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Chapter 3

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Lovaye Kajiura

Biology Chapter 3: Protein Structure and Function Beginning of Life  Theory can be broken down into four steps o Chemical evolution began with production of small organic compounds o Simple organic compounds reacted to form mid-sized molecules called amino acids, sugars and nitrogenous bases  Accumulated in the waters of ancient oceans, forming prebiotic soup o Mid-sized building block molecules linked to form the types of large molecules found in cells today (proteins, nucleic acids, complex carbohydrates) o Life became possible when one of these large, complex molecules acquired the ability to self-replicate Functions of Proteins Function Protein Type Role in Cell or Organism Defence Antibodies and Destruction of disease causing viruses and complement proteins bacteria Movement Contractile proteins and Moving the cell itself or for moving large motor proteins molecules and other types of cargo inside the cell (Actin and myosin) Catalysis Enzymes Catalyze chemical reactions (salivary amylase) Signalling Hormones/Receptor Act as signals that help coordinate the proteins activities of many cells Receive chemical signals from outside cell and initiate response Structure Structural proteins Provide support for cells and tissues; form structures such as hair, feathers, cocoons and spider webs Keeps cells flexible and in their normal shape Transport Transport proteins Move substances across cell membrane and throughout body (haemoglobin) Origin of Life Experiments  Miller experimented to see if complex organic compounds could be synthesized from simple molecules present in Earth’s early atmosphere and ocean  Large glass flask containing methane, ammonia and hydrogen, all of which have high free energy  Connected to a smaller flask by glass tubing; flask held liquid water (ocean) o Miller boiled water constantly so water vapour was added to mix of gases in large flask and as vapour cooled and condensed, it would flow back into small flask  Miller sent electrical discharges across the electrodes he had inserted into the atmosphere (lightning) o Added pulses of intense electrical energy  After some time, the solution in the boiling flask became pink, then red and cloudy  He found large quantities of HCN and H CO a2 well as several complex carbon-carbon compounds and most importantly, amino acids  Results and those of subsequent researchers supported chemical evolution  Other hypotheses included hydrothermal vents and meteorites Amino Acids  All 21 amino acids have a similar backbone structure o Central carbon attached to a NH func2ional group, a COOH functional group, a hydrogen atom and an R group  At pH 7, amino group gains a proton to become NH and c3rboxyl group loses a proton to become COO (zwitterion)  Amino acids with nonpolar side chains cannot form hydrogen bonds with water and thus are hydrophobic o Tend to coalesce in aqueous solution  Amino acids with polar or charged side chains interact readily with water and are hydrophilic o Dissolve easily in water  Nature of side chain influences chemical reactivity o R groups consisting of mainly carbon and hydrogen atoms rarely participate in chemical reactions  Chemical behaviour thus depends primarily on size and shape o R groups containing hydroxyl, amino, carboxyl or sulfhydryl functional groups are more reactive Isomers  Structural isomers o Same atoms, but differ in order in which covalently bonded atoms are attached  Geometric isomers o Same atoms, but differ in the arrangement of atoms or groups on either side of a double bond or ring structure (trans vs. cis)  Optical isomers o Same atoms, but differ in arrangement of atoms or groups around a central carbon atom that has four different groups attached (mirror images) o In cells, only the “left handed” form of amino acids exist o If the right handed form is introduced, the cell does not function properly  Real world example o L-Dopa and D-Dopa to treat Parkinson’s Disease o Thalidomide  One optical isomer prevented morning sickness  Other optical isomer inhibited blood vessel development, leading to birth defects  Investigations on implementing it for cancer research (therapeutic use)  Targeting thalidomide to cancer tumours by blocking the nourishment of blood from reaching cancer cells  Will be able to alleviate bad side effects from using other methods such as chemotherapy or radiation Polymerization  Amino acids (monomers) link to form proteins (polymers) through polymerization  Condensation reaction occurs, water as biproduct  Reverse reaction is hydrolysis, water breaks the polymer  Peptide bond is formed from the C-N bond between the carboxyl and the amino group  When amino acids are linked by peptide bonds into a chain, the amino acids are referred to as residues and the resulting molecule is called a polypeptide  Three points about the polypeptide backbone o Side chains present in each residue extend out from it o It has directionality  Amino group on left end (N-terminus) and carboxyl group on right end (C- terminus) o It is flexible  Polypeptides with fewer than 50 amino acids are called oligopeptides or peptides Protein Structure  Proteins can serve diverse functions in cells because they are diverse in size and shape as well as in chemical properties of their amino acids  Primary s
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