KH1: Introduction to Biological Biopolymers

Informational Biopolymers

Have more than one kind of monomer

Characteristic and common elements

Common - Shared by all monomers

Characteristic - Makes each monomer different from another

Are informational polymers branched or linear? Why?

Linear, as monomers have only two asymmetric joining sites

How to draw polymers?

The orientation of the growing chain should always be to the right

Nucleotides - Common/Characteristic element

Common - Penrose sugar backbone

Characteristic - Heterocyclic base

Joining sites on nucleotide?

The 5’ phosphate (negative charge) the 3’OH

Direction of growth in DNA

Always addition of polymers in 3’ end

DNA vs RNA

DNA has an -H instead of an -OH, is double stranded and has thymine instead of uracil (RNA opposite)

Two types of heterocyclic bases

Purines - Pair of fused carbon rings (A, G)

Pyrimidines - Single carbon ring (U, T, C)

Bond between sugar and bases

N-Glycosidic bond

Bond between phosphate and sugar

Phosphodiester bond

Amino acids - Common/Characteristic elements

Common - Carbon linked with carboxyl & amino group

Characteristic - Amino acid side chain (R)

Amino acid joining sites

Amino terminus and Carboxyl terminus

Types of amino acids

Hydrophobic

Hydrophilic

Special

Bond between adjacent amino acids

Peptide bond

High energised DNA monomers are found as…

Nucleoside triphosphates, of whcih the two outer phosphates are then kicked out when NTP is incorporated

High energised amino acid monomers are found as…

Amino acyl-tRNA esters, which contain a high energy ester bond. t-RNA molecule is then kicked out

Enzymes for monomers to join polymers

DNA = DNA polymerase

RNA = RNA polymerase

Protein = Ribosome

How are DNA strands held together

By Watson-Crick bases, which contain hydrogen

Number of hydrogen bonds between bases

A-T = 2 double bonds

C-G= 3 double bonds

What is Tm and how can it be influenced?

The temperature at which half the DNA is melted. Depends on the amount of C-G bases

examples of informational biopolymers?

DNA, RNA (nucleic acids) and proteins

max number of binding sites in informational biopolymers

2

Informational biopolymers are made up of _ {symmetric/ asymmetric} monomers

asymmetric

how are different nucleotides joined together to form DNA? (which bond and between what groups)

joined via phosphodiester bonds to form DNA

there will be two phosphodiester bonds-

1. between the 3’ OH and the 5’ phosphate group

2. the 5’ phosphate groups and the 5’ hydroxyl on the pentose sugar

Difference in the pentose sugar between RNA and DNA?

RNA → contains ribsose sugar (has an extra ‘OH group on the second carbon)

DNA → contains ribose sugar (with an H in the place of the ‘OH in the second carbon)

What advantage does DNA have over RNA due to the absence of the 2’-OH

increases the stability of DNA and helps to prevent hydrolysis and degradation by enymes

Advantage of DNA having T over U?

Thymine can be easily recognised for fixation if there is gene mutation, uracil is more prone to mispairing and is less stable

what are the two stereoisomers of amino acids? which one is used for protein synthesis?

L and D stereoisomers

only L stereoisomer of amino acids are used in protein synethesis

to what terminus are monomers added during protein polymer growth?

carboxyl terminal

how many different amino acids are there? classification of amino acids? + number of amino acids in each class

• 20 different amino acids

• Main classes of amino acids: 

  • Hydrophobic (8 amino acids) 

  • Hydrophilic (includes acidic and basic side chains) (9 amino acids) 

  • Special (3 amino acids) 

what happens when NTPs are added to the polymer chain?

high - energy NTPs formed which has two extra phosphate groups attached to it (tri-phosphates formation)

The extra two phosphates are kicked out when NTP is added to chain 

how are amino acids added to the growing polypeptide chain?

• Form high-energy aminoacyl-tRNA esters 

• The tRNA molecule is “kicked out” when the next amino acid is incorporated at the end of a growing protein chain 

structure of high-energy aminoacyl tRNA esters?

How can base pair sequences in DNA be identified without separating the two strands of DNA?

DNA binding proteins can make contact with base pairs at the major or minor grooves to identify specific sequences without having to separate the strands 

Tm ? What does the Tm depend on?

• Tm = temperature at which the DNA is one-half melted 

• Tm depends on DNA’s base composition 

• DNA with higher proportions of G-C base pairs have a higher Tm

  • 3 hydrogen bonds instead of 2 

  • Takes more energy to separate G-C

structural difference between thymine and uracil?

• DNA contains T instead of U as it makes some chemical damage easier to repair 

  • Thymine contains an extra methyl group than uracil 

how are monomers activated during protein/ dna elongation?

by phosphorylation

What bonds are broken during denaturation?

hydrogen bonds between the nucleotides on the two strands

Parts of an amino acid?

• Central alpha carbon atom  (C_a )  

  • All alpha carbons are optical/ asymmetric (except that in glycine) 

  • Forms two mirror images: 

    • Dextro (D) isomers 

      • Found mostly in bacterial cell wall 

    • Levo (L) isomers 

      • Found in amino acids in proteins 

  • Cannot be interconverted without breaking and reforming the bond 

• NH2 / amino group 

• COOH / carboxyl group 

• H atom 

• R group / side chain 

unique properties of the special amino acids?

• List of special amino acids: 

  • Cysteine: 

    • Contains a reactive sulfhydryl group (-SH) 

    • When H+ is released, sulfhydryl group is converted into a thiolate anion (S^-) 

    • In proteins, two adjacent sulfhydryl groups can form a covalent disulfide bond (-S-S-) [releases 2H] 

    • Disulfide bonds serve to cross-link regions - 

      • both intramolecular and intermolecular 

      • Stabilizes the folded structure

  • Glycine:

    • Only has an H in its side chain 

    • Very small so can fit into tight spaces 

  • Proline: 

    • Alpha carbon atom forms a ring with the side chain 

    • Very rigid 

    • Cannot take part in hydrogen bonding 

how are bases attached to the pentose sugars?

via the N-glycosidic bonds