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DNA Flashcards

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1
Q

Who discovered the structure of DNA?

A

Rosalind Franklin, but died before she could publish her results. Her results were them stolen by a Watson & Crick, who took the credit and earned a noble prize.

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2
Q

What is the structure of DNA?

A

DNA is a Double Helix:
\__/
_/
/\
/___\

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3
Q

DNA is made up of nucleotides. What are the three components of nucleotides?

A
  1. A nitrogenous base
  2. A five-carbon sugar
  3. A phosphate backbone
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4
Q

What are the nitrogenous bases in DNA?

A

Adenine, Thymine, Guanine, and Cytosine (Note that these are also amino acids)

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5
Q

What are the nitrogenous bases in RNA?

A

Adenine, Uracil, Guanine, and Cytosine (Note that these are also amino acids)

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6
Q

What is Chargaff’s rule?

A

The nitrogenous bases are linked in base pairs of Adenine-Thymine/Uracil and Guanine-Cytosine. If this pattern does not follow, that is a genetic mutation.

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7
Q

What is point mutation?

A

A singular example of Chargaff’s rule being broken

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8
Q

What is the template strand and what is the complementary strand?

A

The template strand is the existing strand of DNA, and the complementary strand is the one that uses the template strand as a reference for its bases.

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9
Q

Are the amino acids in DNA acidic, basic, or neither?

A

Basic

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10
Q

Is it possible for uracil to mutate onto DNA/thymine to mutate onto RNA?

A

No, it’s one of the few truly impossible things in science

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11
Q

DNA replication is anti-parallel. What does it mean by anti-parallel?

A

DNA being anti-parallel means it’s parallel but moves in opposite directions of polarity, so one DNA strand moves in the 5’ to 3’ direction, while the other moves in the 3’ to 5’ direction.

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12
Q

How can you tell how many carbons there are in a carbon sugar?

A

You can count the corners, so a 5-carbon sugar had 5 carbons.

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13
Q

What is the main difference in the structure of RNA and DNA?

A

RNA is single-stranded, while DNA is double-stranded

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14
Q

What does RNA have that DNA doesn’t?

A

RNA has a 5 prime cap and a poly A (Adenine) tail, with no specific length.

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15
Q

What does DNA stand for?

A

Deoxyribonucleic Acid

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16
Q

What does RNA stand for?

A

Ribonucleic Acid

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17
Q

DNA strands are polynucleotides. What is a polynucleotide?

A

A polynucleotide is something made up of many individual units called nucleotides.

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18
Q

Where is the Nitrogenous base attached to the Five-carbon sugar

A

They are attached at the 1’ carbon of the sugar.

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19
Q

Where is the phosphate located in DNA?

A

Between the 5’ carbon of one sugar and the 3’ carbon of the neighboring nucleotide.

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20
Q

How are nucleotides attached to each other in DNA?

A

They attach to each other through phosphodiester bonds.

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21
Q

How are the nitrogenous bases in base pairs connected?

A

They are connected via hydrogen bonds.

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22
Q

Why do base pairs such as A-G or C-T not work?

A

They don’t work because the nitrogenous bases are not able to connect to each other strongly

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23
Q

What are pi-pi interactions?

A

pi-pi interactions form when the aromatic rings of the bases stack next to each other and share electron probabilities

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24
Q

The regularity of DNA’s structure causes two repeating and alternating spaces to form. What are they and what do they do?

A

They are called the major & minor grooves, and they can be used for base pair recognition and as a binding site for proteins.

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25
Q

DNA replication is semiconservative. What does that mean?

A

When DNA replicates, one strand is from an old DNA strand (the template strand) and one is newly synthesized (the complementary strand)

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26
Q

Match the nucleotides to their correct counterparts to make base pairs

5’ - G T C A C A G A T C T G A A - 3’

A

3’ - C A G T G T C T A G A C T T - 5’

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27
Q

DNA replication proceeds bi-directionally. what does that mean?

A

DNA replication occurs in both directions, with each strand going in a different direction

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28
Q

What does the helicase enzyme do?

A

The helicase enzyme separates the two DNA strands by breaking the hydrogen bonds that hold the base pairs together

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29
Q

When the DNA strands begin to separate, torsional strain is created. What enzyme solves this?

A

DNA gyrase solves this by reducing the torsional strain

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30
Q

What purpose do Single Stranded Binding Proteins (SSB Proteins) have?

A

SSB Proteins protect the separated stands from cleaving and stabilize the isolated strands in order to prevent them from sticking back together.

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31
Q

When the DNA is split up, what is the name of the newly split strands where DNA replication occurs?

A

The replication fork

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32
Q

What does DNA replication require to begin producing nucleotides?

A

DNA replication requires an RNA primer in order to begin, as it triggers DNA Polymerase III to begin making nucleotide strands.

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33
Q

What triggers DNA polymerase 3 and what does it do?

A

DNA polymerase is triggered once it sees the RNA primer, and it begins to synthesize a new strand in the direction that the DNA strand is being cut open, and does so in the opposite prime direction of the template strand. This strand is the leading strand.

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34
Q

What enzyme creates the RNA primer?

A

primease

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35
Q

When the leading strand begins making its nucleotide chain, what does the other strand do?

A

The other strand makes a primer that begins DNA polymerase in the direction opposite of the cutting, which is made in the opposite prime direction of their template strand. This strand is the lagging strand. As the replication fork is cut forward, more space is left behind the lagging strand, so another primer is placed, where DNA polymerase also starts. This repeats until the DNA strand is fully split

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36
Q

DNA replication is semi-discontinuous. what does that mean?

A

The leading strand makes nucleotides continuously, while the lagging strand makes them, then has to make another primer, making DNA replication semi-discontinuous.

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37
Q

When the RNA primers finish their job, what happens to them?

A

DNA polymerase 1 removes the RNA primers and replaces them with DNA material.

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38
Q

During DNA replication, there are spaces left between the lagging strands. What are they called and how are they fixed?

A

The spaces are known as Okazaki fragments and an enzyme known as DNA ligase seals the space between the primers

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39
Q

What part of DNA replication has exonuclease activity and what does it do?

A

DNA Polymerase 1 & 3 have exonuclease activity for the leading strand’s template strand and DNA Polymerase 1 also has exonuclease activity for the lagging strand. Exonuclease activity is done by an exonuclease enzyme that can remove incorrect nucleotides from a strand and replace them with the correct ones.

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40
Q

What does DNA Polymerase III do?

A

DNA polymerase III is activated by the RNA primers and makes nucleotide chains during DNA replication.

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41
Q

What does DNA Ligase do?

A

DNA ligase joins the sugar-phosphates of the Okazaki fragments in the lagging strand.

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42
Q

What does Primease do?

A

Primease makes the primers that begin the RNA chain from starch. Primease will be replaced by DNA material at the end of DNA replication.

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43
Q

What does Helicase do?

A

Helicase unwinds the double helix by breaking the hydrogen bonds that hold the base pairs together, creating the replication fork.

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44
Q

What does Topoisomerase do?

A

In the form of DNA gyrase, Topoisomerase relieves the DNA strand ahead of the replication fork in order to reduce the strain caused by the DNA strand splitting up.

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45
Q

Explain the steps of DNA replication

A
  1. The Helicase splits up the two DNA strands by breaking their hydrogen bonds
  2. Topoisomerase, in the form of DNA gyrase, relieves the DNA strand of stress due to it being split up.
  3. SSB proteins bind to the unzipped strands to keep them separated
  4. Primease adds primer on the DNA’s leading strand, and DNA Polymerase III adds nucleotide strands in the direction of the split
  5. A second primer is added to the other strand and DNA Polymerase makes nucleotide strands in the direction away from the split
  6. More primers are added to the lagging strand along with DNA polymerase to fill in the newly split parts.
  7. DNA polymerase I replace the primers with DNA material
  8. DNA ligase fills in the Okazaki fragments between the lagging strand’s primers
  9. An exonuclease enzyme checks for incorrect nucleotides and fixes them.
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46
Q

What are Amino Acids?

A

Essentials of the body that build muscles, prevent illnesses, and transport nutrients, among other things. They cannot naturally be made by the body and have to be consumed via other sources.

47
Q

What are Nucleotides?

A

Any member of a class of organic compounds made up of three subunits: a nitrogenous base, a five-carbon sugar, and a phosphate group. Nucleotides form the basic structural unit of nucleic acids such as DNA.

48
Q

What is RNA Polymerase?

A

RNA polymerase is similar to DNA polymerase, but it can add the nitrogenous bases found in RNA. It transcribes genetic information from DNA to RNA. RNA polymerase can also split the DNA during transcription.

49
Q

What is mRNA?

A

mRNA means messenger RNA. mRNA carries the genetic information outside of the nucleus to the rest of the body.

50
Q

What is tRNA?

A

tRNA means transfer RNA. Transfer RNA reads the mRNA sequence, then delivers amino acids to the protein synthesis machinery during translation.

51
Q

What is rRNA?

A

rRNA means ribosomal RNA. rRNA binds to mRNA during protein synthesis and translates the information in mRNA into protein.

52
Q

What is a Monomer?

A

A monomer works as a singular building block. For DNA, this would be a single nucleotide.

53
Q

What is a Polymer?

A

A polymer is a group of monomers. For DNA, this would be a set of nucleotides.

54
Q

What is Protein Synthesis?

A

The creation of protein cells with the support of DNA, RNA, and other enzymes. It begins in the nucleus, continues in the cytoplasm, and end in the ribosomes.

55
Q

What is a Replication Fork?

A

The replication fork is the unwound area of DNA during DNA replication and is where DNA polymerase and RNA primers create the new nucleotide strands.

56
Q

What are Okazaki Fragments?

A

Okazaki fragments are spaces left between the primers of the lagging strand. To fix this, an enzyme known as DNA ligase seals the space after the primers are replaced with DNA.

57
Q

What is the Leading(Template) Strand?

A

The leading strand is the strand that makes nucleotides in the direction of the split. The leading strand’s nucleotide production is continuous and goes along with the split, only requiring one primase.

58
Q

What is the Lagging (Complementary) Strand?

A

The lagging strand is the strand that makes nucleotides in the direction away from the split. Because the DNA keeps splitting even while the strand’s primer is placed, there are multiple primers placed, making the lagging strand discontinuous.

59
Q

What does DNA Polymerase 1 do?

A

DNA polymerase 1 removes the RNA primers and replaces them with DNA material during DNA replication.

60
Q

What does DNA gyrase do?

A

DNA Gyrase reduces strain on the unsplit DNA while the Helicase splits the rest of the DNA.

61
Q

What are proteins made of?

A

Proteins are made of a string of amino acids connected to each other by peptide bonds

62
Q

What are polypeptides?

A

Polypeptides are chains of amino acids

63
Q

What is mRNA?

A

mRNA is a copy of DNA that can leave the nucleus

64
Q

Where does the creation of mRNA take place?

A

The creation of mRNA takes place in the nucleus

65
Q

Why is mRNA needed?

A

mRNA is important because it can leave the nucleus while DNA can’t

66
Q

What is a gene?

A

A gene is a sequence of DNA that codes for a trait that you have. These genes can also wear down after a while and result in traits like hair color shutting down, which is why some people’s hair is white.

67
Q

What is a 5’ Cap?

A

a 5’ Cap is a nucleotide on the 5’ end of RNA

68
Q

What is a poly-A tail?

A

A poly-A tail is a string of Adenines (A) attached to the end of an RNA strand.

69
Q

How do genes make cloning possible?

A

Genes make cloning possible through copying the genes and giving them to someone else of the same species, such as with Dolly the sheep

70
Q

Simply put, what is transcription and what is its purpose?

A

Transcription is the process by which a strand of DNA is copied into mRNA. This is so DNA can leave the nucleus and the body can get important information, which is known as gene expression

71
Q

Why is RNA ribonucleic but DNA is deoxyribonucleic?

A

DNA is missing an oxygen molecule at the 2’ of its 5’ sugar, which RNA does have.

72
Q

What is RNA polymerase?

A

RNA polymerase is like DNA polymerase, except it adds the nitrogenous bases found in RNA.

73
Q

What are Promoters?

A

Promoters (AKA the T A T A Box) are nitrogenous base sequences in DNA that signal the beginning of a gene, that sequence being Thymine, Adenine, Thymine, Adenine.

74
Q

What are terminators?

A

Terminators are nitrogenous base sequences in DNA that signal the end of a gene.

75
Q

What are introns?

A

Introns are removed portions of the RNA sequence that stay in the nucleus.

76
Q

What are exons?

A

Exons are portions of the RNA sequence that exit the nucleus.

77
Q

What are the three main steps of transcription?

A
  1. Initiation
  2. Elongation
  3. Termination
78
Q

What is the first step of transcription and what does it do?

A

The first step of transcription is initiation. Initiation is when the RNA polymerase binds to the DNA at the promoter/TATA box. (One should also note that there are many other factors and molecules that aid in the initiation.)

79
Q

What is the second step of transcription and what does it do?

A

The second step of transcription is elongation. Elongation involves the RNA polymerase adding RNA strands to the template strand according to Chargaff’s rules. (One should also note that Thyamine is replaced with Uracil when building the mRNA strand.)

80
Q

What is the third step of transcription and what does it do?

A

The third step of transcription is termination. Termination happens when the RNA polymerase reaches a terminator, making the RNA polymerase stop adding RNA bases, detaching itself from the DNA strand. After this step, the mRNA strand is complete and exits the nucleus.

81
Q

How does mRNA exit the nucleus?

A

The mRNA exits the nucleus through the nuclear pores to be translated.

82
Q

Simply put, what is translation?

A

Translation is the process of taking the mRNA strand and turning them into a chain of amino acids that become a protein. This protein will then do its job and helps define our traits.

83
Q

What is a codon?

A

A codon is a set of three nitrogenous bases that are code for our amino acids. (Examples: UGA, CAG, CUG, CAU)

84
Q

What is a start codon?

A

A start codon (AUG) signals the beginning of a gene sequence

85
Q

What is a stop codon?

A

A stop codon (UAA, UAG, UGA) signals the end of a gene sequence

86
Q

What is an anticodon?

A

An anticodon is a detector that binds to the mRNA. It’s located on the tRNA and is the opposite of the mRNA message.

87
Q

What is a ribosome?

A

Ribosomes are protein factories that assemble amino acids together in a chain.

88
Q

What are the steps of transcription?

A

The steps of transcription are:
1. Initiation
2. Elongation
3. Termination

89
Q

What’s the first step of transcription and what does it do?

A

The first step of transcription is initiation. Initiation involves the ribosome attaching to the strand of the mRNA to be read, binding the first tRNA to the start codon and forming the initiation complex.

90
Q

What’s the second step of transcription and what does it do?

A

The second step of transcription is elongation. Elongation involves the frame for the first mRNA strand shifting over one codon for the next one to be read, and another tRNA brings the next corresponding amino acid. The ribosome then attaches the second amino acid to the chain, and the first tRNA leaves. This process repeats for the entire gene sequence until a STOP codon is read.

91
Q

What’s the third step of transcription and what does it do?

A

The third step of transcription is termination. Termination occurs when a STOP codon is read, releasing the polypeptide sequence. Now released, the polypeptide sequence goes to the Golgi Body where its folded/processed into a protein so it can do its job.

92
Q

What codon begins a polypeptide chain?

A

Methionine (AUG) begins the polypeptide chain.

93
Q

What are genetic mutations?

A

Genetic mutations are problems/mistakes in RNA/DNA strands that can have big effects!

94
Q

What is a silent mutation?

A

A silent mutation is a base change that does not change the outcome because the same codon is produced. (Example: GCT becoming GCC is a silent mutation because they both produce the same codon, Alanine)

95
Q

What is a nonsense mutation?

A

A nonsense mutation is a point mutation that creates a STOP codon early, ending the protein strand and canceling any future codons from being read. (Example: TGC [Cystine] becoming TGA [STOP] and ending the polypeptide chain early.)

96
Q

What is a missense mutation?

A

A missense mutation is a point mutation where a different amino acid is created. (Example: AGT [Serine] becoming AGA [Arginine] is a missense mutation because it changes the amino acid being produced.)

97
Q

What is frameshift deletion?

A

Frameshift deletion involves a nitrogenous base being missing from a codon, shifting all the codons being read to the left. (Example: AUG TC_ CGA gets read as AUG TCC GA_)

98
Q

What is frameshift insertion?

A

Frameshift insertion involves a nitrogenous base being randomly added to a codon, shifting all the codons being read to the right. (Example: AUG TCG A__ CAG gets read as AUG TCG ACA G__)

99
Q

What is the purpose of proteins?

A

Proteins can do a lot depending on the type, including transport, building, acting with chemicals, and more!

100
Q

All cells have DNA except what type of cell?

A

Red Blood Cells

101
Q

What are the two big steps of protein synthesis?

A

Transcription and Translation

102
Q

Where does transcription occur?

A

Transcription occurs in the nucleus

103
Q

Where does translation occur?

A

Translation occurs in the cytoplasm and ribosomes

104
Q

What are the monomers for proteins?

A

The monomers for proteins are Amino Acids

105
Q

Where does tRNA stay while waiting for Protein Synthesis?

A

While not doing protein synthesis, tRNA is floating around the cytoplasm

106
Q

What are amino acids made of?

A

Carbons, Hydrogens, Oxygens, and Nitrogens

107
Q

Simply defined, what is a mutation?

A

A mutation is a permanent mistake/change to the original DNA and can occur in any gene sequence.

108
Q

What makes mutations dangerous?

A

Mutations can cause things like proteins to fail to work and even a single mutation can cause disorders such as Cystic Fibrosis, Tay-Sachs Disease, and Color-Blindness.

109
Q

What are chromosomal mutations?

A

Chromosomal mutations are mutations that occur during crossing over, where chromosomes cross over to the incorrect pairs (Example: Mom’s gene 6 crosses over to Dad’s gene 9). When this happens, the chromosomes become unequal and are called translocated, and can be extremely dangerous.

110
Q

What is a mutagen?

A

Mutagens are agents in the environment that can affect DNA. (Examples: UV Radiation/X-Rays [Radiations], Cigarettes/Nitrate [Chemicals], HPV/H. Pylori [Infectious Agents])

111
Q

What is gene regulation?

A

Gene regulation begins with the promoters (TATA Box) helping signal the beginning of gene expression in transcription. When this happens, the introns of mRNA are removed and kept within the nucleus. While this happens, the exons are spliced together, a 5’ cap and poly-A tail are added and the mRNA exits the nucleus.

112
Q

What ratio are chromosome pairs between parents?

A

1/2 Mom, 1/2 Dad. Other ratios can be problematic, see mutations.

113
Q

Where are amino acids made?

A

Amino acids are made in the cytoplasm and are gotten from consumed proteins.

Biology Honors (4 decks)

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