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M1 > Nucleic Acid Structures > Flashcards

Nucleic Acid Structures Flashcards

1
Q

join the 3’-carbon of one sugar to the 5’-carbon of the next sugar

A

Phosphodiester bonds

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2
Q

DNA chains are ______ meaning on side runs from 5’ to 3’ while the other side runs from 3’ to 5’ end

A

antiparallel

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3
Q

located on the outside of the double helix

A

phosphate groups. Used in phosphodiester bonds

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4
Q

is right-handed and contains ______ per turn.

A

B form of DNA; 10 base pairs

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5
Q

Alkali or heat causes the strands of DNA to separate but does not break phosphodiester bonds.

A

Denaturing

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6
Q

If strands of DNA are separated by heat and then the temperature is slowly decreased under the appropriate conditions, base pairs reform, and complementary strands of DNA come back together.

A

Renaturing/annealing

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7
Q

A single strand of DNA or RNA pairs with complementary base sequen- ces on another strand of DNA or RNA.

A

Hybridization

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8
Q

a segment of a DNA molecule that contains the information required for the synthesis of a functional biological product, whether protein or RNA

A

gene

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9
Q

only known functions of DNA:

A

storage of biological information transmission of that information to the next generation

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10
Q

Pneumococcus type:

  • Live (smooth bacteria):
  • Heat-killed (smooth bacteria:
  • Live (rough bacteria)
  • Mixture of Heat-killed (smooth bacteria) + Live (rough bacteria)

Mouse fate?

A
  • Mouse dies
  • Mouse lives
  • Mouse lives
  • Mouse dies
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11
Q
  • protein injection:
  • lipids injection:
  • carbohydrates injection:
  • nucleic acids fraction:
A
  • mouse lives
  • mouse lives
  • mouse lives
  • mouse dies
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12
Q

Gene flow

A

replication (DNA) transcription/reverse transcription (RNA) translation protein

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13
Q

associated with gene silencing

A

methylation (5-methylcytosine)

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14
Q
A
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15
Q

Catalyzes the formation of DNA chains

A

DNA Polymerase

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16
Q

short (typically < 50 nucleotides) nucleic acid

A

oligonucleotide

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17
Q

longer nucleic acid

A

polynucleotide

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18
Q

All nucleic acid sequences are written in a ________ direction

A

5’ to 3’ direction

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19
Q

Severs p-type linkage

A

Endonuclease

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20
Q

severs d-type linkage

A

exonucleases (cleavage on the edges of the strand)

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21
Q

Classes of RNA:

A
  • ribosomal RNAs (rRNAs) = components of ribosomes
  • messenger RNAs (mRNAs) = intermediates in protein synthesis
  • transfer RNAs (tRNAs) = adapter molecules that translate the information in mRNA into a specific amino acid sequence
  • noncoding RNAs (ncRNAs) = wide variety of functions
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22
Q

4 Basic Molecular Genetic Processes

A
  1. Transcription
  2. RNA Processing
  3. mRNA translation
  4. Replication
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23
Q

Formation of 3’ to 5’ Linkage

A

How phoshodiester bonds are linked 3’ to 5’ dispite the strand still going from 5’ to 3’ end.

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24
Q

The normal form of DNA found in mammals

Most stable for a random-sequence DNA molecule under physiological conditions

characteristic:

A

B form

perpendicular bases

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25
Q

right-handed double helix with a wider helix, 11 bp/turn, and a tilted plane

favored in solutions devoid of water

A

A-form DNA

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26
Q

left-handed helix with 12 bp/turn and a backbone with a zig-zag appearance

appears more slender and elongated

A

Z-form DNA

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27
Q

Comparison of A, B, and Z forms of DNA

A
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28
Q

Stabilizing Forces of DNA

A
  • Hydrophobic Interactions Among the Bases
  • Electrostatic Interactions of the Negatively Charged Phosphate Groups; Counter-ions Such as Mg++; and Basic Proteins
  • Hydrogen Bonds (weak forces)
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29
Q

the observed decrease in the absorption of UV light when complementary strands are paired

A

hypochromic effect

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30
Q

Stabilization of the DNA Double Helix

A
  • metal cations that shield the negative charges of backbone phosphates
  • base stacking interactions between successive base pairs
    • successive G≡C or C≡G are stronger than successive A=T or T=A
    • duplexes with higher G≡C context are more stable
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31
Q

the observed increase in the absorption of UV light when a double-stranded nucleic acid is denatured

A

hyperchromic effect

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32
Q

monitoring UV absorption at ______nmcan detect the transition from double-stranded to single-stranded DNA

A

260 nm

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33
Q

Absorption of light in different forms of DNA

Describe the graph for the following

  • Single stranded DNA
  • Double stranded DNA
A
  • linear graph
  • sigmoidal curve
34
Q

An increase in the percentage of C + G bonds _______ the melting point.

35
Q

Consists of short (~20 nts or less) that are repeated many thousands or several million times. Located mostly in centromeres. Sometimes called satellite DNA

A

Highly Repetitive DNA

36
Q

DNA sequences that are repeated from 100 - 1000x times. The sequences are several hundred to several thousands bps long. Usually found in tandem arrays among transcribed single-copy DNA

A

Moderately Repetitive DNA

37
Q

DNA sequences that are present in only one copy are referred to an unique or single copy DNA. Usually, code for proteins; pseudogenes (not expressed) and introns (found within functional genes)/spacers (between genes).

A

Single - Copy DNA

38
Q

Defined Order Sequences

39
Q

region of DNA that is identical when read either forward or backward

applied to regions of DNA with inverted repeats

A

palindrome

40
Q

sequence when the inverted repeat occurs within each individual strand

A

mirror repeat

41
Q

Secondary Structures of DNA

A
  • Hairpin
  • Stem-Loop
42
Q

Tertiary Structure or DNA

A
  • Pseudoknot
43
Q

Types of Histones

A
  • H1
  • H2A
  • H2B
  • H3
  • H4

evolutionary conserved

44
Q

Histone octamer

A

2 copies of H2A, H2B, H3, and H4 bound up in an octet and tied by one copy of HI

45
Q

Histones

A
  • Genes are highly conserved
  • Expressed during the S-phase of the cell cycle
  • The mRNAs contain no poly-A tails
  • Genes have no introns and occur in tandem repeats
  • NOT associated with bacterial or mitochondrial DNAs
46
Q

Organization of chromatin in the cell

48
Q

The linear chromosomes of eukaryotes have many origins of replication usually spaced about _________ kilobase pairs (kb) apart.

49
Q

At each replication fork synthesis of the leading strand is ________ and synthesis of the lagging strand is _________.

A

continuous; discontinuous

50
Q

Short discontinuous segments, which later are joined

A

Okazaki fragments

51
Q

BAsic principles that apply to DNA synthesis in every organism

A
  • DNA replication is semiconservative
  • replication begins at an origin and usually proceeds bidirectionally
  • DNA synthesis proceeds in a 5′→3′ direction and is semidiscontinuous
52
Q

each DNA strand serves as a template for the synthesis of a new strand

produces two new DNA molecules, each with one new strand and one old strand

established by Meselson and Stahl in 1957

A

semiconservative replication

53
Q

DNA replication and histone synthesis in the mammalian cell cycle takes place during the

54
Q

The programmed suicide of cells

55
Q

General Characteristics of DNA Replication

A
  1. Occurs in a 5’ —-> 3’ direction
  2. DNA repln. requires:
    1. a DNA template
    2. Mg++
    3. all 4 dNTPs
    4. ATP
    5. many proteins
    6. RNA primers
    7. most importantly, DNA-dependent DNA polymerases.
56
Q

a structure that would allow molecules to be lined up in a specific order and joined to create a macromolecule with a unique sequence and function

A

template

the structure of DNA revealed one strand is the complement of the other.

each strand provides the template for a new strand

57
Q

a strand segment with a free 3′-OH group to which a nucleotide can be added

must be complementary to the template

many are RNA oligonucleotides

58
Q

the free 3′ end of the primer

A

primer terminus

59
Q

DNA Polymerases

60
Q

removes RNA until it gets to a single RNA nucleotide

61
Q

Removes single RNA nucleotide after RNase H removal of RNA

A

Flap endonuclease 1

62
Q

fill in the gaps in the removal of RNA primers

a reverse transcriptase that has its own RNA template

A

telomerase

63
Q

Characteristics of Coronavirus Virion

A

~125 nm diameter, 30 Kb (+) RNA genome

with :

  • Ribonucleoprotein complex (RNP)
  • Membrane Glycoprotein (M)
  • Envelope protein (E)
  • Spike protein (S)
  • C-terminal and Transmembrane domains
64
Q

Coronavirus Replication

A

RNA-dependent RNA Polymerase or Replicase

The CoV replicase requires functional integration of RNA polymerase, capping and proof-reading.

65
Q

Unusual/Modified RNA Bases

66
Q

process by which an enzyme system converts the genetic information in dsDNA into an RNA strand with a complementary base sequence

A

transcription

67
Q

RNA is synthesized by RNA polymerases using

A

DNA templates and ribonucleoside 5’-triphosphates

68
Q

RNA can be used as a template for synthesis of DNA by

A

reverse transcriptases

69
Q

RNA can act as both a

A

catalyst and carrier of genetic information

70
Q

Major types of RNAs

73
Q

responsible for cleavage in tRNA processing

A

Nucleotidyl transferase

74
Q

In prokaryotes, messenger RNA undergo ________ processing at all

A

little or no

75
Q

Formation of the 5′ Cap

A

formed by condensation of a molecule of GTP with the triphosphate at the 5′ end of the transcript

methylation occurs at the N-7 guanine and often the 2′-OH groups of the two nucleotides adjacent to the cap

methyl groups are derived from S-adenosylmethionine

76
Q

A single polypeptide protein with 3 different catalytic domains

A

DNA Polymerase I

77
Q

Palindrome & Palindrome-like Sequences

A
  1. EcoRI restriction site
  2. Single and double stranded inverted repeats
    1. Hairpin
    2. Cruciform
  3. Mirror repeat
78
Q

separate double-stranded DNA into single strands allowing each strand to be copied

79
Q

catalyze and guide the unknotting or unlinking of DNA by creating transient breaks in the DNA using a conserved tyrosine as the catalytic residue

A

topoisomerase

80
Q
  • RNase D cuts at the :
  • RNase P cuts at the :
  • Nucleotidyl transferase:
  • Final structure of Transfer RNA is ______ long
A
  • RNase D cuts at the 3’ end
  • RNase P cuts at the 5’ end
  • Nucleotidyl transferase adds the 3’-CCA to all mature tRNA
  • Final structure is 70-90 nucleotides long
81
Q

As DNA polmerase extends the strand, it does so by

A

releasing a pyrophosphate molecule

M1 (48 decks)

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