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biochem 3g03 > Chapter 3 - From Genes to Proteins > Flashcards

Chapter 3 - From Genes to Proteins Flashcards

1
Q

two types of bases?

A

purines and pyrimidines

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2
Q

types of purines

A

adenine (A), guanine (G)

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3
Q

types of pyrimidines

A

cytosine (C), thymine (T), uracil (U)

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4
Q

bases of RNA

A

adenine, cytosine, guanine, uracil

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5
Q

bases of DNA

A

adenine, cytosine, guanine, thymine

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6
Q

nucleoside

A

sugar + base

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7
Q

nucleotide

A
  • a nucleoside with one or more phosphate groups attached
  • usually at C5 of the sugar
  • can also be at other positions
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8
Q

nucleic acid

A

polymer of nucleotides

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9
Q

phosphodiester bonds

A
  • links nucleotides by sugar
  • creates a nucleic acid in which its sequences are read 5’ to 3’
  • these bonds are high in energy because they include phosphate groups that are high in energy
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10
Q

how are two nucleotide strands held together?

A
  • they are held together by hydrogen bonds
  • 3 hydrogen bonds form between guanine and cytosine
  • 2 hydrogen bonds form between adenine and thymine or adenine and uracil
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11
Q

chargaff’s rule

A
  • the amount of A+G = C+T
  • base pairs contain a purine (A, G) and a pyrimidine (C, T, U)
  • A-T, A-U, G-C are the possible base pairs
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12
Q

model of DNA

A

double-stranded, antiparallel, right-handed, diameter of 20 Å, major and minor grooves, backbone exposed to solvent

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13
Q

model of RNA

A

single-stranded, can fold back on itself, intricate 3D shapes

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14
Q

order of duplex stability from most stable to least stable

A

RNA-RNA, RNA-DNA, DNA-DNA

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15
Q

X-ray crystallography

A
  • dominant method for deducing high-resolution protein structures
  • X-rays scatter as they pass through crystallized protein
  • the resulting waves interfere with each other, creating a diffraction pattern from which the position of atoms is deduced
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16
Q

cryo-electron microscopy

A
  • used instead of X-ray crystallography
  • beam of electrons is fired at frozen protein solution
  • emerging scattered electrons pass through a lens to create a magnified image on the detector, allowing the structure to be deduced
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17
Q

what does the stability of the DNA helix rely upon?

A

stacking interactions. does not really depend on the hydrogen bonds between base pairs

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18
Q

which base pair is stronger?

A

G-C

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19
Q

what drives the double helical conformation of DNA?

A

entropic forces that induce base stacking

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20
Q

different forces that stabilize DNA

A
  • predominant forces: hydrophobicity, base stacking, entropy
  • hydrogen bonding in base pairs
  • ionic interactions: cations, polyamines
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21
Q

denaturation/renaturation of DNA

A
  • apply high heat to melt DNA and denature it
  • cooling the denatured DNA to 20-25 C below Tm will cause renaturation
  • sometimes rapid cooling of the denatured DNA to temperatures much lower than Tm leads to improper base pairing
  • this improper base pairing can be fixed by rewarming the base pairs to 20-25 C below Tm to cause renaturation
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22
Q

genes

A

sequences of DNA

23
Q

replication

A

process for copying DNA

24
Q

transcription

A

process that converts DNA into RNA

25
Q

reverse transcription

A

process that covers RNA into DNA. this does not happen in our body

26
Q

translation

A

process that makes proteins from RNA template

27
Q

DNA replication (In vivo)

A
  • DNA must be copied in order to sustain life

- excessive DNA replication can be indicative of cancer

28
Q

DNA replication (In vitro)

A
  • polymerase chain reaction (PCR) has allowed researchers to study Nucleic Acids and genes
  • PCR amplifies DNA
29
Q

3 types of RNA

A

messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA)

30
Q

mRNA

A

encodes for polypeptide sequences

31
Q

tRNA

A

carries amino acids to ribosome

32
Q

rRNA

A

aids in polypeptide synthesis

33
Q

genetic code

A
  • use to translate mRNA into an amino acid sequence
  • 64 codons
  • codon has 3 nucleotides
  • a lot of codons are redundant
34
Q

how are genes identified?

A
  • scan for open reading frame: start codon (ATG) or stop codon (TAA, TAG, TGA)
  • comparison with known genes
35
Q

what is gene number roughly correlated with?

A

organismal complexity

36
Q

relationship between noncoding DNA and the organism

A

proportion of noncoding DNA generally increases with complexity of the organism

37
Q

sequence strategy for polymer

A

1) cleave polymer into small fragments
2) separate fragments
3) determine the sequence of resides in each of the fragments
4) determine the order of fragments in original polymer by overlapping fragments

38
Q

restriction enzymes

A

they cut DNA at specific sequences

39
Q

role of restriction enzymes in nature

A
  • aid in defence for bacteria
  • bacteria methylate their own DNA
  • bacteriophages (viruses that infect bacteria) have unmethylated DNA
  • bacterial restriction enzymes can recognize and excise viral DNA
40
Q

type 1 restriction enzymes

A
  • activity: endonuclease, methylase

- cleavage site: ≥1000 bp from recognition sequence

41
Q

type 2 restriction enzymes

A
  • activity: endonuclease
  • cleavage site: within or near recognition sequence
  • cleave 4-8 bp of dsDNA
  • palindromic recognition sequences
  • forms blunt or sticky ends
42
Q

type 3 restriction enzymes

A
  • activity: endonuclease, methylase

- cleavage site: approximately 24-26 bp from recognition sequence

43
Q

EcoRI

A
  • recognizes 5’-GAATTC-3’
  • complimentary sequence is implied
  • EcoRI cuts both strands after the 5’-G
  • each fragment has sticky ends
44
Q

EcoRV

A
  • recognizes 5’-GATATC-3’
  • complimentary sequence is implied
  • EcoRV cuts both strands after the 5’-T
  • each fragment has blunt ends
45
Q

gel electrophoresis

A

technique used to separate DNA fragments or other macromolecules based on their size or charge. a current is run through the Gell containing molecules of interest, creating a positively-charged side and a negatively-charged side. this allows attraction/repulsion forces to cause the molecule to travel to the opposite end of the cell accordingly

46
Q

pyrosequencing

A
  • method determines the sequence of residues in each DNA fragment
  • steps:
    1) DNA polymerase incorporates a complementary nucleotide into the new DNA chain (extends the primer). this releases a inorganic pyrophosphate (PPi).
    2) sulfurylase converts the PPi reaction product to ATP
    3) luciferase uses the ATP to power a reaction that produces light. the intensity of the light released is used to determine the number of nucleotides incorporated, etc.
47
Q

illumina sequencing

A
  • used to determine the series of base pairs in the DNA
  • steps:
    1) DNA polymerase incorporates a complementary nucleotide into the new DNA chain and unreacted nucleotides are washed away
    2) the incorporated nucleotide is detected by its fluorescence, then the fluorescent group is removed
    3) a new solution of nucleotides is introduced
48
Q

cloning techniques

A

1) a fragment of DNA is generated
2) the fragment is incorporated into a vector
3) the vector with the inserted DNA is introduced into cells, where it is replicated
4) cells containing the desired DNA are identified or selected

49
Q

types of cloning vectors

A

plasmid, cosmid, bacterial artificial chromosome, yeast artificial chromosome

50
Q

recombinant DNA

A
  • DNA fragments are joined to produce this
  • plasmid, foreign DNA are cut
  • then the pieces are annealed in such a way that now the plasmid and foreign DNA are combined into one
  • ligation occurs to produce recombinant DNA. this is done by DNA ligase as it facilitates the joining of DNA fragments by catalyzing the formation of the phosphodiester bond
51
Q

PCR

A
  • polymerase chain reaction

- amplifies DNA to make billions of copies of DNA efficiently and accurately

52
Q

requirements for PCR

A
  • heat-stable DNA polymerase (ex: Taq DNA polymerase)
  • primers (DNA oligonucleotides)
  • deoxynucleotide triphosphates (dATP, dGTP, dCTP, dTTP)
  • DNA template
  • buffer
  • thermal cycler: device that heats and cools sample
53
Q

chemical reactions used and repeated in PCR

A

1) denaturation:
- dsDNA separates at high temperatures to form ssDNA
- 92-95 C
2) annealing:
- primers can base pair to ssDNA
- approximately 55 C
3) extension:
- optimal temperature for heat-stable DNA polymerases to work
- new strand is synthesized
- 72 C

54
Q

CRISPRs

A

Clustered Regularly Interspersed Short Palindromic Repeats

biochem 3g03 (3 decks)

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