Chapter 5: What Are the Major Types of Organic Molecules?

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Chapter 5: What are the major types of organic molecules?

 polymers

 four major classes of biologically important organic molecules:

 carbohydrates

 lipids

 proteins (and related compounds)

 nucleic acids (and related compounds)

. • Discuss hydrolysis and condensation, and the connection between them.

. many biological molecules are polymers

 polymers: long chains w/ repeating subunits (monomers)

 example: proteins - amino acids  example: nucleic acids – nucleotides

 macromolecules: very large polymers (100s of subunits)

. Polymers  hydrolysis (“break with water”)

. Polymers

 condensation (dehydration synthesis)

. . • Discuss hydrolysis and condensation, and the connection between them.

. Chapter 5: What are the major types of organic molecules?

 four major classes of biologically important organic molecules:

 carbohydrates

 lipids

 proteins (and related compounds)

 nucleic acids (and related compounds)

. • For each organic molecule class, address what they are (structure) and what they are used for (function).

. • Carbohydrates: what are they, and what are they used for?

• What terms are associated with them (including the monomers and the polymer bond name)?

• Give some examples of molecules in this group.

. Carbohydrates

 carbohydrates: carbon, hydrogen, and oxygen

 ratio typically (CH2O)n

 sugars, starches, and cellulose

. Carbohydrates

 main molecules of life for energy storage; consumed for energy production

 some used as building materials

 monosaccharides, disaccharides, and polysaccharides

. Carbohydrates  monosaccharides single monomer

 3, 4, 5, 6, or 7 carbons

 trioses, tetroses, pentoses, hexoses, and heptoses

 pentose examples:

 ribose and deoxyribose

 hexose examples:

 glucose, fructose, and galactose

. Carbohydrates  structural formulas for glucose, fructose, and galactose

 isomers of each other

 glucose and galactose are structural isomers of fructose

 glucose and galactose are diastereomers

. Carbohydrates

 pentose and hexose sugars form ring structures in solution  carbons given position numbers

. Carbohydrates

 ring structures in solution  often creates diastereomers  example: a-glucose and b-glucose

. Carbohydrates

 disaccharides: two monosaccharide units  joined by a glycosidic linkage or bond  condensation  oxygen atom is bound to a carbon from each momomer  linkage typically carbon 1 to carbon 4

. Carbohydrates

 maltose, sucrose, lactose: common disaccharides

 maltose (malt sugar): two glucose subunits

 sucrose (table sugar): glucose + fructose

 lactose (milk sugar): glucose + galactose + . Carbohydrates

 polysaccharides

 number of subunits varies, typically thousands

 can be branched or unbranched

 some are easily broken down and are good for energy storage (examples: starch, glycogen)

 some are harder to break down and are good as structural components (example: cellulose)

. Carbohydrates

 starch: main energy storage carbohydrate of plants

 polymer made from α-glucose units, mostly α1-4 linkages  amylose = unbranched starch  amylopectin = branched starch (branches usually 1-6 linkages)  amyloplasts, a type of plastid for starch storage

. Carbohydrates

 glycogen: main energy storage carbohydrate of animals  very highly branched  more water-soluble  is NOT stored in an organelle  mostly found in liver and muscle cells

. Carbohydrates

 cellulose: major structural component plant cell walls

 b-glucose units

 similar to starch, but note that the b1-4 linkage makes a huge difference

. Carbohydrates

 unlike starch, most organisms cannot digest cellulose

 cellulose is a major constituent of cotton, wood, and paper

 cellulose contains ~50% of the carbon in found in plants

. Carbohydrates

 fibrous cellulose is the “fiber” in your diet  some fungi, bacteria, and protozoa make enzymes that can break down cellulose

 animals that live on materials rich in cellulose, e.g. cattle, sheep and termites, contain microorganisms in their gut that are able to break down cellulose for use by the animal

. Carbohydrates

 carbohydrates can be modified from the basic (CH2O)n formula  many modified carbohydrates have important biological roles

 example: chitin – structural component in fungal cell walls and arthropod exoskeltons

 example: galactosamine in cartilage

 example: glycoproteins and glycolipids cellular membranes

. • Carbohydrates: what are they, and what are they used for?

• What terms are associated with them (including the monomers and the polymer bond name)?

• Give some examples of molecules in this group.

. • Lipids: what are they, and what are they used for?

• What terms are associated with them (including majors classes and bond names)?

• Give some examples of molecules in this group.

. Lipids

 lipids defined by solubility, not structure  oily or fatty compounds  lipids are principally hydrophobic  mainly carbon and hydrogen  some do have polar and nonpolar regions  some oxygen and/or phosphorus, mainly in polar regions

. Lipids

 roles of lipids include serving as:

 membrane structural components

 signaling molecules

 energy storage molecules

. Lipids  major classes of lipids that you need to know are: triacylglycerols (fats) phospholipids

terpenes and terpenoids

. Lipids

 triacylglycerols: glycerol + 3 fatty acids

 glycerol: 3C sugar alcohol w/ 3 (-OH) groups

 fatty acid: long, unbranched hydrocarbon chain w/ (-COOH) at end

. Lipids  saturated fatty acids: no carbon-carbon double bonds (usually solid at room temp)

. Lipids  unsaturated fatty acids: one or more double bonds (usually liquid at room temp)  monounsaturated – one double bond  polyunsaturated – more than one double bond

. Lipids

 about 30 different fatty acids are commonly found in triacylglycerols; most have an even number of carbons

. Lipids  condensation results in an ester linkage between a fatty acid and the glycerol

. Lipids

 names based on number of attached fatty acids:

 one = monoacylglycerol

 two = diacylglycerol

 three = triacylglycerol

. Carboxyl

Glycerol Fatty acid (a) Ester linkage

Palmitic acid

Oleic acid

Linoleic acid

(b) A triacyglycerol

 triacylglycerols (also called triglycerides) are the most abundant lipids, and are important sources of energy

. Lipids

 phospholipids consist of:

 a diacylglycerol molecule

 a phosphate group esterified to the third -OH group of glycerol

 an organic molecule (such as choline) esterified to the phosphate . Lipids

 phospholipids are amphipathic  polar end (the phosphate and organic molecule)  nonpolar end (the two fatty acids)

 this is often drawn with a polar “head” and two nonpolar “tails” . Lipids

 the nonpolar (or hydrophobic) portion of phospholipids tends to stay away from water  the polar (or hydrophilic) portion of the molecule tends to interact with water  this, along with shape, causes phospholipids to form bilayers when mixed with water  because of this character phospholipids are important constituents of biological membranes

. Lipids terpenes are long-chained lipids built from 5-carbon isoprene units  many pigments, such as chlorophyll, carotenoids, and retinal, are terpenes or modified terpenes (often called terpenoids)

. Lipids

 other terpenes/terpenoids include natural rubber and “essential oils” such as plant fragrances and many spices

. Lipids

 steroids are terpene derivatives that contain four rings of carbon atoms  side chains extend from the rings; length and structure of the side chains varies  one type of steroid, cholesterol, is an important component of cell membranes  other examples: many hormones such as testosterone, estrogens . • Lipids: what are they, and what are they used for?

• What terms are associated with them (including majors classes and bond names)?

• Give some examples of molecules in this group.

. • Polypeptides: what are they, and what are they used for?

• What terms are associated with them (including the monomers and the polymer bond name)?

• Give some examples of molecules in this group.

. Proteins (polypeptides)

 macromolecules formed from amino acid monomers

 proteins have great structural diversity and perform many roles

 roles include enzyme catalysis, defense, transport, structure/support, motion, regulation

 protein structure determines protein function . . proteins are polymers made of amino acid monomers linked together by peptide bonds

 amino acids consist of a central or alpha carbon bound to:  a hydrogen atom

 an amino group (-NH2)  a carboxyl group (-COOH)  and a variable side chain (R group)

. proteins are polymers made of amino acid monomers linked together by peptide bonds

 the R group determines the identity and much of the chemical properties of the amino acid  there are 20 amino acids that commonly occur in proteins

 pay attention to what makes an R group polar, nonpolar, or ionic (charged) and thus their hydrophobic or hydrophilic nature

. • Discuss how to tell which of these categories an amino acid falls into: hydrophobic or hydrophilic (and within the hydrophilic, polar or charged).

.  cysteine and tyrosine are actually essentially nonpolar

. Alpha carbon

R group POLAR POLAR hydrophilic = Asparagine Glutamine Tyrosine Serine Theonine Asn Gln Tyr Ser Thr

Exception: mainly hydrophobic ACIDIC BASIC

ELECTRICALLY CHARGED= hydrophilic ELECTRICALLY Aspartic Glutamic Acid Arginine Lysine Histidine Asn Glu Arg Lys His Glycine Alanine Valine Leucine Isoleucine

Gly Ala Val Leu Ile NONPOLAR NONPOLAR = hydrophobic

Tryptophan Proline Cysteine Methionine Phenylalanine Trp Pro Cys Met Phe • Discuss how to tell which of these categories an amino acid falls into: hydrophobic or hydrophilic (and within the hydrophilic, polar or charged).

. proteins are polymers made of amino acid monomers linked together by peptide bonds

 most amino acids have optical isomers; when this is so, the amino acids found in proteins are of the L-configuration  plants and bacteria can usually make their own amino acids; many animals must obtain some amino acids from their diet (essential amino acids)

. proteins are polymers made of amino acid monomers linked together by peptide bonds

 the peptide bond joins the carboxyl group of one amino acid to the amino group of another by a condensation reaction

. proteins are polymers made of amino acid monomers linked together by peptide bonds

 two amino acids fastened together by a peptide bond is called a dipeptide, several amino acids fastened together by peptide bonds are called a polypeptide

. • Discuss the four levels of protein structure.

. Proteins (polypeptides)

 the sequence of amino acids determine the structure (and thus the properties) of a protein

 proteins have 4 levels of organization or structure

. proteins have 4 levels of organization or structure

 primary structure (1) of a protein is the sequence of amino acids in the peptide chain

. proteins have 4 levels of organization or structure

 secondary structure (2) of a protein results from hydrogen bonds involving the backbone, where the peptide chain is held in structures  either a coiled α-helix or  folded β-pleated sheet  proteins often have both types of secondary structure in different regions of the chain

. proteins have 4 levels of organization or structure

 tertiary structure (3) of a protein is the overall folded shape of a single polypeptide chain

 determined by secondary structure combined with interactions between R groups

 NOTE: book defines this in a confusing way, use my way

. interactions between R groups

. proteins have 4 levels of organization or structure  quaternary structure (4) of a protein results from interactions between two or more separate polypeptide chains

 the interactions are of the same type that produce 2 and 3 structure in a single polypeptide chain

 when present, 4 structure is the final three-dimensional structure of the protein (the protein conformation)

. proteins have 4 levels of organization or structure  quaternary structure (4)

 example: hemoglobin has 4 polypeptide chains

 not all proteins have 4 structure

. • Discuss the four levels of protein structure.

. proteins have 4 levels of organization or structure  ultimately the secondary, tertiary, and quaternary structures of a protein derive from its primary structure  …but molecular chaperones may aid the folding process

. proteins have 4 levels of organization or structure  protein conformation determines function  denaturation is unfolding of a protein, disrupting 2, 3, and 4 structure  changes in temperature, pH, or exposure to various chemicals can cause denaturation  denatured proteins typically cannot perform their normal biological function  denaturation is generally irreversible . . Proteins (polypeptides)

 enzymes are biological substances that regulate the rates of the chemical reactions in living organisms

 most enzymes are proteins (covered in some detail later in this course)

. Proteins (polypeptides)

 “related compounds”

 individual amino acids

 modified amino acids

 polypeptides too short to be considered true proteins

 modified short polypeptides

. • Polypeptides: what are they, and what are they used for?

• What terms are associated with them (including the monomers and the polymer bond name)?

• Give some examples of molecules in this group.

. • Nucleic acids: what are they, and what are they used for?

• What terms are associated with them (including the monomers and the polymer bond name)?

• Give some examples of molecules in this group.

. Nucleic acids

 hereditary information

 two classes

 DNA carries the genetic information

 RNA functions in protein synthesis

. Nucleic acids  nucleotide monomers

 ribose or deoxyribose (5-carbon sugar)

 phosphate groups (one or more)

 nitrogenous base

. Nucleic acids

 purines

 pyrimidines

. Nucleic acids

 DNA typically AGCT  RNA typically AGCU

. • What are 5’ and 3’ ends?

• What does “antiparallel” mean in DNA?

. Nucleic acids

 phosphodiester bonds

 condensation

 sugar-phosphate backbone

 specificity in the bases (= genes)

. A nucleotide

Ribose Uracil

Ribose Adenine

A phosphodiester linkage

Cytosine Ribose

Ribose Guanine Nucleic acids  DNA double helix  hydrogen bonds  antiparallel

 RNA  usually single strand  DNA template  folding . • What are 5’ and 3’ ends?

• What does “antiparallel” mean in DNA?

. Nucleic acids

 “related compounds”

 nucleotides

 dinucleotides

 modified nucleotides

. • What are ATP, cAMP, and NAD+? What are their roles in cells?

. some single and double nucleotides have important biological functions

 ATP

 adenosine triphosphate

 important energy carrying compound

. some single and double nucleotides have important biological functions

 cAMP

 cyclic adenosine monophosphate

 hormone intermediary compound

. some single and double nucleotides have important biological functions

 NAD+

 nicotinamide adenine dinucleotide

 electron carrier (metabolic redox)

. • What are ATP, cAMP, and NAD+? What are their roles in cells?

. • Nucleic acids: what are they, and what are they used for?

• What terms are associated with them (including the monomers and the polymer bond name)?

• Give some examples of molecules in this group.