3.13 - Amino Acids, Proteins & DNA Flashcards
Why do some enzymes require Organic co-factors?
Form weak intermolecular forces to the active site & aid in catalysis
Why are enzymes Specific?
They act upon Particular Substrates
Define: Isoelectric point
pH at which a molecule has no net electrical charge
How are Peptide links formed?
Condensation reaction between Amino Acids
What is the Secondary structure of Proteins held together by?
Hydrogen Bonding
Reagents: Acid Hydrolysis of Peptides
HCl(aq)
Diluted Strong Acid
Conditions: Acid Hydrolysis of Peptides
Reflux
What is the Primary structure of Proteins held together by?
Strong Covalent Bonds
Amino Acids Dissolve well in ____ but poorly in ____ solvents?
Water
Non-polar
How can the Side Effects of Cisplatin be Reduced?
|> Using very low dosages
|> Targeting delivery of the drug directly to the cancer cells
a β-pleated sheet has a ____ arrangement of the ____ backbone?
Planar Arrangement
Polypeptide Backbone
What are Genes?
Sections of DNA that holds the code for the amino acid sequence for certain proteins
What is the Lock & Key hypothesis?
That only One Substrate can Bind to One Enzyme due to its Specific shape
How can the Secondary structure of a Protein be disrupted?
|> Gentle Heating
|> Changes in pH
Reagents: Alkaline Hydrolysis of Peptides
NaOH(aq)
Moderately Concentrated Base
What is a Co-factor?
Molecules required by certain Enzymes to carry out Catalysis
Define: Hydrolysis
Breaking of a Bond using Water
In the Condensation reaction between 2-deoxyribose & the organic base, ____ is eliminated?
Water
Why do different Amino Acids have different Polarities?
Have different Side chains
How can Strand Separation occur without breaking the Polynucleotide chain?
Hydrogen bonds between Strands are Much weaker than the Covalent bonds between Nucleotides
What is an Inhibitor?
A molecule w/ a similar Shape to the Substrate which makes similar interactions w/ the active site, Preventing the Subtrate from Binding
What does Hydrogen Bonding in the Secondary Structure occur between?
The NH of one Peptide link
& the C=O of an adjacent Peptide link
What is DNA?
a Polymer of Four Different Nucleotides that contains the Genetic information of an organism
Base Pairings of DNA?
A-T
&
G-C
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
DNA exists as two ____ strands in the form of a ____ ?
Polynucleotide
Double Helix
Hydrogen bonding in the Secondary Structure occurs between the ____ of one Peptide link & the ____ of ____ Peptide link?
N-H
C=O
An adjacent
What must be used for Amino Acid solutions to be visible?
Ninhydrin - Developing Agent
UV Light
Why is Cisplatin still used for Chemotherapy considering its side effects?
Balance of long-term positive effects
Outweigh
the negative short-term effects
An α-helix has a ____ structure w/ ____ of amino acid residues ____ ____ ?
Spiral
R groups
Pointing Out
Why can Thymine only Hydrogen Bond with Adenine?
Has the right atoms in the right places to form two Hydrogen Bonds
Where do Van der Waals occur in the Tertiary Structure of a Protein?
Between non-polar amino acid R-groups
non-polar sidechains
Where do Ionic bonds occur in the Tertiary Structure of a Protein?
Between Sidechains w/ Charged groups
(e.g. NH₂ |> NH₃⁺
COOH |> COO⁻)
What causes Cancer?
The uncontrollable dividing of cells in the body
Features of a β-pleated sheet?
|> Planar arrangement of the Polypeptide backbone
|> R-groups of amino acid residues point above & below the plane
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
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
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
At the Isoelectric point, what do Amino Acids exist as?
Dipolar ions/Zwitterions
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
Why do Amino Acids Dissolve well in Polar solvents?
Zwitterions interact strongly with polar solvent molecules, allowing the amino acid to dissolve
Define: Stereoisomerism
Compounds w/ same structural formula but a different arrangement of atoms in space
Define: Optical isomer
Non-superimposable mirror image isomers
Why can Cytosine only Hydrogen Bond with Guanine?
Has the right atoms in the right places to form three Hydrogen Bonds
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
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
Define: Secondary Structure
How the Primary Structure folds & twists to form an α-helix or β-pleated sheet held together by Hydrogen bonds
Polynucleotides are ____ polymers of nucleotides?
Condensation
Why must a Locating Agent be used on Amino Acid Solutions?
They are Colourless
Products of Condensation reaction between Amino Acids?
Water & Amino Acid Residue
Where do Sulfur-Sulfur bonds occur in the Tertiary Structure of a Protein?
Between Thiol (-SH) groups of a pair of Cysteine residues
How do Inhibitor drugs work?
Block the Active site of an Enzyme that Catalyses harmful reactions
What is Structure-directed drug design?
Chemists use computer modelling to design molecules that will inhibit enzymes known to cause disease
Functional Group: Peptide
R-C(=O)-NH-
How do chemists make use of Enzymatic Stereospecificity?
Synthesis Chiral Compounds
What are Nucleotides made up of?
Phosphate ion
Pentose Sugar = 2-deoxyribose
a Base
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
What can the Tertiary Structure of Proteins be held together by?
|> van der Waals
|> Hydrogen Bonds
|> Ionic Bonds
|> Sulfur-Sulfur bonds
Only Substrate molecules w/ a ____ shape can fit in the active site’s precise ____ shape & bind to the ____ ?
Complementary
Three-Dimensional
Enzyme
How does a Substrate bind to the Active Site of an Enzyme?
|> van der Waals
|> Permanent dipole-dipole
|> Hydrogen Bonds
|> Ionic Bonds
Proteins have ____ ____ ____ shapes that are ____ for their function
Complicated Three Dimensional
Vital
Amino Acids contain both an ____ group & a ____ ____ group?
Amine
Carboxylic Acid
What is Eliminated in the Condensation Polymerisation of Nucleotides?
Water
What does DNA stand for?
Deoxyribonucleic Acid
A β-pleated sheet has ____ of amino acid residues pointing ____ ?
R groups
Above & below the plane
Amino acids are Crystalline ____ with ____ ____ melting points?
Solids
Relatively High
Conditions: Alkaline Hydrolysis of Peptides
Reflux
Dipeptides contain:
____ amino acid residues &
____ peptide link
Two
One
Tripeptides contain:
____ amino acid residues &
____ peptide links
Three
Two
How are the Strands in DNA held together?
Hydrogen Bonds
An α-helix has ____ amino acid residues per ____ ____ ____ ____ ?
3.6
Turn of the Helix
Polypeptides are ____ polymers of amino acids?
Condensation
Why do amino acids exhibit Optical Isomerism?
Contain a Chiral Carbon
Define: Tertiary Structure
How the Secondary Structure folds & twists to form a 3D molecule of a single Polypeptide chain
How do Co-factors work?
They Bind to the Active Site of the Enzyme & participate in Catalysis
In α-amino acids, the amine & carboxylic acid are attached to ____ ?
The same Carbon
How can Cisplatin be used as an Anticancer drug?
Cisplatin can bind to DNA, blocking replication & transcription & triggering programmed cell death (apoptosis)
What is a Chiral Carbon?
Carbon atom bonded to four different groups of atoms
Define: Amphoteric
A species that can act as an Acid or Base
What are the 4 different Bases of DNA?
Adenine
Guanine
Cytosine
Thymine
In the Condensation reaction between Phosphate ions & 2-deoxyribose, ____ is Eliminated?
Water
What are the Three levels of Structure all Proteins have?
Primary Structure
Secondary Structure
Tertiary Structure
Two different amino acids can form ____ different dipeptides?
Two
Define: Active Site
Region responsible for an Enzyme’s Catalytic activity
- usually a creft or crevice on the Enzyme’s surface
Define: Stereospecificity
Many Enzymes can only Catalyse the reaction of one Enantiomer of an Optically Active compound due to an extremely Selective Active Site
Three different amino acids can form ____ different tripeptides?
Six
What does Cisplatin do to DNA?
Binds to it & causes the DNA double helix to Kink meaning it Cannot Unwind & be copied properly
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)
What is a peptide?
Compound made of Amino Acids joined by Peptide Links
Why are Amino Acids Amphoteric?
Can react with both Acids & Bases
Define: Primary Structure
Sequence of Amino Acids in a Protein Chain
Why can the Secondary Structure of a Protein be disrupted relatively easily?
Hydrogen bonds are weak in comparison to covalent bonds
How does an Active Site work?
Contains R groups from Amino Acid residues which react w/ the substrate & hold it in place
Deinfe: Enzyme
Protein-based Catalyst which Speeds up the rate of a Particular reaction
What do Enzymes consist of?
One or more Polypeptide chains
-may also contain a co-factor such as a metal ion or organic molecule
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
At a pH higher than the Isoelectric point, the amino acid acts as a ____ & ____ H⁺ ions
Acid
Donates
At a pH lower than the Isoelectric point, the amino acid acts as a ____ & ____ H⁺ ions
Base
Accepts
What are Proteins?
Naturally Occurring Polymers of Amino Acids
What are Polynucleotides held together by?
Phosphodiester Bonds
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
Amino Acids are ____ solids with relatively high ____ ____ ?
Crystalline
Melting Points
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)
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
Exception to amino acids exhibiting Stereoisomerism?
Glycine
Proteins with more than one ____ also have ____ ____ ?
Polypeptide
Quatenary Structure
Why do Amino Acids have relatively High Melting Points?
Zwitterions form strong Ionic bonds that require a lot of energy to break
Define: Substrate
The compound an Enzyme acts upon
Define: Sulfur-Sulfur bond
Covalent bond formed from the thiol (-SH) groups of a pair of cysteine residues
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
Simplified Structure of a Nucleotide?
Circle(phosphate ion) - pentagon(2-deoxyribose) - rectangle(base)
How can a Mixture of Amino Acids be Separated after Hydrolysis?
Thin Layer Chromatography
What is the Main Product in the Condensation Polymerisation of Nucleotides?
Polynucleotides
held together by phosphodiester bonds
