BIOCHEM 2280 FINAL
REVIEW
December 17, 2022
,Nucleic Acids
Nucleotide Monomers = monosaccharide + nitrogenous base +
phosphate
• Nucleic acid polymers are composed of nucleotide monomers
• Nucleotides consist of 3 components: monosaccharide + nitrogenous base + phosphate
Nucleoside = sugar + nitrogenous base
1) Monosaccharide
• Ribonucleotides contain the pentose sugar ribose
o OH on 2’ carbon
• Deoxyribonucleotides contain the pentose sugar deoxyribose
o H on 2’ carbon
2) Nitrogenous base
There are two types of nitrogenous bases:
Purines: 2 rings (larger nitrogenous bases)
• Adenine (A) + Guanine (G)
Pyrimidines: 1 ring (smaller nitrogenous bases)
• Cytosine (C) + Thymine (T) + Uracil (U)
o Thymine found in DNA; Uracil found in RNA
▪ Uracil is identical to Thymine, but lacks CH3 group
*not required to memorize structure of nitrogenous bases
1
, • All nitrogenous bases are planar (lots of rings and double bonds) and relatively
hydrophobic
Nucleoside (sugar + nitrogenous base) Structure
• Nitrogen (N) of nitrogenous base is joined to the anomeric carbon (1’ C) of the pentose
sugar via an N-glycosidic bond
• Sugar is always in the β configuration (OH on anomeric carbon same side as CH2OH)
when joined to a nitrogenous base
• Nucleoside names are: adenosine, guanosine, cytidine, thymidine, uridine
• Carbons of pentose sugar are numbered 1’ (anomeric carbon) – 5’ (CH2OH)
o Primes (‘) used as convention to differentiate from numbering of nitrogenous base
Nucleotide = nucleoside (sugar + nitrogenous base) + phosphate
3) Phosphate
• Phosphate group(s) are attached to the 5’ carbon of the pentose sugar via a
phosphodiester linkage
• Nucleotide = nucleoside (sugar + nitrogenous base) + phosphate
• Nucleotides are named by naming (or abbreviating with letter of) the nucleoside,
followed by the number of phosphates
o Ie., cytidine triphosphate (CTP)
• Sometimes, the abbreviation for a deoxyribonucleotide will begin with a small d
o Ie., deoxycytidine triphosphate dCTP
2
, Polynucleotide Structure
• Mononucleotides are linked to form an unbranched polynucleotide polymer
• Mononucleotides are joined by phosphodiester bonds
o A phosphate group attached to the 5’ carbon of one pentose forms a
phosphodiester bond with the OH group off the 3’ carbon of the pentose sugar in
the next mononucleotide
• Creates a phosphate-sugar backbone, with the nitrogenous bases sticking out the side
• A polynucleotide has “polarity” because the 5’ and 3’ ends are different
o 5’ end: end of the polynucleotide at which the 5’ carbon is free (not attached to
another mononucleotide)
▪ Phosphate group may or may not be present
o 3’ end: end of the polynucleotide at which the 3’ carbon is free (not attached to
another mononucleotide)
▪ Phosphate group may or may not be present
• The sequence of a polynucleotide is written by listing the letter for each nucleotide’s
nitrogenous base always in the 5’→3’ direction from left to right
o Context (presence of T vs. U in sequence) tells us whether DNA or RNA
• If there is a sequence with its complementary sequence written below it, the top sequence
will be 5’→3’
If asked what the complementary sequence is to a given sequence and 5’→3’ not labelled,
assume the complementary sequence is written in the 5’→3’ direction
• What is the complementary sequence to ATCGCA?
5’ATCGCA3’
3’TAGCGT5’ Answer: TGCGAT (5’→3’)
Palindromic sequence: read the same on both strands in the 5’ → 3’ direction
5'AAATTT3' = both AAATTT 5’→3’
3'TTTAAA5'
3
REVIEW
December 17, 2022
,Nucleic Acids
Nucleotide Monomers = monosaccharide + nitrogenous base +
phosphate
• Nucleic acid polymers are composed of nucleotide monomers
• Nucleotides consist of 3 components: monosaccharide + nitrogenous base + phosphate
Nucleoside = sugar + nitrogenous base
1) Monosaccharide
• Ribonucleotides contain the pentose sugar ribose
o OH on 2’ carbon
• Deoxyribonucleotides contain the pentose sugar deoxyribose
o H on 2’ carbon
2) Nitrogenous base
There are two types of nitrogenous bases:
Purines: 2 rings (larger nitrogenous bases)
• Adenine (A) + Guanine (G)
Pyrimidines: 1 ring (smaller nitrogenous bases)
• Cytosine (C) + Thymine (T) + Uracil (U)
o Thymine found in DNA; Uracil found in RNA
▪ Uracil is identical to Thymine, but lacks CH3 group
*not required to memorize structure of nitrogenous bases
1
, • All nitrogenous bases are planar (lots of rings and double bonds) and relatively
hydrophobic
Nucleoside (sugar + nitrogenous base) Structure
• Nitrogen (N) of nitrogenous base is joined to the anomeric carbon (1’ C) of the pentose
sugar via an N-glycosidic bond
• Sugar is always in the β configuration (OH on anomeric carbon same side as CH2OH)
when joined to a nitrogenous base
• Nucleoside names are: adenosine, guanosine, cytidine, thymidine, uridine
• Carbons of pentose sugar are numbered 1’ (anomeric carbon) – 5’ (CH2OH)
o Primes (‘) used as convention to differentiate from numbering of nitrogenous base
Nucleotide = nucleoside (sugar + nitrogenous base) + phosphate
3) Phosphate
• Phosphate group(s) are attached to the 5’ carbon of the pentose sugar via a
phosphodiester linkage
• Nucleotide = nucleoside (sugar + nitrogenous base) + phosphate
• Nucleotides are named by naming (or abbreviating with letter of) the nucleoside,
followed by the number of phosphates
o Ie., cytidine triphosphate (CTP)
• Sometimes, the abbreviation for a deoxyribonucleotide will begin with a small d
o Ie., deoxycytidine triphosphate dCTP
2
, Polynucleotide Structure
• Mononucleotides are linked to form an unbranched polynucleotide polymer
• Mononucleotides are joined by phosphodiester bonds
o A phosphate group attached to the 5’ carbon of one pentose forms a
phosphodiester bond with the OH group off the 3’ carbon of the pentose sugar in
the next mononucleotide
• Creates a phosphate-sugar backbone, with the nitrogenous bases sticking out the side
• A polynucleotide has “polarity” because the 5’ and 3’ ends are different
o 5’ end: end of the polynucleotide at which the 5’ carbon is free (not attached to
another mononucleotide)
▪ Phosphate group may or may not be present
o 3’ end: end of the polynucleotide at which the 3’ carbon is free (not attached to
another mononucleotide)
▪ Phosphate group may or may not be present
• The sequence of a polynucleotide is written by listing the letter for each nucleotide’s
nitrogenous base always in the 5’→3’ direction from left to right
o Context (presence of T vs. U in sequence) tells us whether DNA or RNA
• If there is a sequence with its complementary sequence written below it, the top sequence
will be 5’→3’
If asked what the complementary sequence is to a given sequence and 5’→3’ not labelled,
assume the complementary sequence is written in the 5’→3’ direction
• What is the complementary sequence to ATCGCA?
5’ATCGCA3’
3’TAGCGT5’ Answer: TGCGAT (5’→3’)
Palindromic sequence: read the same on both strands in the 5’ → 3’ direction
5'AAATTT3' = both AAATTT 5’→3’
3'TTTAAA5'
3
