Biochem LEC

• Enzymes


  Proteins that serve as biological catalysts for reactions in all living organisms
• Enzymes


  • Increase the rate of reaction (10^6 to 10^12 times faster), but are unchanged themselves
  • Very specific - each enzyme catalyzes a certain reaction or type of reaction only
  • Undergo all the reactions of proteins - can be denatured/coagulated by heat, alcohol, strong acids, alkaloidal reagents
  • Names of most enzymes end with the suffix -ase (e.g. peptidase, lipase, hydrolase)
• Cofactor


  Metal ion or organic molecule needed for an enzyme-catalyzed reaction to occur
• NAD+


  Cofactor that oxidizes lactate to pyruvate with the aid of the enzyme lactate dehydrogenase
• Properties of enzymes


  • Highly increases the rate of the reaction (10^6 to 10^12 times faster) without themselves being changed in the overall process
  • Very specific with the reaction it catalyzed
  • Formation of side product is rare
  • Have a very complex structure and is capable of being regulated
• Classifications of enzymes


  • Based on substrate (e.g. urease - urea, lactase - lactose, lipase - lipid)
  • Based on reaction they catalyzed (oxido-reductases, transferases, hydrolase, lyases, isomerases, ligases)
• How enzymes work


  1. Lowers the activation energy - energy required for a chemical reaction to occur

  2. Provides active site, a unique bonding surface, where the substrate, reactant molecule, binds into

  3. Enzymes contain an active site that binds the substrate to form an enzyme-substrate complex

  4. Once the reaction is complete, the catalyst will release the product/s

  5. There are 2 models to explain the specificity of a substrate for an enzyme's active site (lock-and-key model, induced-fit model)
• Catalytic activity of some enzymes

  • Depend only on the interaction between the active site and substrate
  • Other enzymes require non-protein component for their activity - known as enzyme cofactors (metal activators, coenzymes)
• Apoenzyme


  Enzyme, protein part, that lacks an essential cofactor
• Holoenzymes


  Formed by the combination of coenzyme and apoenzyme, intact enzymes with their bound cofactors
• Zymogens


  Proenzymes, inactive form of an enzyme that can be converted to the active form when needed
• Factors affecting rate of enzyme-catalyzed reaction

  • Substrate and enzyme concentration
  • Temperature (optimum temperature at which the rate of enzyme's activity is at maximum)
  • pH (optimum pH at which the rate of enzyme's activity is at maximum)
• Enzyme inhibitors


  • Bonds to the enzyme and alters or destroys the enzyme's activity
  • Inhibition can be reversible or irreversible
  • Noncompetitive inhibitor bonds to the enzyme but not to the active site
  • Competitive inhibitor has shape and structure similar to substrate, competes with the substrate for binding to the active site
• Enzyme levels as diagnostic tools

  Certain enzymes are present in higher amounts in particular cells, if these cells rupture and die, enzymes are released into the bloodstream and can be detected (e.g. creatine phosphokinase - heart attack, alkaline phosphatase - liver or bone disease, acid phosphatase - prostate cancer)
• Drugs that interact with enzymes

  • Penicillin (inhibits the enzyme that forms the cell walls of bacteria)
  • ACE (angiotensin-converting enzyme, causes blood vessels to narrow to increase blood pressure)
  • ACE inhibitors (prevent ACE's synthesis from its zymogen)
  • HIV protease (essential enzyme that allows the virus to make copies of itself)
  • HIV protease inhibitors (interfere with the copying, decreases virus population in the patient)
• Nucleic acids


  • Unbranched polymers composed of repeating monomers called nucleotides
  • DNA (deoxyribonucleic acid) stores the genetic information of an organism and transmits that information from one generation to another
  • RNA (ribonucleic acid) translates the genetic information contained in DNA into proteins needed for all cellular functions
• Sources of nucleic acids


  • Meat, fish, seafood, legumes, and mushrooms
  • More processed food = less nucleic acids
• Nucleotide monomers in DNA and RNA

  • Monosaccharide
  • N-containing base
  • Phosphate group
• DNA molecules contain several million nucleotides, RNA molecules have only a few thousand nucleotides
• DNA is contained in the chromosomes of the nucleus, each chromosome have a different type of DNA
• Gene


  Portion of the DNA molecule responsible for synthesis of a single protein
• Nucleosome


  DNA wrapped in histones
• Chromosome


  Collection of nucleosome
• Nucleosides


  • Nucleic acid + sugar (monosaccharide in RNA is the aldopentose D-ribose, in DNA is the aldopentose D-2-deoxyribose)
  • N-containing bases (cytosine, uracil, thymine are based on pyrimidine, adenine and guanine are based on purine)
  • Formed by joining the anomeric carbon of the monosaccharide with the N atom of the base
• Nucleotides


  • Formed by adding a phosphate group to the 5' OH of a nucleoside (e.g. cytidine 5'-monophosphate is CMP, deoxyadenosine 5'-monophosphate is dAMP)
  • ADP - adenosine 5'-diphosphate, ATP - adenosine 5'-triphosphate
• Nucleic acids


  DNA and RNA, polymers of nucleotides joined by phosphodiester linkages, polynucleotide contains a backbone of alternating sugar and phosphate groups, identity and order of bases distinguish one polynucleotide from another (primary structure), has one free phosphate group at the 5' end and one free OH group at the 3' end
• DNA


  • Sequence of bases carries the genetic information of the organism
  • Consists of two polynucleotide strands that wind into a right-handed double helix, two strands run in opposite directions
  • Sugar-phosphate groups lie on the outside of the helix and the bases lie on the inside
  • Bases always line up so that a pyrimidine derivative can hydrogen bond to a purine derivative on the other strand (complementary base pairs - adenine pairs with thymine with 2 hydrogen bonds, cytosine pairs with guanine using 3 hydrogen bonds)
• Information stored in DNA

  1. Used to direct the synthesis of proteins

  2. Replication - process by which DNA makes a copy of itself when a cell divides

  3. Transcription - ordered synthesis of RNA from DNA, genetic information stored in DNA is passed onto RNA

  4. 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 new molecule contains a strand from the parent DNA and one new strand

  2. Formation of replication fork as the two strands split apart

  3. Synthesis of lagging strand in segments known as Okazaki fragments

  4. Identity of the bases on the template strand determines the order of the bases on the new strand, A must pair with T, G must pair with C

  5. New phosphodiester bond is formed between the 5'-phosphate of the nucleoside triphosphate and the 3'-OH group of the new DNA strand, occurs in only direction on the template strand - from the 3' end to the 5' end

  6. New strand is either a leading strand - grows continuously, or a lagging strand - grows in small fragments
• RNA


  Monosaccharide is ribose, thymine base is not present instead Uracil base is used, single strand and smaller than DNA, has three types
• DNA replication


  1. Before replication

  2. Formation of replication fork

  3. Synthesis of lagging strand

  4. Final product
• Replication fork


  Forms as the two DNA strands split apart
• Lagging strand


  Replicated in segments known as Okazaki fragments
• DNA replication


  • Identity of the bases on the template strand determines the order of the bases on the new strand
  • A must pair with T
  • G must pair with C
  • New phosphodiester bond is formed between the 5'-phosphate of the nucleoside triphosphate and the 3'-OH group of the new DNA strand
  • Occurs in only direction on the template strand - from the 3' end to the 5' end
  • New strand is either a leading strand - grows continuously, or a lagging strand - grows in small fragments
• RNA


  • Monosaccharide is ribose
  • Thymine base is not present instead Uracil base is used
  • Single strand and smaller than DNA
  • Has three types: Ribosomal RNA, Messenger RNA, Transfer RNA
• Ribosomal RNA


  • Provides the site where polypeptides are assembled during protein synthesis
• Messenger RNA


  • Carries the information from DNA to the ribosome
• Transfer RNA


  • Bring specific amino acids to the ribosomes for protein synthesis
  • Drawn as a cloverleaf shape, with an acceptor stem at the 3' end (carries the amino acid) and an anticodon (identifies the needed amino acid)
• Transcription


  1. Splits into two strands - template strand used to synthesize RNA, information strand not used

  2. Proceeds from the 3' end to the 5' end of the template

  3. Forms a mRNA with a complementary sequence to the template DNA strand and an exact sequence as the informational DNA strand

  4. Base U replaces T on mRNA
• Genetic code


  • Sequence of three nucleotides codes for a specific amino acid
  • Each triplet is called a codon
  • Codons are written from the 5' end to the 3' end of the mRNA molecule