BIOL 200 Lecture 1 Building Blocks and Linear biopolymers

What are the three informational biopolymers?

DNA, RNA and protein

What is a polymer?

Covalent bon-linked chain of monomers

What makes informational polymers able to store information in their sequence?

they have more than one type of monomer

What is the information in DNA, RNA and protein?

The sequence

What are the two elements that make up informational biopolymer generic structure?

A common element shared among all the monomers and a characteristic element that is different from other monomers

Which element forms the polymer backbone by covalent bonding between monomers?

The common element

Which element forms side chains that protrude from the polymer backbone?

The characteristic element

What is polymerization?

process of reacting monomer molecules together in a chemical reaction to form polymer chains

If the monomer has one joining site, can a polymer be made?

No, only a dimer

If a monomer has two joining sitesin the common element what type of polymer can be made?

A linear polymer of potentially infinite length

If a monomer has three joining sites in the common element what type of polymer can be made?

A branched polymer

Are informational polymers linear or branched?

They are linear though branched polymers can be made by cells

Why are informational biopolymers linear molecules?

They are easier to package such as coiled coils.

How can the bacterial genome be circular if the informational biopolymers are linear?

They have two chemically distinct ends

What shape of monomers are in informational biopolymers?

They are made from asymmetric monomers - the two joining sites are different

Are polymers symmetrical?

No, they are asymmetrical - the asymmetry of the monomers drives the asymmetry of the polymer with two chemically distinct ends

Can an informational biopolymer experience growth at both ends of the chain?

No, polymer growth is always unidirectional

What is the convention when showing biopolymer representations on paper?

The way that growth happens is always to the right

What are the major types of informational biopolymer units?

Nucleotides and amino acids

How long is DNA usually?

1000 to 100 million monomers

How long is RNA usually?

20 - 10 000/20 000/ 30 000 units

How long are proteins usually?

100 - 2000

What is the characteristic element of nucleotides?

Heterocyclic base such as adenine

What is the common element in nucleotides?

pentose sugar phosphate like ribose and phosphate

What are the two joining sites in the common element of nucleotides?

The 5’ phosphate (acid in nucleic acid) with a negative charge and the 3’ OH hydroxyl group. These are maintained in the polymer

Where does nucleic acid polymer growth occur?

Addition of monomers to the 3’ hydroxyl end

What is the main difference between DNA and RNA nucleotides? What does this cause?

Deoxyribose is missing the 2’ hydroxyl of ribose. DNA is much more stable because of its resistance to chain cleavage by hydrolysis.

What are the purines?

Adenine and guanine. 2 fused heterocyclic rings. Big.

What are the pyrimidines?

Uracil (RNA), Thymine (DNA) and Cytosine. One heterocyclic ring. Smaller

How does T vs U help DNA?

Makes some chemical damage easier to repair

What is a phosphodiester bond?

Link between adjacent nucleotides. Diester because phosphate is joined in an ester linkage to 5’ OH.

What is the common element in amino acids?

Alpha carbon linked to carboxyl(COOH)and amino NH2 and 1 H.

Which stereoisomers of amino acids are used in protein synthesis?

L not the D

What is the characteristic element of an amino acid?

The amino acid side chain

What are the two joining sites on the common element?

The amino and carboxyl group. (amino and carboxyl terminus)

Where does protein growth occur?

The addition of monomers to the carboxyl end.

What are the three main classes of the 20 amino acid side chains?

Hydrophobic (8), Hydrophilic (acid and basic - 9), Special (3)

What is the link between adjacent amino acids called?

A peptide bond - a type of amide bond.

What is a nucleoside?

Base and sugar with a phosphate

How are monomers energized to be incorporated into the growing polymer chain?

Nucleotide monomers are in the form of high-energy nucleoside triphosphates (NTPs). the outer two phosphates are lost when the NTP is incorporated into a growing nucleotide chain. This helps the polymer to form rather than unform.

How are amino acid monomers energized to be incorporated to the growing polymer?

They are in the form of amino acyl-tRNA esters. tRNA is kicked out when monomer is incorporated

How is an energized monomer added to the chain?

A specific enzyme catalyzes the reaction. The enzyme is associated with a template biopolymer that directs the enzyme to incorporate the correct flavour monomer.

Name all three biopolymers and their template and enzyme.

DNA: DNA: DNA polymerase

RNA:DNA: RNA polymerase

protein: mRNA: ribosome

What type of helix is DNA?

a right handed helix generally. Termed B DNA.

What are Watson-Crick base pairs?

Complementary bases held together by H-bonds. ALways one purine and one pyramidine.

What is the orientation of the DNA strands?

antiparallel.

What can DNA binding proteins do to read the sequence without unravelling the strands?

Make contact with base pairs at the major or minor grooves to sense the bases.

How can the strands separate?

DNA strands are held together with weak H bonds. Denaturation can occur when DNA is heated up. THis can happen at below the boiling point of water.

When can renaturation happen?

Denatured DNA strands can accurately re-form base-paired duplex DNA by formation of H-bonds between complementary base-pair sequences. At reasonable temperature in reasonable time.

When is DNA denaturation and renaturation important?

During biological processes like DNA replication and transcription. Also exploited for techniques in molecular biology and genomics.

What is Tm?

The temperature at which the DNA is half melted

What does Tm depend on?

Base pair composition. More G-C base pairs = higher Tm. (more H-bonds which take more energy)

Are informational biopolymers capable of dynamic motion?

Yesm DNA can bend about its long axis - RNA is even more dynamic