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Biochemistry > Chapter 6 > Flashcards

Chapter 6 Flashcards

1
Q

Nucleosides

A
  • Composed of a 5 carbon sugar (pentose) bound to a nitrogenous base
  • Formed by covalently linking base to C1 of the sugar
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2
Q

Nucleotides

A
  • Formed when one or more phosphate groups are attached to C5 of a nucleoside
  • Often named by the number of phosphates bound
  • High-energy compounds because of teh energy associated with the repulsion between closely associated negative charges on the phosphate groups
  • Nucleotides are the building blocks of DNA
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3
Q

Backbone of DNA

A
  • Alternating sugar and phosphate groups
  • Always read 5’ to 3’

-Formed as nucleotides are joined by 3’ to 5’ phosphodiester bonds

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4
Q

Purines

A
  • Contain two rings

- Adenine and guanine

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5
Q

Pyrimidines

A
  • Contain only one ring
  • Cytosine, thymine and uracil

-Thymine is only found in DNA and Uracil is only found in RNA

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6
Q

Watson-Crick model

A
  • Two strands of DNA are antiparallel (oriented in opposite directions)
  • Sugar phosphate backbone is on the outside (hydrophilic) of the helix with nitrogenous bases on the inside (hydrophobic)
  • A with T (2 H bonds) and G with C (3 H bonds) thus C/G is a stronger bond
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7
Q

Chargaff’s Rules

A

The total amount of purines will be equal to the total pyrimidines overall

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8
Q

B-DNA

A
  • Right-handed helix

- Makes a turn every 3.4 nm and contains 10 bases within that span

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9
Q

Denaturation

A
  • Conditions that disrupt h bonds and base-pairing
  • “melting” of the double helix into two single strands (none of the nucleotides in the backbone break)

-Heat, alkaline pH and chemicals like formaldehyde/urea are most commonly used

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10
Q

Reannealing

A
  • DNA can be brought back together if the denaturing condition is slowly removed
  • Important step in laboratory processes like polymerase chain reactions (PCR)
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11
Q

DNA Replication- Heterochromatin and euchromatin

A
  • During the S phase of interphase
  • Small percentage of chromatin remains compacted during interphase and is referred to as heterochromatin (Transcriptionally silent)

-Dispersed chromatin is euchromatin- contains genetically active DNA

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12
Q

Telomere

A
  • Repeating unit TTAGGG at the end of DNA
  • Some lost in each round of replication but can be replaced by the enzyme telomerase
  • Progressive shortening of telomeres contributes to aging
  • High GC content creates strong strand attractions at the end of chromosomes to prevent unraveling
  • Think of telomeres as “knotting off” the end of the chromosome
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13
Q

Centromeres

A
  • Found at the center of chromosomes
  • Composed of heterochromatin- which is composed of tandem repeat sequences that contain high GC content (why microtubules have to separate the chromatids during anaphase)
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14
Q

Replisome/Replication Complex

A

Set of specialized proteins that assist the DNA polymerases

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15
Q

Origins of replication

A
  • Where DNA begins unwinding (Where replication begins)

- Generation of new DNA proceeds in both directions- creating replication forks

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16
Q

Helicase

A

-Enzyme responsible for unwinding DNA, generating two single stranded template strands ahead of the polymerase

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17
Q

Nucleases

A

Degrade DNA

18
Q

DNA gyrase/DNA topoisomerase II

A

introduces negative supercoils by working ahead of helicase, nicking both strands, passing dna through the strands and releasing it

19
Q

DNA polymerase

A
  • Responsible for reading the DNA template (parent strand) and synthesizing the new daughter strand
  • Reads template 3’ to 5’ while synthesizing in the 5’ to 3’ direction
20
Q

DNA Ligase

A
  • Closes the gaps between Okazaki fragments

- Lacks proofreading ability so likelihood of mutations in lagging strand is considerably higher

21
Q

Single Stranded DNA binding proteins

A

Bind to unraveled DNA strands, preventing both the reassociation of the strands and degradation by nucleases

22
Q

Supercoiling

A
  • Wrapping of DNA on itself (as its helical structure is pushed further toward the telomeres during replication
  • Picture telephone cord wrapping on itself
23
Q

DNA gyrase/DNA topoisomerase II

A

introduces negative supercoils to reduce the risk of strand breakage

24
Q

Leading strand

A
  • strand that is copied in a continuous fashion, same direction as the replication fork
  • read 3’ to 5’ and replicated 5’ to 3’
25
Q

Primase

A
  • Synthesizes RNA primer that is laid down to start DNA replication
  • RNA primers are constantly added to lagging strands because each Okazaki fragment must start with a new primer
26
Q

DNA polymerase III (prok) & DNA polymerases alpha and delta (euk)

A

Synthesize daughter strand in 5’ to 3’ manner

27
Q

DNA polymerase I (prok) & RNase H (euk)

A

Remove RNA primer

28
Q

DNA polymerase I (prok) & DNA polymerase delta (euk)

A

Add DNA nucleotides where RNA primer had been

29
Q

Methylation

A

Parent strand has been around longer so it is more methylated than the daughter strand.
-also plays a role in transcriptional activity of DNA

30
Q

Metastasis

A

Migration to distant tissues by the bloodstream or lymphatic system

31
Q

Cancer cells

A

Proliferate excessively b/c they are able to divide without stimulation from other cells
-Over time cancer cells tend to accumulate mutations

32
Q

Oncogenes

A

Mutated genes that cause cancer

-encode cell cycle related proteins

33
Q

Proto-oncogenes

A

oncogenes that are not yet mutated

34
Q

Tumor suppressor genes

A

Genes like p53 or Rb
-encode proteins that inhibit the cell cycle

-normally function to stop tumor progression and can be called antiongogenes

35
Q

Mismatch Repair

A

-Machinery in the G2 phase (encoded by MSH2 and MLH1 which detect and remove errors introduced in replication that were missed during the S phase)

36
Q

Nucleotide Excision Repair

A 
Thymine dimers (induced by ultraviolet light) that interfere with DNA replication are removed from DNA
-Recognized by bulge in the strand

-Excision endonuclease nicks the phosphodiester backbone of damaged strand and removes defective oligonucleotide

37
Q

Base Excision Repair

A
  • Uracil found in DNA
  • Affected base is recognized and removed by a glycosylase enzyme- leaving an AP site

-AP site recognized by an AP endonuclease that removes damage sequence

38
Q

Palindromic

A

The 5’ to 3’ sequence of one strand is identical to the 5’ to 3’ sequence of the other in antiparallel orientation

39
Q

Restriction enzymes/restriction endonucleases

A
  • Enzymes that recognize specific double stranded DNA sequences
  • Isolated from bacteria, their natural source

-Some produce offset cuts, yielding sticky ends on framents

40
Q

DNA libraries

A

-Large collections of known DNA sequences- these sequences could equate to the genome of an orangism

41
Q

Hybridization

A

The joining of complementary base pair sequences
-Uses two single stranded sequences and is a vital part of PCR and southern blotting

-Can be DNA-DNA recognition or DNA-RNA recognition

42
Q

Southern Blot

A

Used to detect the presence and quantity of various DNA strands in a sample
-DNA cut by restriction enzymes and then separated by gel electrophoresis.

Biochemistry (3 decks)

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