Nucleotides, Nucleic Acids and Heredity

Bettelheim, Brown, Campbell and Farrell

Chapter 25—part 2

DNA and RNA

• The three differences in structure between DNA and RNA are– DNA bases are A, G, C, and TT; the RNA

bases are A, G, C, and UU– the sugar in DNA is 2-deoxy-D-ribose2-deoxy-D-ribose; in RNA

it is D-riboseD-ribose– DNA is always double strandeddouble stranded; there are

several kinds of RNA, all of which are single-single-strandedstranded

RNA

• RNA molecules are classified according to their structure and function

RNA type Size Function

Transfer(tRNA)

Ribosomal(rRNA)

Messenger(mRNA)

from 73 to 93 base pairs

very large;MW up to 106

combines with proteinsto form ribosomes

750 base pairson average

transports amino acidsto the site of proteinsynthesis

directs amino acidsequence of proteins

Ribozymes(catalytic RNA)

catalyze cleavage of partof their own sequencesin mRNA and tRNA

very large

Other RNAs• RNA molecules are classified according to their

structure and function

• snRNA –small nuclear RNA (100-200 b)Combine to make snRNPs to help processing of mRNA for

export from nucleus

• miRNA—microRNA• Bind to mRNA in development

• siRNA—small interfering RNA• Knock out mRNA for genes that are undesirable

t-RNA Structure• Contains some modified nucleotides, such as

1-methylguanosine• Actual 3-D shape is an L• Often shown as a 2-D “clover leaf” shape with

three “loops”• Some H-bonding between bases at base of loops• Anticodon bases contained on middle loop • 3’ end has CCA as terminal bases• 3’ end carries the amino acid

“Clover Leaf” Structure of tRNA

Fig. 24.10

Nucleic Acids and Heredity

• Chromosomes exist in pairs (23 pairs in humans) • Inherit one DNA copy from each parent. • Most cells in our body contain copies of both • Genetic information is carried in the sequence of

bases along the DNA strands. • Information is passed to daughter cells when cell

divides.

Genes, Exons, and Introns• Gene:Gene: a segment of DNA that carries a base

sequence that directs the synthesis of a particular protein, tRNA, or mRNA– there are many genes in one DNA molecule– in bacteria the gene is continuous– in higher organisms the gene is discontinuous

• Exon:Exon: a section of DNA that, when transcribed, codes for a protein or RNA

• Intron:Intron: a section of DNA that does not code for anything functional

Genes, Exons, and Introns

– introns are cut out of mRNA by ribozymes before the protein is synthesized

Central Dogma of Molecular Biology

DNA → RNA → Protein

Processes involved in transfer of hereditary information

• Replication: DNA → DNA (identical copy)

• Transcription: DNA → RNA (m-RNA)

• Translation: RNA → protein

DNA Replication• ReplicationReplication 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 replicationorigin of replication– DNA replication is bidirectionalbidirectional: chains are synthesized

in both directions from the origin of replication– At each origin of replication, there are two replication replication

forksforks where where new polynucleotide strands are formed

Two NEW Strands Formed

Steps in Replication1.Weaken DNA-Histone interactions

– Histone Acetylase interferes with +/- interaction by adding acetyl group to lysine amino groups

2.Relax higher DNA superstructure– Topoisomerases (gyrases) eliminate supercoiling of DNA by

binding to one strand (via tyrosine and phosphate bond), nicking DNA, uncoiling DNA and rejoining DNA segments

3.Unwind Double Helix– Helicases attach to one strand and separate the two strands

(uses ATP for energy)

DNA Replication

Steps in Replication4.Primer/Primases

– Short RNA sequences needed to start DNA synthesis– Catalyzed by Primase

5.Polymerization (actual synthesis of new DNA strands)– DNA Polymerase– Catalyzes attachment base to new strand– New base is complementary to template base– Short Okasaki fragments formed (ca 200 bases)

6.Ligation– DNA ligase joins Okasaki fragments

DNA Replication– DNA is synthesized from its 5’ -> 3’ end (from the 3’ -> 5’

direction of the template)– the leading strand leading strand is synthesized continuously in the 5’ ->

3’ direction toward the replication fork – the lagging strand lagging strand is synthesized discontinuously as a

series of Okazaki fragmentsOkazaki 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 ligaseDNA ligase

– replication is semiconservativesemiconservative:: each daughter strand contains one original template strand and one newly synthesized strand

DNA Replication

Leading strand

Lagging strand

DNA ReplicationLeading strand (new strand synthesized from 5’ to 3’)

Lagging strand (new strand runs from 3’ to 5’ but synthesis of individual Okasaki fragments is 5’ to 3’)

Fig. 24.9

DNA Replication

Bond Formation in Replication

DNA Replication

Old strand:New strand:

ATTCGTAAAGGTCTAAGCATT

DNA Repair• Cells have DNA repair enzymes that can

detect, recognize, and repair mutations in DNA• Base excision repairBase excision repair (BER)(BER): one of the most

common repair mechanisms– DNA glycosylase recognizes the “damaged” base

and cuts out the base, leaving the sugar-phosphate backbone

APAP (apapurinic or apapyrimidinic) sitesite created

DNA Repair• EndonucleasEndonuclease catalyzes the hydrolysis of the

backbone

– an exonucleaseexonuclease liberates the sugar-phosphate unit of the damaged site

– DNA polymerase inserts the correct nucleotide

– DNA ligase seals the backbone to complete the repair

DNA Repair• NERNER (nnucleotide eexcision rrepair) removes

and repairs up to 24-32 units by a similar mechanism involving a number of repair enzymes