chapter 5: what are the major types of organic molecules? polymers polymers four major classes of...

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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)

http://www.auburn.edu/academic/classes/biol/1020/bowling/

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• 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)


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Polymers hydrolysis (“break with water”)


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Polymers condensation (dehydration synthesis)


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


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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)


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


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• 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.


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Carbohydrates carbohydrates: carbon, hydrogen, and

oxygen

ratio typically (CH2O)n

sugars, starches, and cellulose


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Carbohydrates main molecules of life for energy storage;

consumed for energy production

some used as building materials

monosaccharides, disaccharides, and polysaccharides


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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


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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


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Carbohydrates pentose and hexose sugars form ring

structures in solution carbons given position numbers


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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


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Carbohydrates

maltose, sucrose, lactose: common disaccharides

maltose (malt sugar): two glucose subunits

sucrose (table sugar): glucose + fructose

lactose (milk sugar): glucose + galactose +


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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)


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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


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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


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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


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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


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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


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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


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




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

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



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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


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Lipids roles of lipids include serving as:

membrane structural components signaling molecules energy storage molecules


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Lipids major classes of lipids that you need to know are:

triacylglycerols (fats) phospholipids

terpenes and terpenoids


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Lipids triacylglycerols:

glycerol + 3 fatty acids

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

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


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Lipids saturated fatty acids: no carbon-carbon double

bonds (usually solid at room temp)


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Lipids unsaturated fatty acids: one or more double

bonds (usually liquid at room temp) monounsaturated – one double bond polyunsaturated – more than one double bond


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Lipids

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


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Lipids condensation results in an ester linkage

between a fatty acid and the glycerol


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Lipids

names based on number of attached fatty acids:

one = monoacylglycerol two = diacylglycerol three = triacylglycerol


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Carboxyl

Glycerol(a)

Fatty acid

Ester linkage

(b) A triacyglycerol

Palmitic acid

Oleic acid

Linoleic acid

(c) Palmitic (d) Oleic (e) Linoleic


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Lipids

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


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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


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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”


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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


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Lipidsterpenes 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)


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Lipids other terpenes/terpenoids include

natural rubber and “essential oils” such as plant fragrances and many spices


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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


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

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



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




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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


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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)


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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


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


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cysteine and tyrosine are actually essentially nonpolar


AsparagineAsn

PO

LAR

= h

ydro

phili

c

GlutamineGln

TyrosineTyr

SerineSer

TheonineThr

R group

Alphacarbon

Exception: mainly hydrophobic

AsparticAsn

ELE

CT

RIC

ALL

Y C

HA

RG

ED

= h

ydro

phili

c

Glutamic AcidGlu

ArginineArg

LysineLys

HistidineHis

ACIDIC BASIC

GlycineGly

NO

NP

OLA

R =

hyd

roph

obic

AlanineAla

ValineVal

LeucineLeu

IsoleucineIle

TryptophanTrp

ProlinePro

CysteineCys

MethionineMet

PhenylalaninePhe

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


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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)


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


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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


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• Discuss the four levels of protein structure.


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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


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


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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


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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


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interactions between R groups


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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)


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quaternary structure (4) example: hemoglobin has 4 polypeptide

chains not all proteins have 4 structure


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• Discuss the four levels of protein structure.


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ultimately the secondary, tertiary, and quaternary structures of a protein derive from its primary structure

…but molecular chaperones may aid the folding process


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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


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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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“related compounds” individual amino acids modified amino acids polypeptides too short to be

considered true proteins modified short polypeptides


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




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




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Nucleic acids

hereditary information two classes

DNA carries the genetic information RNA functions in protein synthesis


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Nucleic acids nucleotide monomers

ribose or deoxyribose (5-carbon sugar)

phosphate groups (one or more)

nitrogenous base


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Nucleic acids purines

pyrimidines


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Nucleic acids DNA typically AGCT RNA typically AGCU


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• What are 5’ and 3’ ends?

• What does “antiparallel” mean in DNA?


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Nucleic acids phosphodiester

bonds condensation

sugar-phosphate backbone

specificity in the bases (= genes)


Ribose

Ribose

Ribose

Ribose Guanine

Cytosine

Adenine

Uracil

A nucleotide

A phosphodiesterlinkage

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Nucleic acids DNA double helix

hydrogen bonds antiparallel

RNA usually single

strand DNA template folding


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• What are 5’ and 3’ ends?

• What does “antiparallel” mean in DNA?


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Nucleic acids “related compounds”

nucleotides dinucleotides modified nucleotides


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


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some single and double nucleotides have important biological functions

ATP adenosine triphosphate important energy carrying compound


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cAMP cyclic adenosine

monophosphate hormone

intermediary compound


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NAD+

nicotinamide adenine dinucleotide electron carrier (metabolic redox)


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


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




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