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
2
Q
Why are enzymes Specific?
A
They act upon Particular Substrates
3
Q
Define: Isoelectric point
A
pH at which a molecule has no net electrical charge
4
Q
How are Peptide links formed?
A
Condensation reaction between Amino Acids
5
Q
What is the Secondary structure of Proteins held together by?
A
Hydrogen Bonding
6
Q
Reagents: Acid Hydrolysis of Peptides
A
HCl(aq)
Diluted Strong Acid
7
Q
Conditions: Acid Hydrolysis of Peptides
A
Reflux
8
Q
What is the Primary structure of Proteins held together by?
A
Strong Covalent Bonds
9
Q
Amino Acids Dissolve well in ____ but poorly in ____ solvents?
A
Water
Non-polar
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
11
Q
a β-pleated sheet has a ____ arrangement of the ____ backbone?
A
Planar Arrangement
Polypeptide Backbone
12
Q
What are Genes?
A
Sections of DNA that holds the code for the amino acid sequence for certain proteins
13
Q
What is the Lock & Key hypothesis?
A
That only One Substrate can Bind to One Enzyme due to its Specific shape
14
Q
How can the Secondary structure of a Protein be disrupted?
A
|> Gentle Heating
|> Changes in pH
15
Q
Reagents: Alkaline Hydrolysis of Peptides
A
NaOH(aq)
Moderately Concentrated Base
16
Q
What is a Co-factor?
A
Molecules required by certain Enzymes to carry out Catalysis
17
Q
Define: Hydrolysis
A
Breaking of a Bond using Water
18
Q
In the Condensation reaction between 2-deoxyribose & the organic base, ____ is eliminated?
A
Water
19
Q
Why do different Amino Acids have different Polarities?
A
Have different Side chains
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
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
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
23
Q
What is DNA?
A
a Polymer of Four Different Nucleotides that contains the Genetic information of an organism
24
Q
Base Pairings of DNA?
A
A-T
&
G-C
25
Where do Hydrogen Bonds occur in the Tertiary Structure of a Protein?
Between C=O & N-H & O-H groups
| on the R group sidechains
26
DNA exists as two ____ strands in the form of a ____ ?
Polynucleotide
| Double Helix
27
Hydrogen bonding in the Secondary Structure occurs between the ____ of one Peptide link & the ____ of ____ Peptide link?
N-H
C=O
An adjacent
28
What must be used for Amino Acid solutions to be visible?
Ninhydrin - Developing Agent
| UV Light
29
Why is Cisplatin still used for Chemotherapy considering its side effects?
Balance of long-term positive effects
Outweigh
the negative short-term effects
30
An α-helix has a ____ structure w/ ____ of amino acid residues ____ ____ ?
Spiral
R groups
Pointing Out
31
Why can Thymine only Hydrogen Bond with Adenine?
Has the right atoms in the right places to form two Hydrogen Bonds
32
Where do Van der Waals occur in the Tertiary Structure of a Protein?
Between non-polar amino acid R-groups
| non-polar sidechains
33
Where do Ionic bonds occur in the Tertiary Structure of a Protein?
Between Sidechains w/ Charged groups
(e.g. NH₂ |> NH₃⁺
COOH |> COO⁻)
34
What causes Cancer?
The uncontrollable dividing of cells in the body
35
Features of a β-pleated sheet?
|> Planar arrangement of the Polypeptide backbone
|> R-groups of amino acid residues point above & below the plane
36
What is Cisplatin?
a Complex of Platinum(II) w/
two Chloride ion ligands next to each other
& two Ammonia ligands
in a Square Planar shape
37
How can the Tertiary Structure of a Protein be Disrupted?
|> Gentle Heating (VDWs, Hydrogen bonds)
|> Changes in pH (ionic bonds, sulfur-sulfur bonds)
|> Changes in Solvent Polarity
38
Why do Enzymes require Metal ion Co-factors?
Form co-ordinate bonds, usually prosthetic groups that are permanently fixed to the active site & aid in catalysis
39
At the Isoelectric point, what do Amino Acids exist as?
Dipolar ions/Zwitterions
40
How are drugs w/ Adverse Effects approved for use?
|> Organisations that license drugs for use consider the balance of the benefits & adverse effects
|> Doctors discuss potential benefits & adverse effects w/ patients
41
Why do Amino Acids Dissolve well in Polar solvents?
Zwitterions interact strongly with polar solvent molecules, allowing the amino acid to dissolve
42
Define: Stereoisomerism
Compounds w/ same structural formula but a different arrangement of atoms in space
43
Define: Optical isomer
Non-superimposable mirror image isomers
44
Why can Cytosine only Hydrogen Bond with Guanine?
Has the right atoms in the right places to form three Hydrogen Bonds
45
Why is Two Dimensional Thin Layer Chromatography advantageous for Amino Acids?
|> 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
46
Why are No other Base-pairings possible?
Others would place the charged atoms too close together or too far apart so could Not Hydrogen Bond properly
47
Define: Secondary Structure
How the Primary Structure folds & twists to form an α-helix or β-pleated sheet held together by Hydrogen bonds
48
Polynucleotides are ____ polymers of nucleotides?
Condensation
49
Why must a Locating Agent be used on Amino Acid Solutions?
They are Colourless
50
Products of Condensation reaction between Amino Acids?
Water & Amino Acid Residue
51
Where do Sulfur-Sulfur bonds occur in the Tertiary Structure of a Protein?
Between Thiol (-SH) groups of a pair of Cysteine residues
52
How do Inhibitor drugs work?
Block the Active site of an Enzyme that Catalyses harmful reactions
53
What is Structure-directed drug design?
Chemists use computer modelling to design molecules that will inhibit enzymes known to cause disease
54
Functional Group: Peptide
R-C(=O)-NH-
55
How do chemists make use of Enzymatic Stereospecificity?
Synthesis Chiral Compounds
56
What are Nucleotides made up of?
Phosphate ion
Pentose Sugar = 2-deoxyribose
a Base
57
When do the two strands of the Double Helix Separate?
|> When DNA is transcribed to make an mRNA template for Protein Synthesis
|> When DNA is Replicated during Cell Division
58
What can the Tertiary Structure of Proteins be held together by?
|> van der Waals
|> Hydrogen Bonds
|> Ionic Bonds
|> Sulfur-Sulfur bonds
59
Only Substrate molecules w/ a ____ shape can fit in the active site's precise ____ shape & bind to the ____ ?
Complementary
Three-Dimensional
Enzyme
60
How does a Substrate bind to the Active Site of an Enzyme?
|> van der Waals
|> Permanent dipole-dipole
|> Hydrogen Bonds
|> Ionic Bonds
61
Proteins have ____ ____ ____ shapes that are ____ for their function
Complicated Three Dimensional
| Vital
62
Amino Acids contain both an ____ group & a ____ ____ group?
Amine
| Carboxylic Acid
63
What is Eliminated in the Condensation Polymerisation of Nucleotides?
Water
64
What does DNA stand for?
Deoxyribonucleic Acid
65
A β-pleated sheet has ____ of amino acid residues pointing ____ ?
R groups
| Above & below the plane
66
Amino acids are Crystalline ____ with ____ ____ melting points?
Solids
| Relatively High
67
Conditions: Alkaline Hydrolysis of Peptides
Reflux
68
Dipeptides contain:
____ amino acid residues &
____ peptide link
Two
| One
69
Tripeptides contain:
____ amino acid residues &
____ peptide links
Three
| Two
70
How are the Strands in DNA held together?
Hydrogen Bonds
71
An α-helix has ____ amino acid residues per ____ ____ ____ ____ ?
3.6
| Turn of the Helix
72
Polypeptides are ____ polymers of amino acids?
Condensation
73
Why do amino acids exhibit Optical Isomerism?
Contain a Chiral Carbon
74
Define: Tertiary Structure
How the Secondary Structure folds & twists to form a 3D molecule of a single Polypeptide chain
75
How do Co-factors work?
They Bind to the Active Site of the Enzyme & participate in Catalysis
76
In α-amino acids, the amine & carboxylic acid are attached to ____ ?
The same Carbon
77
How can Cisplatin be used as an Anticancer drug?
Cisplatin can bind to DNA, blocking replication & transcription & triggering programmed cell death (apoptosis)
78
What is a Chiral Carbon?
Carbon atom bonded to four different groups of atoms
79
Define: Amphoteric
A species that can act as an Acid or Base
80
What are the 4 different Bases of DNA?
Adenine
Guanine
Cytosine
Thymine
81
In the Condensation reaction between Phosphate ions & 2-deoxyribose, ____ is Eliminated?
Water
82
What are the Three levels of Structure all Proteins have?
Primary Structure
Secondary Structure
Tertiary Structure
83
Two different amino acids can form ____ different dipeptides?
Two
84
Define: Active Site
Region responsible for an Enzyme's Catalytic activity
| - usually a creft or crevice on the Enzyme's surface
85
Define: Stereospecificity
Many Enzymes can only Catalyse the reaction of one Enantiomer of an Optically Active compound due to an extremely Selective Active Site
86
Three different amino acids can form ____ different tripeptides?
Six
87
What does Cisplatin do to DNA?
Binds to it & causes the DNA double helix to Kink meaning it Cannot Unwind & be copied properly
88
Adverse Effects of Cisplatin?
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
What is a peptide?
Compound made of Amino Acids joined by Peptide Links
90
Why are Amino Acids Amphoteric?
Can react with both Acids & Bases
91
Define: Primary Structure
Sequence of Amino Acids in a Protein Chain
92
Why can the Secondary Structure of a Protein be disrupted relatively easily?
Hydrogen bonds are weak in comparison to covalent bonds
93
How does an Active Site work?
Contains R groups from Amino Acid residues which react w/ the substrate & hold it in place
94
Deinfe: Enzyme
Protein-based Catalyst which Speeds up the rate of a Particular reaction
95
What do Enzymes consist of?
One or more Polypeptide chains
-may also contain a co-factor such as a metal ion or organic molecule
96
Why is the Primary Structure of a Protein relatively Stable?
Each amino acid residue is linked to the next by a peptide link
Lots of energy required to break strong covalent bond
97
At a pH higher than the Isoelectric point, the amino acid acts as a ____ & ____ H⁺ ions
Acid
| Donates
98
At a pH lower than the Isoelectric point, the amino acid acts as a ____ & ____ H⁺ ions
Base
| Accepts
99
What are Proteins?
Naturally Occurring Polymers of Amino Acids
100
What are Polynucleotides held together by?
Phosphodiester Bonds
101
Features of an α-helix
Spiral Structure w/ R groups of amino acid residues pointing out
3.6 amino acid residues per turn of the helix
102
Amino Acids are ____ solids with relatively high ____ ____ ?
Crystalline
| Melting Points
103
How does Cisplatin bind to DNA?
|> 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
How do Zwitterions form?
At the Isoelectric Point, the Carboxyl group of one amino acid donates its proton to the amine of anotehr amino acid molecule
105
Exception to amino acids exhibiting Stereoisomerism?
Glycine
106
Proteins with more than one ____ also have ____ ____ ?
Polypeptide
| Quatenary Structure
107
Why do Amino Acids have relatively High Melting Points?
Zwitterions form strong Ionic bonds that require a lot of energy to break
108
Define: Substrate
The compound an Enzyme acts upon
109
Define: Sulfur-Sulfur bond
Covalent bond formed from the thiol (-SH) groups of a pair of cysteine residues
110
What is the Induced Fit model?
|> 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
Simplified Structure of a Nucleotide?
Circle(phosphate ion) - pentagon(2-deoxyribose) - rectangle(base)
112
How can a Mixture of Amino Acids be Separated after Hydrolysis?
Thin Layer Chromatography
113
What is the Main Product in the Condensation Polymerisation of Nucleotides?
Polynucleotides
| held together by phosphodiester bonds
