Nucleotides and nucleic acids Nucleotides have three parts

Nucleotides and nucleic acids

Nucleotides have three parts Phosphate group Monosaccharide D-ribose nitrogenous base

D-ribose or 2 -deoxy-D-ribose 5’ 1’ 4’ 3’ 2’ deoxy-ribonucleic acid DNA ribonucleic acid RNA

Nitrogenous bases Pyrimidines Purines adenine (A) guanine (G) cytosine (C) thymine (T) uracil (U)

Nucleoside = sugar + base linked by β-glycosidic bond at the 1’ anomeric carbon Adenosin 2 -deoxyadenosine

Phosphate + Nucleoside = Nucleotide 5’ adenosine triphosphate (ATP) cyclic adenosine monophosphate (AMP)

Nucleotides and Nucleic Acids NH 2 Nucleotides -O OP O - O Phosphate -O Adenine OP O O CH 2 O Ribose Adenosine monophosphate (AMP)

Nucleotides and Nucleic Acids NH 2 Nucleotide diphosphate: -O O- Adenine O- P O O O CH 2 O Ribose Adenosine diphosphate (ADP)

Nucleotides and Nucleic Acids NH 2 Nucleotide diphosphate: -O OP O - O Phosphate -O O- Adenine O- P O O O CH 2 O Ribose Adenosine diphosphate (ADP)

Nucleotides and Nucleic Acids NH 2 Nucleotide triphosphate: -O O- O- Adenine O- P O P O O CH 2 O Ribose Adenosine tr. Iphosphate (ATP)

Nucleotides and Nucleic Acids NH 2 Nucleotide triphosphate: -O O- O- O- P O P O O O Energy Unit Adenine O CH 2 O Ribose Adenosine tr. Iphosphate (ATP)

Nucleotides and Nucleic Acids NH 2 Nucleotide diphosphate: -O OP O - O Phosphate Negative Charge -O O- Adenine O- P O O O CH 2 O Ribose Adenosine diphosphate (ADP) Negative Charge

Electrophoresis is based on the molecules charge

Nucleic Acids Nucleic acid polymers contain nucleotides connected by phosphate esters Connects the 3’ hydroxyl of one ribose to the 5’ hydroxyl of another 3’ 5’

Bases vary according to the order of the nucleosides Backbone made up of ribose and phosphate groups We can list the sequence of bases

Frequency of bases in human DNA • adenine (A) = 30 % • thymine (T) = 30 % • cytosine (C) = 20 % • guanine (G) = 20 % WHY? DNA must be two strands DNA must be complementary

AT pairs makes two hydrogen bonds GC pairs makes three hydrogen bonds

AC pairing and GT pairing make repulsive instead of attractive interactions

Nucleotides and Nucleic Acids Rosalin Franklin 1952: x-ray of DNA suggested helical twisted shape

Nucleotides and Nucleic Acids Watson and Crick 1953 Used Rosalind Franklin's x-ray diffraction photo of DNA to identify DNA structure. Movie: Photo 51

DNA molecule contains millions of base pairs One strand is a complementary to the other antiparallel strands 5’ 3’ 3’ 5’

DNA T G C T A C G A T A G G A T G C T A Base pairs

DNA T G C T A C G A T G C T A Base pairs

DNA Sequence: TGCTACGAT Base pairs

Structural variation in DNA • B-DNA – Most commonly occurring • Z-DNA – Helix winds to the left in a zigzag pattern • A-DNA – Shorter, more compact – Favored in water-poor environments

Others • Triplex DNA – Transient molecule – Has been implicated in the regulation of several genes • G-quadruplex – quadruple-stranded structures formed by a guanine-rich sequences of nucleic acids

ribose deoxyribose

RNA forms structures • RNA has structure variation due to not having limitations of stereochemistry • RNA structure influences gene expression • Critical roles in processes --- ligand sensing, regulation of translation, polyadenylation, splicing