Chapter 5 The Structure & Function of Large Biological Molecules PDF

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What are the structures and functions of the 4 important classes of biological molecules? Carbohydrates: source of energy and provide structural support a. Monomer: Glucose Proteins: wide range of functions such as catalyzing reactions and transporting substances into and out if cells b. Monomer: Amino Acid Nucleic Acids: store genetic information and function in gene expression c. Monomer: Nucleotide Lipids: provide energy, makeup cell membranes, and act as hormones *Classes 1-3 are macromolecules that are polymers made up of monomers. Lipids are NOT polymers and they are NOT macromolecules Concept 5.1 How would we expect these large molecules to behave under certain conditions? Macromolecules- large carbohydrates, protein, and nucleic acids; form polymers Polymer- a  long molecule consisting of similar or identical building blocks linked by covalent bonds (the whole train) - Nature of polymers is based on nature of monomers (the repeating units) - Built through dehydration synthesis/reaction - Broken down by hydrolysis Monomer- r epeating units that serve as the building blocks of a polymer (the train cars) How do we generate macromolecules? Polymerization- how cells make polymers (chemical mechanisms)

Condensation reaction- when two molecules are covalently bonded to each other with the loss of a small molecule Dehydration reaction- when a water molecule is lost during a condensation reaction - When 2 monomers bond together through the loss of a H2O molecule - The resulting covalent bond is formed through the removal of a hydroxyl group of an H atom - Every monomer (subunit) joined together results in the generation of H2O molecule - Enzymes are needed to help hold the monomers in close proximity to one another, in order to ensure that the correct bonds are broken Hydrolysis- when the bond between monomers is broken by the addition of a water molecule (reverse of dehydration) (can be used to generate monomers) i.e in the digestive system where enzymes attack polymers of food, speeding up hydrolysis, in order for the monomers of food to be digested and released/absorbed into the bloodstream to be distributed throughout the body *Dehydration reactions and hydrolysis can be also involved in the formation/ breakdown of non-polymer molecules (i.e lipids) -

The length of a polymer can contribute to how it may fold or interact with itself if found in close proximity to each other, but the sequence is essential

How would you expect to take large biological molecules and break them down? What would you yield?

Concept 5.2 Carbohydrates- sugars and polymers of sugars Monosaccharides- simplest carbohydrates(simple sugars); the monomers of more complex carbohydrates - Contains a carbonyl group (>C=O) and multiple hydroxyl groups (─OH) -

The C-H bonds in carbs make them ideal for energy storage (can be released through oxidation) The position of the carbonyl group in the ring structure allows carbon to exist in 2 different forms

Can vary in: 1) The location of the carbonyl group - Can either an a  ldose (aldehyde sugar) or a ketose (ketone sugar) 2) Length - The carbon skeleton ranges from 3-7 carbons long (Hexoses[6], Trioses[3], and Pentoses[5] are common) 3) Arrangement around asymmetric carbons - can differ simply in the way their parts are arranged spatially around asymmetric carbons -

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Generally have molecular formulas that are a multiple of CH2O (i.e G  lucose= C6H12O6 ) Glucose is the most common monosaccharide/ central importance in the chemistry of life* In aqueous solution, glucose molecules and most other 5-6 C sugars, form rings, because this is the most stable form of sugar for them under physical conditions*

Disaccharide- consists of two monosaccharides joined by a glycosidic linkage Glycosidic linkage- a covalent bond formed between two monosaccharides by a dehydration reaction - Most prevalent disaccharide is sucrose (table sugar)(glucose & fructose) - Disaccharides must be broken into monosaccharides to be used for energy by organisms - i.e Lactose intolerance is due to the lack of lactase, the enzyme that breaks down lactose. The sugar is instead broken down by intestinal bacteria, causing formation of gas and cramping - Can be treated by 1) taking lactase supplements or 2) consume lactose-free products Dehydration reaction in the synthesis of maltose -joining the glucose monomers in a different way would result in a different disaccharide - putting sugar into water will not cause hydrolysis (it doesn’t dissociate, it just dissolves - the OH is an entire hydroxyl group, and the H atoms is part of a hydroxyl group - this event will occur in the presence of an enzyme, which will allow for the components of each glucose to dissociate Dehydration reaction in the synthesis of sucrose - The difference between the 1-4 and 1-2 linkages, has to do with the position in which the components are found on each sugar

Oligosaccharides - more than 2 but less than a forever changing number of subunits that are bonded together

Polysaccharide- macromolecules with many polymers linked through dehydration reactions, which form glycosidic linkages (covalent bond) - Some serve as storage material, hydrolyzed as needed to provide monosaccharides for cells - Others serve as building material for structures that protect the cell or the whole organisms - structure and function are determined by its monosaccharides and the positions of its glycosidic linkages Starch- a polymer of glucose monomers; stored by plants - Most animals, including humans, can hydrolyze plant starch, making plant starch available as a nutrient for cells - Most of the glucose monomers in starch are joined by 1-4 linkages (i.e maltose) - These numbers indicate which C positions are participating in that covalent bond - Starch can readily react with water, which allows for hydrolysis and release of energy that a plant can use to drive its own cellular events Amylose, the simplest form of starch, is unbranched Amylopectin, a more complex starch, is branched with 1-6 linkages Glycogen- a polysaccharide stored by animals, a polymer of glucose - Vertebrates store glycogen mainly in: - The liver to be used as a source of glucose to help maintain blood sugar levels - Muscle cells to be used as a source of fuel to generate ATP molecules which is needed for muscles contraction - However this stored fuel cannot sustain an animal for long (i.e in humans, glycogen stores are depleted in about a day unless they are replenished by eating, an issue in low-carb diets) -

Both starch and glycogen are readily hydrolyzed into their monomers, which can also be broken down more in order to release the energy stored in their bond - In both scenarios, the organization of both polysaccharides allows for the ease of breaking the covalent bonds and acquiring the potential energy that was stored there

Cellulose - polymer of glucose; the most abundant organic compound on Earth - Never branched, but some hydroxyl groups on its glucose monomers are free to H-bond with the hydroxyls of other cellulose molecules lying parallel to it

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The parallel branching of cellulose makes them more suitable as structural material (high level of rigidity)

- The difference in spacing between cellulose and starch impacts the ability of certain enzymes to hydrolyze those glycosidic linkages and access the monomers - The cellulose in our food passes through the digestive tract and is eliminated with the feces→the cellulose abrades the wall of the digestive tract and stimulates the lining to secrete mucus, which aids in the smooth passage of food through the tract -

Humans are not able to hydrolyze the beta linkages in cellulose (but we can digest the alpha linkages in starch)

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Some microorganisms can digest cellulose, breaking it down into glucose monomers - i.e A cow harbors cellulose-digesting prokaryotes and protists in its gut. These microbes hydrolyze the cellulose of hay and grass and convert the glucose to the other compounds that nourish the cow - A termite has the same cellulose-digesting prokaryotes, which allows it to turn wood into food

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This all relates to form and function, as the alpha and beta linkages are not one size fits all Chitin - carbohydrate used by arthropods to build their exoskeletons (hard cases that surround the soft parts of an animal - Also found in fungi, which use it to build their cell walls rather than cellulose -

How are chitin and cellulose similar/ different? - They both have β linkages - The glucose monomer of chitin has an N-containing attachment

Concept 5.3 Lipids - the one class of large biological molecules that do not include true polymers - Are not macromolecules because we cannot take any monomers and link them together through dehydration synthesis reactions a limitless amount of times - Hydrophobic because they contain mostly hydrocarbon regions with relatively non-polar C-H bonds (although they may have some polar bonds associated with oxygen) - Nonpolar - Relatively insoluble in water Fats - consists of a glycerol  m  olecule joined to 3 fatty acids (triacylglycerol) (triglyceride) - Not polymers; they are large molecules assembled from smaller molecules by dehydration reactions

Glycerol - an alcohol, where each of its 3 C’s bears a hydroxyl group - The major function of fats is long term energy storage

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Stored in adipose cells Can also be used to cushion our organs and insulate our body

Fatty Acid - has a long C skeleton (usually 16 or 18 carbon atoms in length) - The carbon at one end of the skeleton is part of a carboxyl group, which gives it the name fatty acid - In making a fat, each fatty acid molecule is joined to a glycerol group by a dehydration reaction - Results in an ester linkage, a bond between a hydroxyl group and a carboxyl group - The fatty acids in a fat can all be the same, or they can be 2 or 3 different kinds - can vary in respect to length and presence of double bonds (amount and location) Saturated fatty acid - If there are no double bonds between C atoms composing a chain, then as many H atoms as possible are bonded to the C skeleton (saturated with H) - no space for C to double bond with each other - This helps stabilize the fat and reduce its ability to move around, because the fats are so tightly packed together - Solid at room temperature, will liquify if the temperature increases (i.e lard or butter) - This is because the kinks where the cis double bonds are located prevent the molecules from packing together closely enough to solidify at room temperature Unsaturated fatty acid - has one or more double bonds, with one fewer H atom on each double-bonded C - Nearly every double bond in naturally occurring fatty acids is a cis double bond, which creates a kink in the hydrocarbon chain - Liquid at room temperature - Fats that are high in fatty acids (oils), can’t pack closely together, allowing them to be liquids (i.e fats of plants and fishes) -

The reason why oil separates from water, is because the water molecules are pushing the oil molecules (lipids) together, so that they do not disrupt the water’s H bonding

Hydrogenated Vegetable Oils - t hese unsaturated fats have been synthetically converted to saturated fats by adding H, allowing them to solidify

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Products like peanut butter and margarine prevent liquids from separating out in liquid (oil) form

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Cis  = H bonds in double bond are located on the same side Trans = H bonds in double bond are on opposite sides

 double bonds (produced by the process of Trans fats - unsaturated fats with trans  hydrogenating vegetable oils) - Cause disease (i.e cardiovascular disease) - Creates a more compact structure of the unsaturated fat Phospholipid - two fatty acids attached to a glycerol (instead of 3 fatty acids like in a fat molecule) - Essential for cells because they are major constituents of cell membranes (forms a barrier between the cell and its external properties) - The third hydroxyl group of glycerol is joined to a phosphate group (“-” charge) - Typically, an additional small charged or polar molecule is also linked to the phosphate group - This allows the formation of a variety of phospholipids that differ from each other - The hydrocarbon tails of a phospholipid are hydrophobic and are excluded from water (they don’t mix with water) - The phosphate group and its attachments form a hydrophilic head that has an affinity for water - When phospholipids are added to water, they self-assemble into a bilayer (double-layered sheet) - The bilayer shields their hydrophobic fatty acid tails from water - Hydrophilic (polar) head - 2 hydrophobic (nonpolar) tails - this particular example shows phosphatidylcholine, which has a choline attached to it phosphate group

How do the components of a phospholipid relate to its assembly in an (aq) solution/water? Steroids - lipids characterized by a carbon skeleton consisting of four fused rings - The variety of steroids is based on the particular chemical groups attached to the ensemble of rings - Will have a polar hydroxyl group attached to the fused rings, but the amount present compared to everything else is not significant enough to make it highly water soluble - Steroids with a hydroxyl group = sterol - Also play a role in cardiovascular disease Cholesterol - a type of steroid, crucial in animals (like in the cell membrane) - The forerunner from which other steroids (i.e the vertebrate sex hormones) are synthesized

Concept 5.4 -

Proteins account for more than 50% of the dry mass of most cells Some play a role in: - Defense (i.e protection against disease) - Storage ( i.e storage of amino acids) - Transport ( i.e transport of substances) - Cellular communication ( i.e response of cell to chemical stimuli) - Movement ( i.e contraction of muscles) - Structural support ( i.e Keratin in hair gives the hair strands their specific shape) - Chemical reactions ( i.e enzymes that speed up a chemical reaction) - Hormonal function ( i.e Insulin, a hormone secreted by the pancreas, regulates blood sugar concentration)

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Most enzymes are proteins - Enzymatic proteins regulate metabolism by acting as catalysts - An enzyme can perform its function over and over again

Catalysts - chemical agents that selectively speed up chemical reactions without being consumed in the reaction -

Proteins are the most structurally sophisticated molecules known - They are all constructed from the same set of 20 amino acids, linked in unbranched polymers

Polypeptide - a polymer of amino acids (with a peptide bond between amino acids) Protein - a biologically functional molecule made up of one or more polypeptides, each folded and coils into a specific three-dimensional structure Amino acid - an organic molecule with both an amino group and a carboxyl group - At the center of an amino acid is an asymmetric C atom called the alpha (𝛼) carbon - Its four partners are: - An amino group - A carboxyl group (acid part of an amino acid) - An H atom - A variable group symbolized by R (side chain)

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The side chain (R) differs with each amino acid - The physical and chemical properties of the side chain determine the unique characteristics of particular amino acid - Affects its functional role in a polypeptide

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In a physiological pH (normal for a cell), both the amino group and the carboxyl group will be in an ionized state - The amino group will be “+” because it gained an H atom - The carboxyl group will be “-” because it lost an H atom

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Amino acids with nonpolar side chains are hydrophobic - Expected behavior is (aq) solutions is that these amino acids will cluster together in order to “hide” from the surrounding polar environment

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Amino acids with polar side chains are hydrophilic - Most likely to face an (aq) solution in order to maximize interactions with water molecules or other polar substances in the environment

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Acidic and basic side chains are hydrophilic - Will be able to donated their H ion (acidic) or accept an H ion (basic) - Acidic* amino acids have side chains that are generally negative in charge due to the presence of a carboxyl group - Usually dissociated (ionized) at cellular pH  mino acids have amino groups in their side chains that are - Basic* a generally positive in charge

 r basic in this context only refers to groups in the side chains, *The term acidic o because all amino acids (as monomers) have carboxyl groups and amino groups

How will these amino acids interact with each other or the environment, based on the properties of their side chains? Peptide bond - when two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, and they become joined by a dehydration reaction (covalent bond) - When this process is repeated over and over, a polypeptide is formed (polymer of many amino acids linked by peptide bonds) - Note that: - one end of the polypeptide chain has a free amino group (the N-terminus of the polypeptide) - while the opposite end has a free carboxyl group (the C-terminus) - The chemical nature of the molecule as a whole is determined by the kind of sequence of the side chains - This determines how a polypeptide folds and thus its final shape and chemical characteristics -

Monomeric or Multimeric refers to how many parts of the protein is made of Protein structure (3D architecture) = it’s function  the term protein The term polypeptide ≠

Space-filling model - provides info on the atoms within the structure Ribbon model - looks at the polypeptide backbone and folding pattern -

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The amino acid sequence of each polypeptide determines what structure the protein will have under normal cellular conditions - i.e where an alpha helix can form, where beta pleated sheets can exist, where disulfide bridges are located, where ionic bonds can form, etc When a cell synthesizes a polypeptide, the chain may fold spontaneously, assuming the functional structure for that protein - A protein’s specific structure determines how it works - In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecule (i.e with antibodies) - i.e Morphine, heroin, and other opiate drugs are able to mimic endorphins because they all have a shape similar to that of endorphins and can thus fit into and bind to endorphin receptors in the brain - This folding is driven and reinforces by the formation of various bonds between parts of the chain (depends on the sequence of amino acids)

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 pherical Globular proteins = S  ong fibers Fibrous proteins = L

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Proteins share 3 superimposed levels of structure: 1) Primary 2) Secondary 3) Tertiary 4) Quaternary - arises when a protein consists of two or more polypeptide chains Primary structure - the sequence of amino acids in a protein - tells us how it's going to fold (personalization of protein power) - The precise primary structure of a protein is determined not by the random linking of amino acids, but by inherited genetic information - Focuses on: - The directionality of elongation - The location of which peptide bonds are being formed

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The idea that we describe certain positions based on where they’re found relative to the start and end site - The primary structure dictates… - secondary structure (𝛼 helices and β pleated sheets) - tertiary structure … due to the chemical nature of the backbone and the side chains (R groups) of the amino acids along the polypeptide Secondary structure - the coils and folds of a protein

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the result of H bonds between the repeating constituents of t...