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7.01 A Level Organic MH > 3.13 - Amino Acids, Proteins & DNA > Flashcards

3.13 - Amino Acids, Proteins & DNA Flashcards

1
Q

Why do some enzymes require Organic co-factors?

A

Form weak intermolecular forces to the active site & aid in catalysis

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2
Q

Why are enzymes Specific?

A

They act upon Particular Substrates

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3
Q

Define: Isoelectric point

A

pH at which a molecule has no net electrical charge

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4
Q

How are Peptide links formed?

A

Condensation reaction between Amino Acids

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5
Q

What is the Secondary structure of Proteins held together by?

A

Hydrogen Bonding

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6
Q

Reagents: Acid Hydrolysis of Peptides

A

HCl(aq)

Diluted Strong Acid

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7
Q

Conditions: Acid Hydrolysis of Peptides

A

Reflux

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8
Q

What is the Primary structure of Proteins held together by?

A

Strong Covalent Bonds

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9
Q

Amino Acids Dissolve well in ____ but poorly in ____ solvents?

A

Water

Non-polar

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10
Q

How can the Side Effects of Cisplatin be Reduced?

A

|> Using very low dosages

|> Targeting delivery of the drug directly to the cancer cells

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11
Q

a β-pleated sheet has a ____ arrangement of the ____ backbone?

A

Planar Arrangement

Polypeptide Backbone

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12
Q

What are Genes?

A

Sections of DNA that holds the code for the amino acid sequence for certain proteins

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13
Q

What is the Lock & Key hypothesis?

A

That only One Substrate can Bind to One Enzyme due to its Specific shape

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14
Q

How can the Secondary structure of a Protein be disrupted?

A

|> Gentle Heating

|> Changes in pH

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15
Q

Reagents: Alkaline Hydrolysis of Peptides

A

NaOH(aq)

Moderately Concentrated Base

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16
Q

What is a Co-factor?

A

Molecules required by certain Enzymes to carry out Catalysis

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17
Q

Define: Hydrolysis

A

Breaking of a Bond using Water

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18
Q

In the Condensation reaction between 2-deoxyribose & the organic base, ____ is eliminated?

A

Water

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19
Q

Why do different Amino Acids have different Polarities?

A

Have different Side chains

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20
Q

How can Strand Separation occur without breaking the Polynucleotide chain?

A

Hydrogen bonds between Strands are Much weaker than the Covalent bonds between Nucleotides

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21
Q

What is an Inhibitor?

A

A molecule w/ a similar Shape to the Substrate which makes similar interactions w/ the active site, Preventing the Subtrate from Binding

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22
Q

What does Hydrogen Bonding in the Secondary Structure occur between?

A

The NH of one Peptide link

& the C=O of an adjacent Peptide link

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23
Q

What is DNA?

A

a Polymer of Four Different Nucleotides that contains the Genetic information of an organism

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24
Q

Base Pairings of DNA?

A

A-T
&
G-C

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25
Q

Where do Hydrogen Bonds occur in the Tertiary Structure of a Protein?

A

Between C=O & N-H & O-H groups

on the R group sidechains

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26
Q

DNA exists as two ____ strands in the form of a ____ ?

A

Polynucleotide

Double Helix

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27
Q

Hydrogen bonding in the Secondary Structure occurs between the ____ of one Peptide link & the ____ of ____ Peptide link?

A

N-H
C=O
An adjacent

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28
Q

What must be used for Amino Acid solutions to be visible?

A

Ninhydrin - Developing Agent

UV Light

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29
Q

Why is Cisplatin still used for Chemotherapy considering its side effects?

A

Balance of long-term positive effects
Outweigh
the negative short-term effects

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30
Q

An α-helix has a ____ structure w/ ____ of amino acid residues ____ ____ ?

A

Spiral
R groups
Pointing Out

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31
Q

Why can Thymine only Hydrogen Bond with Adenine?

A

Has the right atoms in the right places to form two Hydrogen Bonds

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32
Q

Where do Van der Waals occur in the Tertiary Structure of a Protein?

A

Between non-polar amino acid R-groups

non-polar sidechains

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33
Q

Where do Ionic bonds occur in the Tertiary Structure of a Protein?

A

Between Sidechains w/ Charged groups
(e.g. NH₂ |> NH₃⁺
COOH |> COO⁻)

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34
Q

What causes Cancer?

A

The uncontrollable dividing of cells in the body

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35
Q

Features of a β-pleated sheet?

A

|> Planar arrangement of the Polypeptide backbone

|> R-groups of amino acid residues point above & below the plane

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36
Q

What is Cisplatin?

A

a Complex of Platinum(II) w/
two Chloride ion ligands next to each other
& two Ammonia ligands
in a Square Planar shape

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37
Q

How can the Tertiary Structure of a Protein be Disrupted?

A

|> Gentle Heating (VDWs, Hydrogen bonds)

|> Changes in pH (ionic bonds, sulfur-sulfur bonds)

|> Changes in Solvent Polarity

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38
Q

Why do Enzymes require Metal ion Co-factors?

A

Form co-ordinate bonds, usually prosthetic groups that are permanently fixed to the active site & aid in catalysis

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39
Q

At the Isoelectric point, what do Amino Acids exist as?

A

Dipolar ions/Zwitterions

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40
Q

How are drugs w/ Adverse Effects approved for use?

A

|> Organisations that license drugs for use consider the balance of the benefits & adverse effects

|> Doctors discuss potential benefits & adverse effects w/ patients

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41
Q

Why do Amino Acids Dissolve well in Polar solvents?

A

Zwitterions interact strongly with polar solvent molecules, allowing the amino acid to dissolve

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42
Q

Define: Stereoisomerism

A

Compounds w/ same structural formula but a different arrangement of atoms in space

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43
Q

Define: Optical isomer

A

Non-superimposable mirror image isomers

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44
Q

Why can Cytosine only Hydrogen Bond with Guanine?

A

Has the right atoms in the right places to form three Hydrogen Bonds

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45
Q

Why is Two Dimensional Thin Layer Chromatography advantageous for Amino Acids?

A

|> Amino Acids can have similar Rf values in a Solvent

|> Chromatogram can be run w/ two different solvents

|> Each spot then has two Rf values

|> Greater confidence identifying amino acid

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46
Q

Why are No other Base-pairings possible?

A

Others would place the charged atoms too close together or too far apart so could Not Hydrogen Bond properly

47
Q

Define: Secondary Structure

A

How the Primary Structure folds & twists to form an α-helix or β-pleated sheet held together by Hydrogen bonds

48
Q

Polynucleotides are ____ polymers of nucleotides?

A

Condensation

49
Q

Why must a Locating Agent be used on Amino Acid Solutions?

A

They are Colourless

50
Q

Products of Condensation reaction between Amino Acids?

A

Water & Amino Acid Residue

51
Q

Where do Sulfur-Sulfur bonds occur in the Tertiary Structure of a Protein?

A

Between Thiol (-SH) groups of a pair of Cysteine residues

52
Q

How do Inhibitor drugs work?

A

Block the Active site of an Enzyme that Catalyses harmful reactions

53
Q

What is Structure-directed drug design?

A

Chemists use computer modelling to design molecules that will inhibit enzymes known to cause disease

54
Q

Functional Group: Peptide

A

R-C(=O)-NH-

55
Q

How do chemists make use of Enzymatic Stereospecificity?

A

Synthesis Chiral Compounds

56
Q

What are Nucleotides made up of?

A

Phosphate ion
Pentose Sugar = 2-deoxyribose
a Base

57
Q

When do the two strands of the Double Helix Separate?

A

|> When DNA is transcribed to make an mRNA template for Protein Synthesis

|> When DNA is Replicated during Cell Division

58
Q

What can the Tertiary Structure of Proteins be held together by?

A

|> van der Waals
|> Hydrogen Bonds
|> Ionic Bonds
|> Sulfur-Sulfur bonds

59
Q

Only Substrate molecules w/ a ____ shape can fit in the active site’s precise ____ shape & bind to the ____ ?

A

Complementary
Three-Dimensional
Enzyme

60
Q

How does a Substrate bind to the Active Site of an Enzyme?

A

|> van der Waals
|> Permanent dipole-dipole
|> Hydrogen Bonds
|> Ionic Bonds

61
Q

Proteins have ____ ____ ____ shapes that are ____ for their function

A

Complicated Three Dimensional

Vital

62
Q

Amino Acids contain both an ____ group & a ____ ____ group?

A

Amine

Carboxylic Acid

63
Q

What is Eliminated in the Condensation Polymerisation of Nucleotides?

A

Water

64
Q

What does DNA stand for?

A

Deoxyribonucleic Acid

65
Q

A β-pleated sheet has ____ of amino acid residues pointing ____ ?

A

R groups

Above & below the plane

66
Q

Amino acids are Crystalline ____ with ____ ____ melting points?

A

Solids

Relatively High

67
Q

Conditions: Alkaline Hydrolysis of Peptides

A

Reflux

68
Q

Dipeptides contain:
____ amino acid residues &
____ peptide link

A

Two

One

69
Q

Tripeptides contain:
____ amino acid residues &
____ peptide links

A

Three

Two

70
Q

How are the Strands in DNA held together?

A

Hydrogen Bonds

71
Q

An α-helix has ____ amino acid residues per ____ ____ ____ ____ ?

A

3.6

Turn of the Helix

72
Q

Polypeptides are ____ polymers of amino acids?

A

Condensation

73
Q

Why do amino acids exhibit Optical Isomerism?

A

Contain a Chiral Carbon

74
Q

Define: Tertiary Structure

A

How the Secondary Structure folds & twists to form a 3D molecule of a single Polypeptide chain

75
Q

How do Co-factors work?

A

They Bind to the Active Site of the Enzyme & participate in Catalysis

76
Q

In α-amino acids, the amine & carboxylic acid are attached to ____ ?

A

The same Carbon

77
Q

How can Cisplatin be used as an Anticancer drug?

A

Cisplatin can bind to DNA, blocking replication & transcription & triggering programmed cell death (apoptosis)

78
Q

What is a Chiral Carbon?

A

Carbon atom bonded to four different groups of atoms

79
Q

Define: Amphoteric

A

A species that can act as an Acid or Base

80
Q

What are the 4 different Bases of DNA?

A

Adenine
Guanine
Cytosine
Thymine

81
Q

In the Condensation reaction between Phosphate ions & 2-deoxyribose, ____ is Eliminated?

A

Water

82
Q

What are the Three levels of Structure all Proteins have?

A

Primary Structure
Secondary Structure
Tertiary Structure

83
Q

Two different amino acids can form ____ different dipeptides?

A

Two

84
Q

Define: Active Site

A

Region responsible for an Enzyme’s Catalytic activity

- usually a creft or crevice on the Enzyme’s surface

85
Q

Define: Stereospecificity

A

Many Enzymes can only Catalyse the reaction of one Enantiomer of an Optically Active compound due to an extremely Selective Active Site

86
Q

Three different amino acids can form ____ different tripeptides?

A

Six

87
Q

What does Cisplatin do to DNA?

A

Binds to it & causes the DNA double helix to Kink meaning it Cannot Unwind & be copied properly

88
Q

Adverse Effects of Cisplatin?

A

Binds to DNA in normal cells as well as cancer cells, meaning healthy cells that replicate frequently are stopped from replicating

(e.g. Hair loss (hair cells)
Immune suppression (white blood cells)
Kidney Failure)

89
Q

What is a peptide?

A

Compound made of Amino Acids joined by Peptide Links

90
Q

Why are Amino Acids Amphoteric?

A

Can react with both Acids & Bases

91
Q

Define: Primary Structure

A

Sequence of Amino Acids in a Protein Chain

92
Q

Why can the Secondary Structure of a Protein be disrupted relatively easily?

A

Hydrogen bonds are weak in comparison to covalent bonds

93
Q

How does an Active Site work?

A

Contains R groups from Amino Acid residues which react w/ the substrate & hold it in place

94
Q

Deinfe: Enzyme

A

Protein-based Catalyst which Speeds up the rate of a Particular reaction

95
Q

What do Enzymes consist of?

A

One or more Polypeptide chains

-may also contain a co-factor such as a metal ion or organic molecule

96
Q

Why is the Primary Structure of a Protein relatively Stable?

A

Each amino acid residue is linked to the next by a peptide link

Lots of energy required to break strong covalent bond

97
Q

At a pH higher than the Isoelectric point, the amino acid acts as a ____ & ____ H⁺ ions

A

Acid

Donates

98
Q

At a pH lower than the Isoelectric point, the amino acid acts as a ____ & ____ H⁺ ions

A

Base

Accepts

99
Q

What are Proteins?

A

Naturally Occurring Polymers of Amino Acids

100
Q

What are Polynucleotides held together by?

A

Phosphodiester Bonds

101
Q

Features of an α-helix

A

Spiral Structure w/ R groups of amino acid residues pointing out

3.6 amino acid residues per turn of the helix

102
Q

Amino Acids are ____ solids with relatively high ____ ____ ?

A

Crystalline

Melting Points

103
Q

How does Cisplatin bind to DNA?

A

|> Cisplatin is Hydrolysed inside the Cell

|> A Ligand Substitution Reaction occurs between an N in a Guanine Base & the Pt ion

|> A 2nd Ligand Substitution Reaction occurs between an N in a nearby Guanine Base on the Same strand & the Pt ion
(intrastrand binding is the most effective)

104
Q

How do Zwitterions form?

A

At the Isoelectric Point, the Carboxyl group of one amino acid donates its proton to the amine of anotehr amino acid molecule

105
Q

Exception to amino acids exhibiting Stereoisomerism?

A

Glycine

106
Q

Proteins with more than one ____ also have ____ ____ ?

A

Polypeptide

Quatenary Structure

107
Q

Why do Amino Acids have relatively High Melting Points?

A

Zwitterions form strong Ionic bonds that require a lot of energy to break

108
Q

Define: Substrate

A

The compound an Enzyme acts upon

109
Q

Define: Sulfur-Sulfur bond

A

Covalent bond formed from the thiol (-SH) groups of a pair of cysteine residues

110
Q

What is the Induced Fit model?

A

|> Substrate changes the Active Site of an Enzyme for a perfect fit

|> Movement of Electrons occurs in the substrate due to the bonds formed between the Enzyme & the Substrate

|> Activation Energy is Lowered to break & form bonds

111
Q

Simplified Structure of a Nucleotide?

A

Circle(phosphate ion) - pentagon(2-deoxyribose) - rectangle(base)

112
Q

How can a Mixture of Amino Acids be Separated after Hydrolysis?

A

Thin Layer Chromatography

113
Q

What is the Main Product in the Condensation Polymerisation of Nucleotides?

A

Polynucleotides

held together by phosphodiester bonds

7.01 A Level Organic MH (18 decks)

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