Biochemistry | Nucleic Acids

What are nucleic acids?

Biomolecules responsible for the storage, transfer, and expression of genetic traits.

What is genetics?

The science of inherited traits.

What are the two major types of nucleic acids?

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

What are nucleic acids made up of?

Nucleotides.

How long is RNA generally?

Quite short; hundred to thousands of nucleotides.

How long can DNA be?

Up to millions of nucleotides long.

What are the three components of a nucleotide?

Phosphate, sugar, and nitrogenous base.

What type of sugar is found in nucleotides?

A 5-carbon/pentose sugar: ribose or deoxyribose.

What are the two chemical types of nitrogenous bases?

What are the two most common nitrogenous bases?

Purine and pyrimidine.

What is a nucleoside?

Sugar + base.

What is a nucleotide?

Phosphate + sugar + base.

What is the structural form of ribose and deoxyribose?

Furanose structures.

What is the difference between deoxyribose and ribose?

The presence and absence of oxygen.

What does “deoxy-” mean?

Without oxygen.

What does ribose contain compared with deoxyribose?

Oxygen.

What is deoxidation?

Removal of oxygen.

What term is not being used for deoxidation?

“Reduced.”

Why are prime locants used?

For clarity or differentiation between the same locants in different parts of the structure.

What does 1 refer to?

The base.

What does 1’ refer to?

The sugar.

How many rings does pyrimidine have?

One ring.

How many rings does purine have?

Two rings: 6- and 5-membered rings.

What is the mnemonic for pyrimidine bases?

PyrCUT — Cytosine, Uracil, Thymine.

What is the mnemonic for purine bases?

PurGA — Guanine, Adenine.

Which pyrimidine has an amino group at the top?

Cytosine.

Which pyrimidine has a methyl group at the side?

Thymine.

Which purine has an amino group at the top?

Adenine.

Which purine has oxygen at the top?

Guanine.

What does “in DNA and RNA” mean for bases?

Those bases are present in both.

Which base is only present in RNA?

Uracil.

What happens to thymine in RNA according to the module?

Thymine becomes uracil once it’s in RNA.

Where should thymine be thought of as being present?

DNA only.

What type of compounds are a lot of drugs?

Modified nucleosides.

What is the nucleoside formed from guanine?

Guanosine.

What is the nucleotide naming form for guanosine?

Guanosine ____phosphate.

What is the nucleoside formed from adenine?

Adenosine.

What is the nucleotide naming form for adenosine?

Adenosine ____phosphate.

What is the nucleoside formed from cytosine?

Cytidine.

What is the nucleotide naming form for cytidine?

Cytidine ____phosphate.

What is the nucleoside formed from uracil?

Uridine.

What is the nucleotide naming form for uridine?

Uridine ____phosphate.

What is the nucleoside formed from thymine?

Thymidine.

What is the nucleotide naming form for thymidine?

Thymidine ____phosphate.

What must be indicated when naming nucleotides?

The number of phosphates: mono, di, or tri.

What are alternative names for cytidine monophosphate?

Cytidylic acid or cytidylate.

What are alternative names for adenosine monophosphate?

Adenylic acid or adenylate.

What prefix is added when deoxyribose is used?

“Deoxy-”.

What bond binds bases to sugar?

Glycosidic bond.

At which carbon does the base bind to the sugar?

1’ carbon.

What bond binds phosphates to sugar?

Phosphoester bond.

At which carbon does phosphate bind to sugar?

5’ carbon.

Where is the base attached?

At 1’.

Where is the phosphate attached?

At 5’.

What bonds form between multiple phosphates?

Phosphoanhydride bonds.

What are the suffixes for purine nucleosides?

-OSINE.

What are the suffixes for pyrimidine nucleosides?

-IDINE.

What is GDP?

Guanosine diphosphate.

What happens if “deoxy” is added to guanosine diphosphate?

It becomes deoxyguanosine diphosphate (dGDP).

What is a polynucleotide strand composed of?

Nucleotides bonded together by phosphodiester bonds between phosphate and sugars.

What does a phosphodiester bond connect?

A phosphate part connected to two sugar parts.

What bond connects two nucleotides?

Phosphodiester bond.

What happens to almost all 3’ and 5’ carbons in a polynucleotide strand?

They are locked by bonds.

What are the exceptions to the locked 3’ and 5’ carbons?

The 5’ end and 3’ end, because they are free ends.

What is the 5’ end of a polynucleotide strand?

The end with a free phosphate.

What is the 3’ end of a polynucleotide strand?

The end with a free OH on 3’.

How are bases represented in a nucleotide sequence?

As a sequence of letters.

In what direction are nucleotides read?

From the 5’ end to the 3’ end.

In what direction are protein sequences read?

From the N-terminus to the C-terminus.

What is the direction of the opposing strand in double-stranded nucleic acid?

3’ end to 5’ end.

What sugar does DNA contain?

Deoxyribose.

What sugar does RNA contain?

Ribose.

What bases does DNA contain?

A, G, C, T.

What bases does RNA contain?

A, G, C, U.

What is the common form of DNA?

Double-stranded.

What is the common form of RNA?

Single-stranded.

What is the purpose of DNA?

Starting point of all genetic material.

What is the purpose of RNA?

Bridges DNA and proteins in the central dogma.

What is the mutual exclusion between T and U?

T and U are not supposed to be present at the same time unless there is a mutation.

What indicates DNA when considering T and U?

T indicates DNA.

What indicates RNA when considering T and U?

U indicates RNA.

What does C base-pair with?

G.

What does A base-pair with?

T.

Which base pairs are possible in DNA?

C-G and A-T.

Which base pairs are not possible?

C-A and G-T.

Why are C-G pairs stronger?

Due to more H-bonds.

What is antiparallel orientation?

The 5’ to 3’ directions of the two strands go in opposite directions.

What is handedness of DNA?

It rotates either clockwise/right-handed or counterclockwise/left-handed.

Which DNA forms are right-handed?

A and B.

Which DNA form is the most common?

B-DNA.

Which DNA form is left-handed?

Z-DNA.

What does Z-DNA mean?

Zigzag DNA.

How common is Z-DNA?

Very rare.

What is B-DNA?

The DNA that convinced earlier scientists that DNA is really double-helix.

What is the central dogma of molecular biology?

The flow of genetic information from DNA through RNA to proteins.

What is the starting point or blueprint of life?

DNA.

What does DNA store?

An organism’s genetic information.

What process allows mRNA to bridge DNA to RNA?

Transcription.

What process converts RNA into proteins?

Translation.

What are the characteristics of DNA replication?

Bi-directional, semi-discontinuous, semi-conservative, and high fidelity.