1510 Biology Module #3 Part 1
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Book: Chapter 5: 5.15.5 Pages 6887 October 10, 2007 5.1
5.2
Polymer : a long molecule consisting of many similar or identical building blocks linked by covalent bonds Monomers : repeating units that serve as the building blocks of a polymer Condensation/dehydration reaction : a process in which monomers are connected by a reaction in which two molecules are covalently bonded to each other through loss of a water molecule Hydrolysis : a process that is essentially the reverse of the dehydration reaction... polymers break w/addition of water
Carbohydrates : include sugars and polymers of sugars o Simple carbs = monosaccharides (single sugars) ex: glucose o Disaccharide : consists of two monosaccharides joined by a glycosidic linkage a
o Polysaccharides : macromolecules Starch : storage polysaccharide of plantsglucose monomers Glycogen : animal storageglucose monomersmore branched than
starch
covalent bond formed btwn two monosaccharides by a dehydration reaction
Cellulose : major component of tough walls that enclose plant cellspolymer of glucosediffers from starch and glycogen b/c of linkage alpha and beta ring forms of glucose glucose switches from up to down Chitin : structural polysaccharide; used by arthropods to build exoskeletons; used by fungi
5.3
Lipids : do not consists of polymers; grouped together because they share one important trait little or no affinity for water (hydrophobic) o Consists mostly of hydrocarbons o Fats, phospholipids, and steroids o Not polymers, but large molecules o is constructed from two kinds of smaller molecules: glycerol and fatty acids Fat Glycerol = alcohol w/3 C each bearing a hydroxyl group
Fatty acid : long carbon skeleton; one end carboxyl group; attached to carboxyl group long hydrocarbon chain
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CH bonds are nonpolar Ester linkage : bond btwn hydroxyl group and carboxyl group 3 fatty acids + glycerol though ester bonds = tricylglycerol Saturated fatty acid: no double bonds btwn C atoms composing the chains as many H atoms as possible are bonded to the C skeleton Unsaturated fatty acid: one or more double bonds less H; kink in chain where double bond occurs
Phospholipids : similar to fats, but only have 2 fatty acids attached to a glycerol; 3rd hydroxyl group of glycerol is joined to a phosphate group (has negative charge); additional small molecules (usually polar) can be linked to the phosphate group o Hydrocarbon tails hydrophobic o Phosphate group hydrophilic o When in water, they selfassemble into a bilayer that shields their hydrophobic portions from water. Steroid : lipids characterized by a carbon skeleton consisting of 4 fused rings o Cholesterol : common component of animal cell membranes o Produces many hormones/other steroids Vary in the functional groups attached to their 4 rings
5.4 Proteins structure, speed up chemical reactions, storage, transport, cellular communications, movement, defense Enzyme : act as a catalyst in a chemical reaction Polypeptide : polymers of amino acids Protein : consists of one or more polypeptides Amino acids : organic molecules possessing both a carboxyl and amino group Peptide bond : covalent bond between amino acids A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape Protein's specific conformation determines how it works Four levels of protein structure: o 1) Primary structure: unique sequence of amino acids o 2) Secondary structure: segments of the polypeptide chain that repeatedly coil and fold into patterns that contribute to the proteins overall formation; result of H bonds helix: coil formed from H bonds btwn every 4th amino acid pleated sheet: 2 or more regions of the polypeptide chain lying side by side are connected by hydrogen bonds btwn parts of the 2 parallel polypeptide backbones 3)Tertiary structure: overall shape of the polypeptide resulting from interactions
o
btwn the side chains (R groups) of the various amino acids
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o
Hydrophobic interaction: amino acids w/hydrophobic (nonpolar) side chains usually end up in clusters at the core of the protein; once nonpolar amino acid side chains are close together, van der Waals interactions help hold them together Disulfide bridge: form where 2 cysteine monomers, amino acids w/sulfhydryl groups (SH) on the side chains, are brought together by the folding of the protein 4) Quaternary structure: overall protein structure that results from the aggregation of its polypeptide subunits; globular of chain
SickleCell Diseaseexample of what can happen w/even a simple change in the primary structure of a protein Protein conformation also depends on the physical and chemical conditions of the protein's environment Denaturation : change in the protein's native conformation due to alteration of the pH, salt concentration, temperature, or other aspects of the protein's environment. Chaperonins : protein molecules that assist in the proper folding of other proteins Xray crystallography : important method used to determine a protein's 3D structure
5.5
Gene : unit of inheritance Nucleic acids : polymer composed of nucleotides (nitrogenous base, pentose/5C sugar, and a phosphate group...portion w/o phosphate group=nucleoside) 2 families of nitrogenous bases: o Pyrimidines: 6 C ring fused to 5 C ring: cytosine (C), thymine (T), and uracil (U)
o Purines: larger; 6 C ring fused to 5 C ring: adenine (A), and guanine (G)
o Differ in functional groups attached to rings
Pentose connected to the nitrogenous base is ribose in the nucleotides of RNA and deoxyribose in DNA; differencedeoxyribose lacks O atom on the second C in the ring
Book: Chapter 6: 6.26.6 Pages 94, 98118 October 10, 2007 6.2
6.3
Eukaryotic cells vs prokaryotic cells
nuclear lamina : a netlike array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope
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6.4
endomembrane system : carries out variety of tasks int eh cell; includes nuclear envelope, ER, golgi apparatus, lysosomes, various kinds of vacuoles, and plasma membrane Smooth ER : synthesis of lipids, metabolism of carbs, and detoxification of drugs and poisons Rough ER : ribosomes attached to rough ER secrete proteins o Glycoproteins : have carb covalently bonded to protein o o After proteins formed, ER membranes keep them separate from the proteins produced by free ribosomes transport Vesicles proteins later on
Golgi apparatus : A Golgi stack has a distinct polarity, with the membranes of cisternae on opposite sides of the stack differing in thickness and molecular composition. The two poles of a Golgi stack are referred to as the cis face and the trans face; these act, respectively, as the receiving and shipping departments of the Golgi apparatus. o Cis face usually near ER
o Trans face : gives rise to vesicles o Cisternal maturation model : the cisternae of the Golgi progress forward from the
cis to the trans face of the Golgi, carrying and modifying their protein cargo as they move
Lysosome : membranous sac of hydrolytic enzymes that an animal cell uses to digest all kinds of macromolecules o Enzymes work best in acidic environments (inside lysosome)
o Phagocytosis : engulfing smaller organisms or other food particles o Autophagy : process in which a lysosoe use their hydrolytic enzymes to recycle
the cell's own organic material
Vacuoles : similar to lysosomes in that they carry out hydrolysis but they also perform other functions: o Food vacuoles : formed by phagocytosis
o Contractile vacuoles : pump excess water out of the cell (commonly found in
freshwater protests) ; maintain appropriate concentration of salts and other molecules Central vacuole : found in mature plant cells; enclosed by membrane called
o
tonoplast ; cell sap inside vacuole; disposal site for metabolic byproducts that would endanger cell if they accumulated in the cytosol allow plant cell to grow with minimal investment in cytosol ratio of membrane surface to cytosolic volume is great, even for a large plant cell because the vacuole takes up so much space
6.5
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mitochondria : sites of cellular respiration o found in nearly all eukaryotic cells o enclosed by two membranes o inner membrane has infoldings called cristae
o intermembrane spacearea between the inner and outer membranes o mitochondrial matrix : enclosed by inner membrane
o o
o
some of the metabolic steps in cellular respiration are catalyzed by enzymes in the matrix other proteins that function in respiration, including enzymes that makes ATP, are built into the inner membrane inner membranehigh surface area; enhances the productivity of cellular respiration
chloroplast : found only in plants and algae; sites of photosynthesis o plastids : family of related plant organelles; chloroplasts are a part of this family o contents partitioned from cytosol by envelope consisting of two membranes separated by very narrow intermembrane space thylakoid : interconnected sacs
o o granum : stacks of thylakoids o stroma : fluid outside the thylakoids; contain chloroplasts DNA and ribosomes +
many enzymes
peroxisomes : special metabolic compartment bounded by a single membrane o contain enzymes that transnfer hyrdrogen from various substrates to oxygen, producing hydrogen peroxide as a byproduct o also contains enzyme that converts hydrogen peroxide to water o glyoxysomes are specialed peroxisomes that are found in the fatstoring tissues of plant seeds o o o contain enzymes fatty acids to sugar unlike lysosomes, peroxisomes do not bud from the endomembrane system grow by: proteins in cytosol, lipids made by ER & by self can split when reach certain size
6.6 cytoskeleton is a network that organizes structures and activities in the cell composed of... o microtubules: thickest of the three types cytoplasm of all eukaryotic cells hollow; constructed of globular proteintubulin
shape and support; serve as tracks along which organelles equipped w/ motor proteins can move compressionresisting role responsible for separation of chromosomes during cell division
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o microfilaments (actin filaments) thinnest
solid rods; twisted double chain built from actin present in all eukaryotic cells bear tension (pulling forces) forms 3D network in cell, maintain shape bundle of them makes up core of microvilli
o
work w/myosin (thicker filaments) in protein cells to contract intermediate filaments: fibers w/diameters in middle range
more permanent than others roles of cytoskeleton o mechanical support in animal cellcan be quickly dismantled and recreated to change the shape of the cell cell motility (movement) changes in cell location and more limited movements of part of the cell
o
o
motor proteins : interact with cytoskeleton for motility regulation of biochemical activities in the cell can transmit mechanical forces exerted by extracellular molecules via surface proteins of the cell to its interior
in many cells, microtubules grow out from a centrosome: region often located near the nucleus that is considered to be a "microtubuleorganizingcenter" o w/in centrosome of an animal cell are a pair of centrioles: composed of nine sets o of triplet centrosomes of plant cells lack centriols
flagella and cilia: locomotor appendages that protrude from some cells o mainly in unicellular eukaryotic cells o the microtubule assembly of cilium or flagellum is anchored in the cell by a basal body which is structurally identical to a centriole in many plant cells basal body = centriole
dynein : large motor protein extending from one microtubule doublet to the next (protein that walks along skeleton) cytoplasmic streaming : circular flow of cytoplasm w/in cells; common in large plant cells; speeds the distribution of materials w/in the cell
Lecture: Macromolecules & Cell Structure October 10, 2007 4 main categories of macromolecules present in living systems are: proteins, nucleic acids, polysaccharides, and proteins Main monosaccharide used by human cells for energy: glucose All lipids...do not dissolve well in water
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Saturated vs. unsaturated fatty acids: o Saturated: all CC bonds are single...max # of Hsolid; animal fats temperatures; plant oils o Cholesterol decreases fluidity; more rigid Proteins o Categorized into nonpolar and polar
o Unsaturated: double bonds btwn C...creates a kink more fluid at low
o Structure: secondaryH bonds, primary sequence of amino acid, tertiary 3D
shape (created by van der Waals, H bonds, disulfide bonds, Ionic bonds Hydrogen bonds Hydrophobic interactions Hydrogen bonds Covalent Bonds Protein tertiary structure Alpha helices Lipid bilayer membranes Protein Tertiary Structure DNA duplexes
Sickle cell disease mutation affects what level of protein structure? A: All 3 Domains of Life: o Bacteria o Archaea o Eucarya Prokaryotes: o Circular genome Eukaryotes: o Linear chromosomes