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.

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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

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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)

(c) Palmitic

A triacyglycerol

(d) Oleic

(e) Linoleic

.

Lipids 

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

.

POLAR = hydrophilic

Alpha carbon

R group

Asparagine Asn

Glutamine Gln

Tyrosine Tyr

Serine Ser

Exception: mainly hydrophobic

Theonine Thr

ELECTRICALLY CHARGED= hydrophilic

ACIDIC

Aspartic Asn

Glutamic Acid Glu

BASIC

Arginine Arg

Lysine Lys

Histidine His

NONPOLAR = hydrophobic

Glycine Gly

Alanine Ala

Valine Val

Leucine Leu

Isoleucine Ile

Tryptophan Trp

Proline Pro

Cysteine Cys

Methionine Met

Phenylalanine 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

.

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)

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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

Ribose

Uracil

Adenine

A phosphodiester linkage

Ribose

Ribose

Cytosine

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. .