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BIO206 > Term Test 1 Prep > Flashcards

Term Test 1 Prep Flashcards

1
Q

A-DNA

A
  • right handed
  • short and broad
  • 26 Å in diameter
  • 11 base pairs/turn
  • 26 Å rise per base pair
  • 20° tilt to helix axis
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2
Q

B-DNA

A
  • right handed
  • longer and thinner
  • most common in living cells
  • has major and minor grooves
  • 20 Å in diameter
  • 10.5 base pairs/turn
  • 34Å rise per base pair
  • 6° tilt to helix axis
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3
Q

Z-DNA

A
  • left handed
  • slim and elongated
  • unknown function
  • distorted
  • 18Å in diameter
  • 12 base pairs/turn
  • 3.7Å rise per base pair
  • 7° tilt to helix axis
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4
Q

How wide is each base pair?

A

10.85 angstroms (1.085 nm)

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5
Q

How many H bonds form between AT and CG?

A

2 H bonds between A and T

3 H bonds between C and G (takes more energy to break apart)

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6
Q

How long is each turn in a DNA helix?

A

34 angstroms or 3.4 nm

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7
Q

Which C and N are involved in N-glycosidic bonds?

A

pyrimidines: C1’ to N1
purines: C1’ to N9

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8
Q

How thick is the whole DNA helix?

A

20 angstroms or 2nm

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9
Q

How many nucleotide bases per turn?

A

10

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10
Q

Angles of the major and minor grooves of B-DNA

A

major: 257°
minor: 103°

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11
Q

What are “zinc fingers”?

A

DNA binding proteins that wrap around DNA and interact specifically within major group

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12
Q

Why is DNA an ideal molecule to carry genetic information?

A
  • stable, doesn’t carry on promiscuous reactions
  • regular structure
  • no evidence of catalytic activity
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13
Q

What type of bond links nucleotides together?

A

phosphodiester

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14
Q

intramolecular base pairing

A

when regions of the same rna molecule complementarily base pair with each other with H bonds
rna folds onto itself forming unique structures

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15
Q

T/F: RNA can catalyze reactions.

A

true

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16
Q

Which optical isomer form are amino acids usually?

A

L form

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17
Q

What type of reaction forms a peptide bond?

A

condensation rxn

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18
Q

N-terminus

A

amino end, (+)

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19
Q

C-terminus

A

carboxyl end, (-)

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20
Q

How are secondary structures formed?

A

by intramolecular hydrogen bonds between small portions of the polypeptide backbone

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21
Q

alpha helix

A
  • N-H forms H bond with C=O 4 peptide bonds away
  • H bonds run parallel to the helix (vertically)
  • each turn is 0.54nm in length
  • can be amphipathic–one side hydrophobic one side hydrophilic (one side will form towards lipids the other side will form towards water)
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22
Q

beta sheet

A
  • H bonds between N-H and C=O of different strands, holding the polypeptide chains together (very rigid)
  • can be parallel, antiparallel or mixed
  • 5 to 10 amino acids per strand
  • each sheet contains approx 2-15 strands
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23
Q

3° structure

A

folding of 2° structures with respect to each other

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24
Q

4° structure

A

overall 3D structure of multiple polypeptide chains; these chains interact with each other to create a stable molecule

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25
Q

The -NH3+ and -COO- can come together to form

A

an ionic/electrostatic bond

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26
Q

Disulfide bonds are formed in ____ conditions and broken in ____ conditions

A

formed in oxidizing condition and broken in reducing conditions

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27
Q

molecular chaperons

A

helps in the folding of proteins (or refolding of misfolded proteins)

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28
Q

How many amino acids are there per turn in an alpha helix?

A

3.6

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29
Q

motif

A
  • recurring/repeating 2° structure in different proteins (e.g. helix-turn-helix)
  • generally specific functions
  • smaller
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30
Q

domain

A
  • subunit of 3° structure that folds independently
  • larger
  • have particular functions
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31
Q

What is each level of protein structure stabilized by?

A

primary: peptide bonds
secondary: H bonding between groups on backbone
tertiary: bonds and interactions involving R groups
quaternary: bonds and interactions involving R groups and peptide backbone of different polypeptide chains

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32
Q

dimer

A

protein with two subunits

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33
Q

nucleases

A

enzymes that cleave phosphodiester bonds between nucleotides

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34
Q

difference between exonucleases and endonucleases

A

exonucleases cleave nucleotides at the end of the chain, endonucleases cleave phosphodiester bonds in the middle of the chain

35
Q

restriction endonucleases/restriction enzymes

A
  • a subset of endonucleases that cut dsDNA at a specific DNA sequence
  • came from bacteria; it was a method for them to protect themselves from viruses (viral DNA)
36
Q

type II restriction endonucleases

A
  • more than 90% REs are type II
  • recognize and cut symmetric/palindromic sequences 4-8 base pairs in length
  • most molecular biology applications use type II endonucleases
37
Q

methylase

A

methylates bacterial DNA to prevent it from being cleaved by endonucleases; REs target unmethylated

38
Q

RE nomenclature

A 
e.g. EcoR1
E-genus
co-species
R-strain
1-order isolated in
39
Q

REs can recognize DNA sequences # to # base pairs in length

A

4 to 8

40
Q

inverted palindrome

A

same nucleotide sequence in antiparallel directions (sequence is read the same way forward and back)

41
Q

EcoRI, BamHI, HindIII produce __ sticky ends (overhang)

A

5’ sticky ends

42
Q

PstI and KpnI produce __ sticky ends (overhang)

A

3’ sticky ends

43
Q

SmaI and AluI produce ___ ends

A

blunt ends (no overhang)

44
Q

isoschizomers

A

REs from different organisms that have the same cut site

45
Q

DNA ligase

A

the enzyme that joins the ends of two strands of DNA to make one continuous strand; catalyzes formation of 3’-5’-phosphodiester bonds; ATP dependent

46
Q

Which parts of eukaryotic cells contain DNA

A

Nucleus, mitochondria and chloroplasts (all segregated/separate)

47
Q

promotor

A

region on DNA where RNA polymerase will bind to begin transcription

48
Q

exon

A

region of the gene that is transcribed to RNA and encodes part or all of a particular protein

49
Q

UTRs

A

untranslated regions; regions that are transcribed but not translated; contain control elements; region before and after area to be translated

50
Q

terminator

A

region of DNA that signals the end of a gene; disengages RNA polymerase

51
Q

introns

A
  • non coding region of a eukaryotic gene that is transcribed but not translated
  • gene expression regulation
52
Q

promotor is typically ~__ nucleotides upstream of transcription site

A

25

53
Q

What does the strength of the promotor have to do with protein production?

A

strong promotors
= strong enhancers
= rapid engagement of rna polymerase
= more protein produced

54
Q

“equation” for transcription

A

dsDNA + RNA polymerase + NTPs (nucleotide triphosphates for energy) –> ssRNA + dsDNA + RNA polymerase

55
Q

primary transcript

A
  • the ssRNA initially produced by transcription
  • may undergo further processing to become mRNA, tRNA, rRNA
  • prokaryotes: primary transcript is mRNA
  • eukaryotes: primary transcript is hnRNA (heterogeneous nuclear) or pre-mRNA –> MUST UNDERGO FURTHER PROCESSING TO BECOME mRNA
56
Q

the coding strand is also known as…

A

non-template, + strand, this is what the sequence of a gene would be

57
Q

the non-coding strand is also known as…

A

template, - strand

58
Q

RNA is polymerized __ to __, DNA template strand is read __ to ___

A

RNA polymerized 5’ to 3’, DNA read 3’ to 5’

59
Q

alpha helices are generally __ amino acids long with __ turns, and __ amino acids per turn

A

11 amino acids long, 3 turns, 3.6 amino acids per turn

60
Q

amino acids that are “helix preference”

A

ala, leu, met, glu

61
Q

amino acids that are “helix breakers”

A

pro, gly, ser, thr

62
Q

What bond/interaction does not directly influence tertiary structure of a protein?

A

peptide bonds (it influences primary structure)

63
Q

consensus sequence

A

sequence of DNA having similar structure and function in different organisms

64
Q

bacterial culture growth phases

A

1) lag phase: 30 minutes following inoculation, no cell growth
2) log phase: cell number doubles every 20-25 minutes
3) stationary phase: nutrients depleted, cells stop dividing
4) death phase: waste products accumulate, cells begin to die

65
Q

intragenic mutation

A

gene can be randomly modified by errors in DNA replication

66
Q

gene duplication

A
  • accidental duplication of a gene in a single cell

- 2 genes may diverge through evolution

67
Q

DNA segment shuffling

A

2 or more genes break and rejoin to make a hybrid gene

68
Q

What did the mitochondria originate from?

A
  • a long time ago it existed as a free living organism
  • was an aerobic bacteria in a symbiotic relationship with an anaerobic ancestral cell (generated energy from oxygen)
  • have their own circular DNA, ribosomes, tRNA
69
Q

hydrophobic force

A

pushing nonpolar surfaces together to push them out of a hydrogen-bonded water network (reducing their contact with water)

70
Q

nucleoside names of each nitrogenous base

A

adenosine, guanosine, cytidine, thymidine, uridine

71
Q

nucleotide names of each nitrogenous base

A

adenylate, guanylate, cytidylate, thymidylate, uridylate

72
Q

nuclear envelope

A
  • made of lipid bilayer membrane
  • punctured by large pores that allow molecules to move between nucleus and cytosol
  • supported by network of filaments (NUCLEAR LAMINA)
  • keeps nuclear and cytosolic enzymes separate
73
Q

domain shuffling

A

evolutionary process where large proteins evolve by joining domains in new combinations

74
Q

protein modules

A

domains repeatedly found in diverse proteins; have versatile structures

75
Q

RNA polymerase

A
  • enzymes that perform transcription; catalyze formation of phosphodiester bonds that link ribonucleotides
  • substrates are ribonucleoside triphosphates
  • hydrolysis of phosphoanhydride bonds release energy to drive this process
76
Q

upstream goes toward the __ end and downstream goes toward the __ end

A

upstream: 5’ end
downstream: 3’ end

77
Q

gene expression

A

process involving the transcription and translation of a discrete DNA sequence

78
Q

core promotor (TATA box)

A
  • TATAAA

- 25 nucleotides upstream

79
Q

CAAT box

A
  • a proximal control element
  • GCCCAATCT
  • 80 nucleotides upstream
80
Q

GC box

A
  • a proximal control element
  • GGGCGG
  • 100 nucleotides upstream
81
Q

What type of interactions contribute to the stability of a DNA molecule along the vertical axis?

A

hydrophobic interactions along the base pairs of the vertical axis

82
Q

types of covalent bonding that can contribute to protein tertiary structure (5)

A
  1. hydrogen bonding between side chain and carboxyl oxygen
  2. hydrogen bonding between two side chains
  3. van der Waals interactions between hydrophobic regions
  4. disulfide bonds
  5. ionic bonds (non covalent)
83
Q

X-ray crystallography is a biophysical technique typically used to determine the 3-D structure of ___.

A

proteins

84
Q

“Phages” are infectious agents that attack __.

A

bacteria

BIO206 (9 decks)

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