA molecules will pass through part of the DNA polymerase enzyme for ?

A

Proofreading

35
Q

What is mismatch repair?

A

A type of machine repair that is available in the G2 phase of the cell cycle. The enzymes encoded here have genes MLH1 and MSH2, which detect and remove errors introduced in replication that were missed in the S phase.

36
Q

When our cell machinery recognizes damage or lesions to our DNA (specifically in the G1/G2 cell cycle phases), there are what two types of repair?

A
  • Nucleotide Excision Repair

- Base Excision Repair

37
Q

Ultraviolet light induces the formaton of dimers between adjacent thymine residues in DNA. These residues are removed by a cut-and-patch mechanism called?

A

Nucleotide Excision Repair (NER)

38
Q

This nuclease makes nicks in the phosphodiester backbone of a damaged DNA strand (on both sides of the thymine dimer) and removes the defective oligonucleotide.

A

Excision Endonuclease

39
Q

Thermal energy can be absorbed by DNA and may lead to cytosine deamination (where cytosine converts to uracil; which is not DNA based). How are these residues repaired?

A

Base Excision Repair

40
Q

When a base deamination is recognized, it is then removed by a glycosylase enzyme. This enzyme leaves behind an apurinic/apyrimidinic site (abasic site). This site can be recognized by a specific nuclease that eliminates the damaged sequence from the DNA. What nuclease is this?

A

“AP” Endonuclease

41
Q

A type of cloning that requires the investigator to ligate the DNA of interest into a piece of nucleic acid. Usually a bacterial or viral plasmid that can be transferred to a host bacterium after insertion of the DNA of interest.

A

Vector

42
Q

Enzymes that are isolated from bacteria and are used to recognize specific double stranded DNA sequences.

A

Restriction Enzymes (AKA Restriction Endonucleases)

43
Q

Contain large fragments of DNA, and include both coding (exon) and noncoding (intron) regions of the genome.

A

Genomic Libraries

44
Q

Constructed by reverse-transcribing processed mRNA. Sometimes lacks noncoding regions, such as introns, and only includes the genes that are expressed in the tissue from which the mRNA was isolated.

A
  • cDNA libraries (complementary DNA)
    or
  • Expression Libraries
45
Q

This is a tool where complemetary base pair sequences are joined. This technique uses two single-stranded sequences and is a vital part of PCR and southern blotting.

A

Hybridization

46
Q

An automated process that can produce millions of copies of a DNA sequence without amplifying the DNA in bacteria. Requires primers, heat and a denovo DNA polymerase.

A

Polymerase Chain Reaction (PCR)

47
Q

What is the preffered gel for DNA (in gel electrophoresis)?

A

Agarose Gel

48
Q

A technique used to seperate macromoleculs by size and charge.

A

Gel Electrophoresis

49
Q

Used to detect the presence and quantity of various DNA strands in a sample.

A

Southern Blot

50
Q

What binds to targeted complemetary sequences and forms a double-stranded DNA helix (hint: indicates the presence of a desired sequence).

A

Probe

51
Q

A cloned gene that is introduced to a developing organism.

A

Transgene

52
Q

Mice that are altered in their germ line by the introduction of a cloned gene into fertilized ova or embryonic stem cell.

A

Transgenic Mice

53
Q

Mice that have been intentionally mutated by the deletion of a gene.

A

Knockout Mice

54
Q

Organisms that contain cells from two different lineages (such as mice formed by integration of transgenic embryonic stem cells into a normal mouse blastocyst).

A

Chimeras

MCAT Biochemistry (7 decks)

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