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MCAT: Biochemistry > Chapter 6: DNA and Biotechnology > Flashcards

Chapter 6: DNA and Biotechnology Flashcards

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MCAT flashcards
1
Q

What does DNA stand for?

A

Deoxyribonucleic acid

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2
Q

Where is the bulk of DNA found in eukaryotic cells? Where is it also present?

A
  • In chromosomes in the nucleus

- Mitochondria and chloroplasts

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3
Q

Define nucleosides.

A
  • Composed of five-carbon sugar (pentose) bound to a nitrogenous base
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4
Q

In nucleosides, how are nitrogenous bases linked to sugars?

A

Covalently linking the base to C-1’ of the sugar

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5
Q

When are nucleotides formed? What is attached to where?

A

When one or more phosphate groups are attached to C-5’ of a nucleoside

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6
Q

How are nucleotides named?

A
  • According to the number of phosphates bound

- ex: Adenosine di- and triphosphate

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7
Q

What are the building blocks of DNA?

A

Nucleotides

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8
Q

Nucleic acids are classified according to what?

A

According to the pentose they contain

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9
Q

What is the difference between the pentose in RNA and DNA?

A

RNA: ribose
DNA: deoxyribose

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10
Q

What is deoxyribose? How is it different than ribose?

A

Ribose with the 2’-OH group replaced by -H

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11
Q

Name the 5 nitrogenous bases. Which one is only present in DNA? Which one is only present in RNA?

A
  • Adenine
  • Guanine
  • Cytosine
  • Uracil (RNA)
  • Thymine (DNA)
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12
Q

What is the backbone of DNA composed of? In what direction is DNA read from?

A
  • Alternating sugar and phosphate groups

- Read from 5’ to 3’

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13
Q

How are nucleotides joined together? What type of bond?

A

3’-5’ phosphodiester bonds

- Phosphate group links the 3’ carbon of one sugar to the 5’ phosphate group of the next incoming sugar

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14
Q

What is the overall charge of DNA and RNA strands? Why?

A
  • Negative

- Phosphates carry a negative charge

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15
Q

What does the 5’ end of DNA contain? What does the 3’ end contain?

A

5’: -OH or phosphate group bound to C-5’ of the sugar

3’: free -OH on C-3’ of the sugar

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16
Q

How would you write (5’-ATG-3’) backwards?

A

3’-GTA-5’

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17
Q

Write the following DNA strand while showing the position of phosphates: 5’-ATG-3’

A

pApTpG

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18
Q

DNA is generally ______-stranded and RNA is generally ______-stranded.

A

double, single

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19
Q

What are the two families of nitrogen-containing bases found in nucleotides?

A

Purines and pyrimidines

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20
Q

How do the ring structures of purines and pyrimidines differ?

A

Purine: two rings
Pyrimidine: one ring

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21
Q

What are the two purines found in nucleic acids?

A

Adenine (A) and Guanine (G)

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22
Q

What are the three pyrimidines found in nucleic acids?

A

Cytosine (C), Uracil (U), and Thymine (T)

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23
Q

Purines and pyrimidines are examples of biological _______ _______

A

aromatic heterocycles

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24
Q

In chemistry, the term aromatic describes any unusually stable ring that adheres to the which four specific rules?

A

1) Compound is cyclic
2) Compound is planar
3) Compound is conjugated
4) Compound respects Huckel’s rule

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25
Q

What is a conjugated compound?

A

Has alternating single and multiple bonds, or lone pairs, creating at least one unhybridized p-orbital for each atom in the ring

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26
Q

What is Huckel’s rule?

A

Compound has 4n + 2 (where n is any integer) pi electrons

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27
Q

What is the cause of the extra stability in aromatic compounds?

A

The delocalized pi electrons, which can travel throughout the entire compound using available p-orbitals

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28
Q

Are aromatic compounds reactive?

A

No, they are fairly unreactive

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29
Q

What are heterocycles?

A

Ring structrues that contain at least two different elements in the ring

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30
Q

Who presented the three-dimensional structure of DNA in 1953?

A

James Watson and Francis Crick

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31
Q

What are the key features of the Watson-Crick model?

A
  • Two strands of DNA are antiparallel (opposite direction)
  • Sugar-phosphate backbone is on the outside of the helix while the nitrogenous bases are on the inside
  • Complementary base pairings
  • Chargaff’s rule
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32
Q

Where is the sugar-phosphate backbone located in DNA? Where are the nitrogenous bases located?

A

Sugar-phosphate backbone: outside of the helix

Nitrogenous bases: inside

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33
Q

What is adenine (A) always paired with? Through how many hydrogen bonds?

A
  • Thymine (T) - DNA or Uracil (U) - RNA

- 2 hydrogen bonds

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34
Q

What is guanine (G) always paired with? Through how many hydrogen bonds?

A
  • Cytosine (C)

- 3 hydrogen bonds

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35
Q

What would be the complimentary strand of DNA for the following strand: 5’-ATCG-3’

A

5’-CGAT-3’

36
Q

Which complementary pair is stronger? Why?

A
  • G-C

- Because of the three hydrogen bonds

37
Q

What does Chargaff’s rules state?

A
  • Total purines will be equal to total pyrimidines
  • %A = %T
  • %G = %C
38
Q

What hand is the DNA helix? What is it called?

A
  • Right-handed helix

- B-DNA

39
Q

How often does the helix in B-DNA make a turn? How many bases does it contain within that span?

A
  • 3.4 nm

- 10 bases

40
Q

How can major and minor grooves be identified? What is their role?

A
  • Between the interlocking strands and are often the site of protein binding
  • Provide binding sites for regulatory proteins
41
Q

Apart from B-DNA, what is another form of DNA? Why is it called that?

A
  • Z-DNA

- For its zigzag appearance

42
Q

What hand is Z-DNA? How often does the helix make a turn? How many bases does it contain within that span?

A
  • Left-handed helix
  • 4.6 nm
  • 12 bases
43
Q

What contributes to the formation of Z-DNA?

A

High GC-content or high salt concentration

44
Q

Has Z-DNA been attributed biological activity? Why or why not?

A

No, partly because it is unstable and difficult to research

45
Q

How can DNA be denatured? What does that result in?

A
  • By conditions that disrupt hydrogen bonding and base-pairing
  • Resulting in the “melting” of the double helix into two single strands that have separated from each other
46
Q

What does not break during DNA denaturation?

A

The covalent links between the nucleotides in the backbone of the DNA

47
Q

What is commonly used to denature DNA?

A

Heat, alkaline pH, and chemicals (formaldehyde)

48
Q

How can denatured be brought back together? What is this called?

A
  • Reannealed

- If the denaturing condition is slowly removed

49
Q

Annealing of complementary DNA strands is an important step in many laboratory processes. Give examples.

A

Polymerase chain reactions (PCR) and the detection of specific DNA sequences

50
Q

How does PCR and detection of specific DNA sequences work?

A
  • Probe DNA (DNA with known sequence) is added to a mixture of target DNA sequences
  • Probe DNA binds to target DNA sequences, evidence of the presence of the gene of interest
51
Q

How many phosphate groups can nucleotides contain?

A

One to three phosphate groups

52
Q

How does the aromaticity of purines and pyrimidines underscore their genetic function?

A
  • Make compounds stable and unreactive

- Important for storing genetic information and avoiding spontaneous mutations

53
Q

If a strand of RNA contained 15% cytosine, 15% adenine, 35% guanine, and 35% uracil, would you violate Chargaff’s rules? Why or why not?

A
  • No

- RNA is single-stranded, so the complementarity seen in DNA does not hold true

54
Q

In humans, DNA is divided up among the ___ chromosomes found in the nucleus of the cell.

A

46

55
Q

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

A

histones, chromatin

56
Q

How many histone proteins are found in eukaryotic cells? What are they?

A
  • H2A, H2B, H3, H4

- H1

57
Q

How does a nucleosome form?

A
  • Two copies each of the histone proteins H2A, H2B, H3, and H4 form a histone core
  • 200 base pairs of DNA are wrapped around this protein complex, forming a nucleosome
58
Q

What does the histone H1 do?

A

Seals off the DNA as it enters and leaves the nucleosome, adding stability to the structure

59
Q

What contributes to the compaction of DNA?

A
  • Supercoiling of the DNA double helix

- Nucleosomes

60
Q

What are nucleoproteins? Give an example.

A
  • Proteins that associate with DNA

- Histones

61
Q

What would be the consequence of a nucleosome without the histone H1?

A

Sensitive to nuclease

62
Q

As a whole, DNA and its associated histones make up ______ in the nucleus

A

chromatin

63
Q

What is heterochromatin? How does it appear under light microscopy?

A

Dense, transcriptionally silent DNA that appears dark under light microscopy

64
Q

What is euchromatin? How does it appear under light microscopy?

A

Less dense, transcriptionally active DNA that appears light under light microscopy

65
Q

A small percentage of the chromatin remains compacted during interphase and is referred to as ____________.

A

heterochromatin

66
Q

Why can’t DNA replication extend all the way to the end of a chromosome? What is the solution?

A
  • Results in losing sequences and information with each round of replication
  • Solution
67
Q

What are telomeres? What do they contain? Why?

A
  • The ends of chromosomes

- Contain high GC-content to prevent unraveling of the DNA

68
Q

What happens to telomeres during replication? How can this be (partially) reversed?

A
  • Slightly shortened

- By the enzyme telomerase

69
Q

In each round of DNA replication, some of the sequence is lost. How can it be replaced?

A

By the enzyme telomerase

70
Q

Telomerase is more highly expressed in which kinds of cells?

A

Rapidly dividing cells

71
Q

Where are centromeres located? What is their major function?

A
  • Located in the middle of chromosomes

- Hold sister chromatids together until they are separated during anaphase in mitosis

72
Q

What contains a high GC-content to maintain a strong bond between chromatids?

A

Centromeres

73
Q

Which histone is not part of the histone core around which DNA wraps to form chromatin?

A

H1

74
Q

What property of telomeres and centromeres allow them to stay tightly raveled, even when the rest of DNA is uncondensed?

A

High GC-content increases hydrogen bonding, making the association between DNA strands very strong at telomeres and centromeres

75
Q

What is the replisome or replication complex?

A

Set of specialized proteins that assist the DNA polymerases

76
Q

To being the process of replication, DNA unwinds at points called _______________

A

origins of replication

77
Q

The generation of new DNA proceeds in ____ directions, creating ______________ on both sides of the origin

A
  • both

- replication forks (2 in total)

78
Q

What enzymes unwound DNA during DNA replication?

A

Helicases

79
Q

Prokaryotes have a ______ chromosome that contains ___ origin of replication

A

circular, one

80
Q

Eukaryotes have a ______ chromosome that contains ___ origin of replication

A

linear, many

81
Q

What are unwound strands of DNA kept from reannealing or being degraded by during DNA replication?

A

Single-stranded DNA-binding proteins

82
Q

During DNA replication, as the replication forks move toward each other and ___________ are created, the chromatids will remain connected at the _________.

A

sister chromatids, centromere

83
Q

What is supercoiling? When does it happen?

A
  • Wrapping of DNA on itself as its helical structure is pushed ever further toward the telomeres during replication
  • As the helicase unwinds the DNA during DNA replication
84
Q

What enzymes introduces negative supercoils to alleviate the torsional stress and reduce the risk of strand breakage?

A

DNA topoisomerase II (DNA gyrase)

85
Q

How does DNA topoisomerase II (DNA gyrase) work?

A

Alleviates torsional stress by working ahead of helicase, nicking both strands, passing the DNA strands through the nick and then resealing both strands

86
Q

Why is the replication process is termed semiconservative?

A

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

87
Q

Which enzyme is responsible for reading the DNA template, or parental strand, and synthesizing the new daughter strand?

A

DNA polymerases

MCAT: Biochemistry (12 decks)

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