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cbe 235 > DNA (pp.4-8, handout 4) > Flashcards

DNA (pp.4-8, handout 4) Flashcards

1
Q

purines

A

Type of nitrogenous base with a double ring found in DNA and RNA

Guanine and Adenine

GAPUR

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2
Q

pyrimidines

A

Type of nitrogenous base with a single ring found in DNA and RNA

cytosine and thymine

PYRCT

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3
Q

DNA

A

deoxyribonucleic acid.
- the central dogma of genetics is that all genes are made of DNA

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4
Q

base pairs

A

adenine and thymine (DNA) / adenine and uracil (RNA) (2 hydrogen bonds)

guanine and cytosine (DNA) (3 hydrogen bonds)

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5
Q

RNA

A

ribonucleic acid.

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6
Q

right-handed helix

A

In a right-handed helix, as the observer looks down, the helix axis (in either direction), each strand turns clockwise as it moves away from the observer

one turn is 34 angstrom and has 10 base pairs

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7
Q

Nucleotides contain…

A

1) a phosphate group
2) pentose (five-carbon sugar)
3) nitrogen-containing base

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8
Q

What is the pentose for DNA

A

deoxyribose

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9
Q

B-form

A

The normal form of the DNA double helix, as originally described by Watson and Crick
- aqueous environments with low salt concentrations

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10
Q

What is the pentose of RNA

A

ribose

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11
Q

What are the nitrogenous bases

A

adenine and thymine (corresponds with DNA)
guanine and cytosine (corresponds with DNA)

uracil (corresponds with RNA)

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12
Q

A-form

A

An alternative form of the double helix, with 11 base pairs per turn, often found for double-stranded RNA, but rarely for DNA

found in DNA in high salt environments

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13
Q

Z-form

A

An alternative form of double helix with left-handed turns and 12 base pairs per turn. Both DNA and dsRNA may be found in the Z-form

occurs when proteins bind to DNA and create a zig-zagged phosphate backbone

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14
Q

What is a phosphodiester bond

A

how phosphate connects to sugars. connect the nucleotides into a chain that runs in the 5’ to 3’ direction.

5’ -OH of one nucleotide’s sugar is linked to a phosphate group by an oxygen. The 3’ -OH of the next nucleotide’s sugar is linked to the other side of the phosphate.

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15
Q

DNA double helix

A

TEAMROSALIND

most stable structure: when one single strand of nucleotides aligns with another strand to form a double stranded molecule.

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16
Q

supercoiling

A

Higher level coiling of DNA that is already a double helix.

The DNA is twisted in a left-handed direction containing around 200 nucleotides per supercoil. The supercoils then forms loops and connects to a protein scaffold.

performed by DNA gyrase.

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17
Q

DNA Gyrase

A

An enzyme that introduces negative (left-handed) supercoils into DNA, a member of the type II topoisomerase family

the only one that can do negative coils…..#biologyissocool

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18
Q

antiparallel

A

as each base forms H-bonds with another base in the other strand, the strands run in opposite directions to each other

5’ ———————- 3’
3’ ———————- 5’

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19
Q

restriction enzymes

A

(also known as restriction endonucleases) allows DNA to be cut and rejoined in predictable ways

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20
Q

antisense strand

A

one of the strands in DNA that contains the complementary sequence to the strand and to the mRNA transcript generated from the gene

the non-coding DNA strand of a gene, serves as the template for producing messenger RNA (mRNA), which directs the synthesis of a protein.

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21
Q

sense strand

A

the strand of DNA that reads as the code for the expressed genes

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22
Q

topoisomerase I

A

Enzyme that alters the level of supercoiling or catenation of DNA (i.e., changes the topological conformation) - removes extra super coils

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23
Q

polymer

A

molecular chain of building blocks stitched from end to end

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24
Q

histones

A

DNA is supercoiled and wrapped around the histones so that everything ‘fits’

Special positively charged protein that binds to DNA (neutralizes negatively charged phosphate) and helps to maintain the structure of chromosomes in eukaryotes

eukaryotic (plant and animal) DNA is too complex for just supercoiling.

tails stick out of nucleosomes to assist in regulation

in regions of dna expression, histones roam freely

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25
Q

monomer

A

the building blocks making the links in the polymer chain

26
Q

chromatin

A

Complex mixture of DNA plus protein that constitutes eukaryotic chromosomes.

dna is supercoiled, wrapped around histones to become chromatin and then all squished up to make chromosomes

looks like beads on a string

27
Q

nucleosome

A

Subunit of a eukaryotic chromosome consisting of DNA coiled around histone proteins (the beads on chromatin)

structural unit of chromatin.

contains of 200 base pairs and 9 histones

28
Q

tetra-nucleotide theory

A

People believed that DNA was simply repeating a nucleotide sequence and could not be complex enough to carry hereditary information

29
Q

heterochromatin

A

condensed histones that prevent other protein from accessing DNA

Tightly packed form of chromatin that is found in centromeres and telomeres; histone 3 is di- and tri-methylated on lysine 9 (H3K9) in these regions of the genome

30
Q

Chargaff’s Rules

A

The number of Adenines always equals the number of Thymines
The number of Guanines always equal the number of Cytosines

31
Q

What is the DNA backbone made up of?

A

A phosphate and a pentose (5-carbon sugar)

32
Q

30-nanometer fiber

A

Chain of nucleosomes that is arranged helically, approximately 30 nm in diameter

chromatin cannot condense enough to fit eukaryotic DNA so it is coiled into this structures that has six nucleosomes per turn.

structure loops back and forth and is tethered to a protein scaffold or chromosome axis

33
Q

How many hydrogen bonds bind Adenine and Thymine?

A

2 hydrogen bonds

34
Q

How many hydrogen bonds bind Guanine and Cytosine

A

3 Hydrogen bonds

35
Q

matrix attachment regions (MAR)

A

Site on eukaryotic DNA that binds to proteins of the nuclear matrix or of the chromosomal scaffold—same as SAR sites

aka place where chromatin loopies from 30nm fiber attach to protein or chromosome.

70% A/T concentration causes bentness and promotes connections between DNA and proteins

36
Q

Semiconservative replication

A

During the replication process each new double helix contains one original strand and one newly synthesized strand

37
Q

purpose of bacteria in biotechnology

A

bacteria are treated as workhorses due to their prevalence on earth and ability to thrive in extreme conditions

38
Q

which enzyme aids in DNA copying from the template strand?

A

DNA Polymerase - proofreads and replicates!

39
Q

DNA polymerase

A

An enzyme that elongates strands of DNA, especially when chromosomes are being replicated - synthesizes a new strand of DNA in the 5’ –> 3’ direction

think DNA replication!!

40
Q

nucleoside

A

a nitrogen base linked to a sugar - no phosphate group!

41
Q

thermostable

A

Able to withstand high temperatures without loss of function

42
Q

nucleotide

A

a nitrogenous base linked to a sugar and one or more phosphate groups

43
Q

nucleoside triphosphate

A

a nitrogenous base linked to a sugar and three phosphates

44
Q

polymerase chain reaction (PCR)

A

Amplification of a DNA sequence by repeated cycles of strand separation and replication

takes one segments and amplifies and replicates it really quickly so you get alot of copies of one dna segment

carried out at high temperatures

45
Q

Nucleophilic attack

A

occurs when an electron-rich species “attacks” an electron-deficient species, forming a new bond between the nucleophile and the carbocation

46
Q

amino acids

A

monomer building blocks (20 different ones) of proteins whose sequence is determine by the nitrogen bases within the genetic code.

sequence of amino acids determine a proteins 3D structure which determines its function.

47
Q

What other enzymes also participate in unzipping and unwinding the double helix?

A

DNA helicase and DNA topoisomerase

48
Q

codons

A

three base sequences that represent amino acids (found inside of DNA sequences is singles or multiples)

49
Q

degeneracy of the genetic code

A

multiple codons specifying the same amino acid

50
Q

The two antiparallel strands are replicated ___________

A

simultaneously

51
Q

What are RNA primers used for?

A

To initiate a new strand

52
Q

The parent strand at the 3’ end determines __________ in a continuous replication

A

the leading strand

53
Q

The parent strand at the 5’ end determines __________ in a continuous replication

A

the lagging strand

54
Q

What are Okazaki fragments

A

the lagging strand fragments

55
Q

what process does the central dogma of biology follow?

A

DNA → transcription → RNA → translation → polypeptide → folding → functional protein (3D)

56
Q

RNA primers are removed by __________ and the fragments are joined by _________

A

DNA polymerase DNA ligase

57
Q

transcription

A

the process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA).

58
Q

walter sutton

A

observed chromosomes in pairs that sorted independently to gametes

59
Q

thomas hunt morgan

A

fly guy!!! bred flies and tracked their phenotypes (worked better than peas bc they reproduce faster and have more traits to consider)

60
Q

what are the ten features of DNA that watson and crick identified?

A

1) double-stranded helix that spirals in the right hand direction
2) anti-parallel
3) backbones outside, bases inside
4) bases perpendicular to helix axis
5) bases held together by hydrogen bond
6) 2nm diameter for double helix
7) base-pairing
8) major and minor grooves
9) one revolution = 10 monomers
10) complementarity

61
Q

what two things does DNA polymerase need?

A

1) template strand to direct the sequence
2) a short piece of stranded DNA to prime the enzyme

62
Q

what is the significance of a covalent bond?

A

because it has chemical potential, breaking the bond releases energy

cbe 235 (27 decks)

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