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Medical Biochemistry > Ch. 21: Structure & Properties Of DNA > Flashcards

Ch. 21: Structure & Properties Of DNA Flashcards

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USMLE® Step 1 flashcards
1
Q

What does the primary structure of DNA consist of?

A

1) 5C deoxyribose sugar
2) Phosphate group attached to 5’ C of deoxyribose
3) Heterocylic nitrogenous base attached to 1’ C of deoxyribose

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2
Q

Which DNA bases are purines?

A

Adenine and Guanine

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3
Q

Which DNA bases are pyrimidines?

A

Cytosine, Thymine, Uracil

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4
Q

What does the secondary structure of DNA consist of?

A

Base pairing ➡️ overall architecture of DNA double helix

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5
Q

What does the tertiary structure of DNA consist of?

A

Superhelical structure (supercoil)

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6
Q

What are the 4 major stages that represent the central dogma of molecular biology? (DNA ➡️ RNA ➡️ pro)

A

1) DNA replication
2) Transcription: DNA codes for mRNA
3) mRNA processed (splicing)
4) Translation: mRNA brings info to ribosomes ➡️ used for pro synthesis

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7
Q

What were the 4 experimental outcomes (with mice) in the 1928 F. Griffith experiment?

A

1) Living S strain (virulent) put in 🐭 ➡️ 🐭 dies (S strain in tissue)
2) Living R strain (avirulent) put in 🐭 ➡️ 🐭 lives
3) Heat-killed S put in 🐭 ➡️ 🐭 lives
4) Mix of heat-killed S & living R put in 🐭➡️ 🐭 dies (S strain in tissue)

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8
Q

What were the 3 experimental outcomes in the 1944 Oswald Theodore Avery experiment?

A

1) Heat-killed S strain + RNAase + R strain (avirulent) ➡️ mix of R + S
2) Heat-killed S + protease + R ➡️ mix of R & S
3) Heat-killed S + DNase + R ➡️ only R

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9
Q

What is the transforming principle Oswald Avery & co discovered, in regards to the Griffith experiment?

A

DNA is agent responsible for genetic transferring (NOT pro!)

explains 4th outcome of experiment: turning avirulent R strain into virulent S strain via S DNA ➡️ kill 🐭

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10
Q

What were the 2 experimental outcomes of the 1952 Alfred Hershey & Martha Chase experiment?

A

1) bacteriophage pro coat radioactively labeled ➡️ pro coat remain outside bacterial host cell ➡️ not in pellet of bacterial cells ➡️ conclude: pro is NOT the genetic material directing production of new bacteriophages
2) bacteriophage DNA radioactively labeled ➡️ DNA injected into bacterial host cell ➡️ in pellet of bacterial cells ➡️ conclude: DNA is the genetic material directing production of new bacteriophages

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11
Q

Who discovered the double helical structure of DNA in 1953?

A

James Watson & Francis Crick

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12
Q

What is the difference between a nucleoside & nucleotide?

A

Nucleoside: Base + deoxyribose sugar

Nucleotide: Base + phosphate + deoxyribose sugar

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13
Q

What type of bond connects bases to form polymerized DNA strands?

A

Phosphodiester bonds: 3’ C of one sugar linked to 5’ C of next sugar

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14
Q

How is uracil obtained from cytosine?

How is thymine obtained from uracil?

A

Deamination of C ➡️ U

Methylation of U ➡️ T

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15
Q

Which DNA base pairs with which? (Chargaff’s rules)

How many H bonds are involved with each pairing?

A

A to T (2 H bonds)

G to C (3 H bonds)

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16
Q

Which are the most frequently methylated DNA bases?

A

Guanine

Cytosine (methylation pattern inherited)

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17
Q

What does DAM methylase act on?

A

Adenine in any GATC sequence

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18
Q

What does DEM methylase act on?

A

Cytosine in CCAGG sequence

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19
Q

Why is methylation important in bacteria?

A

Causes inactivation of DNA expression, protects against restriction endonucleases

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20
Q

What is genomic imprinting?

A

Different methylation pattern in maternal & paternal chromosomes at CpG nucleotides

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21
Q

What diseases involve faulty imprinting?

A

Prader-Willinsyndrome
Angelmann’s syndrome
Beckwith-Wiedemann syndrome

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22
Q

Example of good DNA methylation?

A

Women born with 2 X chromosomes ➡️ cells randomly pick one X chromosome to inactivate via methylation ➡️ one working X chromosome in each cell

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23
Q

Example of bad DNA methylation?

A

Fragile X syndrome: CpG island (regulatory site) is methylated ➡️ cell can’t make mRNA copy of FMR1 gene (fragile X mental retardation 1 gene) ➡️ FMRP (fragile X mental retardation protein) not made ➡️ fragile X syndrome

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24
Q

How do females, being mosaic, impact the severity of fragile X syndrome if they have the mutation?

A

Females who have most cells turn off X chromosome with fragile X mutation ➡️ most cells produce FMRP ➡️ limited impact of fragile X syndrome

Females who have most cells turn off X chromosome with working FMR1 ➡️ ⬇️ cells producing FMRP ➡️ greater impact of fragile X syndrome

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25
Q

What is a base analogue?

A

Molecules that can substitute for normal bases in nucleus acids

Usually leads to altered base pairings & structural changes ➡️ affect DNA replication & gene transcription

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26
Q

Which base analog is used to treat herpes virus infection?

A

Acycloguanosine (acyclovir)

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27
Q

Which base analogue is used to treat HSV & HIV?

A

3’-deoxy-3’-azidothymidine (AZT)

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28
Q

Which base analogue is used to treat leukemia?

A

6-mercaptopurine

29
Q

Which base analogue is used to treat cancer & acne?

Which base is it an analog of? What enzyme does it irreversibly inhibit?

A

5-fluorouracil

analog of thymine, ➖ thymidylate synthetase

30
Q

What base analogue is non-mutagenic/weakly mutagenic for eukaryotes & is mutagenic for bacteria?

What base is it an analog of?

A

2-aminopurine

analog of adenine

31
Q

What are the 2 DNA sequencing methods discussed in class?

A

Maxam-Gilbert method (old, used for short fragments)

Dideoxy chain termination (uses fluorescent color tags for each of the 4 DNA bases)

32
Q

What did we learn from completing the Human Genome Project?

A

1) 0.1% of our genome contains polymorphisms ➡️ we are all different (one gene can give rise to more than 1 protein)
2) Discovered fewer genes (25,000-35,000) than expected (100,000)

33
Q

Physical structure of DNA:
? base pairs per helical turn
? diameter
? gap between bases

A

10 bp per helical turn

  1. 0 nm diameter
  2. 34 nm gap between bases
34
Q

Physical structure of DNA: Difference between major & minor grooves?

A

Major groove: has more exposed space ➡️ DNA binding proteins can bind via H bonding w/exposed bases

35
Q

What are the 3 types of DNA helixes?

A

B: Watson-crick DNA helix, R handed, main form under physiological conditions, 10.5 bases per turn

A: similar to B, R-handed, more compact, dehydrated, 11 bases per turn

Z: L-handed, zigzag structure, formed under high salt conditions, 12 bases per turn

36
Q

What are intercalating agents? Examples?

A

Resemble ring structure of of base pairs ➡️ Insert between stacked base pairs ➡️ distorts DNA double helix ➡️ introduce mutations

Ethidium bromide, acridine orange, actinomycin D

37
Q

What is plasmid DNA? What are the 3 physical structures?

A

Circular DNA (in bacteria), contains only a few to >100 genes ➡️ antibiotic resistance genes

Relaxed, relaxed open, supercoil

38
Q

How are plasmids transferred from one bacteria to another?

A

Transferred via conjugation (use conjugation tube)

39
Q

DNA supercoils: positive versus negative supercoil?

A

Positive: Add more twists to typical relaxed DNA helix (overwinding)

Negative: Remove extra twists (underwinding)

40
Q

What enzyme catalyzes the formation of negative supercoiled DNA ahead of replication fork? (To relieve stress)

A

Topoisomerase II (DNA gyrase)

41
Q

What is an inhibitor of topoisomerase?

A

Camptothecin

42
Q

What factors can denature DNA?

A

pH: >11.5 and <2.3
Temperature: causes DNA to melt
Ionic strength

43
Q

What ⬆️ the melting temperature (Tm) of DNA?

What ⬇️ Tm of DNA?

A

⬆️ GC content

⬇️ ionic strength

44
Q

What is renaturation of DNA an indicator of?

What 3 things is it used to do?

A

Indicator of DNA sequence complexity

1) Determine frequency of certain sequences
2) Locate specific base sequences
3) Detect certain species of RNA

45
Q

Where are short, highly competitive sequences of DNA found?

A

Telomeres (end)

Centromere (site of attachment of spindle fiber)

46
Q

What are histones?

What is chromatin?

A

Very basic proteins with (➕) charged lysines & arginines, help to compact DNA

Chromatin = DNA + histones

47
Q

What are the 5 major classes of histones?

A

H1, H2A, H2B, H3, H4

All exist as pairs except H1

48
Q

What is a nucleosome?

A

Beadlike structure from resting nuclei, 10 nm diameter

Segment of DNA wrapped around histone octamer

49
Q

What makes up the 30 mm chromatin filament? (Stage in condensing DNA to form chromosome)

A

Spring-shaped solenoid w/6 nucleosomes per turn

Stabilized via head to tail associations of H1 histone

50
Q

of repetitive DNA sequences can be divided into 3 classes, based on the reassociation rate ➡️ Name & describe these 3 classes

A

1) Highly repetitive: 10-15% of mammalian DNA; includes tandem repeats
2) Moderately repetitive: 25-40% of mammalian DNA; includes interspersed repeats
3) Single copy (or very low copy #): 50-60% of mammalian DNA

51
Q

What are the 3 subclasses of tandem repeats?

A

1) Satellites: Very highly repetitive, organized as large clusters (up to 100 million bp), near centrosomes & telomeres, abundant on Y chromosome
2) Minisatellites: Moderately repetitive, moderate size (9-100 bp), most highly polymorphic sequences elements yet discovered
3) Microsatellites: Moderately repetitive, short repeats (2-6 bp)

52
Q

What characterizes the fragile X gene (FMR1)?

A

Tandem repeat sequence (CGG) near 5’ end

53
Q

What is involved in a Southern blot analysis?

A

DNA + DNA

54
Q

What is involved in a Northern blot analysis?

A

DNA + RNA

55
Q

What is involved in a Western blot analysis?

A

Protein + protein

56
Q

What is involved in a Southwestern (Eastern) blot analysis?

A

DNA + protein

57
Q

5 Steps of isolation of total genomic DNA?

A

1) Lyse cell & nucleus w/detergent or lytic enzymes
2) Degrade DNA bound protein & nucleases w/proteinase K
3) Extract DNA w/column or phenol/chloroform
4) Precipitate DNA w/ethanol
5) Dry & redissolve DNA in aqueous buffer

58
Q

What is a restriction enzyme?

A

Bacterial enzymes (Exonucleases and endonucleases) that cut ds DNA in sequence specific manner

Restrict entry of foreign DNA via cleaving at recognition site not found in host bacterium

Cuts asymmetrically (➡️ sticky ends) or symmetrically (blunt ends)

59
Q

What does DNA ligase do?

A

Attaches 2 pieces of DNA covalently to each other

60
Q

What does DNA polymerase do?

A

Uses sDNA as template, w/primer ➡️ extends DNA sequence

61
Q

What does reverse transcriptase do?

A

Uses RNA as template, w/primer ➡️ makes cDNA

62
Q

What is cloning?

What can it be used for (in lab)?

A

Process of making a genetically identical DNA by nonsexual means

Can make large # of DNA copies (for analysis & manipulation)
Remove DNA sequences from genome ➡️ put into vector ➡️ put into host (E. coli, yeast) ➡️ multiplied

63
Q

What are examples of vectors used in DNA cloning?

A

Plasmid (most used)
Bacteriophage
Artificial chromosome

64
Q

3 main steps of polymerase chain reaction (PCR)?

A

1) Denaturation
2) Annealing (forward & reverse primers)
3) Extension (DNA polymerase)

Repeat for 30-40 cycles

65
Q

Detecting sequence polymorphisms example: RFLP-sickle cell anemia

What is the point mutation? What are its effects in the body?

A

Glu ➡️ Val, position 6 of beta-globin pro chain

Insoluble in O2-free form, crystallized, form sickle shaped RBCs ➡️ anemia, thrombotic vaso-occlusion & hemolysis

66
Q

What is an example of variable numbers of tandem repeats?

A

Huntington’s Disease

36-125 CAG (= glu) repeats (normal 11-30) ➡️ produces huntingtin pro ➡️ “polar zipper”

67
Q

What are the 2 types of replication slippage that cause micro satellite polymorphism?

A

1) backward slippage ➡️ insertion mutation (longer than normal)
2) forward slippage ➡️ deletion mutation (shorter than normal)

68
Q

What is a DNA Library?

What are the 2 types?

A

Collection of cloned DNA fragments

1) genomic library: DNA fragments of entire genome of organism
2) cDNA library: only complementary DNA made from mRNA in cell

69
Q

What is a DNA vaccine?

A

Made of single or multiple genes of immunologic proteins inserted into commercially available DNA expression plasmid

Medical Biochemistry (23 decks)

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