3.8 - Amino acids, Proteins + DNA

What is an Amino Acid?

Molecules with a central Carbon atoms, bonded directly to an amine group, carboxylic acid group, hydrogen atom and changeable “R” group

What 2 properties does the “R” group in an amino acid dictate? (how)

1. Size → Larger R group increases amino acid size

2. Polarity → R group can contain atoms that induce different IMFs (Hydrogen bonding, Permanent Dipole-Dipole etc)

How many amino acids does the body use?

• Of these how many are essential (non-dietary)

• Of these how many are non-essential (dietary)

21:

• 9 essential

• 12 non-essential

What type of isomerism do the Amino acids in our body observe?

• What is the exception?

Optical Isomerism:

• 20 amino acids observe Optical isomerism, bar glyceine → since its “R” group is a hydrogen

***NAMING AMINO ACIDS IN CHEM NOTES 1***

***NAMING AMINO ACIDS IN CHEM NOTES 1***

What is a Zwitterion?

A molecule containing both positive (NH₃⁺) and negative (COO^-) charged groups of an amino acid, resulting in no overall electrical charge

In what conditions do Zwitterions exist?

Neutral conditions → for example: amino acids in water

What is the trend of Mp + Bp of Zwitterions? (why)

Tend to have High Mp + Bp:

• The oppositely charged COO^- and NH₃⁺ have a strong attraction to eachother - requiring large amounts of energy to overcome the ionic force

When drawing zwitterions which groups change to their ions?

• Rule of THUMB for this

NH₂ and COOH groups directly bonded to the central Carbon atoms change to their ions:

• R groups that contain amine or carboxyl groups dont change to their ions

Which group changes for the following conditions in an Amino acid:

• Acidic conditions

• Alkaline conditions

• Acidic conditions = COOH group is kept (Amine group is turned ionic)

• Alkaline conditions = NH₂ group is kept (Carboxyl group is turned ionic)

What is the general equation for an Amino acid + Acid?

Amino acid + Acid → Amino acid salt

What is the general equation for an Amino acid + Base?

Amino acid + Base → Amino acid (basic) salt + Water

Are Zwitterions soluble in water? (why)

Yes:

• The unlike charges of the polar water molecules and ionic amine and carboxyl groups attract to form ion dipole forces, making it soluble

What type of bond forms to make protiens between Peptides?

Peptide link (a specific type of amide link)

What are the 3 types of Protein structures?

1. Primary

2. Secondary

3. Tertiary

Describe the Primary Protein structure (+ display)

Peptide links form between amino acids:

• - - - glu-ala-ser-glu-cyt- - - 

2 types of Secondary Protein structures (+ describe)

1. Alpha Helix chain = H-Bonds between different points of the peptide links negative carboxyl group and positive amine group

2. Beta pleated sheet = “ ⬆ ”

How is the Tertiary Protein structure formed?

The bending and winding of a proteins secondary structure

What 4 factors effect Tertiary Structure? (how)

1. H-Bonding (in R groups)

2. Ionic interactions between NH₃⁺ and COO^-

3. Disulfide Bonds between Cysteine units (strong bonding)

4. VDW (When amino acids are large enough, form noticeable Dipole-Dipole forces)

Give the summary of Bonding that occurs in:

• Primary Proteins

• Secondary Proteins

• Tertiary Proteins

1. Primary Proteins = Covalent

2. Secondary Proteins = H-Bonding of R groups

3. Tertiary Proteins = R group IMF interaction (H-Bonding, Ionic interactions of Amine and Carboxyl ion groups, DiSulfide bonds)

What type of Polymerisation reaction do Amino acids undergo between eachother?

Condensation polymerisation (+ water byproduct)

Give the conditions in the Hydrolysis of Proteins into its Amino acids (2 conditions)

• How to identify the reactants that form the Polymer

1. 24 hr reflux

2. 6M HCL

• When identifying the amino acids that make up the peptide link, we use the same method as Amides to find the reactants that formed it

Enzymes

Enzymes

What are Enzymes?

Stereospecifc proteins that catalyse metabollic reactions without being used up/changed. Their active sites are complimentary to a specific substrate that binds to it to form an “enzyme-substrate” complex

How does an Enzymes active site form?

The folding of a polypeptide chain - Tertiary structure

What part of the Amino Acid/Substrate binds to the substrate? (how)

The “R” group of a substrate attract to the active site of the complimentary enzyme via IMFs:

• H-Bonding

• VDW

• Ionic

Give + explain an example where enzymes work biologically

• Prevention?

Bacterium Enzymes:

• React with substrates to form products that contribute to the formation/regen of its cell wall

• Prevention = Use of inhibitors

How do Inhibitor molecules work?

They bind with + prevent the enzyme reacting with the substrate, preventing cell wall formation + bursting the bacterium to prevent it from multiplying

What are the 3 requirements of Inhibitors?

1. Must not be a shape which is complimentary to enzymes which play a role in key reactions in the body

2. Must be stereospecific

3. Must be made up of 100s of amino acid residues

What makes Inhibitors?

Computers

Describe the layout of a DNA molecule

What does the reaction between Phosphates + Sugars form?

Sugar-Phosphate + Water

***HOW TO PAIR BASES + SUGARS IN IRL FC***

***HOW TO PAIR BASES + SUGARS IN IRL FC***

What is a Nucleotide?

The sugar-phosphate-base molecule

How many bonds form between bases?

• (List the base pairs + Number of bonds)

• A-T → 2 bonds

• G-C → 3 bonds

What is the Anti-Cancer drug we’re required to know:

• Shape

• Bond angles + Co-ordinate number

• Describe structure

Cisplatin:

• Square Planar

• 90^o - Coordinate Number = 4

• 2 NH₃ on the same side /// 2 Cl on same side

What does Cisplatin do? (explain)

Cisplatin triggers programmed cell death, by causing a kink in the Cancerous DNA chain, preventing enzymes from interacting with DNA. Preventing cell division + DNA unwinding

(EXTRA QUESTION)

• How does Cisplatin attach to the Cancer DNA?

Cisplatin enters a cell where its Cl ligands undergo substitution for H₂O molecules → forming “Cis-diamminediaquaplatinum(II)” which then locates 2 guanine bases in the cancer DNA. Replacing the waters with the Nitrogen of these bases