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This 7 page Class Notes was uploaded by Shira Clements on Wednesday February 17, 2016. The Class Notes belongs to BSCI105 at University of Maryland taught by Norma Allewell in Fall 2015. Since its upload, it has received 16 views. For similar materials see Principles of Biology I in Biology at University of Maryland.
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Date Created: 02/17/16
Shira Clements BSCI105 Chapter 5- The Structure and Function of Large Biological Molecules Macromolecules- huge molecules - Carbohydrates, proteins, nucleic acids Polymers- long molecules (macromolecule) consisting of many similar building blocks linked by covalent bonds (with loss of water molecule)- Lipids don’t have polymers - Monomers- the repeating unit, smaller units of polymer - Breaking and making polymers are facilitated by enzymes- macromolecules that speed up chemical reaction - Dehydration reaction- when a bond forms between two monomers, each monomer contributes part of the water molecule that is released during the reaction- one monomer provides hydroxyl group (-OH), other monomer provides hydrogen group (-H)- repeated as monomers are linked to make polymer - Hydrolysis- dissembles polymers into monomers- reverse of dehydration reaction o Break polymers by adding water- H from water attaching to one monomer and hydroxyl group attaching to adjacent monomer o Digestion is an example - Huge variation of polymers- each cell has so many even o 40 to 50 monomers in common monomers, so arrangement matters (like letters in words) Carbohydrates- include sugars and polymers of sugars - Monosaccharides- simple sugars (end in –ose), monomers from which more complex carbohydrates are made o Usually have molecular formula that is multiple of CH O 2 Glucose (C H 6 12 6rademarks of a sugar in the makeup with carbonyl group (C=O) and multiple hydroxyl groups (-OH) aldose sugar (carbonyl group at end of carbon skeleton) while fructose is a ketone sugar (carbonyl group within carbon skelton) 6 C so hexose- a ring shape nutrients for cells- extract energy starting with glucose can help with synthesis of other organic molecules such as fatty and amino acids o ranges from 3-7 Cs long o diversity also stems from the placement of parts around C - Disaccharides- two monosaccharides joined by glyscosidic linkage- covalent bond formed between two monosaccharides by dehydration reaction o Maltose- two glucose together o Sucrose – glucose and fructose - Polysaccharides- macromolecules, polymers with hundreds of monosaccharides formed by glyscodic linkage o Storage material, provides sugar for cells o Building material for structures that protect cell o Plants store starch- polymer of glucose monomers- as granules within cellular structures known as plastids (include chloroplasts) Synthesizing starch helps plant store excess glucose Starch is stored energy basically and get be accessible through hydrolysis or enzymes that can hydrolyze plant starch- glucose would be available as nutrients for cell 1-4 linkages of C usually o Animals store polysaccharides called glycogen- polymer of glucose that is like amylopectin but with more branches Store in liver and muscle cells Hydrolysis releases glucose when demand for sugar increases- depletes in day and then replenishes from food (so concern of low-carb diet) - Structural Polysaccharides- cellulose- major component for the toughness on the cell walls Polymer of glucose but the glysosidic linkages differ- glucose monomers in cellulose is in beta configuration (while it is in the alpha configuration in starch), so every glucose monomer is upside down. Cellulose is never crooked Some hydroxyl groups on end of glucose can hydrogen bond with hydroxyl of other cellulose monomers parallel to it- called microfibrils (important for plants and humans because cellulose is major constituent of paper and only component of cotton) o Alpha and beta placements really matter- enzymes that digest starch with alpha linkages can’t digest one with beta linkages. Few organisms have enzyme to digest cellulose, but still important in diet (helps with mucus) o Chitin- carbohydrate used by insects to build exoskeleton- hard case that protects soft parts of animal. Similar to cellulose with beta linkages except that glucose monomer of chitin has a nitrogen containing addition Lipids- one class of large biological molecules that does not include true polymers (not big enough to be a macromolecule) - Mix poorly with water (hydrophobic)- mostly hydro-carbon regions - Wax in pigments - Fats- large molecules from smaller molecules by dehydration reactions o Glycerol (alcohol- 3 C bears hydroxyl) and fatty acids (long carbon skeleton with carboxyl group at end- rest is hydrocarbon chain, so hydrophobic because hydrogen bonds to one another and exclude the fats) o Ester linkage- fatty acids are joined to glycerol by this- results in triacylglycerol A bond between hydroxyl and carboxyl group o Structure of hydrocarbon chain of fatty acids- Saturated fats- no double bonds (so flexible and can pack many together) between carbon atoms with however many hydrogens attached- saturated fatty acid- most animal fats- solid at room temp Unsaturated fatty acid- one or more double bonds with one fewer hydrogen on each doubly bonded C (cis double bonds which cause kink in hydrocarbon)- most plant and fish- liquid at room temp because kink doesn’t allow it to solidify Can cause heart disease- plaques impede blood flow and reduce resilience of vessels Is not made in human body so people must bring some in- omega-3 (against cardiovascular disease) o Major functions are energy storage and cushion for organs - Phospholipids- essential for cells because they make up cell membrane o Similar to fat but only has two fatty acids attached to glycerol instead of 3- 3 hydroxyl group is joined to phosphate (neg charge in cell) and charged molecules can be joined to phosphate to give a variety of phospholipids o Hydrocarbon tail is hydrophobic, while the phosphate group is a hydrophilic head, so when added to water, they self assemble into bilayers- shielding hydrophobic from water- two phospholipids on top of each other - Steroids- lipids characterized by a carbon skeleton consisting of 4 fused rings o cholesterol- crucial molecule in animal’s cell membranes precursor from which other steroids are synthesized liver and contained through diet high level in blood can contribute to disease Proteins- every living thing depends on proteins, 50% of dry mass in cell - unbranched polymers made from same set of 20 amino acids - some speed up chemical reactions and others defend, store, transport, communicate, move, and give structural support. - Catalysts- enzymes, which are proteins, that regulate metabolism by speeding up reaction and not getting consumed - Polypeptides- polymers of amino acids, o protein consists of one or more of them- folded and coiled into 3D structure - Amino Acid Monomers- organic molecule that has amino group and carboxyl group and in middle is the alpha C (symmetrical) also connected to H and a variable- side chain makes amino acid unique which are usually negative because of carboxyl group which is usually ionized (dissociated) at cellular pH, but basic amino acids are usually positive. o All amino acids have carboxyl group and amino group o Acidic and basic are only determined by side chains- hydrophilic - Peptide bond- two amino acids are positioned next to each other so the carboxyl group of one is next to the amino acid of the other, this covalent bond occurs by dehydration reaction (with removal of water bonds) o Amino acids are connected and one end of polypeptide has free amino group (N terminus) and other end has free carboxyl group (C terminus) o Chemical nature is determined by side chains because there are so many of them - Function results from 3D architecture- proteins are a few polypeptides precisely twisted, folded, coiled into a unique shape- amino acid sequence determines structure under normal circumstances o Chain folds when polypeptide forms getting structure for protein Folding is driven by bonds between parts of chain, which in turn depends on amino acids o Structure depends on ability to recognize and bind to other molecules - 4 Levels of protein structure- o Primary structure- linked series of amino acids with a unique sequence (order of letters in long word)- precise structure is determined by inherited genetic information Sickle cell is a disease caused by a substitution of one amino acid for another in hemoglobin, causing blood cells to crystalize and be sickle shape instead of disk shape o Secondary Structure- the coils and folds in polypeptide chains from hydrogen bonding (O has partial neg charge and H has partial + charge and together can support shape of protein) between repeating constituents of polypeptide backbone. Alpha helix is a type of coil between every 4 amino acid. Beta pleated sheet- type of structure where two chains lying side by side as connected through H bonding between polypeptide backbones o Tertiary Structure- overall shape of polypeptide result from interactions of side chains Hydrophobic interaction-polypeptide folds into function shape and amino acids with the nonpolar parts end up in the core of protein and van der Waals interactions help hold them together, and the polar bonds between side chains and amino acids also help hold the polypeptide together. All weak interactions but together it’s fine. Disulfide Bridges- type of covalent bond that might help hold shape of protein o Two cysteine monomers- sulfhydryl groups (- SH) are brought close together by folding protein- S of one bonds to S of other, so disulfide bridge fastens protein together o Quaternary Structure- overall protein structure that results from aggregation of all polypeptide subunits o Overall- a polypeptide chain of given amino acids sequence can spontaneously arrange itself into a 3D shape determined and maintained by interactions responsible for secondary and tertiary structure. Fold occurs as protein is being synthesized in crowded environment within a cell. But, also depends on physical and chemical conditions around- if aspects are altered, then bonds are weak and whole protein will denature- fall apart and lose native shape and become inactive. When denaturing agent is removed, the protein can sometimes reform. o Folding- chaperonins- protein molecules that help proper folding in proteins by keeping new polypeptide separated from “bad influences” in the cytoplasmic environment when it folds spontaneously- puts cap over hole so nothing besides for the polypeptide can get in. Misfolding causes diseases Structure is also very detailed and can be figured out by using xray crystallography Gene- unit of inheritance - amino acid sequence of polypeptide that programs primary structure - consists of DNA, which is a Nucleic Acid- polymers made of monomers called nucleotides Nucleic Acid- two types- DNA and RNA- that enable living organisms reproduce their complex components from one generation to next - DNA- provides directions for own replication o Directs RNA synthesis, and then, can control protein synthesis o Genetic material that organisms inherit from parents o Each chromosome contains one long DNA molecule (carrying numerous genes) o When cell reproduces, DNA copies and travels on to the next generation too o Proteins are needed to implement to genetic program o Synthesis occurs in ribosomes, but DNA is in nucleus - RNA- each gene on DNA directs the creation of mRNA (messenger RNA), which communicates with proteins to make a polypeptide which will fold into part of a or a full protein. It also conveys genetic instructions for building proteins from nucleus to cytoplasm (or for prokaryotes, from parts that translate coded information into amino DNA to mRNA to acid sequences). protein - Macromolecules that exist as polymers called polynucleotides - Nucleotide- composed of 3 parts- nitrogen containing base (nitrogenuous), 5 C sugar (pentose), one or more phosphate group. Nucleotide without phosphate is nucleoside- just nirtorgen base and sugar. o Nitrogen base- one or two rings including N and tend to take up H+ Pyrimidines- has one 6 membered ring of C and nitrogen atoms- cytosine, thymine, and uracil. Purines- larger with 6 membered ring fused to 5 member ring. nd o Sugar- DNA=deoxyribose (lacks Oxygen in 2 C ring), RNA=ribose o Phophate group- add to 5’ carbon of sugar and now nucleotide o Adjacent nucleotides are joined by a phosphodiester linkage- phosphate group that links sugar to two nucleotides- creates backbone for repeating pattern of sugar-phosphate units (nitrogen bases are not part of backbone). One end has a phosphate attached to a 5’ C and other has a hydroxyl group attached to 3’ C (5’ C end and 3’ C end) goes from 5’ end to 3’ end- along the backbone are additions consisting of the Nirtrogen bases o Genes are thousands nucleotides long and each different one means something else RNA molecules- single polynucleotide chain - Base paring of RNA allows it to become 3D and function - A (adenine) runs with U (uracil), and T (thymine) is not in RNA - Variable in shape DNA molecules- two polynucleotide chain that spiral around an axis- forming a double helix (held together by hydrogen bonds). - Sugar phosphate are on outside and nitrogenous bases are on inside of helix. - RNA and DNA run in opp directions- one has 5’ C to 3’C and other has 3’ to 5’ C- aka antiparallel - A (adenine) always pairs with T (thymine), G (guamine) always pairs with C (cytocine) on the opposite helix- complement each other, which makes it possible to generate two of the same DNA molecules when dividing. - Always double helix