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BIOL 122 > Unit 2: Nucleic Acids and DNA > Flashcards

Unit 2: Nucleic Acids and DNA Flashcards

1
Q

What are the 2 major biological functions of DNA?

A
  • DNA stores genetic information that is encoded in the sequence of subunits along its length
  • DNA transmits genetic information to other molecules and from one generation to the next
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2
Q

genetic information (2)

A
  • information carried in DNA, organized in the form of genes

- some information in DNA encodes proteins that provide structure and do much of the work of the cell

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3
Q

genes (3)

A
  • unit of heredity
  • the stretch of DNA that affects one or more traits in an organism, usually through an encoded protein or noncoding RNA
  • genes can exist in different forms in different individuals, even within a single species
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4
Q

gene expression

A
  • production of a functional gene product
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5
Q

gene regulation

A
  • various ways in which cells control gene expression
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6
Q

How do genes affect an organism? (2)

A
  • usually have no affect on the organism until they are “turned on” and their product is made
  • turning on of a gene is called gene expression
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7
Q

nucleotides

A
  • constituent of nucleic acids, consisting of a 5-carbon sugar, a nitrogen-containing base, and one or more phosphate groups
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8
Q

what forms the backbone of the DNA structure

A
  • the 5-carbon sugars and the phosphate groups for the backbone of the molecule with each sugar being linked to the phosphate group of the neighbouring nucleotide
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9
Q

what is role of each base that sticks out from the sugar

A
  • give each nucleotide its chemical identity
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10
Q

Which carbon in the sugar is the phosphate group bonded to?

A
  • the 5’ carbon
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11
Q

which carbon in the sugar is the base bonded to?

A
  • the 1’ carbon and the base projects above the sugar ring
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12
Q

deoxyribose

A
  • the sugar in DNA
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13
Q

what is the shape of the sugar in the nucleotide and how do you read the carbons (2)

A
  • indicated by an pentagon where 4/5 of the vertices represent the position of a carbon atom
  • carbon atoms of the sugar ring are numbered clockwise with the primes
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14
Q

How does the sugar in DNA differ from the sugar in RNA (2)

A
  • chemical group projecting downward from the 2’ carbon is a hydrogen atom (–H) in DNA
  • chemical group projecting downward from the 2’ carbon group is a hydroxyl group (–OH) in RNA
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15
Q

Why is DNA a mild acid (2)

A
  • at cellular pH the free hydroxyl groups attached to the phosphorus atom are ionized by the loss of a proton and become negatively charged
  • phosphate group has negative charges on 2 of its oxygen atoms
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16
Q

mild acid

A
  • molecule that tends to lose protons to the aqueous environment
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17
Q

purines (2)

A
  • bases that have a double-ring structure

- adenine and guanine

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18
Q

pyrimidines (2)

A
  • bases that have a single-ring structure

- thymine and cytosine

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19
Q

what are the 4 kinds of bases

A
  • adenine
  • guanine
  • thymine
  • cytosine
20
Q

nucleoside

A
  • molecule consisting of a 5-carbon sugar and a base
21
Q

how to nucleosides and nucleotides differ

A
  • a nucleoside with one or more phosphate groups is a nucleotide
22
Q

what is a nucleotide with 1, 2, and 3 phosphate groups called

A
  • nucleotides:
    1. nucleoside monophosphate
    2. nucleoside diphosphate
    3. nucleoside triphosphate
23
Q

phosphodiester bond (4)

A
  • bond that forms when a phosphate group in one nucleotide is covalently joined to the sugar unit in another nucleotide
  • whole connection between the 3’ carbon of one nucleotide to the 5’ of another in line through the 5’-phosphate group (C–O–P–O–C)
  • relatively stable and form the backbone of a DNA strand
  • cause polarity in DNA strands
24
Q

polarity

A
  • asymmetry where one end of a structure differs from the other
25
Q

5’ end

A
  • the end of a nucleic acid strand containing a free 5’ phosphate group
26
Q

3’ end

A
  • end of the nucleic acid strand that carries a free 3’ hydroxyl
27
Q

How can we write AGCT in 2 different ways to signify directionality

A
  • 5’-AGCT-3’ (AGCT can be written without prime ends assuming 5’ is the starting end)
  • 3’-TCGA-5’
28
Q

What does the Watson-Crick structure tell us

A
  • DNA structure consist of 2 DNA strands that are wrapped around the other in the form of a helix coiling to the right
  • the sugar-phosphate backbones are winded around the outside of the molecule
  • bases point inward
  • A pairs with T and G pairs with C
29
Q

major groove

A
  • the larger of two uneven grooves on the outside of a DNA duplex
  • allows proteins to easily access the core of the DNA strand and detect or “read” the base pair sequence
30
Q

minor groove

A
  • the smaller of two unequal grooves on the outside of a DNA duplex
31
Q

why are the grooves in DNA important

A
  • proteins that interact with DNA often recognize a particular sequences of bases by making contact with the bases by the major or minor group or both
32
Q

what is Chargaff’s rule?

A
  • each base pairing contains a purine and a pyrimidine: the pairing of A with T and of G with C
33
Q

how does Chargaff’s rule maintain the structure of the double helix (2)

A
  • pairing 2 purines would cause the backbones to bulge and pairing 2 pyrimidines would cause them to narrow, putting excessive strain on the covalent bonds in the sugar-phosphate backbone
  • pairing of one pyrimidine to one purine preserves the distance between the backbones along the length of the entire molecule
34
Q

anitparallel (2)

A
  • oriented in opposite directions

- the strands in a DNA duplex are antiparallel

35
Q

How many hydrogen bonds form between A and T, and C and G amd how are they formed in DNA (4)

A
  • 2 hydrogen bonds form between A and T
  • 3 hydrogen bonds form between C and G
  • formed when 1 electronegative atom (O or N) in one base shares a hydrogen atom (H) with another electronegative atom in the base across the way, typically weak and can be disrupted by high pH or heat
  • many hydrogen bonds together along the molecule contribute to the stability of the DNA double helix
36
Q

base stacking

A
  • stabilizing hydrophobic interactions between bases and in the same strand of DNA
  • occurs because nonpolar, flat surfaces of the bases tend to group together away from water molecules, and stack on top of one another as tightly as possible
37
Q

what are the three key structural features of DNA

A
  1. DNA is made up of subunits called bases
  2. DNA is a linear polymer of nucleotides linked by phosphodiester bonds
  3. cellular DNA is a double helix with 2 strands that are antiparallel to each other
38
Q

RNA (3)

A
  • polymer of nucleotides linked by phosphodiester bonds, similar to DNA
  • polarity determined by which end of the chain carries the 3’ hydroxyl group and which end carries the 5’ phosphate group
  • RNA molecules can act as enzymes
39
Q

Why is RNA less stable then DNA

A
  • 2’ hydroxyl group are a reactive functional group
40
Q

How do the bases in RNA differ from those in DNA? (2)

A
  • the base uracil (U) in RNA replaces thymine in DNA

- uracil pairs with adenine in RNA just as thymine pairs in adenine in DNA

41
Q

How do the phosphate groups in RNA differ from those in DNA? (2)

A
  • the 5’ end of a DNA strand is typically a monophosphate

- the 5’ end of an RNA molecule is typically a triphosphate

42
Q

What are physical attributes that differ DNA from RNA? (2)

A
  • RNA molecule is much shorter than DNA molecule

- most RNA molecules in the cell are single stranded, whereas the DNA molecule is double stranded

43
Q

which carbon in the ribose ring links to the base?

A
  • the 1’ carbon
44
Q

which type of interaction contributes the most to the stability of a double stranded DNA helix

A
  • hydrophobic interactions
45
Q

A always pairs with T, and G always pairs with C, why?

A
  • an A-T pair has the same geometry as a G-C pair
46
Q

What happens when improper geometry between base pairs occur?

A
  • DNA helix is unable to form properly around a region containing a mismatched pair, messing up the base stacking and hydrogen bonding
47
Q

why does it matter that DNA sequences have directionality? (2)

A
  • information stored in DNA is stored in the sequence of the bases so it is critical that the cell (via enzymes) can determine which direction to read the sequence
  • reading in one direction will have a completely different meaning as compared to the other direction

BIOL 122 (20 decks)

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