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KIN 217

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Kin 217 – Lecture 2 Small Molecules • Carbohydrates • Lipids • Amino acids Fig. 1.2 Dark blue – nitrogen (proteins have N) Grey – carbons Macromolecules • Large structures made of smaller units -monomers • Polymers -Simple (ie: glycogen and starch) -Complex (ie: ptroteins amino acids, DNA) Proteins • Theses are polymers of 20 diff AA • Once they have been synthesized they fold into defined 3D structures • :pProteins rang in size (50-a lot) Fig 1.3 Dehydration rxn – losing water (carboxyl and amine group, lose water  dipeptide bond) Catalysis of rxn by enzyme proteins is central to the existence of life • Biological rxns tend not o occur spontaneously • Esseentially all events that occur in cells require a protein or proteins • Usually one protein catalyses a single rxn o Enzymes are usually very efficient catalysts • 20 AA X (35-several thousands in length) = A LOT of possibilities DNA • DNA: base-sugar-phosphate • DNA is made up of 4 nucleotides • Adenine (A) • Thymine (T) • Guanine (G) • Cytosine (C) Fig 1.5 • DNA and Information Flow • DNA can: -relicate -semiconservative (separation of strands and synthesis of individ strands) -Direct protein synthesis - 3 bases code for each AA -4 X 4X 4 = 64 diff combinations Protein Synthesis • DNA – mRNA – polypeptide – folded protein • RNA differ from DNA? • Different structures: primary, ternary, quaternary (review) Proteins and Genes • Each polypeptide chain is coded by a gene - proteins may contain more than 1 polypeptide chain • Changes in the DNA (mutations) result in changes in protein structure Evolution of proteins • Most mutations are unfavourable o Rare occasions when a favourable mutation occurs the organism is advantaged and selection occurs • Gene duplication allows mutation to occur in a way that is less likely to disadvantage the organism -ie: being heterozygous for sickle cell anemia makes you immune to malaria -ie: diabetes – in cold temp, protect against frostbite -ie: cystic fibrosis – protection against cholera Molecular recognition by proteins • Proteins have the capacity to bind to other molecules in a highly specific manner -includes recognition of growth actors and hormones, substrate binding by enzymes and gene regulation • This binding is readily reversible and is achieved via chemical bonds -ionic bonds -H bonds -van der Waals forces How did it all start? • Replication materials together -need to be contained • During the evolution of life the appearance of membranes must have been an early event • RNA has some catalytic activity o Could have catalysed its own replication o RNA vs DNA Fig 1.8 – phospholipids ( head – phosphate, tail – fatty acids) The new ‘Omics’ phase of biochemistry and molecular biology • Ie: genomic, proteomicsProtein and DNA databases have been established on an international basis o Genomics, proteomics • Vast amt of information - new science called bioinformatics -microarrays • Other areas -Transcriptomics, metablomics, lipidomics Chapter 2: Viruses and __ Cells are the units of all living systems • Bacterial cells tend to be small • Animal and plants cells larger o Volume is 1000X bigerr • Physical reason • Surface area to volume • Accommodate diffusion • Transport of macromolecules • Cells from higher org cannot rely on diffusion for macromolecule transport • Example mothra -insects rely on passive respiration -oxygen diffusion is absolute limit on insect size • Classifications of organisms • Prokaryotes • Bacteria • Eukaryotes • Fig 2.2 September 14 Wednesday, September 14, 2005 8:36 AM • Read Chapter 3 by Friday • 5% bonus o The person who asks the "tough" or "good" question gets the opportunity o Must answer the question and provide detail on the question in 10 min presentation in the next lecture o Class gives thumbs up/down for whether the person gets the 5% bonus o Individual can only do this once • Small molecules o Carbohydrates make up beer…what other molecules make up beer which we talked about? There were 3 major small molecules in biochemistry… • Water (although we leave this on its own since its so important) • Lipids Proteins/amino acids • o So in total: carbs, lipids, proteins/aa's • Fig 1.2 o The structure of compounds…and their components… o Grey --> carbons o Dark blue on L-alanine --> nitrogen…because proteins have nitrogens! • Macromolecules o OK these are larger structures made of smaller units… o The small repeating unit is a monomer… o Polymers… • Can be simple (a couple monomers)…or one kind of monomer repeated over and over  i.e. Starch is just glucose over and over…so glucose is the simple monomer • Complex  This is different kinds of monomers repeating over and over… • Proteins o Polymers of 20 different aa's o Once they have been synthesized they fold into defined 3D structures… o They can be from 50 amino acids to several thousand… • Fig 1.3 o Here we have a dehydration reaction…we're losing water… • Catalysis of reactions by enzyme proteins is central to the existence of life… o Enzymes are proteins and proteins are enzymes! And this is essential to life… o Because biological reactions don't occur spontaneously! o Essentially all events that occur in cells require a protein (or proteins!) o Usually, one protein catalyzes a single reaction…and enzymes are very efficient catalysts… biological systems need to be efficient! • Like…pharmaceutical companies try to develop stuff which can react very specif
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