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Introduction to Cells & MicroscopyNucleotide and Nucleic Acid Structure

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Structural Components of Nucleotides

Glycosidic bond

Base Sugar

Phosphate

H

H

NUCLEOTIDE

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Table 3-1

RNA

DNA

Nucleic acid – polymer of nucleotides – directionality 5’à3’

When you write a sequence:

ATCG

It is assumed that the 5’-end is on the left and the 3’-end is on the right, unless otherwise labeled.

5’-ATCG-3’Phosphodiester bonds

Composition of DNA?

3’-GCTA-5’ same molecule

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Chargaff’s Rules

DNA is Double Stranded Helix

http://higheredbcs.wiley.com/legacy/college/voet/0470129301/kinemages/exercise_2.html

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Figure 3-8

Computer-simulated space-filling model of DNA.

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• The crucial piece of evidence for DNA structure came from X-ray “crystallography.” Wilkins learned how to purify DNA and make regular fiber patterns. Rosalind Franklin performed the X-ray diffraction and deduced there was a helix.

• Francis Crick saw the data at a seminar Wilkins gave and also deduced there was a helix and the size parameters.• James Watson discovered how the

bases went together (complementarity) using Chargaff rules (A=T, G=C).• Watson & Crick published their

structure in 1953. Beautiful example of how structure predicted function.

Video: Computer-simulated space-filling model of DNA.

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SUMMARY

(34 Å)

Right-handed, antiparallel, double-stranded helix. With the “basecomplementarity,” it explains genetic material:• Storage of genetic information• Replication• Information retrival

sugar–phosphate backbone (phosphodiester bonds)

Introduction to Cells & MicroscopyCentral Dogma of Molecular Biology

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From DNA to Protein: Gene Expression

• Central Dogma: from Genes to Proteins• Replication of the genes (DNAàDNA)• Transcribing the information (DNAàRNA)• Translating the nucleotide sequence into

protein sequence (RNAàProtein)– The Genetic Code– Protein Biosynthesis

Central Dogma

The central dogma of molecular biologyReplication

Information Flow

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Replication

DNA replication is semiconservative (Meselson-Stahl Expt)

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Arthur Kornberg showed that DNA contains information for its own replication.

He combined in a test tube: DNA, the four deoxyribonucleoside triphosphates (dNTPs–monomers), DNA polymerase, salts (Mg+2), and buffer.

The DNA served as a template for synthesis of new DNA.

DNA Replication

Each New DNA Strand Grows from Its 5´ End to Its 3´ End

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ALL polymerases add nucleotides to the 3’ end

(Direction is termed 5’ g 3’)

Pyrophosphatase

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Each New DNA Strand Grows from Its 5´ End to Its 3´ End

Transcription

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Central Dogma


Messenger RNA (mRNA)

Transfer RNA (tRNA)

Ribosomal RNA (rRNA)

RNA is key to this process:• Messenger RNA (mRNA)—carries

copy of a DNA sequence to site of protein synthesis at the ribosome

• Transfer RNA (tRNA)—carries amino acids for polypeptide assembly

• Ribosomal RNA (rRNA)—catalyzes peptide bond formation and provides structure for the ribosome

Central Dogma

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Central Dogma


Transcription


Transfer RNA (tRNA)


Transcription

Transcription components:• A DNA template for base pairings—one of the two

strands of DNA• Nucleoside triphosphates (ATP,GTP,CTP,UTP) as

substrates• An RNA polymerase enzyme

Transcription process:• RNA polymerase unwinds DNA about ten base pairs at a

time; reads template in 3’ to 5’ direction, synthesizes RNA in the 5’ to 3’ direction.

• The RNA transcript is antiparallel to the DNA template strand, and adds nucleotides to its 3’ end.

• NTPs incorporate NMP and PPi is a product!

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• Production of mRNA transcript by RNA polymerase

Transcription

Coding Region5' Flanking 3'-flanking

Transcription: Where to start?

Promoter

prokaryotes

The consensus sequence for each element in human genes (N is any nucleotide)

eukaryotes

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Transcription

Translation

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Central Dogma


Translation


Transfer RNA (tRNA)


What is the relationship between a DNA sequence and an amino acid sequence?

• The Code• The Adaptors (tRNA)• The Ribosome (rRNA + rProteins)

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Translation: The Genetic Code

The genetic code: Specifies which amino acids will be used to build a protein

Codon: A sequence of three bases—each codon specifies a particular amino acid.

Start codon: AUG—initiation signal for translation.

Stop codons: UAA, UAG, UGA—stop translation and polypeptide is released.

Translation: The Genetic Code

The genetic code is redundant. The genetic code is universal.

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Translation: tRNA

tRNAs must deliver amino acids corresponding to each codon

The conformation (three-dimensional shape) of tRNA results from base pairing (hydrogen bonding) within the molecule.

3‘-end is the amino-acid attachment site—binds covalently.

At the other end (middle of the tRNA sequence) is the Anticodon—site of base pairing with mRNA. Unique for each species of tRNA.

Translation: tRNA

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tRNAanticodon

Template for mRNA –read 3’à5’

Translation: tRNA

N C

Translation: Ribosome

Ribosome: the workbench—holds mRNA and charged tRNAs in the correct positions to allow assembly of polypeptide chain.

Ribosomes are not specific, they can make any type of protein.

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Translation: Protein Biosynthesis: Ribosome Structure

Ribosomes have two subunits, large and small. When not active in translation, the subunits exist separately.• The small subunit (40S) has one ribosomal RNA (rRNA) (18S) and 33

proteins.• The large subunit (60S) has three molecules of rRNA (28S, 5.8S, 5S)

and 49 different proteins.• Ribosomal subunits are held together by ionic and hydrophobic forces

(not covalent bonds) (80S).

Translation: Ribosome

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Translation: Protein Biosynthesis; Elongation

Decoding(GTP hydrolysis)

Peptidyltransferase

GTPEF-Tu

Translation: Protein Biosynthesis; Elongation

Translocation(GTP hydrolysis)

ELONGATION

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Central Dogma


Animated videos of DNA structure and Central Dogma

(https://wileyassets.s3.amazonaws.com/Voet_Fundamentals_of_Biochemistry_5e_ISBNEPROF12533/media/Guided_Tour/dnaStructure.html)

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