Nucleotide and Nucleic Acid Structure
IntroductionNucleotide to Cells & Microscopy and Nucleic Acid Structure
Adapted from Prof. Dean Tolan • Outline of today’s supplemental lecture
• Nucleotide and nucleic acid structure
• Central Dogma
• Replication • Transcription • Translation
• Quiz at the end of the lecture Structural Components of Nucleotides
Glycosidic bond Table 3-1 Nucleic acid – polymer of nucleotides – directionality 5’3’
When you write a sequence:
ATCG
It is assumed that the 5’-end is on the left and the 3’-end is on Phosphodiester bond the right, unless otherwise labeled.
5’-ATCG-3’ Chargaff’s Rules B-Form DNA
http://higheredbcs.wiley.com/legacy/college/voet/0470129301/kinemages/exercise_2.html Figure 3-8 Computer-simulated space-filling model of DNA. Video: Computer-simulated space-filling model of DNA. SUMMARY
(34 Å)
Right-handed, antiparallel, double- sugar–phosphate stranded helix. With the “base backbone complementarity,” it explains genetic material: (phosphodiester • Storage of genetic information bonds) • Replication • Information retrival IntroductionCentral to Cells Dogma & Microscopy of Molecular Biology From DNA to Protein: Gene Expression
• Central Dogma: from Genes to Proteins • Replication of the genes (DNADNA) • Transcribing the information (DNARNA) • Translating the nucleotide sequence into protein sequence (RNAProtein) – The Genetic Code – Protein Biosynthesis Central Dogma
The central dogma of molecular biology
Replication
Information Flow Replication DNA replication is semiconservative (Meselson-Stahl Expt) DNA Replication
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. Each New DNA Strand Grows from Its 5´ End to Its 3´ End Each New DNA Strand Grows from Its 5´ End to Its 3´ End
ALL polymerases add nucleotides to the 3’ end (Direction is termed 5’ 3’)
Pyrophosphatase
34 Transcription Central Dogma
The central dogma of molecular biology
Replication
Messenger RNA (mRNA) Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
• What is the relationship between a DNA sequence and an amino acid sequence? Central Dogma
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 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! Transcription • Production of mRNA transcript by RNA polymerase Transcription: Where to start?
5' FlankingCoding Region 3'-flanking
Promoter
The consensus sequence for each element in human genes (N is any nucleotide) Transcription Translation Central Dogma
The central dogma of molecular biology
Replication
Messenger RNA (mRNA) Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
• What is the relationship between a DNA sequence and an amino acid sequence? • The Code • The Adaptors (tRNA) • The Ribosome (rRNA + rProteins) 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. 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 Translation: tRNA
Template for mRNA – read 3’5’
tRNA anticodon
NC 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. 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 Translation: Protein Biosynthesis; Elongation
EF-Tu GTP Decoding (GTP hydrolysis)
Peptidyltransferase Translation: Protein Biosynthesis; Elongation
ELONGATION
Translocation (GTP hydrolysis) Central Dogma
The central dogma of molecular biology
Replication
Animated videos of DNA structure and Central Dogma