Biochemistry of Cells- III presentation IV presentation

Biochemistry of Cells:

Biochemistry of Cells Copyright Cmassengale 1

Organic Compounds:

Organic Compounds Compounds that contain CARBON are called organic . Although a cell is mostly water (60-90 %) , the rest of the cell consists mostly of carbon-based molecules copyright cmassengale 2

Comparison of Major Properties of Organic and Inorganic Compounds:

Comparison of Major Properties of Organic and Inorganic Compounds 10.1 The Chemistry of Carbon

Uses of Organic Molecules:

Uses of Organic Molecules Americans consume an average of 140 pounds of sugar per person per year Cellulose, found in plant cell walls, is the most abundant organic compound on Earth Copyright Cmassengale 4

Uses of Organic Molecules:

Uses of Organic Molecules A typical cell in your body has about 2 meters of DNA A typical cow produces over 200 pounds of methane gas each year Copyright Cmassengale 5

Carbon (C):

6 Carbon (C) Carbon has 4 electrons in outer shell Carbon can form covalent bonds with as many as 4 other atoms (elements). Usually with C, H, O or N . Simple example: CH 4 (methane) copyright cmassengale

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Outermost electron level that contains electrons in an atom is called valence shell, electrons called valence electrons Elements that contain 8 electrons in the valence shell are stable and unreactive Most atoms are not stable in their natural state Tend to react (combine) with other atoms in order to become more stable (undergo chemical reactions) Octet rule

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Elements with 8 valence electrons – stable Elements with 1,2,3 valence electrons – losing them- form cations Elements with 6 or 7 valence electrons- gain more- anions Elements with 4 or 5 valence electrons- share

Covalent Bonds:

Covalent Bonds Formed when two atoms share one or more pairs of electrons Single bond – 2 electrons Double bond – 4 electrons Triple bond – 6 electrons

Covalent Bonds:

Covalent Bonds Polar – often when two atoms of different types, electrons are shifted toward the atom which attracts them more strongly Nonpolar- atoms of same type share electrons, equal

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Carbon can form four covalent bonds with other atoms Copyright Cmassengale 12

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The simplest carbon compounds- hydrocarbons – contain only carbon and hydrogen atom The general molecular formula for simple hydrocarbon alkane is C n H 2n+2 C-C bond is quite stable and the result is carbon chains can be quite long Copyright Cmassengale 13

Hydrocarbon Saturation:

Hydrocarbon Saturation Compounds that contain only carbon-carbon and carbon-hydrogen single bonds = saturated hydrocarbon Unsaturated hydrocarbons contain at least one carbon to carbon double or triple bond

Cyclic Structure of Hydrocarbons:

Cyclic Structure of Hydrocarbons Some hydrocarbons are cyclic Form a closed ring 10.1 The Chemistry of Carbon

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Copyright Cmassengale 16 endless diversity of carbon skeletons can be form

Formulas Used in Organic Chemistry:

Formulas Used in Organic Chemistry Molecular formula - lists kind and number of each type of atom in a molecule, no bonding pattern Condensed formula - shows all the atoms in a molecule in sequential order indicating which atoms are bonded to which Structural formula - shows each atom and bond in a molecule 10.2 Alkanes

Isomers:

Isomers Many carbon compounds exist in the form of isomers Isomers are compounds with the same molecular formula but different structures An isomer example: both are C 4 H 10 but have different structures Butane Isobutane (Methylpropane) 10.1 The Chemistry of Carbon

Isomers:

Isomers All have the same molecular formula: C 4 H 10 10.1 The Chemistry of Carbon

Functional Groups:

Functional Groups One or more hydrogens in hydrocarbon can be replaced with another group Groups of atoms that give properties to the compounds to which they attach Reactivity of organic molecules is dependent on the attached groups They also determine the polarity of the molecule and hydrophobic properties Copyright Cmassengale 20

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Alcohols:

Alcohols An organic compound containing a hydroxyl group Alcohols have the general formula R-OH

Physical Properties:

Physical Properties R-O-H has a structure similar to that of water Hydroxyl group is very polar Hydrogen bonds can form readily As a result, alcohols have abnormally high boiling points, because the large amount of heat is needed to break hydrogen bond 12.1 Structure and Physical Properties

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In each water molecule, the oxygen atom attracts more than its "fair share" of electrons The oxygen end “acts” negative The hydrogen end “acts” positive Causes the water to be POLAR However, Water is neutral (equal number of e- and p+) --- Zero Net Charge Water

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Hydrogen Bonds Exist Between Water Molecules Negative Oxygen end of one water molecule is attracted to the Positive Hydrogen end of another water molecule to form a HYDROGEN BOND

Some Important Alcohols:

Some Important Alcohols Methanol Used as a solvent Toxic, can cause blindness and death if ingested Can be used as a fuel Ethanol Widely used as a solvent The alcohol in alcoholic beverages 1,2,3-propanetriol (glycerol) Very viscous, thick Has a sweet taste Non-toxic Used in cosmetics, pharmaceuticals, lubricants

Thiols:

Thiols Thiols have the formula R-SH Similar in structure to alcohols with S replacing O Disulfides have the formula R-S-S-R R may be aliphatic or aromatic 3-methy-1-butanethiol

Thiols and Scent:

Thiols and Scent Thiols, as many other sulfur-containing compounds can have nauseating aromas Defensive spray of North American striped skunk Onions and garlic Compare with pleasant scents below 12.9 Thiols

Aldehydes and Ketones:

Aldehydes and Ketones

Physical Properties:

Physical Properties Aldehydes and ketones are polar compounds The carbonyl group is polar Can hydrogen bond to water Hydrogen bond

Carboxylic Acids:

Carboxylic Acids Carboxylic acid groups consist of two very polar functional groups Carbonyl group Hydroxyl group Carboxylic acid groups are very polar Carboxylic acid – Ester – propanoic acid methyl ethanoate

Physical Properties:

Physical Properties Low molecular weight carboxylic acids Sharp, sour taste Unpleasant aromas High molecular weight carboxylic acids Fatty acids important in biochemistry Low molecular weight carboxylic acids are water soluble due to hydrogen bonding with: Water Each other 1 4 .1 Carboxylic Acids

Some important carboxylic acids:

Some important carboxylic acids Methanoic acid (formic) – stinging sensation of an ant bite Ethanoic acid (acetic) – acidic zip to vinegars Propanoic acid – product of bacterial fermentation of milk products Butanoic acid – foul odor, rancid butter Pentanoic acid (valeric) – in valerian plant, aroma as over-ripe cheese or a “wet dog”

Some Important Carboxylic Acids:

Some Important Carboxylic Acids 14.1 Carboxylic Acids

Some Important Carboxylic Acids:

Some Important Carboxylic Acids 14.1 Carboxylic Acids

Reactions Involving Carboxylic acids:

Reactions Involving Carboxylic acids Carboxylic acids react with alcohols to produce esters A molecule of water is also released as a product: reaction is a dehydration 14.2 Esters

Hydrolysis of Esters:

Hydrolysis of Esters The main reaction of esters is hydrolysis, reaction with water This reaction is also called hydration = cleavage of any bond by the addition of a water molecule 14.2 Esters

Esters:

Esters Frequently found in natural foodstuffs Many have pleasant aromas Isoamyl acetate = banana oil (= 3-methylbutyl ethanoate) Ethyl butanoate = pineapple aroma (= Ethyl butanoate) Isobutyl formate = raspberry aroma (= Isobutyl methanoate)

Amines:

Amines Class of the organic molecules containing nitrogen Amines are derivatives of ammonia Most important type of organic base found in nature Amines form hydrogen bonds but not as strongly as alcohols Nitrogen is less electronegative than oxygen

Heterocyclic Amines:

Heterocyclic Amines Cyclic compounds Have at least one N in the ring MANY are physiologically active and many are critical in biochemistry

Medically Important Amines :

Medically Important Amines Decongestants shrink the membranes lining the nasal passages Sulfa drugs (first chemicals used to fight infections) are also made from amines 15.1 Amines

Medically Important Amines :

Medically Important Amines Amphetamines stimulate the central nervous system – treat depression and epilepsy Analgesics (pain relievers) and anesthetics (pain blockers) 15.1 Amines

Giant Molecules - Polymers:

Giant Molecules - Polymers Large molecules are called macromolecules The largest of the macromolecules are called polymers Polymers are built from smaller molecules called monomers Copyright Cmassengale 43

Polymerization :

Polymerization Copyright Cmassengale 44 From the perspective of the organic chemical industry, the single most important reaction of alkenes is polymerization:

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Copyright Cmassengale 45

Examples of Biological Polymers:

Examples of Biological Polymers Proteins Copyright Cmassengale 46 Lipids Carbohydrates Nucleic Acids

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Polymers are made by stringing together many smaller molecules-monomers Cells link monomers by a process called condensation or dehydration synthesis (removing a molecule of water) Copyright Cmassengale 47 H 2 O Forms Remove OH Remove H

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Cells break down macromolecules by a process called hydrolysis (adding a molecule of water) Copyright Cmassengale 48 Water added to split a double sugar

Carbohydrates:

Carbohydrates Carbohydrates include: Small sugar molecules in soft drinks Long starch molecules in pasta and potatoes Copyright Cmassengale 49

Basic Carbohydrate Types:

Basic Carbohydrate Types Monosaccharides e.g., glucose, fructose One sugar (saccharide) molecule Disaccharides e.g., sucrose, lactose Two monosaccharides linked together Linkage is called a glycosidic bond Oligosaccharides Three to ten monosaccharides linked by glycosidic bonds Polysaccharides e.g., starch, glycogen, cellulose Chains of linked monosaccharide units

Monosaccharides::

Monosaccharides: Called simple sugars Composed of: Carbon Hydrogen Oxygen Include glucose, fructose, & galactose Have the same chemical, but different structural formulas Copyright Cmassengale 51 C 6 H 12 O 6

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Glucose is the most important sugar in the human body Found in many foods Several common names include: dextrose and blood sugar Its concentration in the blood is regulated by insulin and glucagon Fructose is also called: Levulose Fruit sugar Found in large amounts in: Honey Corn syrup Fruits The sweetest of all sugars

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Galactose is the principal sugar found as a component of the disaccharide lactose, in mammalian milk Copyright Cmassengale 53

Isomers:

Isomers Glucose & fructose are isomers because they’re structures are different, but their chemical formulas are the same Copyright Cmassengale 54

Rings:

Rings In aqueous (watery) solutions, monosaccharides form ring structures

Cyclization of Glucose :

Cyclization of Glucose

Cellular Fuel:

Cellular Fuel Monosaccharides are the main fuel that cells use for cellular work Copyright Cmassengale 57 ATP

Disaccharides:

Disaccharides A disaccharide is a double sugar They’re made by joining two monosaccharides Involves removing a water molecule (condensation) Bond called a GLYCOSIDIC bond Copyright Cmassengale 58

Disaccharides:

Disaccharides Sucrose is composed of glucose + fructose Lactose is made of galactose + glucose Maltose is composed of 2 glucose molecules Copyright Cmassengale 59 GLUCOSE

Disaccharides:

Disaccharides Sucrose (table sugar) Lactose (Milk Sugar) Maltose (Grain sugar) For use as an energy source, lactose must be hydrolyzed to glucose and galactose, lactose intolerance results from lack of lactase to hydrolyze the glycosidic link of lactose, lactose intolerance Galactose must be converted to glucose molecule , when enzymes necessary for this conversion are absent, the genetic disease galactosemia results Copyright Cmassengale 60

Polysaccharides:

Polysaccharides Complex carbohydrates Composed of many sugar monomers linked together Copyright Cmassengale 61

Examples of Polysaccharides:

Examples of Polysaccharides Copyright Cmassengale 62 Starch Glycogen Cellulose Glucose Monomer

Starch:

Starch Starch is an example of a polysaccharide in plants It is polymer of linked glucose Plant cells store starch for energy Potatoes and grains are major sources of starch in the human diet Copyright Cmassengale 63

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Starch If the polymer is linear = amylose If the polymer structure is branched = amylopectin

Comparison of Amylose to Amylopectin:

Comparison of Amylose to Amylopectin

Glycogen:

Glycogen Glycogen is an example of a polysaccharide in animals Animals store excess sugar in the form of glycogen Glycogen is similar in structure to starch because BOTH are made of glucose monomers A highly branched chain polymer like amylopectin , more frequent branching Copyright Cmassengale 66

Cellulose:

Cellulose Cellulose is the most abundant organic compound on Earth Cellulose is the major structural polymer in plants It is a major component of wood It is also known as dietary fiber Copyright Cmassengale 67

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Copyright Cmassengale 68 Simple sugars

Dietary Cellulose:

Dietary Cellulose Most animals cannot derive nutrition from fiber In contrast to glycogen, amylose and amylopectin, animals lack the enzymes necessary to hydrolyze cellulose They have bacteria in their digestive tracts that can break down cellulose Copyright Cmassengale 69

Lipids:

Lipids Fats store energy help to insulate the body and cushion and protect organs Copyright Cmassengale 70

Classification of Lipids:

Classification of Lipids Four Main Groups Fatty Acids Saturated Unsaturated Glycerides glycerol-containing lipids Nonglyceride lipids Sphingolipids Steroids Waxes Complex lipids lipoproteins

Fatty Acids:

Fatty Acids Long straight-chain carboxylic acids , no branching Most common chains range from 10–20 carbons in length Usually, an even number of carbons in the chain, including the carboxyl carbon Can be saturated or unsaturated , but usually no other functional groups present Any fatty acid that cannot be synthesized by the body is called an essential fatty acid (linoleic acid)

Carboxylic Acids:

Carboxylic Acids Carboxylic acid groups consist of two very polar functional groups Carbonyl group Hydroxyl group Carboxylic acid groups are very polar Carboxylic acid – Ester – propanoic acid methyl ethanoate

Some Important Carboxylic Acids:

Some Important Carboxylic Acids 14.1 Carboxylic Acids

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Saturated fatty acids have the maximum number of hydrogens bonded to the carbons (all single bonds between carbons) Unsaturated fatty acids have less than the maximum number of hydrogens bonded to the carbons (a double bond between carbons) Double bonds lower the melting temperature, doesn’t allow fatty acids to pack as close together, lower intermolecular attractions

Types of Fatty Acids:

Types of Fatty Acids Copyright Cmassengale 76 Single Bonds in Carbon chain Double bond in carbon chain

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Glycerides:

Glycerides Composed of Glycerol & fatty acid chains Glycerol forms the “backbone” of the fat Esterification may occur at one, two, or all three alcohol positions producing: Monoglyceride Diglyceride Triglyceride

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Triglycerides Fats mainly come from animals , unless from fish, and are solid at room temperature Oils mainly come from plants , and are liquid at room temperature Copyright Cmassengale 79

Triglycerides:

Triglycerides Glycerol part Fatty acid chains

Triglyceride (nonpolar molecules):

Triglyceride (nonpolar molecules) Copyright Cmassengale 81 Glycerol Fatty Acid Chains

Fats in Organisms:

Fats in Organisms Most animal fats have a high proportion of saturated fatty acids & exist as solids at room temperature (butter, margarine, shortening) Copyright Cmassengale 82

Fats in Organisms:

Fats in Organisms Most plant oils tend to be low in saturated fatty acids & exist as liquids at room temperature Copyright Cmassengale 83

Phospholipids:

Phospholipids Contain: Glycerol Fatty acid Phosphoric acid with an amino alcohol Replace an end fatty acid of a triglyceride with a phosphoric acid linked to an amino alcohol G l y c e r o l Fatty Acid Fatty Acid Phosphoric Acid Alcohol

Phospholipids:

85 Phospholipids Make up the cell membrane Contains 2 fatty acid chains that are nonpolar Head is polar - contains a –PO 4 Suspended in water, they spontaneously rearrange Hydrophobic group to center Hydrophilic group to water copyright cmassengale

Semipermeable Membrane:

86 Semipermeable Membrane copyright cmassengale

Nonglyceride lipids -Steroids:

Nonglyceride lipids -Steroids The carbon skeleton of steroids is bent to form 4 fused rings Cholesterol is the “base steroid” from which your body produces other steroids Estrogen & testosterone are also steroids Copyright Cmassengale 88 Cholesterol Testosterone Estrogen

Proteins:

Proteins Protein means “ of first importance ” Proteins are made from monomers - amino acids Proteins play a crucial role in biological processes Enzymes – biological catalysts Antibodies – defense proteins Transport proteins Regulatory proteins Structural proteins Movement proteins Nutrient proteins

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Copyright Cmassengale 90 Structural Contractile Storage Transport

Amino Acids:

Amino Acids As the name implies, these compounds contains both an amine and an acid They have a central carbon with 4 things boded to it: Amino group –NH 2 Carboxyl group -COOH Hydrogen -H Side group -R Hundreds are formed both naturally and synthetically Only 20 are common in nature

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Copyright Cmassengale 92 Amino group Carboxyl group R group Side groups Leucine -hydrophobic Serine-hydrophillic

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Copyright Cmassengale 93 Nonpolar -hydrophobic Polar neutral

Linking Amino Acids:

Linking Amino Acids Proteins are polymers Peptide bond links monomers to form polymers (proteins) The process is called condensation or dehydration two amino acids produces a dipeptide more amino acids -polypeptide 94 Carboxyl Amino Dehydration Synthesis Peptide Bond

Primary Structure of Proteins:

Primary Structure of Proteins Primary structure is the amino acid sequence of the polypeptide chain A result bonding between the amino acids Each protein has a different primary structure with different amino acids in different places along the chain

Secondary Structure of Proteins:

Secondary Structure of Proteins When the polypeptide coils or folds into regularly repeating structures, secondary structure is formed Secondary structure results from hydrogen bonding between the amide hydrogens and carbonyl oxygens Different regions of a protein chain may have different types of secondary structures

a-Helix:

a -Helix

b-Pleated Sheet:

b -Pleated Sheet

a-Helices in Fibrils:

a -Helices in Fibrils Human hair, typical example of a- keratins consist of polypeptide chains coiled up into a -helixes

Tertiary and Quaternary Structures:

Tertiary and Quaternary Structures Copyright Cmassengale 100 When protein chains -polypeptides join together, the tertiary structure forms because R groups interact with each other In the watery environment of a cell, proteins become globular in their quaternary structure

Interactions Involved in Tertiary Structure:

Interactions Involved in Tertiary Structure

Hemoglobin - Demonstrating the Four Levels of Protein Structure:

Hemoglobin - Demonstrating the Four Levels of Protein Structure

Poisoning of Proteins:

Poisoning of Proteins Hydrolysis : peptide bonds are disrupted Changes in pH, Enzymes, Temperature Denaturation : they lose their secondary and tertiary structure Temperature, Heavy metals, Detergents, Organic Solvents, Mechanical Stress Coagulation-protein molecules unfold and became entangled – they are no longer in solution, they aggregated to become a solid High temperature vs. eggs pH vs. milk

Some Important Proteins:

Some Important Proteins Blood sugar level is controlled by a protein called insulin -Insulin causes the liver to uptake and store excess sugar as Glycogen The cell membrane also contains proteins -Receptor proteins help cells recognize other cells Copyright Cmassengale 104

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Copyright Cmassengale 105 INSULIN Cell membrane with proteins & phospholipids

Proteins as Enzymes:

Proteins as Enzymes Copyright Cmassengale 106 Enzymes are globular proteins Enzymes control the rate of chemical reactions by weakening bonds, thus lowering the amount of activation energy needed for the reaction Their folded conformation creates an area known as the active site The nature and arrangement of amino acids in the active site make it specific for only one type of substrate

Enzyme + Substrate = Product:

Enzyme + Substrate = Product Copyright Cmassengale 107

Nucleic Acids:

108 Nucleic Acids Polymers of nucleotides Contain information for making all the body’s proteins DNA (deoxyribonucleic acid) Double-stranded helical spiral (twisted ladder) Serves as genetic information center In chromosomes RNA (ribonucleic acid) Part single-stranded, part double-stranded Serves primarily in assembly of proteins In nucleus and cytoplasm of cell

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The Nucleotides of Nucleic Acids:

110 The Nucleotides of Nucleic Acids Three components: A phosphate group, A pentose sugar (ribose or deoxyribose), and A nitrogenous base Nucleotide subunits connected end-to-end to make nucleic acid Sugar of one connected to the phosphate of the next Sugar-phosphate backbone

Nucleotide – Nucleic acid monomer:

Nucleotide – Nucleic acid monomer Copyright Cmassengale 111

Nucleotides:

112 Nucleotides pentose sugar nitrogen- containing base phosphate deoxyribose (in DNA) ribose (in RNA) cytosine thymine in DNA uracil in RNA a. Nucleotide structure c. Pyrimidines versus purines b. Deoxyribose versus ribose adenine guanine Pyrimidines Purines Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

RNA – Ribonucleic Acid:

RNA – Ribonucleic Acid Ribose sugar has an extra – OH or hydroxyl group It has the base uracil (U) instead of thymine (T) (DNA) Copyright Cmassengale 113 Nitrogenous base (A,G,C, or U) Sugar (ribose) Phosphate group Uracil

RNA Structure:

114 RNA Structure Guanine Uracil Adenine Cytosine Ribose Phosphate P S Backbone Nitrogen-containing bases S S S S P P P P G C A U Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

DNA structure , Hydrogen Bonds:

115 DNA structure , Hydrogen Bonds The bases attract each other because of hydrogen bonds Hydrogen bonds are weak but there are millions and millions of them in a single molecule of DNA When making hydrogen bonds, cytosine always pairs up with guanine Adenine always pairs up with thymine

Complementary Base Pairing:

116 Complementary Base Pairing N adenine (A) sugar sugar thymine (T) cytosine (C) guanine (G) sugar sugar c. Complementary base pairing Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

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DNA Structure:

118 DNA Structure A T b. Double helix a. Space-filling model A A T T G G C C G P C Guanine Thymine Adenine Cytosine Sugar Phosphate S Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. © Photodisk Red/Getty Images

Double helix:

Model proposed by Watson & Crick, 1953 Two sugar-phosphate strands, next to each other, but running in opposite directions. Specific Hydrogen bonds occur among bases from one chain to the other. Due to this specificity, a certain base on one strand indicates a certain base in the other. The 2 strands intertwine, forming a double-helix that winds around a central axis Double helix

Important nucleotide- ATP – Cellular Energy:

Important nucleotide- ATP – Cellular Energy Adenosine triphosphate Made of a nucleotide with 3 phosphate groups Copyright Cmassengale 120

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Energy is stored in the chemical bonds of ATP The last 2 phosphate bonds are HIGH ENERGY Breaking the last phosphate bond releases energy for cellular work and produces ADP and a free phosphate ADP (adenosine Di phosphate ) can be rejoined to the free phosphate to make more ATP Copyright Cmassengale 121