Chapter 5

The Structure and Function of Macromolecules

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macromolecules = smaller organic molecules that are joined together to make larger molecules

four major classes:proteinscarbohydrateslipidsnucleic acids

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Polymer principles

­most macromolecules are polymers­polymers= many similar or identical building blocks linked together by covalent bonds

­each unit repeated is a monomer

­cells can make and break polymers by reactions­condensation/dehydration reaction = connect monomers together

­requires energy­aided by enzymes­ water is taken out

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Example of a condensation reaction

Example of a hydrolysis reaction

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Hydrolysis reaction = breaks the covalent bonds between the monomers of a polymer

­water is used to break apart polymers

­used greatly in the digestive system aided by enzymes

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Carbohydrates

Function ­ fuel and building material

­ include sugars and polymers­monosaccharides, disaccharides, polysaccharides

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Monosaccharides = simple sugarsgeneral molecular formula = CH O

ex. glucose C H O

­ most sugars end in ­ose­ have a carbonyl group and many hydroxyl groups

­if carbonyl gp is at end = aldose­if not = ketose

­classified by number of carbons in backboneie. glucose = hexose

five carbons = pentosesthree carbons = trioses

­can exist as enantiomers ie. glucose and galactose

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function of monosaccharidesa. fuel = glucose

b. for synthesis of other monomersie. amino acids

fatty acids

­joined together by glycosidic linkage to form a disaccharide (dehydration reaction)

­in aqueous solutions tend to form ring structures

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glucose galactose

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linear vs. ring structure of glucose

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Disaccharides

­made from two monosaccharides­examples

­maltose (malt sugar) = 2 glucoses­sucrose (table sugar) = glucose and fructose

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Polysaccharides

= polymers of hundreds/thousands of monosaccharides (1­4 glycosidic linkages)

­store energy ­ broken down to release energy­are building materials for cell/organism

starch= storage polysaccharide­stored in plants in plastids

glycogen = stored polysaccharide of glucose ­in liver and muscles (1 day supply)

main monomer in polysaccharides is glucose

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cellulose =polysaccharide in plant cell wall­insoluble in humans ­ no enzymes to break

down beta linkages­helps to stimulate mucus production in

digestive tract

­cellulase digests cellulose in some organisms

chitin=polysaccharide used in exoskeletons of arthropods and cell walls of fungi

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cellulose

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use of chitin in exoskeletons of insects and suture thread

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Lipids

­do not have polymers­do not like water; have non polar covalent

bonds­are large molecules

Fat = made of glycerol and fatty acidsglycerol = 3­C skeleton with OH group

attached to each Cfatty acids = COOH gp. attached to long C

skeleton

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ex. triacylglycerol = 3 fatty acids + glycerol joined by an ester linkage

­fatty acids can be same or differentcan have double bonds in different places

Saturated fatty acid = no double bonds; maximum # of hydrogens attached

­are straight chains

unsaturated fatty acid=has double bonds due to hydrogens being removed

­are kinked chains where double bonds located

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Saturated fats­found in animal fats­solid at rm. temp.­can contribute to heart disease

Unsaturated fats­are plant, fish fats­aka = oils­liquid at rm. temp.­can't pack tightly together due to kinks

function = energy storage = cushion organs = insulation

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Phospholipids

­glycerol with two fatty acids and a phosphate gp.(neg. charge)­has hydrophobic tail end (fatty acids)­has hydrophilic head end (phosphate gp)

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­if put in water tails point inward away from water to form a micelle­bilayer arrangement in cell membrane (major components)

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Steroids

= lipids with carbon skeleton (four fused carbon rings)­can have different functional gps. added

cholesterol ­ in cell membranes­precursor for all other steroids­high levels lead to cardiovascular disease

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Proteinsfunctions=

structural support, storage, transport of substances, cell signaling, movement, defensemechanisms

­structurally complex ­ 3D shape

­all made from 20 amino acids

polypeptides = polymers of proteinsprotein= one or more polypeptides folded and coiled into a specific conformation

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Amino acid­four components around a carbon

­hydrogen atom­carboxyl group­amino group­R group (differences in these make the different amino acids

­character of R group determine characteristics of the amino acid

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R groups can be:1. hydrophobic2. hydrophilic3. bases4. acids

amino acids are joined by a dehydration reactionto form peptide bonds

at one end of chain is a carboxyl group and the other end is a amino group

­can be very long chains

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making a polypeptide

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Protein Function

­depends on specific conformation

­order of amino acids determines 3D conformation(emergent property)

­relys on ability to recognize and bind to another molecule

­when it binds it helps a chemical reaction

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Levels of protein structure

Primary structure= the sequence of the amino acids

­determined by the inherited genetic information

Lysozyme (enzyme that attacks bacteria) made of polypeptide of 129 amino acids

hard to predict the 3D structure based on amino acid sequence alone

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Primary structure of a protein

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­sickle cell anemia = abnormal hemoglobin­develops due to a single amino acid change from hemoglobin

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secondary structure = results from hydrogen bonds along the polypeptide backbone

two types:1. coils (an alpha helix)­

right handed coil, R groups extend outward from backbone, hydrogen of N­H of one amino acid is attracted to the oxygen of C=O of another

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2. folds (a beta pleated sheets)­formed from two or more polypeptide chains that are extended and lying next to each other­stabilized by hydrogen bonds between N­H gps on one chain and C=O on the other

ex. silk's structural properties are due to beta pleated sheets (lots of hydrogen bonds)

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spider's silk ­ protein

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Tertiary structure ­ determined by interactions among and between the R groups and the polypeptide backbone

include weak interactions:­hydrogen bonds among polar and/or charged areas­ionic bonds between charged R groups­hydrophobic interactions and van der Waals interactions among hydrophobic R groups

strong covalent bonds ­ disulfide bridges that are between sulfhydryl groups (SH) of cysteine mononers = stabilize the structure

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Tertiary structure

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Quarternary Structure­ happens due to two or more polypeptide subunits coming together

Ex. collagen­ found in connective tissue (tendons, ligaments)­fibrous protein of three polypeptides supercoiled like a rope

hemoglobin ­ globular protein with two copies of two kinds of polypeptides

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Quarternary structure

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Review of protein structure

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Physical and chemical conditions can change the conformation of the protein

pH, salt concentration, temperature and other factors can denature (change the conformation of) the protein

break the hydrogen bonds, ionic bonds, and disulfide bridges that hold the shape together

some proteins can get back their shape, others can't

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Effect on protein

temperature ­ increases molecular movements so breaks hydrogen bonds and hydrophobic interactions

pH ­ changes pattern of ionization of carboxyl and amino groups in R groups; disrupts ionic attractions and repulsions

high conc. of polar substances­ disrupts hydrogen bonds

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­proteins undergo intermediate changes before they reach quarternary structure

chaperonins=proteins that shield out bad influences while the protein structure is being made (form a "cage" until folded properly)

­protein is vulnerable 1. following denaturation, hydrophobic gps

on inside are exposed to outside,so can bind and form aggregates that are

insoluble2. when a protein is just being made and has not folded correctly

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How chaperonins work

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X­ray crystallography ­ tool used to look at protein structure

­form crystal then hit it with x­rays

­pattern of diffraction by the atoms can determine the location of the atoms and a computer then builds a structure

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photo 51 ­ X­ray diffraction of sodium salt of DNA by Rosalind Franklin

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Nucleic Acids

function: store and transmit hereditary information

two types:1. RNA ­ ribonucleic acid

used in protein synthesissingle polynucleotide chain

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2. DNA­ deoxyribonucleic acidused for replication of DNA directs RNA synthesishas information for all cell activities, but proteins

are responsible for implementing the instructions for the DNA

double helix (Watson and Crick ­ 1953)Adenine pairs with thymineCytosine pairs with guanineComplementary strands

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Crick and Watson

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Rosalind Franklin

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structure of nucleic acids

­are polymers of monomers of nucleotides­nucleotide = nitrogen base, a pentose sugar and a phosphate group

Nitrogen bases = rings of carbon and nitrogentwo types:

1. purines: adenine and guaninehave a six­membered ring joined to a

five membered ring2. pyrimidines: thymine, cytosine & uracil

have a single six membered ring

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Pentose sugar:Ribose in RNADeoxyribose in DNA

a pentose sugar + a nitrogen base = nucleoside

a pentose sugar + nitrogen base + phosphate = nucleotide

polynucleotides form by phosphodiester linkages(sugar of one nucleotide attached to phosphate of other nucleotide)

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­each gene has a unique sequence of nitrogen bases and can be hundred or thousands of nucleotides long

DNA and proteins can be used as markers for evolution due to the heredity of it from parents to offspring

­two species that are closely related based on fossil evidence should also be alike in having similar DNA and protein sequences

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