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CHEM 441A > Midterm 1 > Flashcards

Midterm 1 Flashcards

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1
Q

What is the optimal distance for Van der Waals interactions?

A

Occurs at a distance slightly greater than the length of the covalent bond.

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2
Q

1 nm = 10-9 m

1 Aº = ?

A

10-10 ​m

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3
Q

Order bond strength from strongest to weakest

A
  1. Covalent
  2. Ionic
  3. Hydrogen Bond
  4. Van Der Walls
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4
Q

Given the Second Law of Thermodynamics, how can reactions that create order (which are entropically unfavorable) occur?

A
  • A favorable enthalpy change overcomes entropic penalty.
  • The unfavorable reaction is coupled to a favorable one.
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5
Q

Plant cell shape is determined by the amount of water stored in the central vacuole. What is directly responsible for maintaining turgor pressure in a leaf?

A

osmotic pressure

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6
Q

What are amino acids and how do they differ from one another?

A

Differ by the R group attached to central carbon

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7
Q

What 3 components make up a nucleotide?

A
  1. Nitrogen Base
  2. Pentose (5-ringed) Sugar
  3. Phosphate (1-3 groups)
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8
Q

Sugars contains what 3 atoms and what is the base molecular formula?

A

C, O, H

CH2O (Glucose is C6H12O6)

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9
Q

What does it mean if a molecule is amphipathic and which molecules usually exhibit this feature?

A

Has both hydrophobic and hydophilic parts.

Fatty acids

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10
Q

Compare saturated, polyunsaturated, and monounsaturated fats.

A

Saturated - No C=C double bonds

Polyunsaturated - Multiple C=C double bonds

Monounsaturated - One C=C double bond

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11
Q

Amino acids are _______ linked through _______ bonds.

A

covalently

peptide

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12
Q

Monosaccharides are _______ linked thorough _______ bonds.

A

covalently

glycosidic

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13
Q

What is supramolecular assembly?

A

NO covalent bonds involved

ex. membranes, DNA + Histones

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14
Q

What is the Organizational Heirarchy in Biochemistry?

A
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15
Q

What are the 3 unique properties of water?

A
  1. Solid water less dense than liquid water
  2. Liquid over wide range of Earth’s temperature
  3. Universal Solvent
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16
Q

What is a cofactor?

A

Any element required in conjuction with an enzyme to perorm a reaction.

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17
Q

When forming a hydrogen bond, there is always a H-bond ______ and H-bond _______.

A

donor

acceptor

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18
Q

In liquid, water makes about ____ H-Bonds

In ice, water makes about ____ H-Bonds.

A

3.4

4

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19
Q

What happens when a crystal of NaCl is dropped in water?

A

A hyrdation layer forms around the ions, preventing them from rejoining the crystal.

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20
Q

What exactly is a hydrogen bond?

A

A noncovalent weak bond that occurs between a hydrogen atom on an electronegative atom (N,O,) and a different electronegative atom.

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21
Q

What are Van Der Waals interactions?

A

Occur when temporary dipoles interact

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22
Q

What is the Van Der Waals radius?

A

Perfect distance between two atoms in order for Van Der Waals interaction to occur.

*Note: If atoms are too close, they will repel. If they are too far, they will not interact*

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23
Q

What are hydrophobic effects?

A

Weak noncovalent interactions between non-polar molecules in which the molecules clump together to reduce the size of the hydration layer.

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24
Q

Cell membranes are made of __________ bilayers.

A

phospholipid

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25
Q

What is Osmosis?

A

When solvent (water) moves from an area of lower solute concentration to an area of higher solute concentration through a semipermeable membrane.

Low Concentration ⇒ High Concentration

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26
Q

What is the Henderson-Hasselbach equation?

A
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27
Q

What is the central dogma of molecular biology?

A

DNA → mRNA → Protein

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28
Q

What 3 parts do nucleic acids consist of?

A
  1. Nitrogen base
  2. Pentose sugar (Ribose or Deoxyribose)
  3. Phosphate group
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29
Q

What bases are purine and which are pyrimidines?

A
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30
Q

What is the difference between ribose and deoxyribose sugars?

A

Ribose - OH at C-2’

Deoxyribose - H at C-2’ (more stable)

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31
Q

What does a nucleoside consist of?

A
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32
Q

Phosphate group + nucleoside =

A

nucleotide

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33
Q

Nucleotides are linked together via ___________ bonds.

A

phosphodiester

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34
Q

How are the phosphoryl groups labeled on a nucleotide?

A
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35
Q

How many base pairs are in eukaryotic DNA?

A

6 billion

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36
Q

Purines have _______ rings while pyrimidines have ______ ring.

A

two

one

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37
Q

How do you name a nucleoside?

A

suffix “osine” or “idine”

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38
Q

How do you name a nucleotide?

A

Nucleoside-5’ “monophosphate”

or

suffix “ylate”

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39
Q

Compare the primary and secondary structure of DNA.

A

Primary - nucleotides in a chain

Secondary - two complementary strands of DNA bind together in an antiparallel fashion to form a double helix.

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40
Q

Compare the minor and major grooves.

A

Minor - backbones closer together

Major - backbones further apart

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41
Q

Base pairs (A-T, C-G) are bonded via ________ bonds.

A

hydrogen

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42
Q

The nitrogen bases are _________, therefore, move to the interior of the DNA molecule.

A

hydrophobic

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43
Q

A complete turn of the helix in B-form DNA contains ____ base pairs.

A

10.5 (36 Aº)

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44
Q

Compare the DNA coding strand and DNA template strand.

A

DNA coding strand runs 5’ → 3’

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45
Q

What is Chargaff’s Rule?

A

Molar ratio of A = molar ratio of T, C=G

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46
Q

A-T has ___ H-Bonds and C-G has ___ H-Bonds.

A

2

3

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47
Q

How does base stacking provides stability for DNA?

A

Hydrophobic effects and Van Der Waals interactions create less interaction with water.

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48
Q

Compare the 3 types of DNA.

A

A - Short, wide, right-handed, dehydrated, bases are tilted 20º

*B - Right-handed, most stable/common

Z - Left handed, narrow

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49
Q

What is DNA denaturation and how does it occur?

A

When a double strand separates into single strands.

Occurs under heat or addition of acid/base.

*Note: Separation can also occur enzymatically via helicases

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50
Q

At what temperature (Tm) is half of DNA double-stranded and half single-stranded?

A

85ºC

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51
Q

The absorbance of DNA ________ as it becomes single stranded.

A

increases

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52
Q

What is renaturation of DNA and when does it occur?

A

2 single strands reform to form a double helix.

Occurs when you decrease temperature.

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53
Q

The phenomenon of UV absorbance increasing as DNA is denatured is known as the ____________.

A

hyperchromic shift

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54
Q

What is the absorbance trend for DNA?

A

single nucleotides > single-stranded > double-stranded

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55
Q

Compare the Linking number (Lk), Twist number (Tw), and Writhe number (Wr) and how are they related.

A

Lk - Number of times DNA strand winds in right-hand direction

Tw - Number of times one strand completely crosses over the other

Wr - Number of times helix crosses over itself

Lk = Tw + Wr

*Note: As long as the DNA backbone is not disrupted, Lk is constant.

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56
Q

Compare positive, negative, and relaxed supercoils.

A

Negative most common

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57
Q

What is a nucleosome?

A

DNA + histone proteins.

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58
Q

What are topoisomerases?

A

Enzymes that relieve positive supercoils through cleavage and reannealing of DNA.

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59
Q

Compare Topoisomerase I and Topoisomerase II.

A

Topoisomerase I - Cleaves 1 strand of DNA and reduces supercoil region by 1 turn

Topoisomerase II - Cleaves 2 strands of DNA and reduces supercoil region by 2 turns

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60
Q

Why is DNA more stable than RNA.

A

Autocleavage can occur in RNA but the absence of the C-2’ OH group in DNA keeps autocleavage from happening.

61
Q

What is the deamination of cytosine and what base is produced?

A

Loss of an amine group.

Uracil

62
Q

What are ribozymes and what do they do?

A

RNA molecules with catalytic activity.

Cleave nucleic acids.

63
Q

What is the function of tRNA?

A

tRNA - anticodon

mRNA - codon

In the process of translation, a tRNA anticodon must match up with each codon in mRNA to add the correct amino acid to a growing protein chain.

64
Q

What is Inosine?

A

Inosine is a nucleoside often found in tRNA that can base pair with A, C and U. This can be used in translation. 2 H-Bonds

65
Q

How can you end up with a triple helix?

A

Triplet interactions can occur between a single stranded region of DNA, or RNA with an RNA, DNA, or RNA-DNA duplex.

Quadraplexes can occur among guanine bases found in particular G-rich DNA sequences.

66
Q

How many genes do humans have?

A

50,000

67
Q

What is a genome?

A

The genome is the collection of genes and it remains constant, however, expression of that gene can change.

68
Q

What is the importance of telomeres?

A

Keep chromosomes intact/stable. Every time a cell divides, telomere length decreases and decreased telomere length contributes to cancer.

*Note: Telomerase increases length of telomere

69
Q

What is the promoter region?

A

A specific DNA sequence upstream of the coding sequence that is necessary to interact with transcription factors.

70
Q

Exons are ________ regions and introns are ________ regions.

A

coding

non-coding

71
Q

RNA polymerase binds to the __________ ____________ which initiates transcription.

A

promoter region (TATA)

72
Q

A ____________ gene has one coding-sequence resulting in one protein.

A __________ gene has multiple coding-sequences resulting in multiple proteins.

A

Monocistronic

Polycistronic

73
Q

What occurs when RNA undergoes processing?

A
  • Remove intron sequences,
  • Add a 5′ cap
  • Add a 3′ poly(A) tail
74
Q

What are transcription factors?

A

Proteins that help initiate transcription by recruiting RNA polymerase.

75
Q

What is a single nucleotide polymorphism (SNP)?

A

One nucleotide substituted for another.

76
Q

What are short tandem repeats (STR)?

A

Deletion or insertion in genome

77
Q

What are 3 major ways that bacteria transfer DNA?

A
  1. Transduction - Bacteriophage brings in DNA
  2. Conjugation - DNA transferred via direct contact
  3. Transformation - exogenous DNA introduced
78
Q

What is a restriction endonuclease?

A

An enzyme that cleaves DNA.

Type I: Recognize and cleaves at different sites (25bp)

Type II: Recognize and cleaves at the same site.

Type III: Recognize and cleaves and different sites (100bp)

79
Q

A nucleosome particle consists of ______ base pairs double-stranded DNA wrapped around 8 histone proteins H2A, H2B, H3, and H4, with H1 (green) on the outside of the structure.

A

147

80
Q

Right-handed twists produce a _______ supercoil and left-handed twists produce a ________ supercoil.

A

negative

positive

81
Q

Many tRNA anticodons contain the nucleoside _________ which is able to base pair with the nucleosides C, U, or A.

A

inosine

82
Q

Plasmids, Cloning?

A

White - DNA insertion has occurred (no functional B-enzyme)

Blue - DNA insertion has NOT occurred (functional B-enzyme)

83
Q

For the _________ nitrogenous bases, the heterocyclic ring contains nine atoms and the _________ nitrogenous bases have six atoms within the ring.

A

purine

pyrimidine

84
Q

The presence of 1.5 M NaCl causes a ________ in the melting temperature of DNA.

A

increase

Curve would shift right

85
Q

Why does mp increase when %G-C increases?

A

3 hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher.

86
Q

Supercoiling DNA is a property of what kind of cells?

A

Both prokaryotic cells and eukaryotic cells

87
Q

What role do Topoisomerases play in DNA replication?

A

Topoisomerase enzymes alleviate the supercoil that develops during DNA replication_. IF inhibited DNA replication cannot occur_.

88
Q

Compare euchromatin and heterochromatin. Which is more susceptible to DNA cleavage?

A

Euchromatin - open structure

Heterochromatin - DNA is compact structure

Euchromatin leaves more DNA exposed and is, therefore, more susceptible to DNA cleavage.

89
Q

Heterochromatin is associated with _________ DNA and the ___________ of a chromosome.

A

non-coding

centromere

90
Q

Outline the steps that eukaryotic DNA take in the progression toward reducing its size and becoming a chromosome.

A
  1. The initial DNA–histone association produces the nucleosome
  2. Nucleosomes join to form looped chromatin
  3. Chromatin coils.
  4. Chromosome
91
Q

What is the formula for the number of DNA molecules generated by PCR?

A

2n

n is the cycle number

92
Q

When making cDNA from mRNA, what is the appropriate primer to use?

A

5’-TTTTTTTTTTTTTTT-3’

93
Q

The Sanger method of DNA sequencing requires what being in the reaction tube?

A
  • template DNA
  • deoxyribonucleotides
  • dideoxyribonucleotides.
94
Q

What are the steps for PCR (Polymerase Chain Reaction)?

A
  1. Denature DNA at high temperature
  2. Primers anneal at lower temperature
  3. Taq DNA polymerase catalyzes the extension of the primer to produce a sequence complementary to each template strand
95
Q

How do you make cDNA from mRNA?

A
  1. mRNA + primer that is complementary to mRNA tail
  2. Treat with reverse transcriptase → 1 strand cDNA
  3. Treat with ribonuclease H to degrade mRNA
  4. Treat with DNA polymerase → 2nd strand cDNA
96
Q

If you start with 6 DNA molecules and do 25 PCR cycles, how many DNA molecules will you end up with?

A

6 X 225 molecules

97
Q

What is the chain-termination method used to determine?

A

The sequence of a region of DNA.

Utilizes ddNTP (dideoxyribonucleoside triphosphate) which has H’s at the 2’ and 3’ Carbons. Terminates elongation of chain.

Random incorporation of a ddNTP in the DNA product terminates synthesis and incorporates a different fluorescent label for each ddNTP.

98
Q

What is the configuration for most amino acids? Which one is the exception?

A

S (L) - amino on left

*Exception is Cysteine which is R (D) configuration

99
Q

What is the abbreviation and formula for Glycine?

A

Gly

G

100
Q

What is the abbreviation and formula for Alanine?

A

Ala

A

101
Q

What is the abbreviation and formula for Valine?

A

Val

V

102
Q

What is the abbreviation and formula for Leucine?

A

Leu

L

103
Q

What is the abbreviation and formula for Isoleucine?

A

Ile

I

104
Q

What is the abbreviation and formula for Proline?

A

Pro

P

105
Q

What is the abbreviation and formula for Methionine?

A

Met

M

106
Q

What is the abbreviation and formula for Phenylalanine?

A

Phe

F

107
Q

What is the abbreviation and formula for Tryptophan?

A

Trp

W

108
Q

What is the abbreviation and formula for Tyrosine?

A

Tyr

Y

109
Q

What is the abbreviation and formula for Serine?

A

Ser

S

110
Q

What is the abbreviation and formula for Threonine?

A

Thr

T

111
Q

What is the abbreviation and formula for Cysteine?

A

Cys

C

112
Q

What is the abbreviation and formula for Aspartic Acid?

A

Asp

D

113
Q

What is the abbreviation and formula for Glutamic Acid?

A

Glu

E

114
Q

What is the abbreviation and formula for Asparagine?

A

Asn

N

115
Q

What is the abbreviation and formula for Glutamine?

A

Gln

Q

116
Q

What is the abbreviation and formula for Histidine?

A

His

H

117
Q

What is the abbreviation and formula for Lysine?

A

Lys

K

118
Q

What is the abbreviation and formula for Arginine?

A

Arg

R

119
Q

Which amino acid makes a disulfide bridge?

A

Oxidation of 2 Cysteine residues

120
Q

_________ are enzymes that add a phosphate group to a protein and _________ are enzymes that remove a phosphate group.

A

Kinases

Phosphatases

121
Q

What is the pKa1 of the C-terminal of amino acids?

A

2.2

122
Q

What is the pKa2 of the N-terminal for amino acids?

A

9.4

123
Q

What is the pKa3 of Aspartic Acid (Asp, D)?

A

3.9

124
Q

What is the pKa3 of Glutamic Acid (Glu, E)?

A

4.07

125
Q

What is the pKa3 of Histidine (His, H)?

A

6.04

126
Q

What is the pKa3 of Lysine (Lys, K)?

A

10.54

127
Q

What is the pKa3 of Arginine (Arg, R)?

A

12.48

128
Q

What is the pKa3 of Tyrosine (Tyr, Y)?

A

10.46

129
Q

What is the pKa3 of Cysteine (Cys, C)?

A

8.37

130
Q

Peptide bonds are formed by _________ between the amine and carboxylic acid groups and catalyzed by _________.

A

condensation

ribozymes

131
Q

Why is free rotation restricted around a peptide bond?

A

It has partial double bond character.

132
Q

What are the 3 stop codons in RNA?

A

UAA

UAG

UGA

133
Q

What is the isoelectric point (pI)?

A

The pH at which a molecule (amino acid) is neutral.

134
Q

How do you calculate pI for an acidic amino acid?

A

pKa1 + pKa3

2

135
Q

How do you calculate pI for a basic amino acid?

A

pKa2 + pKa3

2

136
Q

What is the Buffering Zone?

A

1 pH above and 1 pH below pI

137
Q

What is the Wobble Hypothesis?

A

There exists unconventional base pairing for the 3rd base of the codon/anticodon. So we don’t need a tRNA for all 61 codons, most cells have around 40 tRNA.

138
Q

What are some characteristics of the alpha-helix?

A
  • Right-handed helix
  • H-Bond between residues n and n+4
  • Favored by MALEK
  • Destabilized by GP

-

139
Q

Alpha-helices have a dipole moment toward which terminus?

A

C-terminus (carbonyl)

140
Q

ß strands form ___________.

A

ß-pleated sheets

141
Q

ß-sheets can be _______ or ________.

A

parallel

antiparallel (MORE STABLE due to H-bonds)

142
Q

What are Beta Turns?

A

Connect 2 ß strands in an antiparallel fashion.

143
Q

What are the two types of ß turns?

A

Type 1 - Carbonyl oxygen facing inward

Type 2 - Carbonyl oxygen facing outward

144
Q

Compare homodimer and heterodimer.

A

homodimer - 2 identical protein subunits

heterodimer - 2 different protein subunits

145
Q

What is the 4 helix bundle?

A

ALL alpha-helices

146
Q

What is the Greek Key fold?

A

4 or more B-strands to form a B-sheet

147
Q

What is the Rossman Fold?

A

Alternating alpha-helices and B-strands (alpha/Beta 50/50)

148
Q

What is the TIM Barrell fold?

A

Protein fold that has alternating alpha helix and beta strand

(α/βbarrel)

CHEM 441A (4 decks)

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