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MOLBIO > 4 | Nucleotides, Nucleic Acid, and Heredity > Flashcards

4 | Nucleotides, Nucleic Acid, and Heredity Flashcards

1
Q

What are the 2 nucleic acid in cells?

A

◆ Ribonucleic acids (RNA)
◆ Deoxyribonucleic acids (DNA)

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2
Q

Both RNA and DNA are polymers built from monomers called (___________) each of which consists of purine or pyrimidine bases, deoxyribose, ribose, and phosphate.

A

Nucleotides

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3
Q

What are 3 substituents with nitrogen and their location?

A
  • Amino group is located at C6
  • Another Nitrogen is located at the 7th position.
  • Hydrogen is attached to the sugar moiety
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4
Q

Adenine IUPAC naming?

A

6-Aminopurine.

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5
Q

Guanine IUPAC naming?

A

2-Amino-6-Oxypurine

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6
Q

N1, start counting clockwise or counterclockwise

A

counterclockwise

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7
Q

Cytosine IUPAC naming?

A

2-Oxy-4-Aminopyrimidine

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8
Q

Thymine IUPAC naming?

A

2,4-dioxy-5-methyl pyrimidine

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9
Q

Uracil IUPAC naming?

A

2,4,-dioxy pyrimidine

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10
Q

Uracil and Thymine are lookalikes, except that there
is no (____________) attached to the 5th position of
the pyrimidine ring.

A

methyl group

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11
Q

Nucleosides is a compound that consists of D-ribose or
2-deoxy-D-ribose bonded to a purine or pyrimidine
base by?

A

β-N-glycosidic bond

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12
Q

β means (?) direction

A

Upward direction

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13
Q

The -OH group of the sugar is bonded to the (?) of sugar moiety of the pyrimidine bases?

A

N1

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14
Q

The -OH group of the sugar is bonded to the (?) of sugar moiety of the purine bases?

A

N9

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15
Q

Cytosine, Uracil, and Thymine is N1 or N9?

A

N1

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16
Q

Adenine and Guanine is N1 or N9?

A

N9

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17
Q

transcribe AMP?

A

Adenosine Monophosphate

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18
Q

transcribe ADP?

A

Adenosine Diphosphat

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19
Q

transcribe ATP?

A

Adenosine Triphosphate

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20
Q

It is currency for energy?

A

ATP

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21
Q

Thymine is present, it’s different from Uracil
because of the presence of methyl group at 5th
position of the pyrimidine ring, connected with N1C1
or NC glycosidic bond.

A

Deoxythymidine 3’-monophosphate (3’-dTMP)

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22
Q

N9 is at the (?) aromatic ring

A

2nd aromatic ring

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23
Q

It is the sequence of nucleotides, beginning with the nucleotide that has the free 5’ terminus.

A

Primary (1 ◌ํ) Structure

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24
Q

It refers to the order of bases in the polynucleotide
sequences

A

Primary (1 ◌ํ) Structure

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25
Q

The backbone of DNA can be seen here (sugar moiety and
phosphate group). The backbone is constant, only
the bases change

A

Schematic diagram of a nucleic acid molecule

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26
Q

The double helix model of DNA 2 ◌ํ structure
was proposed by? and what year?

A

James Watson and Francis Cricks in 1953

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27
Q

Three dimensional structure of the DNA double
helix. The blue and reddish ribbons represent the
sugar phosphate “backbone.”

A

DNA Double Helix

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28
Q

What rule said that: For each adenine on one chain, a
thymine is aligned opposite it on the other chain;
Each guanine on one chain has a cytosine aligned
with it on the other chain.

A

Chargaff’s rule

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29
Q

It is the most common and most stable form.

A

B-DNA

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30
Q

With B-DNA, a distinguishing feature is the presence of a (__________ and ___________), which arise because the two strands are not equally spaced around the helix.

A

major groove and a minor groove

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31
Q

Histones are rich in the basic amino acids
Lys and Arg, whose side chains have a

A

Positive charge

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32
Q

The negatively-charged DNA molecules are provided by the?

A

phosphate ions depending if it is monophosphate, diphosphate, or triphosphate

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33
Q

The negatively-charged DNA molecules are
provided by the phosphate ions depending
if it is monophosphate, diphosphate, or
triphosphate and positively-charged
histones attract one another and form units called ?

A

nucleosomes

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34
Q

A core of with histone molecules around which the
DNA helix is wrapped.

A

Nucleosome

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35
Q

Nucleosomes are further condense into

A

chromatin

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36
Q

DNA double helix nm?

A

2 nm

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37
Q

Nucleosome nm?

A

11 nm

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38
Q

“beads on a string” chromatin form nm?

A

11 nm

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39
Q

Loops (50 turns per loop) nm?

A

250 nm

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40
Q

Selonoid (6 nucleosomes per turn) nm?

A

30 nm

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41
Q

Chromosome (stacked minibands) nm?

A

840 nm

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42
Q

Transfer RNA molecules contain not
only cytosine, guanine, adenine, and uracil, but also
several other modified nucleotides, such as

A

1-methylguanosine

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43
Q

Miniband nm?

A

840 nm

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44
Q

Transports amino acids to site of protein synthesis

A

Transfer (tRNA)

45
Q

Size of Transfer (tRNA)

A

Small

46
Q

Combines with proteins to form ribosomes, the site of protein synthesis

A

Ribosomal RNA (rRNA)

47
Q

Size of rRNA

A

several kinds-variable in size

48
Q

Directs amino acid sequence of proteins

A

messenger RNA (mRNA)

49
Q

SIZE OF messenger RNA (mRNA)

A

small

50
Q

Processes initial mRNA to its mature form in eukaryotes

A

small nuclear RNA (snRNA)

51
Q

SIZE OF small nuclear RNA (snRNA)

A

small

52
Q

PROTECTS ANIMAL GENOMES AGAINST TRANSPOSONS

A
  • Piwi-associated RNA(piRNA)
53
Q

Affects gene expression; important in growth and development

A

micro RNA (miRNA)

54
Q

Affects gene expression; used by scientists to knock out a gene being studied

A

small interfering RNA(siRNA)

55
Q

SIZE OF small interfering RNA(siRNA)

A

SMALL

56
Q

SIZE OF micro RNA (miRNA)

A

SMALL

57
Q

Involved in activating or silencing specific genes

A

Long non-coding RNA (IncRNA)

58
Q

SIZE OF Long non-coding RNA (IncRNA)

A
  • VARIABLE
59
Q

Acts as miRNA sponge, controlling the effects of miRNA

A
  • CIRCULAR RNA
60
Q

SIZE OF Piwi-associated RNA(piRNA)

A
  • Small
61
Q

SIZE OF CIRCULAR RNA

A
  • VARIABLE
62
Q

The BER pathway contains two parts:

A
    1. A specific DNA glycolase (1) recognizes the damaged base and catalyzes the hydrolysis of the glycosidic bond between that base and the deoxyribose, then releases the damaged base completing the excision. The sugar-phosphate backbone is still intact. At the AP site (apurinic or apyrimidinic site) created in this way, (2) the backbone is cleaved by a second enzyme, endonuclease. A third enzyme, exonuclease (3), liberates the sugar-phosphate unit of the damaged site.
    1. In the synthesis step, the enzyme DNA polymerase (4) inserts the correct nucleotide, cytidine, and the enzyme DNA ligase seals (5) the backbone to complete the repair.
63
Q

Nucleotide of Adenine(DNA)

A
  • Deoxyadenosine 5’-monophosphate
64
Q

Nucleoside of Guanine(DNA)

A
  • Deoxyguanosine
65
Q

Nucleotide of Cytosine(DNA)

A
  • Deoxycytidine 5’-monophosphate
65
Q

Nucleotide of Guanine(DNA)

A
  • Deoxyguanosine 5’-monophosphate
65
Q

Nucleoside of Thymine(DNA)

A
  • Deoxythymidine
66
Q

Nucleotide of Thymine(DNA)

A
  • Deoxythymidine 5’-monophosphate
66
Q

Nucleoside of Guanine(RNA)

A
  • guanosine
67
Q

Nucleoside of Cytosine (DNA)

A
  • Deoxycytidine
68
Q

Nucleotide of Adenine(RNA)

A
  • adenosine 5’-monophosphate
68
Q

Nucleoside of Adenine(RNA)

A
  • adenosine
69
Q

Nucleotide of Guanine(RNA)

A
  • guanosine 5’-monophosphate
70
Q

Nucleoside of Uracil (RNA)

A
  • Uridine
71
Q

Nucleotide of Cytosine(RNA)

A
  • cytidine 5’-monophosphate
71
Q

Nucleotide of Uracil (RNA)

A
  • Uridine 5’-monophosphate
71
Q

Nucleoside of Cytosine (RNA)

A
  • cytidine
71
Q

It temporarily introduce either single or
double strand breaks in DNA.

A
  • Topoisomerases (also called gyrases)
71
Q

The structure of a typical prokaryotic ribosome. The
individual components can be mixed, producing
functional subunits. Reassociation of subunits gives
rise to an intact ribosome. The designation S refers to
Svedberg, a unit of relative size determined when
molecules are separated by centrifugation.

A
  • Structure of rRNA
72
Q

The designation S refers to
_______, a unit of relative size determined when
molecules are separated by centrifugation.

A
  • Svedberg
72
Q

a segment of DNA that carries a base sequence that
directs the synthesis of a particular protein, tRNA, or mRNA

A
  • gene
72
Q

a unit of relative size determined when
molecules are separated by centrifugation

A

Svedberg

73
Q

In bacteria, the gene is ______ (continuous or discontinuous)

A
  • continuous
74
Q

a section of DNA that, when transcribed, codes for a
protein or RNA

A
  • Exon
74
Q

In higher organisms, the gene is ______ (continuous or discontinuous)

A
  • discontinuous
75
Q

a section of DNA that does not code for anything
functional.

A
  • Intron
76
Q

The DNA in the chromosomes carries out two
functions:

A
  • 1) It reproduces itself. This process is called replication.
  • 2) It supplies the information necessary to make all the RNA and the proteins in the body, including enzymes.
76
Q

What are the 6 distinct steps in replication of DNA

A
  • 1) Opening up of the superstructure of the
    chromosomes.
  • 2) Relaxation of Higher-Order Structures of DNA.
  • 3) Unwinding the DNA Double Helix
  • 4) Primers/Primases
  • 5) DNA Polymerase
  • 6) Ligation
77
Q

One key step in this process is
_______________. This reaction eliminates some
of the positive charges on histones and
weakens the strength of the DNA-histone
interaction.

A
  • acetylation-deacetylation of lysine residues on histones
77
Q

Replication begins at a point in the DNA called

A
  • the origin of replication or a replication fork
78
Q

One key step in this process is
acetylation-deacetylation of lysine residues
on histones. This reaction eliminates some
of the positive charges on histones and
weakens the strength of the DNA-histone
interaction.

A
  • Opening up of the superstructure of the
    chromosomes.
78
Q

Topoisomerases (also called gyrases)
temporarily introduce either single or
double strand breaks in DNA. Once the
supercoiling is relaxed, the broken strands
are joined together and the topoisomerase
diffuses from the location of the replication
fork.

A
  • Relaxation of Higher-Order Structures of DNA.
79
Q

Replication of DNA molecules starts with
the unwinding of the double helix which
can occur at either end or in the middle.
Special unwinding proteins called
helicases attach themselves to one DNA
strand and cause the separation of the
double helix.

A
  • Unwinding the DNA Double Helix
80
Q

Special unwinding proteins called ____

A
  • Helicases
80
Q

They are short 4 to 15 nucleotides long
oligonucleotides synthesized from
ribonucleoside triphosphates. They are
needed to initiate the primase-catalyzed
synthesis of both daughter strands.

A
  • Primers/primases
80
Q

Once the two strands are separated at the
replication fork, the DNA nucleotides must
be lined up. In the absence of DNA
polymerases, this alignment is extremely
slow. The enzyme enables complementary
base pairing with high specificity. While
bases are being hydrogen bonded to their
partners, polymerases join the nucleotide
backbones. Along the lagging strand 3’—>5”,
the enzymes can synthesize only short
fragments, because the only way they can
work is from 5’ to 3’. These resulting short
fragments consist of about 200 nucleotides
each, named Okazaki fragments after their
discoverer.

A
  • DNA Polymerase
81
Q

They are short DNA segments
made of about 200 nucleotides in higher
organisms (eukaryotes) and of 2000
nucleotides in prokaryotes.

A
  • Okazaki fragments
82
Q

The 39-hydroxyl group at the end of the growing DNA chain is a

A
  • nucleophile
82
Q

The Okazaki fragments and any nicks
remaining are eventually joined by DNA
ligase.

A
  • Ligation
83
Q

It attacks at the
phosphorus adjacent to the sugar in the nucleotide,
which will be added to the growing chain.

A
  • 39-hydroxyl group at the end of the growing DNA chain
84
Q

Millions of copies of selected DNA fragments can be made within a few hours with high precision by a technique called ______

A
  • polymerase chain reaction (PCR)
84
Q

What temperature is required to
unwind the double helix to hybridize the primer to the target DNA.

A
  • 95°
84
Q

How many cycles are there in PCR?

A
  • 3 CYCLES
85
Q

What cycle is this- Oligonucleotides complementary to a
given DNA sequence prime the synthesis of only that sequence.

A
  • Cycle 1&2
86
Q

What cycle is this–Heat-stable Taq DNA polymerase survives many cycles of heating. Theoretically, the amount of the specific primed sequence is doubled in each cycle.

A
  • Cycle 2&3
87
Q

How Is DNA Repaired?

A

➔ The viability of cells depends on DNA repair
enzymes that can detect, recognize, and
remove mutations from DNA.
➔ Externally, UV radiation or highly reactive
oxidizing agents, such as superoxide, may
damage a base.
➔ Errors in copying or internal chemical
reactions, such as deamination of a base, can
create damage internally deamination of
cytosine turns it into uracil, which creates a
mismatch. The former C-G base pair becomes
a U-G mispairing that must be removed.

88
Q

One of the most common base repair preparation means.

A
  • BER (Base Excision Repair)
89
Q

The BER pathway contains two parts:

A
    1. A specific DNA glycolase (1) recognizes the damaged base and catalyzes the hydrolysis of the glycosidic bond between that base and the deoxyribose, then releases the damaged base completing the excision. The sugar-phosphate backbone is still intact. At the AP site (apurinic or apyrimidinic site) created in this way, (2) the backbone is cleaved by a second enzyme, endonuclease. A third enzyme, exonuclease (3), liberates the sugar-phosphate unit of the damaged site.
    1. In the synthesis step, the enzyme DNA polymerase (4) inserts the correct nucleotide, cytidine, and the enzyme DNA ligase seals (5) the backbone to complete the repair.

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