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Biochemistry > Final > Flashcards

Final Flashcards

1
Q

Nucleic acids

A
  • linear polymers of nucleotides that function in the storage and expression of genetic information and its transfer from one generation to the next
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2
Q

Phosphodiester bonds

A
  • link between the two monomers/nucleotides
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3
Q

Two Categories of Heterolytic/Nitrogenous Bases

A
  1. Purines

2. Pyrimidines

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4
Q

Purines

A
  • Adenine and Guanine

- 2 fused rings: a 6 membered and 5 membered heterocyclic C and N rings fused together

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5
Q

Pyrimidines

A
  • Cytosine, Thymine and Uracil

- single 6 membered heterocyclic rings of C and N

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6
Q

Nucleoside

A
  • nitrogenous bases attached to sugars via Beta 1-N glycosidic bond
  • rotation about glycosidic bond is possible, resulting in syn or anti configuration (anti is favored!)
  • pyrimidines can’t form syn configuration because of steric hindrance
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7
Q

Nucleotide

A

Contains

  1. Phosphate Group
  2. Sugar
  3. Nitrogenous Base
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8
Q

Primary nucleotide structure

A
  • this structure is the nucleotide sequence

- read 5’ to 3’

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9
Q

Secondary Nucleotide Structure

A
  • this structure is the 3D arrangement of nucleotide residues
  • short-term folding interactions
  • only DNA because RNA is single stranded
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10
Q

Tertiary Nucleotide Structure

A
  • this structure is the longer range 3D interactions between proteins and DNA
  • superhelixes forms, cruciforms, etc.
  • Sugar-phosphates form the backbone
  • DNA has a “rise” one base pair to another is the rise
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11
Q

B-DNA

A
  • this DNA form is seen in DNA fibers prepared under high humidity (PREDOMINANT FORM)
  • double helix
  • individual helixes form major and minor grooves
  • right handed helix
  • watson and crick described this
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12
Q

A-DNA

A
  • dsRNA forms this and DNA-RNA hybrids
  • right-handed helix
  • shorter than B form (more compact)
  • bases lie farther outside of axis
  • major and minor grooves are equal in width
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13
Q

Z-DNA

A
  • left handed helix
  • longer than B form
  • pyrimidines are anti and purines are syn
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14
Q

cruciform DNA

A
  • cross-like DNA structures formed when DNA contains a PALINDROME
  • palindromic sequences form a double hairpin
  • involved in protein binding to DNA
  • serves as recognition sites for restriction enzyme
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15
Q

triple helix DNA

A
  • usually unstable DNA form
  • forms from partially unwound duplex DNA under “super-helical” state
  • third strand occupies major groove
  • possible role in crossing over
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16
Q

super-coiled DNA

A
  • DNA + protein coiled on itself several times
  • functions: compacts DNA to occupy less space
  • inactive (prevents replication and transcription)
  • protects DNA when not replicated or transcribed
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17
Q

Bacterial DNA packaging

A
  1. in the NUCLEOID
    - negative supercoilng and separating loops of supercoiled DNA bound to a protein to a compact genome
  2. exists in CYTOSOL with small number of attachment points to membrane
18
Q

Eukaryotic DNA packaging

A
  1. in HISTONES

- DNA is confined to nucleus and wrapped around these protein assemblies

19
Q

satellite DNA

A
  • DNA with multiple tandem repeats of short, simple nucleotide sequences
  • makes up 10-20% of genome in higher eukaryotes
20
Q

introns

A
  • these repetitive sequences interrupt most eukaryotic genes

- noncoding regions

21
Q

restriction-modification systems

A

3 types of these systems
system has 2 enzymes: DNA endonuclease and DNA methylase
1. Phage with unmodified DNA infects a bacterium with restriction systems that recognize the DNA sequence 5’GAATTC-3’
2. most phage DNA is cleaved by host restriction nuclease
3. but the few that are methylated on innermost A are protected from attack
4. phage that emerges with methylated DNA

22
Q

restriction fragment length polymorphism (RFLP)

A
  • genetic polymorphism detected by southern blotting and used to screen for genetic diseases
  • based on fact that alleles often have different restriction endonuclease cleavage sites and produce different arrays of fragments upon cleavage with appropriate endonucleases
23
Q

Euchromatin vs Heterochromatin

A
  1. Euchromatin- transcriptionally active

2. Heterochromatin- thicker and transcriptionally inactive

24
Q

PCR (polymerase chain reaction)

A
  • this process can exponentially make small amounts of DNA in vitro
  • requires thermostable DNA polymerase (Taq pol), a pair of oligonucleotide primers that flank the region to be amplified, dNTPs, and DNA template
    1. denaturing
    2. annealing
    3. extension
25
Q

replication fork

A
  • point of separation on dsDNA at which incorporation of nucleotides occurs during DNA replication
26
Q

Semiconservative replication

A
  • this DNA characteristic means each strand-separated polynucleotide serves as a template for synthesis of new complementary strand
27
Q

semidiscontinuous replication

A
  • this DNA characteristic means the synthesis of DNA fragments that occurs in the lagging strand during DNA replication
28
Q

okazaki fragments

A
  • discontinuous fragments of DNA synthesized in the lagging strand
29
Q

Dna replication in prok

A
  1. initial unwinding, separation, and stabilization of duplex DNA (origin of rep is AT rich)
  2. primer synthesis
  3. DNA synthesis
  4. replace RNA primers with DNA
  5. ligase seals gaps between okazaki fragments
  6. termination of proteins
30
Q

initiation factors

A
  • DNAa proteins that bind to the origin of replication
31
Q

Helicase

A
  • DNAb proteins that catalyze ATP-dependent unwinding of duplex DNA
32
Q

topoisomerase

A
  • prevents supercoiling and tangling of DNA during unwinding

- binds ahead of fork, nicks supercoiling DNA, relaxes stress by allowing uncoiling

33
Q

ssB proteins

A
  • prevents single strands from reannealing, protect against nuclease degradation
34
Q

primase

A
  • RNA polymerase synthesizes a short (10 nucleotide) RNA primer
35
Q

DNA pol I

A
  • this polymerase fills in gaps, repairs mismatched bases, replaces primer RNA during replication
  • main replicative enzyme of lagging strand
  • requires template DNA and DNA or RNA primer
36
Q

DNA pol II

A
  • this polymerase is involved in some repair processes

- prevalent during stationary phase

37
Q

DNA pol III

A
  • this polymerase extends RNA-primed chain; main polymerase in elongation of leading strand
  • major replicative enzyme in bacteria (beta unit, sliding clamp, etc)
38
Q

telomerase

A
  • DNA polymerase adds a short repeating segment to the 3’ end at either of chromosome DNA molecule, creating a single-stranded overhang, which gives room for priming origin of final Okazaki fragments
  • advantage over PROKARYOTIC TERMINATION (they have problem completing the synthesis of the 5’ ends)
39
Q

Prok termination

A
  • Ter binding proteins bind to ter sites (20 bp inverted sequences) on opposite side of DNA loop, inhibit helices, and prevent progression of replication forks
40
Q

Euk termination

A
  • DNA pol runs off ends of DNA; replication bubbles fuse as polymerases collide; involves telomeres
41
Q

Retrovirus

A
  • possess reverse transcriptase to produce DNA from RNA template
  • replicase copies the RNA viruses RNA starting form from 3’ end so the strand is laid in 5’ to 3’ direction

Biochemistry (15 decks)

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