Chapter 17 Nucleotides Nucleic Acids and Heredity Introduction

Chapter 17 Nucleotides, Nucleic Acids, and Heredity

Introduction • each cell of our bodies contains thousands of different proteins • how do cells know which proteins to synthesize out of the extremely large number of possible amino acid sequences? • from the end of the 19 th century, biologists suspected that the transmission of hereditary information took place in the nucleus, more specifically in structures called chromosomes • the hereditary information was thought to reside in genes within the chromosomes • chemical analysis of nuclei showed chromosomes are made up largely of proteins called histones and nucleic acids

Introduction • by the 1940 s it became clear that deoxyribonucleic acids (DNA) carry the hereditary information • other work in the 1940 s demonstrated that each gene controls the manufacture of one protein • thus, the expression of a gene in terms of an enzyme protein led to the study of protein synthesis and its control

Nucleic Acids • There are two kinds of nucleic acids in cells • ribonucleic acids (RNA) • deoxyribonucleic acids (DNA) • Both RNA and DNA are polymers built from monomers called nucleotides • A nucleotide is composed of • a base • a monosaccharide • a phosphate

Pyrimidine/Purine Bases • The nitrogen bases in nucleotides consist of two general types: - purines: adenine (A) and guanine (G) - pyrimidines: cytosine (C), thymine (T) and Uracil (U)

Pentose Sugars • There are two related pentose sugars - RNA contains ribose - DNA contains deoxyribose • The sugars have their carbon atoms labeled with primes to distinguish them from the nitrogen bases

Nucleosides • Nucleoside: a compound that consists of D-ribose or 2 -deoxy-D-ribose bonded to a purine or pyrimidine base by a -N-glycosidic bond

Nucleotides • Nucleotide: a nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’ or the 5’-OH

Nucleotides • deoxythymidine 3’-monophosphate (3’-d. TMP)

AMP, ADP and ATP • • Additional phosphate groups can be added to the nucleoside 5’monophosphates to form diphosphates and triphosphates ATP is the major energy source for cellular activity

Naming nucleosides and nucleotides • Nucleosides are named by changing the nitrogen base ending to –osine for purines and –idine for pyrimidines • Nucleotides are named using the name of the nucleoside followed by 5’-monophosphate

Names of nucleosides and nucleotides

Structure of DNA and RNA • Primary Structure can be divided into two parts: 1) sugar-phosphate backbone 2) side-chain bases • Nucleic acids are polymers of nucleotides • Their primary structure is the sequence of nucleotides • The backbone of DNA or RNA has two ends: a 5’-OH end a 3’-OH end • base sequence is read from the 5’ end to the 3’ end

Nucleic Acid - 1° Structure • A schematic diagram of a nucleic acid

Primary Structure The nucleotides in nucleic acids are joined by phosphodiester bonds • The 3’-OH group of the sugar in one nucleotide forms an ester bond to the phosphate group on the 5’-carbon of the sugar of the next nucleotide •

RNA Primary Structure • In RNA, A, C, G, and U are linked by 3’-5’ ester bonds between ribose and phosphate

DNA Primary Structure • In DNA, A, C, G, and T are linked by 3’-5’ ester bonds between deoxyribose and phosphate

Reading Primary Structure • A nucleic acid polymer has a free 5’-end a free 3’-end • The sequence is read from the free 5’-end using the letters of the bases • This example reads 5’—A—C—G—T— 3’

DNA - 2° Structure • Secondary structure: the ordered arrangement of nucleic acid strands • the double helix model of DNA 2° structure was proposed by James Watson and Francis Crick in 1953 • Double helix: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled about the same axis • Base pairing: the two strands are held together by hydrogen bonding between base pairs

The DNA Double Helix

Base Pairing

Higher Structure of DNA • DNA is coiled around proteins called histones • histones are rich in the basic amine acids Lys and Arg, whose side chains have a positive charge • the negatively-charged DNA molecules and positivelycharged histones attract each other and form units called nucleosomes • nucleosome: a core of eight histone molecules around which the DNA helix is wrapped • nucleosomes are further condensed into chromatin • chromatin fibers are organized into loops, and the loops into the bands that provide the superstructure of chromosomes

Chromosomes

Chromosomes

Chromosomes

Chromosomes

DNA and RNA • The three differences in structure between DNA and RNA are • DNA bases are A, G, C, and T; the RNA bases are A, G, C, and U • the sugar in DNA is 2 -deoxy-D-ribose; 2 -deoxy-D-ribose in RNA it is Dribose • DNA is always double stranded; stranded there are several kinds of RNA, all of which are single-stranded

RNA • RNA molecules are classified according to their structure and function

Structure of t. RNA

Genes, Exons, and Introns • Gene: a segment of DNA that carries a base sequence that directs the synthesis of a particular protein, t. RNA, or m. RNA • there are many genes in one DNA molecule • in bacteria the gene is continuous • in higher organisms the gene is discontinuous • Exon: a section of DNA that, when transcribed, codes for a protein or RNA • Intron: a section of DNA that does not code for anything functional

Genes, Exons, and Introns • introns are cut of m. RNA before the protein is synthesized

DNA Replication • Replication involves separation of the two original strands and synthesis of two new daughter strands using the original strands as templates • DNA double helix unwinds at a specific point called an origin of replication • polynucleotide chains are synthesized in both directions from the origin of replication; that is, DNA replication is bidirectional • at each origin of replication, there are two replication forks, forks points at which new polynucleotide strands are formed

DNA Replication • DNA is synthesized from its 5’ -> 3’ end (from the 3’ -> 5’ direction of the template) • the leading strand is synthesized continuously in the 5’ -> 3’ direction toward the replication fork • the lagging strand is synthesized semidiscontinuously as a series of Okazaki fragments, fragments also in the 5’ -> 3’ direction, but away from the replication fork • Okazaki fragments of the lagging strand are joined by the enzyme DNA ligase • replication is semiconservative: each daughter strand contains one template strand one newly synthesized strand

DNA Replication

Replisomes • Replisomes are assemblies of “enzyme factories”

DNA Replication • Opening up the superstructure • during replication, the very condensed superstructure of chromosomes is opened by a signal transduction mechanism • one step of this mechanism involves acetylation and deacetylation of key lysine residues • acetylation removes a positive charge and thus weakens the DNA-histone interactions

DNA Replication • Relaxation of higher structures of DNA • topoisomerases (also called gyrases) facilitate the relaxation of supercoiled DNA by introducing either single strand or double strand breaks in the DNA • once the supercoiling is relaxed by this break, the broken ends are joined and the topoisomerase diffuses from the location of the replication fork

DNA Replication • Unwinding the DNA double helix • replication of DNA starts with unwinding of the double helix • unwinding can occur at either end or in the middle • unwinding proteins called helicases attach themselves to one DNA strand cause separation of the double helix • the helicases catalyze the hydrolysis of ATP as the DNA strand moves through; the energy of hydrolysis promotes the movement

DNA Replication • Primer/primases • primers are short oligonucleotides of four to 15 nucleotides long • they are required to start the synthesis of both daughter strands • primases are enzymes that catalyze the synthesis of primers • primases are placed at about every 50 nucleotides in the lagging strand synthesis

DNA Replication • DNA polymerases are key enzymes in replication • once the two strands have separated at the replication fork, the nucleotides must be lined up in proper order for DNA synthesis • in the absence of DNA polymerase, alignment is slow • DNA polymerase provides the speed and specificity of alignment • along the lagging (3’ -> 5’) strand, the polymerases can synthesize only short fragments, because these enzymes only work from 5’ -> 3’ • these short fragments are called Okazaki fragments • joining of the Okazaki fragments and any remaining nicks is catalyzed by DNA ligase

DNA Repair • The viability of cells depends on DNA repair enzymes that can detect, recognize, and repair mutations in DNA • Base excision repair (BER): (BER) one of the most common repair mechanisms • a specific DNA glycosylase recognizes the damaged base • it catalyzes the hydrolysis of the -N-glycosidic bond between the incorrect base and its deoxyribose • it then flips the damaged base, completing the excision • the sugar-phosphate backbone remains intact

DNA Repair • BER (cont’d) • at the AP (apurinic or apyrimidinic) site thus created, an ap ap endonuclease endonucleas catalyzes the hydrolysis of the backbone • an exonuclease liberates the sugar-phosphate unit of the damaged site • DNA polymerase inserts the correct nucleotide • DNA ligase seals the backbone to complete the repair • NER (nucleotide excision repair) removes and repairs up to 24 -32 units by a similar mechanism involving a number of repair enzymes

Cloning • Clone: a genetically identical population • Cloning: a process whereby DNA is amplified by inserting it into a host and having the host replicate it along with the host’s own DNA • Polymerase chain reaction (PCR): an automated technique for amplifying DNA using a heat-stable DNA polymerase from a thermophilic bacterium

Cloning

Nucleic Acids End Chapter 17