Biochem

• DNA


  A kind of guidebook or a blueprint on how to build a life
• From plants to animals, DNA defines us all
• Deoxyribonucleic acid


  Folds itself into paired packages called chromosomes
• Chromosomes


  • Transmitted by and stored in the nucleus of the cells
  • Each species have different number of chromosomes
  • Humans have 46 chromosomes that contains our genes
• Meischer is the first to extract crude DNA
• Yeast extract crude extract of RNA
• Pork/Beef/Fruits/Saliva = extract crude extract of DNA
• Replication


  1. Breakdown of Double helix

  2. Transcription

  3. Translation
• Nucleic Acids


  • Vital biopolymers found in all living things
  • Function to encode, transfer, and express genes
  • Large molecules
  • First identified inside the nucleus cells
  • Also found in: Mitochondria, Chloroplast, Bacteria, Viruses
• Puranose


  5 carbons, pentagon
• Principal Nucleic acids


  • Deoxyribonucleic acid (DNA)
  • Ribonucleic Acid (RNA)
• Nucleic Acid


  • Unbranched polymers composed of repeating monomers called Nucleotides
  • A polynucleoride contains a backbown consisting of alternating sugar and phosphate group
  • The identity and order of the bases distinguish one polynucleotide from another (primary structure)
  • A polynucleotide has a one free phosphate group at the 5' end and one free OH group at the 3' end
  • Phosphodiester linkage joins the 3' C of one nucleotide to the 5' C of another nucleotide
• Nucleotide


  Formed by adding a phosphate groupt to the 5'-OH of a nucleoside
• 46 chromosomes: 23 pairs, each made up of many genes
• Each chromosomes contains one molecule of DNA
• Gene


  The portion of the DNA molecule responsible for the synthesis of a single protein
• RNA


  • Translates the genetic information contained in DNA into proteins needed for all cellular function
  • Contains few thousand of nucleotides
• Acronyms


  • AMP - Adenosine 5' monophosphate
  • GMP - Guanosine 5' monophosphate
  • CMP - Cytidine 5' monophosphate
  • UMP - Uridine 5' monophosphate
  • TMP - thymidine 5' monophosphate, not valid because RNA does not contain Thymine
  • dAMP - deoxyadenosine 5' monophosphate
  • dGMP - deoxyguanosine 5' monophosphate
  • dCMP - deoxycytidine 5' monophosphate
  • dTMP - deoxythymidine 5' monophosphate
  • dUMP - deoxythymidine 5' monophosphate, not valid because DNA does not contain Uracil
• DNA


  • Stores genetic Information of an organism and transmits that information from one generation to another
  • DNA molecules contain several million nucleotides while RNA molecules have only a few thousand
  • Contain in the chromosomes of the nucleus, each chromosome having a different type of DNA
• RNA


  Found primarily in the cytoplasm
• 1. Containing Base (Nitrogenous Base)


  • Pyrimidine - Cytosine, Uracil, Thymine
  • Purine - Adenine, Guanine
• Nucleoside


  Formed by joining the anomeric carbon of the monosaccharide with a N atom of the base
• DNA contains the sugar deoxyribose, while RNA contains the sugar ribose. The only difference between ribose and deoxyribose is that ribose has one more -OH group than deoxyribose, which has -H attached to the second (2) carbon in the ring.
• DNA is a double-stranded molecule, while RNA is a single-stranded molecule.
• DNA is stable under alkaline conditions, while RNA is not stable.
• DNA and RNA perform different functions in humans. DNA is responsible for storing and transferring genetic information, while RNA directly codes for amino acids and acts as a messenger between DNA and ribosomes to make proteins.
• DNA and RNA base pairing is slightly different since DNA uses the bases adenine, thymine, cytosine, and guanine; RNA uses adenine, uracil, cytosine, and guanine. Uracil differs from thymine in that it lacks a methyl group on its ring.
• DNA Double Helix


  • Initially proposed by Watson and Crick in 1953
  • DNA consist of two polynucleotide strands that win into a right-handed double helix
  • The two strand run in opposite direction; one runs from 5' end to the 3' end and the other runs from 3' end to the 5' end
  • The sugar-phosphate groups lie on the outside of the helix and the bases lie on the inside
  • The bases always line up so that a pyrimidine derivative can hydrogen bond to a purine derivative on the other strand
  • There are complementary base pairs that always hydrogen bond together in a particular manner
• Complementary Base Pairs


  • Adenine - Thymine (2 hydrogen bonds)
  • Cytosine - Guanine (3 hydrogen bonds)
• There is some evidence DNA may have occurred first, but most scientists believe RNA evolved before DNA.
• RNA has a simpler structure and is needed in order for DNA to function.
• RNA is found in prokaryotes, which are believed to precede eukaryotes.
• RNA on its own can act as a catalyst for certain chemical reactions.
• DNA evolved since having a double-stranded molecule helps protect the genetic code from damage. If one strand is broken, the other strand can serve as a template for repair. Proteins surrounding DNA also confer additional protection against enzymatic attacks.
• Unusual DNA and RNA

  • Branched DNA
  • Quadruplex DNA
  • Molecules made from triple strands
  • DNA in which arsenic substitutes for phosphorus
  • Double-stranded RNA (dsRNA) found in some viruses
  • Circular single-strand RNA (circRNA) found in both animals and plants
• Central Dogma of Protein Synthesis

  1. Replication - DNA makes a copy of itself when a cell divides

  2. Transcription - Ordered synthesis of RNA from DNA; genetic information stored in DNA is passed onto RNA

  3. Translation - Synthesis of proteins from RNA; genetic information determines the specific amino acid sequence of the protein
• Replication


  1. Original DNA molecule forms two new DNA molecules, each of which contains a strand from the parent DNA and one new strand

  2. Formation of Replication Fork - Helicase enzyme unwinds the DNA strands

  3. Synthesis of Lagging strand - Okazaki fragments joined together with aid of DNA Ligase

  4. Leading strand - Replicated towards the replication fork of the other template strand, starting from 3' end (3' to 5' end)
• The identity of the bases on the template strand determined the order of the bases on the new strand. Must pair: A-T and G - C.
• A new phosphodiester bond is formed between the 5' phosphate of the nucleoside triphosphate and the 3'- OH group of the new DNA strand.
• Replication occurs in only one direction on the template strand, from the 3' end to the 5' end.