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Study Cards > Molecular Bio Midterm #1 > Flashcards

Molecular Bio Midterm #1 Flashcards

Lectures 1-11

1
Q

what is a local energy minimum

A

a state with less energy than its surrounding neighbours in protein folding

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2
Q

what Is a chaperone

A

proteins that assist in proper folding of other proteins

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3
Q

what is a homodimer

A

two of the same proteins

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4
Q

what is a heterodimer

A

two different proteins

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5
Q

what is kinase

A

an enzyme used to add a phosphate group to an amino acid

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6
Q

what is a phosphatase

A

an enzyme used to remove phosphate groups from certain amino acids

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7
Q

5 post-translational modifications

A

methylation, acetylation, phosphorylation, glycosylation, hydroxylation

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8
Q

primary structure does what

A

encodes all information needed for proper protein folding

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9
Q

what are the two forces driving protein folding

A

hydrophobic and van der waals interactions

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10
Q

what does extreme electronegativity allow you to predict?

A

the type of bond that will form

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11
Q

what is separation of positive and negative charges called

A

electric dipole moment

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12
Q

how does electronegativity on the periodic table increase

A

left to right and bottom to top

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13
Q

what is the separation of positive and negative charges called

A

electric dipole moment

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14
Q

what are the three weak non-covalent bonds

A

hydrogen bonds, van Der Waals forces, hydrophobic interactions

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15
Q

hydrogen bond (of H-bond) is primarily what the of force?

A

an electrostatic force of attraction between a hydrogen atom which is covalently bonded to a more electronegative “donor” atom or group (Dn), and another electronegative atom bearing a lone pair of electrons – the hydrogen bond acceptor (Ac)

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16
Q

order the bond strength strongest to weakest

A

covalent, ionic, hydrogen and hydrophobic, van der waals

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17
Q

polar compounds are water soluble so they are…?

A

hydrophilic

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18
Q

non-polar compounds are not water soluble so they are..?

A

hydrophobic

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19
Q

do proteins have hydrophobic or hydrophilic regions and why

A

have both hydrophobic and hydrophilic regions due to structure and function once folded

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20
Q

5 functional groups

A

hydroxyl, amino, methyl, carboxyl, phosphate

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21
Q

why is cysteine chemically unique

A

cysteine is the only amino acid that can form covalent bonds

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22
Q

why is proline conformationally unique

A

part of essential things like collagen

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23
Q

why is glycine conformationally unique

A

R group is H- nothing else can fit and it is flexible (can fit in many different spots)

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24
Q

alpha carbons have what type of group

A

R- groups

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25
Q

what type of bond is formed between the c-terminus and the n-terminus

A

covalent peptide (C-N) partial double bond

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26
Q

is the peptide bond between the C-terminus and the N-terminus rotatable? why?

A

non-rotatable because carbon and oxygen are stuck at there respective sides

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27
Q

can other bonds rotate

A

the single bonds around the molecule are all rotatable

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28
Q

what is life

A

a chemical system capable of darwinian evolution

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29
Q

evolutionary processes depend on what

A

changes in genetic variability and allele frequencies over time

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30
Q

what are the three properties of life

A

multiplication, mutation, heredity

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31
Q

what we know about DNA

A

it is not the origin of like but provides stability and storage

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32
Q

RNA

A

reactive in a way DNA is not, capable of diversity, storage, and catalysis

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33
Q

which biomolecules are capable of diversity and storage but not catalyst?

A

RNA

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34
Q

life requires chemicals capable of what

A

storing information, replicating information, modifiability

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35
Q

what is RNA structure

A

highly evolved ribozyme

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36
Q

what is a ribozyme

A

RNA molecule that catalyzes things

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37
Q

p generation

A

parents used in a cross

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38
Q

F1 generation

A

progeny resulted from a cross in p gen

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39
Q

F2 generation

A

progeny resulting from a cross in the f1 generation

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40
Q

purebred

A

individual homozygous for a given trait or set of traits

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41
Q

hybrid

A

progeny resulting from a cross of parents with different genotypes

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42
Q

gene

A

section of DNA encoding a protein or functional RNA

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43
Q

allele

A

variant of the gene encoding a trait

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44
Q

phenotype

A

outward appearance of an organism

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45
Q

genotype

A

alleles contained in an organism

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46
Q

homozygous

A

having two identical copies of a allele for a gene

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47
Q

heterozygous

A

having two different alleles for a gene

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48
Q

dominant allele

A

allele expressed in the phenotype of a heterozygous organism

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49
Q

recessive allele

A

allele masked in the phenotype of a heterozygous organism

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50
Q

what does an atomic number stand for

A

number of proteins in its nucleus

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51
Q

how many bonds does H, O, N, and C need

A

H - 1
O - 2
N - 3
C - 4

52
Q

what happens in a covalent bond

A

electrons are shared

53
Q

what happens in ionic bond

A

electrons transferred

54
Q

what is electronegativity

A

different affinities of the bonded atoms for electrons

55
Q

what scale is electronegativity measured on

A

pauling scale

56
Q

structural isomer

A

molecules with the same molecular formulas (number and type of atoms), but different bonding arrangements of atoms. They have different properties

57
Q

what happens in extreme electronegativity

A

atom loses electron, and one becomes positive whereas the other becomes negative and forms an ionic bond

58
Q

stereoisomers

A

molecules with the same molecular forms and bonding of atoms but different spatial arrangement. They have different properties

59
Q

chiral molceule vs chiral molecule

A

a chiral molecule cannot be superimposed on its mirror image whereas an achiral molecule can be superimposed

60
Q

what are the 4 unique amino acids

A

glycine, cystein, histamine, proline

61
Q

how is a dihedral angle between two planes defined

A

defined by atoms 1,2, and 3 and atoms 2, 3, and 4 respectively

62
Q

how are amide or peptide bond planes joined

A

joined by the dihedral bonds of the alpha carbon

63
Q

how is a dihedral angle determined

A

between lines perpendicular to each plane

64
Q

why are many possible conformations of an alpha carbon between two peptide planes are forbidden

A

few combinations are possible because of steric crowding/ hindrance

65
Q

in an alpha helix, where does the hydrogen bond form

A

hydrogen on amide N forms a hydrogen bond with the carbonyl O of the 4th residue towards the N-terminus

66
Q

amino acid residues in an alpha helix have conformations with what

A

ψ = -60° and ∅ = -45 to -50°

67
Q

what is the N terminus

A

the nitrogen of the first amino group

68
Q

what do helices exploit

A

maximum hydrogen bonding among groups

69
Q

what is the N terminus

A

the nitrogen of the first amino group

70
Q

when making a peptide bond where would you never add a new amino group

A

H2N

71
Q

how are bonding strands in an antiparallel strand shown

A

straight

72
Q

when making a peptide bond where would you add a new amino group

A

the OH of the first alpha carbon

73
Q

how are bonding strands in a parallel strand shown

A

oblique (diagonal)

74
Q

where does the R group of the helix pop out

A

towards the axis not outside

75
Q

how do R groups alternate

A

up and down

76
Q

how many angstroms are there per residue

A

3.5

77
Q

how many angstroms are between R groups on the same side

A

7

78
Q

where is the Phi angle around

A

the -N-CA- bond (where ‘CA’ is the alpha-carbon)

79
Q

where is the psi angle around

A

around the -CA-C- bond.

80
Q

what is a motif

A

particularly stable and common arrangements of multiple secondary structural elements (aka super secondary structures). motifs are structural but not necessarily functional characteristics

81
Q

what is a domain

A

independent folding units with a defined function a domain can have one or more motifs

82
Q

what is a protein

A

a functional polypeptide. it can have one or more domains

83
Q

helical structures have R residues facing what way

A

outside

84
Q

beta sheets (sheet motifs) have R residues facing what way

A

both inside and outside

85
Q

what does a zinc finger motif do

A

reads DNA and shows alpha and beta

86
Q

what is protein folding

A

the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil

87
Q

all information needed for proper protein folding is encoded by what

A

primary structure

88
Q

what are molten globules

A

compact, partially folded conformations of proteins that have near-native compactness, substantial secondary structure, dynamic tertiary structure and increased solvent-exposed hydrophobic surface area relative to the native state

89
Q

what collapses during protein folding

A

postulated hydrophobic collapse

90
Q

what is a local energy minimum

A

a dip that has less energy than its surrounding neighbours

91
Q

what does a massive dip mean

A

protein has misfolded

92
Q

what is methylation

A

addition of a methyl group

93
Q

what is acetylation

A

addition of an acetyl group

94
Q

what is phosphorylation

A

addition of a phosphate group

95
Q

what is glycoslation

A

addition of a sugar molecule

96
Q

what is hydroxylation

A

addition of a hydroxide (OH) group

97
Q

what electronegativity range is non polar covalent

A

<0.4

98
Q

what electronegativity range is polar covalent

A

0.4 - 1.8

99
Q

what electronegativity range is ionic

A

> 1.8

100
Q

what is alpha-keratin

A

key structural material making up scales, hair, nails, feathers, horns, claws, hooves, and the outlet layer of skin among vertebrates.

101
Q

what is alpha-keratin found in

A

vertebrates

102
Q

what is beta-keratin found in

A

birds and reptiles

103
Q

what is collagen

A

a fibrous structural protein with modified amino acids. it is the main structural protein in the extracellular space in the various connective tissues in animal bodies

104
Q

what percent of whole body protein does collagen make up

A

25% - 35%

105
Q

what three consistencies can collagen tissues be

A

depending on degree of mineralization, can be rigid (bones), compliant (tendon), or have a gradient from rigid to compliant (cartilage)

106
Q

how many amino acid residues does each collagen helix consist of

A

~1000

107
Q

what post-translational modification needs vitamin C as a reactant

A

hydroxylation of Pro and Lys

108
Q

what can cause wrinkles

A

collagen levels decreasing and cross linking not being rebuilt properly

109
Q

what happens at carbon 1’

A

the carbon that leads to the base – the pyrimidine or purine base is linked here

110
Q

what happens at carbon 2’

A

tell you if it’s a ribonucleotide or deoxynucleotide
- ribonucleotide will have one hydroxy and one hydrogen
- deoxy will have two hydrogens

111
Q

what happens at carbon 3’

A

it has a hydroxy which in involved in the phosphodiester bond – related to the 3’ molecule of DNA

112
Q

what happens at carbon 4’

A

nothing

113
Q

what happens at carbon 5’

A

the phosphate is attached here
- bond between the phosphate of the 5’ and the hydroxy of the 3’ is formed here

114
Q

what are the purine bases

A

adenine and guanine

115
Q

what are the pyrimidine bases

A

cytosine, thymine (DNA), uracil (RNA)

116
Q

what does a nucleoside have

A

base and a sugar

117
Q

what does a nucleotide have

A

base, sugar, and phosphate

118
Q

what are the base names

A

adenine, guanine, cytosine, thymine, uracil

119
Q

what are the nucleoside RNA names

A

adenosine, guanosine, cytidine, thymidine, uridine

120
Q

how do the nucleoside DNA names differ from the RNA names

A

“deoxy” is added onto the front the names but the names stay the same as in RNA

121
Q

what are the three-letter abbreviations for nomenclature of bases

A

adenosine - AMP
guanosine - GMP
cytidine - CMP
thymidine - TMP
uracil - UMP

122
Q

how do the three letter abbreviations change when talking about DNA

A

a “d” is added in front of the three letter abbreviations which stay the same

123
Q

what is the orientation of the DNA molecule

A

5’ to 3’

124
Q

why is DNA helical

A

protect the hydrophobic bases from water while exposing the backbone of the phosphodiester bonds

125
Q

antiparallel orientation

A

one strand going 5’ - 3’ and the other going 3’ to 5’

126
Q

what is the secondary structure of DNA

A

two antiparallel polynucleotide chains wound around the same axis with a sugar-phosphate backbone wrapped around the outside

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