Aim: How can we describe carbohydrates and how they are associated with life? Do Now: Draw an animal cell membrane in as much detail as possible and describe. Homework: Review notes.

Carbon and the Molecular Diversity of Life Chapter 3 Carbon and the Molecular Diversity of Life

Macromolecules Are large, complex molecules composed of smaller molecules. Figure 5.1

Macromolecules Most macromolecules are polymers, built from monomers Four classes of life’s organic molecules are polymers: Carbohydrates Lipids Proteins Nucleic Acids

Specific monomers make up each macromolecule. A polymer Is a long molecule consisting of many similar building blocks called monomers. Specific monomers make up each macromolecule. Ex: amino acids are the monomers make up proteins

The Synthesis and Breakdown of Polymers Monomers form larger molecules by condensation reactions called dehydration synthesis. (a) Dehydration reaction in the synthesis of a polymer HO H 1 2 3 4 H2O Short polymer Unlinked monomer Longer polymer Dehydration removes a water molecule, forming a new bond Figure 5.2A

The Synthesis and Breakdown of Polymers Polymers can disassemble by: Hydrolysis (addition of water molecules) (b) Hydrolysis of a polymer HO 1 2 3 H 4 H2O Hydrolysis adds a water molecule, breaking a bond Figure 5.2B

Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers An immense variety of polymers can be built from a small set of monomers

1. Carbohydrates First source of energy Serve as fuel and building material Include both sugars and their polymers (starch, cellulose, etc.)

Sugars Monosaccharides Are the simplest sugars Can be used for fuel Can be converted into other organic molecules Can be combined into polymers

Examples of monosaccharides: Triose sugars (C3H6O3) Pentose sugars (C5H10O5) Hexose sugars (C6H12O6) H C OH H C OH HO C H H C OH C O HO C H H C O Aldoses Glyceraldehyde Ribose Glucose Galactose Dihydroxyacetone Ribulose Ketoses Fructose Figure 5.3

Monosaccharides May be linear Can form rings 4C 3 2 OH Figure 5.4 H C OH HO C H H C O C 1 2 3 4 5 6 OH 4C 6CH2OH 5C H OH 2 C 1C 3 C 2C 1 C CH2OH HO 3 2 (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5. Figure 5.4

Disaccharides Consist of two monosaccharides Are joined by a glycosidic linkage

Figure 5.5 CH2OH O H H OH HO OH H2O Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. (a) (b) H HO H OH OH O CH2OH H2O 1 2 4 1– 4 glycosidic linkage 1–2 glycosidic linkage Glucose Fructose Maltose Sucrose Figure 5.5

Polysaccharides Polysaccharides Are polymers of sugars Serve many roles in organisms

Storage Polysaccharides Chloroplast Starch Amylose Amylopectin 1 m (a) Starch: a plant polysaccharide Figure 5.6 Starch Is a polymer consisting entirely of glucose monomers Is the major storage form of glucose in plants

(b) Glycogen: an animal polysaccharide Consists of glucose monomers Is the major storage form of glucose in animals Mitochondria Giycogen granules 0.5 m (b) Glycogen: an animal polysaccharide Glycogen Figure 5.6

Structural Polysaccharides Cellulose Is a polymer of glucose and is a structural polysaccharide. Found in the cell wall of plants

 Figure 5.8 About 80 cellulose molecules associate Plant cells 0.5 m Cell walls Cellulose microfibrils in a plant cell wall  Microfibril CH2OH OH O Glucose monomer Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. A cellulose molecule is an unbranched  glucose polymer. Cellulose molecules Figure 5.8

Cellulose is difficult to digest Cows have microbes in their stomachs to facilitate this process, we however do not have these same microbes. Figure 5.9

Chitin, another important structural polysaccharide Is found in the exoskeleton of arthropods (invertebrate with an exoskeleton). Can be used as surgical thread. (a) The structure of the chitin monomer. O CH2OH OH H NH C CH3 (b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. Figure 5.10 A–C

Aim: How can we describe lipid and protein structure and function Aim: How can we describe lipid and protein structure and function? Do Now: Do the number of fat cells increase, decrease, or remain the same as you age? Justify your response. Homework: Review notes.

2. Lipids Lipids are a diverse group of hydrophobic molecules. Lipids: Are the one class of large biological molecules that do not consist of polymers. Share the common trait of being hydrophobic.

Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids. Vary in the length and number and locations of double bonds they contain

(a) Saturated fat and fatty acid Saturated fatty acids Have the maximum number of hydrogen atoms possible. Have NO double bonds. (a) Saturated fat and fatty acid Stearic acid Figure 5.12 Why are saturated fats bad for us?

(b) Unsaturated fat and fatty acid Unsaturated fatty acids Have one or more double bonds (b) Unsaturated fat and fatty acid cis double bond causes bending Oleic acid Figure 5.12 Why are unsaturated fats good for us?

Phospholipids Have only two fatty acids. Have a phosphate group instead of a third fatty acid.

(a) Structural formula (b) Space-filling model Phospholipid structure Consists of a hydrophilic “head” and hydrophobic “tails”. CH2 O P CH C Phosphate Glycerol (a) Structural formula (b) Space-filling model Fatty acids (c) Phospholipid symbol Hydrophobic tails Hydrophilic head Hydrophobic tails – Hydrophilic head Choline + Figure 5.13 N(CH3)3

The structure of phospholipids: Results in a bilayer arrangement found in cell membranes. Hydrophilic head WATER Hydrophobic tail Figure 5.14

Steroids Steroids: Are lipids characterized by a carbon skeleton consisting of four fused rings. Steroids" has more than one meaning. Your body naturally produces some steroids, to help you fight stress and grow bigger during puberty. (But your body knows just the right amount that you need, so there's no need to take any extra.) There's also a type of medicine called steroids that people might take if they have pain, asthma, or a skin problem. But these aren't the kind of steroids getting attention in sports. When people say steroids (say: STARE-oydz), they often mean illegal anabolic steroids. Anabolic steroids are artificially produced hormones that are the same as, or similar to, androgens, the male-type sex hormones in the body. The most powerful of these is testosterone (say: tes-TOSS-tuh-rone). Anabolic steroids can be taken in the form of pills, powders, or injections. Anabolic steroids are always illegal, meaning that you could get arrested for buying, selling, or taking them.

One steroid, cholesterol Is found in cell membranes Is a precursor for some hormones HO CH3 H3C Figure 5.15

3. Proteins Proteins have many structures, resulting in a wide range of functions. Proteins do most of the work in cells and act as enzymes. Proteins are made of monomers called amino acids.

An overview of protein functions Table 5.1

Enzymes Are a type of protein that acts as a catalyst, speeding up chemical reactions. Substrate (sucrose) Enzyme (sucrase) Glucose OH H O H2O Fructose 3 Substrate is converted to products. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate binds to enzyme. 2 4 Products are released. Figure 5.16 All enzymes are proteins, but not all proteins are enzymes.

Polypeptides Polypeptides A protein Are polymers (chains) of amino acids A protein Consists of one or more polypeptides

Amino acids Are organic molecules possessing both carboxyl and amino groups Differ in their properties due to differing side chains (variable groups), called R groups

Twenty Amino Acids 20 different amino acids make up proteins H H3N+ C CH3 CH CH2 NH H2C H2N Nonpolar Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro) H3C Figure 5.17 S 20 different amino acids make up proteins

Polar Electrically charged OH CH2 C H H3N+ O CH3 CH SH NH2 Polar Electrically charged –O NH3+ NH2+ NH+ NH Serine (Ser) Threonine (Thr) Cysteine (Cys) Tyrosine (Tyr) Asparagine (Asn) Glutamine (Gln) Acidic Basic Aspartic acid (Asp) Glutamic acid (Glu) Lysine (Lys) Arginine (Arg) Histidine (His)

Amino Acid Polymers Amino acids Are linked by peptide bonds.

Protein Conformation and Function A protein’s specific conformation (shape) determines how it functions.

Four Levels of Protein Structure 1. Primary structure: Is the unique sequence of amino acids in a polypeptide. Figure 5.20 – Amino acid subunits +H3N Amino end o Carboxyl end c Gly Pro Thr Glu Seu Lys Cys Leu Met Val Asp Ala Arg Ser lle Phe His Asn Tyr Trp Lle

2. Secondary structure: Is the folding or coiling of the polypeptide into a repeating configuration. Includes the  helix and the  pleated sheet. O C  helix  pleated sheet Amino acid subunits N H R H Figure 5.20

Is the overall three-dimensional shape of a polypeptide. 3. Tertiary structure: Is the overall three-dimensional shape of a polypeptide. Results from interactions between amino acids and R groups. CH2 CH O H O C HO NH3+ -O S CH3 H3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hyrdogen bond Ionic bond Disulfide bridge

4. Quaternary structure: Is the overall protein structure that results from the aggregation of two or more polypeptide subunits. Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme

Review of Protein Structure +H3N Amino end Amino acid subunits helix

Sickle-Cell Disease: A Simple Change in Primary Structure Results from a single amino acid substitution in the protein hemoglobin

Sickle-cell hemoglobin Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin A Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen   10 m Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced.  subunit 1 2 3 4 5 6 7 Normal hemoglobin Sickle-cell hemoglobin . . . Figure 5.21 Exposed hydrophobic region Val Thr His Leu Pro Glul Glu Fibers of abnormal hemoglobin deform cell into sickle shape.

What Determines Protein Conformation? Protein conformation Depends on the physical and chemical conditions of the protein’s environment. Temperature, pH, etc. affect protein structure.

Denaturation is when a protein unravels and loses its native conformation (shape). Renaturation Denatured protein Normal protein Figure 5.22

The Protein-Folding Problem Most proteins: Probably go through several intermediate states on their way to a stable conformation. Denatured proteins no longer work in their unfolded condition. Proteins may be denatured by extreme changes in pH or temperature.

Chaperonins: Are protein molecules that assist in the proper folding of other proteins Hollow cylinder Cap Chaperonin (fully assembled) Steps of Chaperonin Action: An unfolded poly- peptide enters the cylinder from one end. The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. Correctly folded protein Polypeptide 2 1 3 Figure 5.23

Aim: How can we describe Nucleic acids and their association with life Aim: How can we describe Nucleic acids and their association with life? Do Now: Is it good to have a very high fever? Why or why not? Homework: Review notes. Short Quiz on FRIDAY Chapters 2 and 3

4. Nucleic Acids Nucleic acids store and transmit hereditary information. Genes: Are the units of inheritance. Program the amino acid sequence of polypeptides. Are made of nucleotide sequences on DNA.

The Roles of Nucleic Acids There are two types of nucleic acids: Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)

Deoxyribonucleic Acid DNA: Stores information for the synthesis of specific proteins. Found in the nucleus of cells. Directs RNA synthesis (transcription) Directs protein synthesis through RNA (translation)

The Structure of Nucleic Acids 5’ end 5’C 3’ end OH Figure 5.26 O Nucleic acids Exist as polymers called polynucleotides (a) Polynucleotide, or nucleic acid

Each polynucleotide Consists of monomers called nucleotides Sugar + phosphate + nitrogen base Nitrogenous base Nucleoside O O O P CH2 5’C 3’C Phosphate group Pentose sugar (b) Nucleotide Figure 5.26

Nucleotide Polymers Nucleotide polymers Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

The DNA Double Helix Cellular DNA molecules: Have two polynucleotides that spiral around an imaginary axis. Form a double helix.

The DNA double helix Consists of two antiparallel nucleotide strands 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand A 5’ end New strands Figure 5.27

A,T,C,G The nitrogenous bases in DNA Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)

DNA and Proteins are Tape Measures of Evolution Molecular comparisons Help biologists sort out the evolutionary connections among species