Biochemistry Nucleotides and Nucleic acids

What is the functional unit of DNA?

Gene

What does DNA stand for?

Deoxyribonucleic acid

How is genetic information often communicated?

It is communicated via RNA

What does RNA stand for?

Ribonucleic acid

Nucleotide

Repeating subunits of the nucleic acid polymers

Pyrimidines

C, T, U

Purines

A, G

What are the two major factors that discriminate DNA from RNA?

1. DNA is DEOXY Ribonucleic acid…that is the pentose has lost a hydroxyl at position 2

2. In DNA, the set of bases are ATGC while in RNA the set of bases are AUGC

ATP

triphosphorylated adenine

What are cyclic forms important in signaling?

cATP and cGMP

The linkage between nucleotides is via a…?

Phosphodiester bond between the 5’ phosphate on one nucleotide and the 3’hydroxyl on the next

Conjugated bonds in nucleotide bases results in high or low absorbance of UV light?

It results in high absorbance of UV light

The bases are hydrophobic and aromatic

Aromatic interactions between bases helps align them

What did Hershey and Chase accomplish?

They used 35S and 32P to track proteins and DNA from bacteriophage

Their results clearly showed DNA was the source of genetic information

What are Chargaff’’s rules?

1. Base composition varies by species

2. DNA from differing tissues in an organism have the same base composition

3. Base composition does not change with age, environment, or nutrition

4. The bases abundance is matched A=T, G=C

Are DNA strands parallel or antiparallel?

They are antiparallel

What are the interface of DNA strands held together by?

They are held together by complementary base interactions (A-T, G-C)

B-form DNA

Most common, right handed double-helical conformation of DNA

A-form DNA

Shorter and wider conformation than B-form, found in polar environments and is more compact.

Z-form DNA

More extended and can be found very infrequently in cells (untwisted double helix)

Palindrome DNA

Nucleic acid sequence where reading from 5’ to the 3’ on one strand matches the 5’ to 3’ direction of its complementary strand

What is it called when palindromic DNA is on opposite strands

Inverted repeat

mRNA

The copy of DNA that is trafficked to the ribosome for protein production

Is mRNA single or double-stranded?

mRNA is single-stranded

mRNAs contain the info for how many genes in eukaryotes?

1 gene in eukaryotes

mRNAs contain the info for how many genes in prokaryotes?

Many genes in prokaryotes

Does RNA have a “regular” secondary structure?

No, but it will fold into complex structures depending on its sequence

Transfer RNA (tRNA)

Brings amino acids to the ribosome during synthesis

Ribosomal RNA (rRNA)

Components of the ribosome involved in rna recognition in protein synthesis

Ribozymes

RNA-only molecules that have catalytic activity

Plasmids

Small circular DNA fragments that can be used to introduce genes

Contain MCS (multiple cloning sites)

Are DNA and RNA highly charged or lowly charged?

They are highly charged

Can DNA double helices and secondary structures fold and denature?

Yes, they can fold and denature

Mutation

Change in DNA sequence and can lead to DNA, RNA, or protein defects

What are the two ways mutation can happen?

1. Chemical modification of the DNA

2. Errors in transcription/replication

Deamination

When nucleic acid bases lose an amino group

What is deamination accelerated by?

It is accelerated by the presence of HNO2

Can purine or pyrimidine bases be hydrolyzed and depurinated?

Purine bases (guanidine and adenine) can be hydrolyzed and depurinated

Oxidation by free radicals

Can alter base structure in DNA (hydrogen bonds affected)

UV Damage to DNA

Creates thymine dimer, disrupting the double bonds to for cyclobutene dimer

How do bacteria use methylated DNA?

They use it to distinguish self-invader DNA as well as handling of mismatched DNA

Methyl-cytosine

Eukaryotes use this to prevent transposon migration

What did Sanger do?

Sanger developed a DNA sequencing method using selective digestion of DNA dideoxy nucleotides

DNA synthase

Make new copies of the DNA you are interested in sequencing

Incorporate a small fraction of ddNTPs at each position terminating the strand

Then the base specific cleavages are performed and sequence is determined by gel mobility

Pyrosequencing

Sequencing by synthesis

What direction is DNA synthesized in in solid phase synthesis?

3’ 5’ direction

3’ Hydroxyl attached to the bead

Uses a DMT protecting group on the 5’ hydroxyl

Cyanoethyl protecting group on the phosphate

How is cellular energy often stored?

It is often stored as adenosine triphosphate (ATP)

Two of the phosphates are bound by high energy anhydride bonds

Nucleotides as enzymatic cofactors

1. CoEnzymeA (CoA)

2. Nicotinamide Adenine Dinucleotide (NAD+)

3. Flavin Adenine Dinucleotide (FAD)

Modified adenosines function as enzymatic co-factors

Nucleotides as Signals

Typically part of a signaling cascade that begins with binding of a ligand OUTSIDE the cell

Includes change in the TM receptor which stimulates production of cAMP