CHAPTER 5: Nucleic acids and nucleotides summary

There are two types of nucleic acids: Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

General functions of nucleic acids

• Controls cellular functions
• Maintains identity of species over a long time
• Is used in the synthesis of proteins

Components of Nucleic Acids

Nucleotides

• Nucleotides are composed of nitrogenous bases, a phosphate group, and a pentose sugar
• Nucleotides are the building blocks of DNA and RNA
• They are the structural components of some coenzymes

Two types of nitrogenous bases:

Purines and pyrimidines

• DNA purines – Adenine and Guanine
• RNA purines – Adenine and Guanine
• DNA pyrimidines – Thymine and Cytosine
• RNA pyrimidines – Uracil and cytosine

Structure of DNA

• DNA is double helix as proposed by Watson and Crick in 1953.
• It is a twisted ladder
• It is right-handed
• The two strands making up the double helix are antiparallel
• In the double helix, the inner core is made up of nitrogenous bases while the outer core is made up of phosphate backbone
• The two strands in the double helix are held together by hydrogen bonds which are formed by the complementary base pairing
• Hydrogen bonds form between the nitrogenous bases
• Chargaff’s rule implies that Adenine content is equal to Thymine content, and Guanine content is equal to cytosine content.
• Genetic information used for the synthesis of protein is usually carried by one strand called the template strand

Organization of DNA

• DNA is organized in a single chromosome
• Proteins associate with DNA to form chromatids
• The double helix is wrapped around histones
• A nucleosome consists of two molecules of histones and is the basic unit of chromatins

Structure of RNA

• Pentose sugar is ribose, with an oxygenated second carbon atom
• Pyrimidines in RNA are Uracil and Cytosine
• It is usually single-stranded
• Does not obey Chargaff’s rule

Types of RNA

• Messenger RNA
• Ribosomal RNA
• Transfer RNA

Messenger RNA (mRNA)

• Has a 5’ cap that stabilizes the molecule and prevents hydrolysis, and also aids in recognition for protein synthesis
• Has a Poly A tail on the 3’ end which protects the molecule against attacks by 3’ exonucleases and provides stability to the molecule

Transfer RNA (tRNA)

• Has Acceptor arm that attaches amino acids
• Anticodon arm which recognizes the mRNA codon triplet
• D arm
• Variable arm

Ribosomal RNA (rRNA) – plays an important role in binding the mRNA to ribosomes

Differences between DNA and RNA

• DNA has Thymine, while RNA has Uracil
• DNA is double-stranded while RNA is single-stranded
• DNA stores genetic information in genes while RNA carries this information for the synthesis of proteins
• DNA has deoxyribonucleic acid as the pentose sugar while RNA has oxygenated ribose sugar

Central Dogma of Life

DNA in the nucleus is converted to mRNA through a process called transcription; this mRNA molecule is transported to the cytoplasm and into the ribosomes where translation forms amino acids that join through a peptide bond to form protein polypeptide.

Revision

Nucleotides=
-nitrogenous base linked to a
-pentose sugar (ribose or deoxyribose)
-one or more phosphate groups.

ROLES OF NUCLEOTIDES (5)
1) Nucleotides, in particular ATP, have a major role in energy transfer reactions in all cell types (!)

2) universal building blocks of nucleic acids (RNA and DNA).

3) Cofactors for enzymes (ATP, GTP)

4) Positive or negative regulators enzymes

5) Signaling molecules (eg, cAMP).

Nucleotide Structure I:The Pentose Sugar
The pentose sugar is a 5-carbon mono-saccharide

It can be either a D-ribose or a 2-deoxy-D-ribose

This oxygen is missing from the second carbon in 2-deoxyribose

the pentose sugar is always in the __ configuration.
Furanose ring configuration.

Ribose vs deoxyribose sugar
The ribose sugar is present in every nucleotide of RNA, and the deoxyribose sugar is present in every nucleotide of DNA. The deoxyribose sugar differs from the ribose sugar in that it does not have a hydroxyl group bonded to its 2′ carbon.

Connection points to pentose sugar

Nucleotide Structure II:The Nitrogenous Base

The five most abundant nitrogenous bases, divided into two major types:
While the same sugar is present in every nucleotide of a nucleic acid (i.e. RNA or DNA), different nitrogenous bases are found in different nucleotides.

PYRIMIDINE
Cytosine
Uracil
Thymine

PURINES
Guanine
Adenine

The Basic Structure
of Pyrimidine Bases

Thymine and Uracil each have a
2ND carbonyl group on their rings (at position 4)

Cytosine has an _ group, instead of a _ group, attached to position 4
Cytosine has an AMINO GROUP, instead of a CARBONYL GROUP, attached to position 4

Structure of Purine Bases
pyrimidine ring and an imidazole group

KNOW #S FOR DEOXYRIBOSE, NOT PURINES/PYRM

TIP- LOOK UP PNEUMONICS
…

Adenine has an _ group attached to position 6
Adenine has an AMINO group attached to position 6

Guanine has a group attached to position 6 and an ___ group attached to position 2
Guanine has a CARBONYL group attached to position 6 and an AMINO group attached to position 2

“close relative” of adenine and guanine
CAFFEINE

N-glycosidic linkage is what type of bond?
is a covalent, glycosidic bond in which two molecules are joined together by a nitrogen atom

connects a nitrogen atom of a nitrogenous base with C-1 of a pentose sugar (ribose or deoxyribose)

N-glycosidic bonds form from the reaction between
a hemiacetal and an amino group, as in the reaction between a pentose sugar and a nitrogen base

An N-glycosidic bond connects a _ to form a __
An N-glycosidic bond connects a nitrogenous base with a pentose sugar to form a nucleoside

A nucleoside=
A nucleoside is simply a nitrogenous base bound to a pentose sugar (ribose or deoxyribose)

nucleoside = pentose sugar + nitrogenous base

Nucleotide Structure III: The Phosphate Group(s)

The phosphorus atom in a phosphate group is an
“easy target” for nucleophilic attacks

An inorganic phosphate group (Pi) can add to organic molecules by a phosphorylation reaction.

esterification reaction is also a _ RXN
esterification reaction is also a condensation (or dehydration synthesis) reaction because a molecule of water is formed

always endergonic (+DG), requires energy.

The reverse reaction (hydrolysis of the ester) is exergonic (-DG)
(not shown)

The phosphate group adds to
carbon 5 of a pentose sugar

nucleotide=
nucleotide is simply a nucleoside bound to one or more phosphate groups

nucleotide = nitrogen base + pentose sugar + phosphate group(s)

Nucleoside Vs Nucleotide
NUCLEOSIDE DOES NOT HAVE PHOSPHATE GROUPS

NUCLEIC ACIDS
DNA: a hetero-polymer of deoxyribonucleotides
RNA: a hetero-polymer of ribonucleotides

The polymerization of nucleotides to nucleic acids requires:

1. A nucleoside triphosphate
   (a.k.a. ribonucleoside triphosphate)
2. A free 3′ -OH end of an acceptor
   nucleotide in an existing polymer

The chemistry of polymerization relies on a two-step mechanism:

1. Energy-yielding hydrolysis of the a phosphate-b phosphate linkage in the joining nucleotide triphosphate
2. Energy-requiring ester formation between the a phosphate in the nucleotide triphosphate and the 3′ -OH of the acceptor nucleotide

the sugar-phosphate backbone of RNA and DNA is made up of what kind of bonds?
Phosphodiester bonds

Chargaff’s Rules
The amount of Adenine must always equal the amount of Thymine (A = T)

The amount of Guanine must always equal the amount of Cytosine (G = C)

This creates a 1:1 ratio of pyrimidine and purine bases within the nucleic acid (RNA or DNA)

DNA Synthesis
DNA synthesis cannot take place without ATP energy.

The two strands of DNA unwind and each will act as a template for a new strand.

New bases add to the chain by matching up with their complementary bases.

Two new strands of DNA are formed to create two new DNA chains that are identical to the original, parent chain.

DNA STRANDS
2 STRANDS
5′ TO 3′
ANTIPARALLEL

Base-pairing also exists in:

1. DNA:RNA (double helix has 1 strand of each)
2. RNA:RNA (double helix has 2 strands of RNA)

major natural form of DNA in living cells
B-DNA

BASE PAIRS AT TURN OF HELIX~10