Topic 3: Biopolymers

Question 1

Name information containing biopolymers and describe their characteristics in terms of length, sequence and synthesis

Answer 1

DNA (deoxyribose nucleic acid), RNA (ribonucleic acid), and Proteins

• They can be very long polymers
• Sequence of the monomers is important in deciding the function
• Synthesis of new molecules is generated from a template

Question 2

Describe the direction in which biopolymers are synthesized in and the specific directions for nucleic acids and proteins

Answer 2

Biopolymers are synthesized in one direction only and written from left to right.

• Nucleic acids: 5’ to 3’
• Proteins: N-terminus to C-terminus

Question 3

How many naturally occuring amino acids are there?

Answer 3

20

Question 4

In polymerization, what is lost and left behind during the reaction?

Answer 4

Some monomers are lost together with some water (dehydration) leaving behind residues incorporated into the growing chain.

Question 5

Are biopolymer synthesis anabolic or catabolic?

Answer 5

Anabolic –> require energy

Question 6

What is the name, structure and properties (charge, acidity, hydrophilicity) of nucleic acid building blocks?

Answer 6

Nucleotides containing phosphate, sugar and base

Has sugar-phosphate backbone, common no matter what base

5’ and 3’ ends

Phosphates have negatively charged –> because of the charge –> acid

Phosphate and base have N and O and H in sugar when going with N and O –> hydrophilic

Question 7

What are some applicaions of the common sugar phosphate backbone in nucleic acids?

Answer 7

Electrophoresis: the charge allows nucleic acids to move in electric field. Distance moved relies on size

Ethanol precipitation: when combined with salts and ethanol, nucleic acids solidify and precipitate.

Question 8

What are building blocks of proteins and what do proteins structure have in common and difference?

Answer 8

Amino acids are building blocks

Proteins have common peptide bone (C-C and N from amino group), but different sidechains group in different amino acids

Question 9

How are peptides and proteins different?

Answer 9

Peptides and proteins are different names for biopolymers.

Short, less than 50 amino acids residues –> peptides
Longer, more amino acids residues –> proteins

Question 10

Describe features of peptide bond formation process and double bond in peptide bond resonance

Answer 10

• Formation: condesation mechanism
  + loses water, requires energy –> not energetically favorable
• Peptide bond resonance: the bond between 2 amino acid form partial double bond
  + alternating double bond between either N (from amino group of amino acid A) - C (from carbonxyl group of amino acid B) or C-O (from carbonxyl group of amino acid B)

–> partial double bond are rigid, flat and the partial charges encourage hydrogen bonding

Question 11

Describe the variability of properties in a small peptide

Answer 11

Even a small peptide combines different properties because each amino acid/subunit/monomers already vary in properties.

Question 12

What structure are protein sidechains and nucleobases and what are some properties of such structure?

Answer 12

Aromatic ring - have alternating single and double bonds
Flat/planar
Have characteristic absorbance in UV

Question 13

Identify the difference between sugar and bases of DNA and RNA

Answer 13

DNA: has deoxyribose sugar (lose 1 O) and contain thymine base

RNA: has ribose sugar and contain uracil base

Question 14

Describe the relationship between A,T,C,G and their proportion in DNA composition

Answer 14

For any species, amount of A=T and C=G

A+G = C+T = 50%

Question 15

What bond and what bases complement each other in base pairing in DNA/RNA?

Answer 15

Hydrogen bonds between complmentary bonds

A complement T/U
C complement G

Question 16

Compare the strength between A-T/U and C-G pair

Answer 16

C-G pairs have 3 hydrogens while A-T/U only have 2
–> C-G pairs are stronger

Question 17

What is the implication of the difference between strength of A-T/U and C-G pairs

Answer 17

The higher content of C-G, or the longer the chain, the higher the melting temperature is, or the double stranded DNA come apart at higher temp

Question 18

Describe the properties of DNA double helix structure (directions, distances, position of bases)

Answer 18

2 strands run in opp. directions

Flat bases stack on top of each other

Negatively charged phosphate repel each other

Right handed double helix

Major grooves have larger distances between the backbone than the minor grooves

Question 19

Describe the structure of RNA and why it is the way it is

Answer 19

No B-type structure due to the extra oxygen on the sugar

More susceptible to degradation

Question 20

What is deamination and does it cause any negative effects?

Answer 20

Deamination if spontaneous change of C to U
Very rare, but does happen, may have build up effect

In DNA, U is unusual –> get repaired
In RNA. U is usual –> not repaired, but still OK because RNA is not the genetic material