BIOA10-Module 2 Exam notes.docx

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Biological Sciences
Clare Hasenkampf

BIOA10 LECTURE CH.1 Chemical Composition of Cells -whether living or non-living, made up of chemicals -H20 is the most important, abundant small molecules (because life occurs in water (aqueous) environment) Macromolecules: - mostly composed of six elements ( C,H,O,N,S,P) -different combinations to form four major classes of macromolecules: - Lipids, Carbohydrates, Proteins, Nucleic acids -Carbon, Hydrogen, Oxygen- - Macromolecules have carbon as one of their elements (organic chemistry) Proteins - most abundant category of large macromolecules. - monomer units are amino acids -workhorses of the cell: -acts as enzymes (catalysts that drive chem.. rxn) -provide structural features of cell (microtubules, intermediate filaments) -serve as signal molecules -help other proteins to achieve their final shapes -impart movement to cells / cellular structures (transportation) -serve as recognition or receptor molecules at cells surface -Proteins are polymers - are polymers made up from 20 different A.A -formed by polypeptides bond. -bonded via condensation (dehydration) -covalent bonded -Form different dimensional shapes Polypeptide: (Greater than 50 A.A bonded together) -one free end of peptide is an A.A (amino terminus, or N-terminus) < N-H 2 -one free end of peptide is carboxyl group ( carboxyl terminus, or C terminus) -COOH Week forces of Interactions in Polypeptides: -week forces, therefore easy to disrupt by environmental conditions -e.g. 1)Heat 2)changes in pH -will be denatured by change its shape and loses its function -can get back into their shape when heat/pH changed back to normal (some proteins need help) Protein Structures: Precise order of A.A determines shape and function of protein Polypeptides will spontaneously fold up into 3D shaped by many types of interactions -Primary Structure (linear A.A) < not usually. Usually in third dimensional - a chain of A.A, quite stable (all bonds are covalent bond) -Secondary: Alpha helix or Beta pleated sheet -linked by hydrogen bond between the nitrogen+O +H (interaction of R group) 2 2 -Tertiary: -range of bonding interactions on R-groups 1) ionic bonds 2)Hydrogen bonds 3)Hydrophobic 4)disulphide bond -conformation -Quaternary: -two or more polypeptide combined -interactions of / disulphide / polar and nonpolar th - e.g. Hemoglobin (four polypeptide with 4 structure) -most enzymes have quaternary structure -Prosthetic Groups: non-protein components that required by proteins -covalently added on the polypeptides -included carbohydrates, lipids, phosphate group/metal ions -e.g. hemoglobin: O b2und to molecule (heme) specifically Chlorophyll: require metal-containing prosthetic groups Examples of Proteins with Prosthetic group: 1) Hemoglobin: - Heme is the prosthetic group, an iron containing molecules (non-protein) -Iron of heme molecules: responsible for hemoglobin to reversible bind O 2 - Covalently bound to globin proteins 2) Ligand: (e.g. Hormones) -molecules that bind non-covalently to its receptor site on protein -binding of ligand: -changes conformation of the receptor -move it into its active form Structural Proteins : 1) Cytoskeletion: major components of plant and animals cells 2) Microtubules: tracks for direct motor proteins (pull vesicles/chromosomes) 3)Intermediate Filaments: -Structural support elements of cells, relatively stable 4) Microfilaments: Important for structure, can changed rapidly Influence cell shape + amoeboid type motion Required for directing big changes of cell mem. shape Un-repairable proteins: -will be broken down into A.A, then recycled to make new protein Improper Shaped Proteins: - not function well / causes trouble in itself -e.g. Alzeihmers disease (misfiled proteins accumulate in brain) Mad cow disease/ prion diseases Size and functions of Protein: -Size of Polypeptide: determined by # of amino acids it contains -Shape + Function of Proteins: determined by which specific A.A are presented determined by the specific order of A.A Conformation: -the distinctive three dimensional shapes (special bonding arrangement -displays limited shape changes (which critical to the function of the protein) Chaperonin Protein : -Proteins that help other proteins to obtain their correct final shapes -interior of Chaperonin complex provides environment for proper folding -Specialize in recognizing denatured proteins (can help them back to proper shape) Amino Acids -different in R group ( fourth group of atoms attached to central (alpha carbon)) - each A.A has its own unique chem.. properties because different in side links 1) +ve/-ve charged 2) acts as acid/base -carboxylic acid (H-C-OH)+ Hydrogen + amino group (H-N-H)+r group Amino acids in aqueous environment: - nitrogen group gains proton (+ve charged) - carbon of carboxyl group loses proton (-ve charged) Condensation(dehydration) -water is lost, peptide linkage (single A.A bond with single A.A) -peptide bond is a covalent bond - 2 A.A bonded (dipeptide) 3 A.A bonded (tripeptide) -many A.A bonded (polypeptide) Cell Connections : 1) Plant Cells: -direct contact with neighbor cells via plasmodesmata 2) Animal Cells: -Many cells may separated/not in direct contact b/c extracellular matrix (ECM) -Common situation, neighbor cells are not in direct cytoplasmic contact 1) Anchoring Junctions: -Hold two cells together, not tightly - Can expand/contract without disrupting junction - Cells can squeeze between (not tight) 2) Tight Junctions: - series of connections that hold 2 cells closely together - Cells cannot pass between two cells 3) Gap Junctions: Protein tunnel, connect cytoplasm of neighbor cells - allow rapid communication between two cells Extracellular Matrix (ECM): - Connection of proteins and carbohydrates (secreted by cells) CH.2 Nucleic Acids : -two types of nucleic acids: DNA and RNA ( Deoxyribonucleotides & Ribonucleotides) -DNA and RNA are examples of polymers (made by bonding monomer units via condensation) - Ribonucleotides (monomers) held by covalent bonds (phosphodiester linkages) - monomer units: Nucleotides Nucleotides: - all elements are connected with covalent bonds (Strong) -to regulate and adjust cellular activities (not directly) -e.g. ATP (adenosine triphosphate), GTP (Guanosine triphosphate) -energy stored in pyrophosphate bond (covalent bond between adjacent monomers) -active form: nucleoside triphospahte -made by 3 different chemical groups 1) 5-carbon, ring sugar (Pentose) 2) Phosphate group th -attached to 5 carbon of sugar
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