Ch. 3 Biological Macromolecules PDF

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Notes from chapter 3 on biological macromolecules...

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Chapter 3: Biological Macromolecules I.

Synthesis of Biological Macromolecules   

Biological macromolecules: large molecules made from smaller organic molecules necessary for life Four macromolecules: carbohydrates, lipids, proteins, and nucleic acids Make majority of cell’s dry mass, water majority of cell’s mass

A. Dehydration Synthesis       

Single building block of most molecules is a monomer Monomers combine through a covalent bond to make polymers Monomer->polymer=dehydration A water molecule is released during dehydration synthesis A hydrogen (H+) of one monomer combines with a hydroxyl group (OH-) of the other Sharing electrons (covalent bond) Formation of new bond requiring energy

B. Hydrolysis   

II.

Water molecules are used to breakdown polymers to monomers One part gains hydrogen atom (H+) and another gains a hydroxyl molecule (OH-) Bond breaking releasing energy

Carbohydrates  

Provide energy to the body mainly through glucose Glucose is a simple sugar of starch

A. Molecular Structures    

Can be represented by stoichiometric (CH2O)n n= the number of Carbon in a molecule Ratio of carbon:hydrogen:oxygen is 1:2:1 Carbohydrates= “carbo” = carbon ”hydrate”= water Classified into three subtypes: monosaccharides, disaccharides, and polysaccharides

1. Monosaccharides    

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Monosaccharides= “mono” = 1 “saccharides” = sweet Most common simple sugar (a monosaccharide) is glucose Normally 3-7 Carbons tend to end with –ose suffix If sugar has… o an aldehyde group: functional group with structure R-CHO, it is known as aldose o a ketone group: functional group with structure RC(=O)R’ it is known as ketose o three carbons = triose o five carbons = pentose o six carbons = hexose monosaccharides classified based on position of their carbonyl group and # of carbons in backbone aldose have a carbonyl group is at the end of carbon chain ketose have carbonyl group in the middle of the chain triose, pentose, and hexose have three, five, and six carbon backbones chemical formula for glucose = C6H12O6 glucose is an important source of energy for humans, it releases energy during cellular respiration, that energy helps make adenosine triphosphate (ATP) plants synthesize glucose using carbon dioxide and water, used for energy requirements for plants excess glucose is stored as starch and catabolized (cell breaks down large molecules) by consumers Galactose (part of lactose, or milk sugar) Fructose (found in sucrose, in fruit)

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Glucose, galactose, and fructose all have same chemical formula C6H12O6 BUT are different chemically and structurally which make them isomers The arrangement of functional groups around the asymmetric carbon is different which also makes the isomers More than one asymmetric carbon They are all hexose but glucose and galactose are aldose while fructose is ketose Monosaccharides can be a linear chain or ring-shaped molecules In aqueous solutions they are found in ring forms Glucose can have two different arrangements of hydroxyl group (OH-) around the anomeric carbon (carbon 1 that becomes asymmetric in ring formation) If the hydroxyl group (OH) is below carbon number 1 in sugar it is in the alpha () position and in the beta () position above Between linear and ring forms, five and six carbon monosaccharides exist When the ring forms, the side change it closes on is locked into either an  or  positon Ribose and fructose form 5 membered rings while glucose forms 6

2. Disaccharides        

Disaccharides= “di-“ = two; two monosaccharides go through dehydration reaction (condensation reaction or dehydration synthesis) Hydroxyl group of one monosaccharide combines with a hydrogen of another monosaccharide realizing a water molecule forming a covalent bond The covalent bond formed between a carbohydrate molecule and another molecule (this case two monosaccharides) is a glycosidic bond (glycosidic linkages) Can be  or  type When a monomer of glucose and a monomer of fructose join in a dehydration reaction forming a glycosidic bond, sucrose is formed Carbon atoms in a monosaccharide are numbered from terminal carbon closest to the carbonyl group In sucrose, a glycosidic linkage forms between carbon 1 in glucose and carbon 2 in fructose Common disaccharides are… o Lactose (found in milk) = glucose and galactose o Maltose (malt sugar) = glucose and glucose o Sucrose (table sugar) = glucose and fructose

3. Polysaccharides    

Long chain of monosaccharides formed by glycosidic bonds are polysaccharides = “poly-“ = many Can be branched or unbranched and contain different types of monosaccharides Molecular weight may be 100,00 daltons or more depending on the number of monomers joined Primary polysaccharides are… o Starch: stored from sugars in plants (excess glucose) and is a mixture of amylose (polymer of glucose) and amylopectin (polymer of glucose)  Stored in different parts of the plant like the roots and seeds  Starch in seeds provides food for the embryo and can be food for consumers  The starch consumed is broken down by enzymes (salivary amylases) into smaller molecules (maltose and glucose) and then the glucose is absorbed by cells  Made up of glucose monomers joined by  1-4 or  1-6 glycosidic bounds  1-4 and 1-6 refer to carbon number of the two that joined from the bond  amylose is starch formed by unbranched chains of glucose monomers (only  1-4) linkages

amylopectin is a branched polysaccharide ( 1-6 linkages at the branch points) has a helical structure Glycogen: made up of monomers of glucose stored in human  Highly branched molecule usually stored in the liver and muscle cells  When blood glucose levels decrease, glycogen is broken down to release glucose through glycogenolysis Cellulose: most abundant natural biopolymer, make of most of cell wall in plants providing structural support  Made up of glucose monomers linked by  1-4 glycosidic bonds  Every other glucose monomer is flipped relatively and packed tightly to give its high strength  Cellulase is the enzyme that breaks down cellulose to glucose allowing it to be used as energy Chitin: polysaccharide that contains nitrogen, made up of repeating units of Nacteyl--d-glucosamine  Makes the exoskeleton for insects 

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B. Benefits of Carbohydrates 

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III.

Contain soluble and insoluble elements o Insoluble: fiber (made of mostly cellulose) regulates rate of consumption of blood glucose and bowel movements, removes excess cholesterol, reduces risk of colon cancer Immediate source of energy through cellular respiration (produces ATP), the energy currency of the cell

Lipids    

Nonpolar (hydrophobic/insoluble) in nature because they are hydrocarbons including mostly nonpolar carbon-carbon or carbon-hydrogen bonds Store energy for long-term use in the form of fats and provide insolation Building blocks of many hormones Include fats, oils, waxes, phospholipids, and steroids

A. Fats and Oils 

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Fat molecule consists of two main components o Glycerol: organic compound (alcohol) with 3 carbons, 5 hydrogens, and 3 hydroxyl groups (OH) o Fatty acids: Have long chain of hydrocarbons with an attached carboxyl group o Range from 4-36 (most common 12-18) In a fat molecule fatty acids are attached to each of the 3 carbons of glycerol molecule with an ester bond through an oxygen atom During an ester bond 3 water molecules are released Fats are called triacylglycerols or triglycerides because of their chemical structure Some fatty acid names specify their origin o Palmitic (saturated fatty acid) from a palm tree o Arachidic acid from arachis hypogea for peanuts Fatty acids can be… o Saturated: single bods between neighboring carbons and hydrogens o Unsaturated: hydrocarbon chain contains a double bond o Most unsaturated fats liquid at room temperature o Monounsaturated fat = one double bond o Polyunsaturated fat = more than one =double bond Fat may contain similar or different fatty acids attached to a glycerol Long straight fatty acids with single bonds normally packed tight (solid at room temperature)

Saturated fat= Animal fat with stearic acid and palmitic acid (common in meat) and fat with butyric acid (common in butter) Adipocytes store fat in animals Unsaturated fat or oil is stored in many seeds Cis and trans fat identify the configuration of the molecule around the double bond o Cis = hydrogens present in the same plane (cause double bond to bend or “kink”) preventing tight packing, liquid at room temperature o Trans = hydrogen atoms are on two different planes Unsaturated fats consist of… o Olive oil o Corn oil o Cod liver oil o Canola oil Unsaturated fats lower blood cholesterol levels Saturated fats contribute to plaque formation in arteries Saturated fatty acid: hydrocarbons connected by single bonds Unsaturated fatty: one or more double bonds, each bond either cis or trans configuration o Cis configuration: both hydrogens on the same side of hydrogen chain and kink present o Trans configuration: hydrogens on opposite sides o

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1. Trans Fats 

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Oils are hydrogenated to form semi-solids o Cis conformation in the hydrocarbon may be converted to double bonds in trans conformation o Some examples of artificially hydrogenated trans fats are margarine and some types of peanut butter Increase of trans fat in diets can lead to increase in levels of low-density lipoproteins (LDL) also known as bad cholesterol o Lead to plaque deposition in arteries

2. Omega Fatty Acids    

Essential fatty acids required but not synthesized by the human body Omega-3 polyunsaturated fatty acid because the third carbon from the end of the hydrocarbon chain is connected to its neighboring carbon by double bond The furthest carbon from the carboxyl group is numbered as omega () Reduce risk of sudden heart attack, reduce triglycerides in the blood, lower blood pressure, prevent thrombosis, reduce inflammation, provide insulation to the body

B. Waxes   

Covers some aquatic birds and leaves of some plants Hydrophobic nature cause water to just fall off Made up of long fatty acid chains esterified to long-chain alcohols

C. Phospholipids    

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Are major constituents of plasma membrane, outermost layer of animal cell Composed of fatty acid chains attached to a glycerol or sphingosine backbone like fats instead of 3 fatty acids, there are 2 (diaclglycerol) and a modified phosphate group Two important phospholipids are Phosphatidycholine and Phosphatidylserine: A phospholipid is a molecule with two fatty acids and a modified phosphate group attached to a glycerol backbone o Phosphate group may be modified by addition of charge or polar chemical groups  Choline:  Serine: Phospholipids are amphipathic: has both a hydrophobic and hydrophilic part

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Fatty acids are hydrophobic Phosphate-containing group is hydrophilic Phospholipid bilayer is the major component of cell membranes, responsible for the dynamic nature of the plasma membrane Forms micelle = hydrophilic phosphate heads face outside and fatty acids face inside

D. Steroids     

IV.

Unlike phospholipids and fats, steroids have a fused ring structure Are hydrophobic and insoluble have several 4 linked carbon rings, have a short tail and many have –OH functional group (sterols) cholesterol and cortisol composed of four fused hydrocarbon rings cholesterol = most common steroid o synthesized in the liver o precursor to many steroid hormones (testosterone and estradiol) and Vitamin o found in the phospholipid bilayer o responsible for transport of materials, cellular recognition, and cell-to-cell communication

Proteins       

One of the most abundant organic molecules in the living system Most diverse range of functions of all macromolecules May be structural, regulatory, contractile, or protective May be transportation, storage, or membranes May be toxins or enzymes Each cell contains thousands of proteins with unique functions and structures They are polymers built from amino acids arranged in a linear sequence

A. Types and Functions of Proteins  

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Enzymes: produced by living cells and catalyst in biomedical reactions like digestion Specific for the substrate, may break down rearrange, synthesis reaction o Help break down: catabolic enzymes o Build more complex molecules: anabolic enzymes o Affect rate of reaction: catalytic enzymes (all enzymes do this … organic catalyst) o synthesis reactions Hormones: chemical-signaling molecules, small proteins or steroids secreted by endocrine cells that control or regulate specific physiological processes o Growth o Development o Metabolism o Reproduction Protein Types and Functions Type Examples Functions Digestive Enzymes Amylase, lipase, pepsin, Help digestion of food by trypsin catabolizing nutrients into monomeric units Transport Hemoglobin, albumin Carry substances in the blood or lymph throughout the body Structural Actin, tubulin, keratin Construct different structures, like the cytoskeleton Hormones Insulin, thyroxine Coordinate the activity of different body systems

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Defense

Immunoglobulins

Contractile Storage

Actin, myosin Legume storage proteins, egg white (albumin)

Protect the body from foreign pathogens Effect muscle contraction Provide nourishment in early development of the embryo and the seeding

Have different shapes and molecular weights Protein shape is critical to its function, its function is maintained by different chemical bonds Change in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape leading to permanent loss of function known as denaturation Made up of different arrangements of the same 20 amino acids

B. Amino Acids        

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Amino acids are the monomers that make up protein Have the same fundamental structure = central carbon atom, the alpha () carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom Each has another atom/atoms bonded to central atom, the R group A central asymmetric carbon, amino group, carboxyl group, hydrogen atom, and a side chain (R group) attached Amino acid comes from amino group and carboxyl-acid group in basic structure Of the 20 amino acids, 10 are essential (body cannot produce them) Each amino acid has a different R group Chemical nature of the side chain determined the nature of the amino acid (whether it is acidic, basic, polar, or nonpolar) o Nonpolar: glycine, valine, methionine, leucine, isoleucine, and alanine  Glycine has a hydrogen atom o Polar: serine, threonine, proline, asparagine, glutamine, and cysteine  Proline is not separate from the side chain o Basic: lysine and arginine Essential amino acids: isoleucine, leucine, and cysteine o Necessary for construction of proteins of the body but not produced by the body Sequence and # of amino acids determine the protein’s shape, function, and size Peptide bonds attach amino acids to each other o The carboxyl group of one amino acid and the amino group of another combine and release a water molecule

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C. Protein Structure 

1. Primary Structure 

2. Secondary Structure 

3. Tertiary Structure 

4. Quaternary Structure 

D. Denaturation and Protein Folding 

V.

Nucleic Acids 

A. DNA and RNA 

B. DNA Double-Helix Structure 

C. RNA ...