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Biochemistry I 4880 > Unit 1 - Chapters 1-6 > Flashcards

Unit 1 - Chapters 1-6 Flashcards

1
Q

In proteins, what “level” of structure refers to the three-dimensional arrangement of all the atoms in a single polypeptide chain?

A

Tertiary

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2
Q

Where can Z -DNA be found?

A

In G:C rich regions of DNA

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3
Q

What is the nucleoside comprised of?

A

Nitrogenous base and sugar

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4
Q

Nucleic acids absorb UV light. Do single or double strands absorb more light?

A

Single stranded (hypochromic shift)

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5
Q

The melting temperature depends on the G:C content. Is the Tm higher or lower for DNA with more G:C content?

A

It is higher with more G:C content

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6
Q

Under physiological conditions DNA is in A, B or Z form?

A

B - DNA

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7
Q

Which of the following “tags” is used as a signal for protein degradation?

  1. SUMO
  2. phosphorylation
  3. Ubiquitin
  4. Selenocysteine
  5. none of the above.
A

Ubiquitin

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8
Q

DNA contains both A:T and G:C base pairs, and each base pair contains a purine and a pyrimidine. Which of the bases are purines?

A

Adenine and Guanine

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9
Q

Hydrophobic interactions between non-polar molecules in aqueous solution result from the stability achieved when

A

they release “caged” water molecules as the hydrophobic surface area decreases.

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10
Q

In a nucleotide, when the nitrogenous base is positioned away from the ribose ring, the base is said to be in what position?

A

Anti

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11
Q

Which DNA structure contains Guanine in a syn conformation?

A

Z-DNA - C stays anti but whole C nucleoside (base and sugar) flips 180 degrees. Result is that G:C H bonds can be preserved in the transition from B-form to Z-form

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12
Q

Cholesterol is weakly amphipathic due to the presence of

A

OH group at C3

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13
Q

Buffers are solutions of weak acids and their corresponding conjugate bases that resist a change in pH. Buffers are most effective:

A

When there is an equal amount of A- and HA present

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14
Q

The hyperchromic effect refers to

A

the increase in absorption at 260 nm by DNA that has been denatured

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15
Q

Glycine and proline are usually present in a common protein secondary structural element.

A

β -bend - A β turn results in a tight 180° reversal in the direction of the polypeptide chain. Glycine is the smallest and thus most flexible amino acid, and proline can readily assume the cis configuration, which facilitates a tight turn.

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16
Q

The end of a polynucleotide (DNA) which possesses a free hydroxy group is the

A

3’ end

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17
Q

The end of a polynucleotide (DNA) which possesses a free phosphate group is the

A

5’ end

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18
Q

A non-protein, large organic molecule associated non-covalently with an enzyme is referred to as a

A

Prosthetic group

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19
Q

The amino acid cysteine plays an important role physiologically in protein structure because

A

It forms intra- or interchain disulfide bonds

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20
Q

Intrinsic membrane proteins are those that

A

are embedded within the lipid bilayer

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21
Q

What is the main difference between an aldose and a ketose?

A

Both, aldose and ketose are monosaccharides that can be differentiated as aldose is the monosaccharide that contains aldehyde group in its structure along with the carbon chain, whereas ketose is the monosaccharide that contains ketone group along with the carbon chain.

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22
Q

Identify the D and L configurations of glyceraldehyde.

A

The OH group on the sterigenic carbon farthest away from the aldehyde group points to the right, it is D configuration. These correspond to the configurations of glyceraldehyde.

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23
Q

Is Cysteine oxidized or reduced when it forms S-S bonds?

A

Oxidized

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24
Q

What is the H-bonding pattern in alpha helix?

A

The C=O binds to the N-H of residue i + 4

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25
Q

Identify where alpha helices appear on the Ramachandran plot below.

A

Right-handed around -60 phi and psi

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26
Q

Identify where Beta strands appear on the Ramachandran plot below.

A

About -120 to –60 phi and +120 to +160 psi

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27
Q

Why are glycine, cysteine and proline “special”?

A

Glycine is the smallest amino acid. Cysteine creates intra and inter disulfide linkages. Proline connects to the backbone twice forming a 5 - membered ring. It forms kinks in proteins.

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28
Q

What is the approximate pKa of Tyrosine?

A

10.1

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29
Q

What is the approximate pKa of Lysine?

A

10.5

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30
Q

What is the approximate pKa of Histidine ?

A

6.00

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31
Q

What is the approximate pKa of Arginine?

A

12.5

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32
Q

What is the approximate pKa of Aspartate?

A

3.7

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33
Q

What is the approximate pKa of Glutamate?

A

4.3

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34
Q

Which nitrogenous bases are pyrimidines?

A

Cytosine, Thymine and Uracil (RNA)

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35
Q

Which nitrogenous bases are purines?

A

Adenine and Guanine

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36
Q

Draw the structure of ATP

A

See structure

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37
Q

Draw Adenine

(Mnemonic: College Students in NC Never Cut Class (Six-membered ring) NC Never! (5 membered ring)

Adenine adds an amine - Think amine flag at top of six membered ring

A

See structure

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38
Q

Draw Guanine

(Mnemonic: College Students in NC Never Cut Class (Six-membered ring) NC Never! (5 membered ring)

Think Guanine has an amine but also needs a Correctional Officer

A

See structure

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39
Q

Draw Cytosine

(Mnemonic: College Students in NC Never Cut Class (Six-membered ring)

Think Cytosine copies Adenine with its amine and guanine with the Correctional Officer. All pyrimidines need Correctional Officers, but Cytosine only needs 1. The others need 2.

A

See structure

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40
Q

Draw Thymine

(Mnemonic: College Students in NC Never Cut Class (Six-membered ring)

Think Thymine doesn’t need a MINE it already has one. It needs 2 correctional officers because it has the “gas” to escape.

A

See structure - Gas is CH3

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41
Q

Draw Uracil

(Mnemonic: College Students in NC Never Cut Class (Six-membered ring)

Think Thymine but without gas to get away.

A

See structure - Gas is CH3

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42
Q

Where is the N-glycosidic bond between the sugar and a pyrimidine and purine?

A

On the number 1 N in pyrimidines and number 9 N (5 membered ring) on purines

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43
Q

Draw the structure of deoxyribose.

A

See structure

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44
Q

Draw the structure of tryptophan?

A

One carbon plus indole ring

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45
Q

What is a nucleotide comprised of?

A

A nucleotide has three characteristic components: (1) a nitrogenous (nitrogen-containing) base, (2) a pentose, and (3) one or more phosphates

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46
Q

How is the glycosidic bond formed between the sugar and nitrogenous base in DNA and RNA?

A

The N-β-glycosyl bond is formed by removal of the elements of water (a hydroxyl group from the pentose and hydrogen from the base), as in O-glycosidic bond formation.

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47
Q

Where is the N-glycosidic bond formed between the nitrogenous base and the sugar in RNA and DNA?

A

The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an N-β-glycosyl bond to the 1’ carbon of the pentose, and the phosphate is esterified to the 5’ carbon.

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48
Q

What is another name for the sugars ribose and deoxyribose when they are nucleotides?

A

In nucleotides, both types of pentoses are in their β-furanose (closed five-membered ring) form.

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49
Q

Draw the structure of cAMP.

A

See structure

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50
Q

How is the phosphodiester linkage formed in DNA and RNA backbones?

A

The successive nucleotides of both DNA and RNA are covalently linked through phosphate-group “bridges,” in which the 5’ -phosphate group of one nucleotide unit is joined to the 3’-hydroxyl group of the next nucleotide, creating a phosphodiester linkage

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51
Q

Why are the phosphodiester bonds in DNA not rapidly hydrolyzed under alkaline conditions like RNA?

A

DNA does not have an OH on the 2’ carbon sugar. In RNA, water can pull the proton from the OH group on the 2’ carbon and hydrolyze the molecule.

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52
Q

The sequence of a single strand of nucleic acid is always written with the _______ end at the left and the ______end at the right — that is, in the _______ direction.

A

The sequence of a single strand of nucleic acid is always written with the 5’ end at the left and the 3’ end at the right — that is, in the 5’ - 3’ direction.

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53
Q

What is a short nucleic acid called?

A

A short nucleic acid is referred to as an oligonucleotide. The definition of “short” is somewhat arbitrary, but polymers containing 50 or fewer nucleotides are generally called oligonucleotides.

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54
Q

At what wavelength do nucleotides absorb UV light?

A

All nucleotide bases absorb UV light, and nucleic acids are characterized by a strong absorption at wavelengths near 260 nm

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55
Q

How does base stacking help to stabilize nucleic acids?

A

Base stacking involves hydrophobic stacking interactions. It also involves a combination of van der Waals and dipole-dipole interactions between the bases.

Base stacking helps to minimize contact of the bases with water, and base-stacking interactions are very important in stabilizing the three-dimensional structure of nucleic acids,

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56
Q

What is the most important complementary interaction between nucleic acids?

A

Hydrogen bonds involving the amino and carbonyl groups are the most important mode of complementary interaction between two (and occasionally three or four) complementary strands of nucleic acid.

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57
Q

What is the most important complementary interaction between nucleic acids?

A

Hydrogen bonds involving the amino and carbonyl groups are the most important mode of complementary interaction between two (and occasionally three or four) complementary strands of nucleic acid.

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58
Q

Draw the hydrogen bonds between Adenine and Thymine

A

See structure

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59
Q

Draw the hydrogen bonds between Guanine and Cytosine

A

See structure

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60
Q

Draw the hydrogen bonds between Adenine and Uracil

A

See structure

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61
Q
  1. Draw the side chain of Glycine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

Smallest amino acid

A
  1. See structure
  2. Nonpolar
  3. Gly, G
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62
Q
  1. Draw the side chain of Alanine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol
A
  1. See structure
  2. Nonpolar
  3. Ala, A
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63
Q
  1. Draw the side chain of Valine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol
A
  1. See structure
  2. Nonpolar
  3. Val, V
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64
Q
  1. Draw the side chain of Leucine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol
A
  1. See structure
  2. Nonpolar
  3. Leu, L
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65
Q
  1. Draw the side chain of Isoleucine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol
A
  1. See structure
  2. Nonpolar
  3. Ile, I
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66
Q
  1. Draw the side chain of Phenylalanine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol
A
  1. See structure
  2. Nonpolar
  3. Phe, F
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67
Q
  1. Draw the side chain of Tryptophan
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol
A
  1. See structure
  2. Nonpolar
  3. Trp, W
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68
Q
  1. Draw the side chain of Methionine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

2-S-1

A
  1. See structure
  2. Nonpolar
  3. Met, M
69
Q
  1. Draw the side chain of Proline
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol
A
  1. See structure
  2. Nonpolar
  3. Pro, P
70
Q
  1. Draw the side chain of Serine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

One carbon + OH

A
  1. See structure
  2. Polar - uncharged
  3. Ser, S
71
Q
  1. Draw the side chain of Threonine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

2 + OH

A
  1. See structure
  2. Polar - uncharged
  3. Thr - T
72
Q
  1. Draw the side chain of Cysteine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

1 + SH

A
  1. See structure
  2. Polar - uncharged
  3. Cys, C
73
Q
  1. Draw the side chain of Asparagine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

2 - End is part of amide

A
  1. See structure
  2. Polar - uncharged
  3. Asn, N
74
Q
  1. Draw the side chain of Tyrosine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol
A
  1. See structure
  2. Polar - uncharged
  3. Tyr, Y
75
Q
  1. Draw the side chain of Glutamine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

3 - End is part of amide

A
  1. See structure
  2. Polar - uncharged
  3. Gln, Q
76
Q
  1. Draw the side chain of Aspartate (aspartic acid)
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

2 - End is carboxylic acid

A
  1. See structure
  2. Polar - negatively charged (acidic)
  3. Asp, D
77
Q
  1. Draw the side chain of Glutamate (glutamic acid)
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

3 - End is carboxylic acid

A
  1. See structure
  2. Polar - negatively charged (acidic)
  3. Glu, E
78
Q
  1. Draw the side chain of Histidine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

5 membered ring with 2 NH

A
  1. See structure
  2. Polar -positively charged (basic)
  3. His, H
79
Q
  1. Draw the side chain of Lysine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

4 + NH<span>3</span> on the end

A
  1. See structure
  2. Polar -positively charged (basic)
  3. Lys, K
80
Q
  1. Draw the side chain of Arginine
  2. Classify as nonpolar, polar-uncharged, acidic or basic
  3. Provide the 3-letter abbreviation and 1 letter symbol

3 + NH + 1 bonded to 2 NH2 (1 NH2 double bonded)

A
  1. See structure
  2. Polar -positively charged (basic)
  3. Arg, R
81
Q

You wish to engineer a protein to increase its thermal stability. One way to do this would be to

A

Substitute proline for other amino acids

The larger the difference in free energy, the greater the thermal stability.

∆G=∆H - T∆S, a smaller ∆S value leads to a flatter slope in the ∆G plot versus temperature close to the melting temperature and thus increases thermal stability of the protein. This is called entropic stabilization.

82
Q

Sphingosine connected to a fatty acid via an amide bond makes up a lipid known as a

A

Cerebroside

83
Q

Double stranded RNA would most likely form a structure similar to:

A

A DNA

84
Q

What type of lipid is shown below?

A

Unsaturated fatty acid

85
Q

Which of the following “tags” is used as a signal for protein degradation?

A

Ubiquitin

86
Q

The free aldehyde of D-glucose can form a reversible intramolecular bond with either the hydroxyl group attached at carbon 4 or 5 to form what is known as a:

A

hemiacetal

87
Q

Nucleic acids are polyanions because

A

The pK1 of the phosphate group is around 2

88
Q

Which of the following is the major force that stabilizes the double helix of DNA?

A

base stacking interactions (van der Waals and hydrophobic)

89
Q

Explain parallel beta-sheets and how to tell if an amino acid sequence has this structure in terms of hydrophobicity.

A

Parallel β-sheet is characterized by two peptide strands running in the same direction held together by hydrogen bonding between the strands.

Both strands are hydrophobic

90
Q

Explain antiparallel beta-sheets and how to tell if an amino acid sequence has this structure in terms of hydrophobicity.

A

Antiparallel β-sheet is characterized by two peptide strands running in opposite directions held together by hydrogen bonding between the strands.

One strand is hydrophobic and the other is hydrophilic.

91
Q

How can you detect a collagen helix in the primary amino acid sequence?

A

It consists of a triple helix made of the repetitious amino acid sequence glycine -X-Y, where X and Y are frequently proline or hydroxyproline.

92
Q

How does CNBr cleave a polypeptide?

A

It cleaves on the carboxy side of Methionine.

93
Q

How does trypsin cleave a polypeptide?

A

It cleaves on the carboxy side of Lysine or Arginine.

94
Q

How does chymotrypsin cleave a polypeptide?

A

It cleaves on the carboxy side of the aromatic amino acids: Phenylalanine, Tyrosine and Tryptophan

95
Q

How does carboxypeptidase cleave a polypeptide?

A

It cleaves amino acids with a free carboxy end, except arg, lys or pro

96
Q

Acid hydrolysis changes Asn and Gln to which amino acids?

A

Asp and Glu

97
Q

Linking two amino acids is a formed by what type of reaction?

A

Amino acids link by a condensation (loss of water) reaction (addition -elimination) in which the OH group is lost from the carboxylic acid (COOH) group of one molecule and a hydrogen atom from the amino (NH).

98
Q

Digestion of amino acids is a formed by what type of reaction?

A

Amino acids are digested by a hydrolysis (addition of water) reaction in which the OH group is added to one amino acid and an H is added to another one.

99
Q

Chiral type of amino acids found in proteins.

A

L- Amino Acids

100
Q

Another name for dipolar molecules.

A

Zwitterions

101
Q

Disulfide bonds are formed by pairs of which amino acid?

A

Cysteine

102
Q

The amino acid with a pKa near neutral pH.

A

Histidine

103
Q

When a peptide bond is formed, what molecule is also made?

A

Water

104
Q

Where are proteins with extensive disulfide links likely to be found?

A

Extracellular

105
Q

This amino acid residue disrupts the α helix because its side chain contains a unique ring structure that restricts bond rotations.

A

proline

106
Q

Name of the plot that allows one to investigate the likely orientation of certain amino acid pairs.

A

Ramanchandran

107
Q

The type of structure to which α helices, β sheets, and turns are referred.

A

Secondary structure

108
Q

The overall structure of a protein is referred to as

A

tertiary structure

109
Q

The amino acid that contains a weakly acidic “phenolic” group is

A

Tyrosine

110
Q

is a fibrous protein and is the primary component of wool and hair.

A

Keratin

111
Q

Every third residue in the protein collagen is

A

glycine

112
Q

Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as

A

β mecaptoethanol

113
Q

A protein is considered to be __________________ when it is converted into a randomly coiled structure without its normal activity.

A

Denatured

114
Q

______________________ is the major fibrous protein present in skin, bone, tendon, cartilage, and teeth.

A

Collagen

115
Q

Collagen contains _____________________, a modified amino acid.

A

Hydroxyproline

116
Q

Agents such as ______________________ and guanidine hydrochloride denature proteins by disrupting the noncovalent interactions.

A

urea

117
Q

_____________________________ refers to the spatial arrangement of subunits and the nature of their interactions

A

Quaternary

118
Q

The ________________________ β-sheet structure occurs when the two strands are oriented in opposite directions (N → C).

A

antiparallel

119
Q

What determines a protein’s function?

A

Structure

120
Q

What charged group(s) are present in glycine at a pH of 7?

A

COO- and NH3+

121
Q

At a pH of 12, what charged group(s) are present in glycine?

A

COO-

122
Q

In what pH range is zwitterionic Alanine the predominate structure?

A

2-9

123
Q

Which amino acids contain reactive aliphatic hydroxyl groups?

A

serine and threonine

124
Q

Name three amino acids that are positively charged at a neutral pH.

A

Lys, Arg, His

125
Q

Why is the peptide bond planar?

A

It contains partial double-bond character, preventing rotation.

126
Q

The configuration of most α-carbon atoms of amino acids linked in a peptide bond is

A

Trans configuration

127
Q

Where are Ω and β turns and loops often found?

A

on the surface of proteins

128
Q

Alpha helices are disrupted by what type of amino acids?

A
  1. Proline - forms kinks in the helix
  2. Large numbers of bulky and/or branched chained amino acids due to steric hindrance
  3. Acidic or basic AA due to repulsion
129
Q

Which of the following amino acid residues would most likely be buried in the interior of a water soluble, globular protein?

Asp, Ser, Phe, Lys, Glu

A

Phe

130
Q

How does a protein’s amino acid sequence influence the tertiary structure?

A

A protein will spontaneously fold into a three-dimensional structure determined by the amino acid sequence.

131
Q

What is the advantage of having 20 different amino acids available to form proteins?

A

The amino acids provide a rich diversity of functional groups, which can independently contribute to protein structure and function. In addition, many can be modified, increasing the diversity of functional groups.

132
Q

How does the protein backbone add to structural stability?

A

The protein backbone contains the peptide bond, which has NH molecules and C=O (ketone) groups. Hydrogen-bond formation between the hydrogen on the nitrogen and the oxygen support the protein conformation.

133
Q

What is the “hydrophobic effect” as it relates to protein structure?

A

The three-dimensional structure of a water soluble protein is stabilized by the tendency of hydrophobic groups to assemble in the interior of the molecule.

134
Q

The ratio of enzyme activity relative to total protein is called

A

specific activity

135
Q

____________ A type of purification that is based on the attraction of the protein for a particular chemical group.

A

affinity chromatography

136
Q

____________ can be added prior to gel electrophoresis to denature the proteins.

A

SDS

137
Q

Exclusion gel or gel-filtration chromatography separates molecules on the basis of
__________________.

A

Size

138
Q

In the Edman procedure for peptide sequence, phenyl isothiocyanate is used to selectively
remove the __________________ residue as a PTH-derivative.

A

N-terminal

139
Q

Disulfide bonds in peptides and proteins are readily oxidized to cysteic acid residues by
treatment with __________________.

A

Performic acid

140
Q

How do gel-filtration and ion-exchange chromatography differ?

A

Although both are used in purification, the properties of the column material determine how the separation is accomplished. Gel filtration is based on porous beads, and molecules are separated by size. In ion-exchange chromatography, the column material is charged with either positively or negatively charged molecules. Separation is based on the protein’s charge and affinity for the column media.

141
Q

The information-carrying intermediates of translation.

A

mRNA

142
Q

The flow of genetic information from DNA to protein is called ____________.

A

gene expression

143
Q

Scientist who noted the A:T and G:C ratios in DNA are approximately 1:1.

A

Erwin Chargaff

144
Q

The temperature at which half the DNA helical character is lost is referred to as ____________.

A

Tm

145
Q

DNA renaturation after melting is called ____________.

A

Annealing

146
Q

Organisms in which the flow of genetic information can be RNA®DNA.

A

retroviruses

147
Q

Codons that specify the same amino acids are termed ____________.

A

synonyms

148
Q

__________________ is the most abundant type of RNA in a cell.

A

rRNA

149
Q

The phenomenon that stacked bases in double-helical DNA absorbed less UV light than the unstacked bases in single-stranded DNA is referred to as _________________.

A

: hypochromism or the hypochromic effect

150
Q

The chemical forces that contribute to the stability of the DNA due to the base stacking present in the DNA helix are

A

van der Waals

151
Q

Draw two nucleotides in DNA showing the linkage between the sugars linked.

A

See structure

152
Q

What advantage do phosphodiesters have compared to other esters?

A

The negative charge serves to repel nucleophilic species such as OH-. Thus the phophodiester linkage is more stable because it is more resistant to hydrolytic cleavage.

153
Q

Briefly describe the Meselson and Stahl experiment that indicated that DNA replication is semiconservative

A

Meselson and Stahl grew bacteria in the presence of 15N, or “heavy” nitrogen. They rapidly replaced the 15N media with 14N, or light nitrogen. DNA was extracted at various time intervals during the growth of the bacteria, representing different stages of replication (generations). They examined the DNA using density-gradient equilibrium sedimentation and observed that no “heavy” DNA was present in the first generation, but that the DNA was intermediate between light and heavy. After the second generation, there were equal amounts of intermediate and light. This confirmed that one strand of the parent DNA is present in each daughter strand of replicated DNA.

154
Q

What does it mean that DNA is semiconservative?

A

DNA replication is a semi-conservative process, because when a new double-stranded DNA molecule is formed: One strand will be from the original template molecule.

155
Q

___________________________ cleave DNA at sites with inverted repeat sequences referred to as palendromic sequences.

A

Restriction endonucleases

156
Q

Complementary, single-strand overhangs that are produced by some restriction endonucleases are referred to as ___________________.

A

sticky ends or cohesive ends

157
Q

The biological role of restriction enzymes in bacteria is to

A

Cleave foreign DNA

158
Q

What do Southern, Northern, and Western blots detect, respectively?

A

DNA, RNA and protein

159
Q

A number of tools are critical to gene exploration. Name at least four.

A

Tools include restriction enzyme analysis, blotting techniques (Southern and Northern), DNA sequencing, solid-phase synthesis of nucleic acid, PCR, and computer analysis.

160
Q

Homologs are different species that perform similar or identical functions.

A

orthologs - - Human and Bovine Ribonuclease are Orthologs

161
Q

Homologs are the same species that different functions.

A

paralogs - The growth factor angiogenin and ribonuclease are
Paralogs

162
Q

Restriction enzymes are ________and do not work on the ends. They are all_______.

A

Restriction enzymes are endodeoxyribonucleases and do not work on the ends. They are all dimers.

163
Q

Why do Cys, Gly, Pro and Trp have the greatest penalties for change.

A

Cysteine - disulfide bonds, glycine is smallest AA, Proline forms kinks and tryptophan is very large.

164
Q

Homology is ultimately determined by _________

A

structure

165
Q

Evolution requires

A
  1. A mechanism that generates change or
    diversity
  2. A selection for “fitness”
  3. Reproduction that enriches for the more “fit”
166
Q

Explain how the hydrophobic effect drives the structure of three different biological molecules.

A

Base stacking of DNA allows the bases to minimize their contact with water which is the main effect of the hydrophobic effect.

Lipid bilayer membrane - the hydrophobic tails gather inside away from the aqueous environment of the cell.

Protein folding - hydrophobic residues hide inside the structure to limit contact with water.

167
Q

Give an example of a molecule that has an alpha helix

A

α-Keratin of hair, feathers, nails (crosslinked by disulfide bonds)

168
Q

Give an example of a molecule that has a beta conformation

A

silk

Biochemistry I 4880 (2 decks)

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