Chapter 5 - Macromolecules

Chapter 5 - Macromolecules

CHAPTER 5 THE STRUCTURE AND FUNCTION OF LARGE BIOLOGICAL MOLECULES OVERVIEW Macromolecule large, complex molecules made from much smaller units that are essential for cellular processes. Some may be so large that they weigh 100,000 daltons (atomic grams). There are four classes of macromolecules: Carbohydrates Proteins Nucleic acids Lipids are technically not macromolecules, but they are vastly important for life processes 5.1 MACROMOLECULES ARE POLYMERS, BUILT FROM MONOMERS MONOMERS AND POLYMERS Polymer chains of repeating molecules that are similar or identical in structure.

The small subunits that make up a polymer are called monomers. Only three macromolecules are made of polymers: carbohydrates, proteins, and nucleic acids. Well see why lipids dont do this. The chemical bonds that form long polymer chains are made through the loss of a water molecule, called a condensation reaction or dehydration synthesis. Each monomer that binds donates part of a water molecule. One monomer loses a hydrogen (-H) and the other loses a hydroxl group (-OH). This takes energy. WATER BONDING When monomers come together and bond by losing a water molecule, its called a condensation reaction or dehydration synthesis. When the opposite occurs, a water molecule is formed and a polymer chain is broken in a hydrolysis reaction. A lone H reacts and bonds with a hydroxl group. Both reactions are used by our digestive systems. Organic polymers in food are too large to be used as nutrients.

Enzymes (specialized proteins) break down the polymers into monomers or smaller polymers which are absorbed by the microvilli in the small intestine. Body cells then build different polymers that perform a specialized function for that cell type. VARIETY IS THE SPICE OF LIFE There are only 40-50 commonly occurring monomers, but thousands of polymers exist. The differences between polymers can be used to distinguish between unrelated members of the same species, as well as different species. Cells within an organism have their own polymers as well. There are other monomers that occur rarely, but the small number of monomers can be combined in hundreds of thousands of ways, making the variety of available polymers virtually limitless. 5.1 WHAT IF? 1. How many molecules of water are needed to completely hydrolyze a polymer that is ten monomers long? 2. Suppose you eat a serving of fish. Describe the reactions that must occur for the amino acid monomers in the protein of the fish to be converted to new proteins in your body. 5.2 CARBOHYDRATES

SERVE AS FUEL AND BUILDING MATERIAL SUGARS Carbohydrates Include both sugars and their polymers Monosaccharides Are the simplest sugars Can be used for fuel Can be converted into other organic molecules Can be combined into polymers Monosaccharides May be linear Can form rings O H 1C

H HO H H H 2 3 4 C C C 5 C 6 C 6 OH 4 OH OH 3 C H H O 5 H H

OH C OH OH CH2OH 6 5C H H CH2OH 1 H 2 C OH C H 4 O 3 C H CH2OH O H

OH C OH C H 1 H C 2 OH 6 H C OH 4 HO H OH 3 H H Figure 5.3 O 5 (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. H 1 OH 2 OH DISACCHARIDES Disaccharides Consist of two monosaccharides Are joined by a glycosidic linkage [covalent bond formed between two monosaccharides by a dehydration reaction] EXAMPLES OF DISACCHARIDES (a) 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. CH2OH CH2OH

H HO O H OH H H H H OH HO H OH H OH H H OHOH H HO H O H H OH H2O H (b) Dehydration reaction H in the synthesis of O sucrose. Sucrose is a disaccharide formed

from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. H O H H O H O H Glucose O H CH2OH H 1 4 1 glycosidic linkage CH2OH H O H HO HO OH H H H OH

H CH2OH H HO H O H O H OH H 12 glycosidic 1 linkage H O OH CH2OH O 2 H Sucrose H HO CH2OH OH H

H2O Fructose O H O H Maltose H H 4 OH CH2OH O H O Glucose Glucose CH2OH Figure 5.5 O CH2OH POLYSACCHARIDES Polysaccharides

Are polymers of sugars Serve many roles in organisms STORAGE POLYSACCHARIDES Chloroplast Starch Is a polymer consisting entirely of glucose monomers Is the major storage form of glucose in plants Starch 1 m Amylose Amylopectin Figure 5.6 (a) Starch: a plant polysaccharide Glycogen Consists of glucose monomers Mitochondria Is the major storage form of glucose in animals

Giycogen granules 0.5 m Glycogen Figure 5.6 (b) Glycogen: an animal polysaccharide STRUCTURAL POLYSACCHARIDES H Cellulose CH2O H O H OH H H 4 Is a polymer of glucose H Has different glycosidic linkages than starch H OH HO O CH2O

H H O OH H 4 1 OH H HO H C OH glucose H C OH HO C H H C OH H C OH H C OH

H OH glucose (a) and glucose ring structures CH2O H O CH2O H O HO 4 1 OH O OH 1 OH OH CH2O H O CH2O H O O 4 1 OH

OH O 4 1 OH O OH (b) Starch: 1 4 linkage of glucose monomers CH2O CH2O OH OH H H O O O O OH OH OH OH 1 4 O HO OH O O CH2O CH2O OH OH H H (c) Cellulose: 1 4 linkage of glucose monomers Cellulose is a major

component of the tough walls that enclose plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. Figure 5.8 Cell walls Cellulose microfibrils in a plant cell wall Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 0.5 m Plant cells CH2OH OH CH2OH OH O O O O OH OH OH OH O O O

O O O CH OH CH2OH OH 2 H CH2OH OH CH2OH OH O O O O OH OH OH O OH O O O O O CH OH CH OH 2 2OH H CH2OH OH OH CH2OH O O O O OH OH OH O O OH O O O O CH OH OH CH2OH 2 H Glucose monomer Cellulose molecules

A cellulose molecule is an unbranched glucose polymer. Cellulose is difficult to digest Cows have microbes in their stomachs to facilitate this process Chitin, another important structural polysaccharide Is found in the exoskeleton of arthropods Can be used as surgical thread CH2O HO OH H H OH H OH H H NH C O CH3 (a) The structure of the (b) Chitin forms the exoskeleton of arthropods. This cicada chitin monomer. is molting, shedding its old exoskeleton and emerging

Figure 5.9 AC in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. 5.2 WHAT IF? 1. A dehydration reaction joins two glucose molecules to form maltose. The formula for glucose is C6H12O6. What is the formula for maltose? 2. After a cow is given antibiotics to treat an infection, a vet gives the animal a drink of gut culture containing various prokaryotes. Why is this necessary? 5.3 LIPIDS ARE A DIVERSE GROUP OF HYDROPHOBIC MOLECULES LIPIDS Lipids Are the one class of large biological molecules that do not consist of polymers Share the common trait of being hydrophobic FATS Fats Are constructed from two types of

smaller molecules, a single glycerol and usually three fatty acids H H C O OH H C OH H C OH HO H C H H C H H C H H C H H C

H H C H H C H H C H H C H H C H H C H H C H H C H H C H Fatty acid (palmitic acid) H Glycerol (a) Dehydration reaction in the synthesis of a fat

Ester linkage O H H C O C H C H O H C O C O H C H Figure 5.10 C O C H C H H C

H C H H H C H C H H H C H H C H H C H H C H C H H H C H H C H

H C H H C H H C H H C H H C H H C H H C H H C H (b) Fat molecule (triacylglycerol) H C H H C H H C H H C H H C H

H C H H C H H C H H C H H C H H C H H C H H C H H H C C H H H C H H C H

H C H H C H H C H H C H H C H H H C H H H C H H H C H H FATTY ACIDS Fatty acids

Vary in the length and number and locations of double bonds they contain Saturated fatty acids Have the maximum number of hydrogen atoms possible Have no double bonds Stearic acid Figure 5.11 (a) Saturated fat and fatty acid Oleic acid Unsaturated fatty acids Have one or more double bonds Figure 5.11 cis double bond (b) Unsaturated fat and fatty acid causes bending PHOSPHOLIPIDS Phospholipids Have only two fatty acids Have a phosphate group instead of a third fatty acid

Phospholipid structure Consists of a hydrophilic head and hydrophobic tails Figure 5.12 Hydrophobic tails Hydrophilic head O + CH2 N(CH3)3 CH2 O P O O CH2 CH2 CH O O C O C O (a) Structural formula Choline Phosphate Glycerol Fatty acids Hydrophilic head Hydrophobic tails (b) Space-filling model (c) Phospholipid symbol

The structure of phospholipids Results in a bilayer arrangement found in cell membranes WATER Hydrophilic head WATER Hydrophobic tail Figure 5.13 STEROIDS Steroids Are lipids characterized by a carbon skeleton consisting of four fused rings One steroid, cholesterol Is found in cell membranes H3C CH3 Is a precursor for some hormones CH3 CH3 Figure 5.14

HO CH3 5.3 WHAT IF? Suppose a membrane surrounded an oil droplet, as it does in the cells of plant seeds. Describe and explain the form it might take. 5.4 PROTEINS INCLUDE A DIVERSITY OF STRUCTURES, RESULTING IN A WIDE RANGE OF FUNCTIONS PROTEINS HAVE A VARIETY OF FUNCTIONS An overview of protein functions Table 5.1 ENZYMES Enzymes Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate (sucrose) 2 Substrate binds to enzyme. Glucose OH

Enzyme (sucrase) H2O Fructose H O 4 Products are released. 3 Substrate is converted to products. POLYPEPTIDES Polypeptides Are polymers of amino acids A protein Consists of one or more polypeptides AMINO ACID MONOMERS Amino acids Are organic molecules possessing both carboxyl and amino groups Differ in their properties due to differing side chains, called R groups 20 different amino acids make up proteins CH3

CH3 H H3N+ C CH3 O H3N+ C H Glycine (Gly) O C H3N+ C H Alanine (Ala) O C CH2 O H3N+ C H Valine (Val) CH2

CH CH3 CH3 O CH3 CH3 O C H3C O H3N+ C H Leucine (Leu) O CH C O C H Isoleucine (Ile) O Nonpolar CH3

CH2 S NH CH2 CH2 H3N+ C H H3N+ C O Methionine (Met) Figure 5.16 CH2 O C H CH2 O H3N+ C O Phenylalanine (Phe) C H O H2C

CH2 H2N C O C H C O Tryptophan (Trp) Proline (Pro) O OH OH Polar CH2 H3N + C CH O H3N+ C C O H

Serine (Ser) CH2 O H3N+ C O H C CH2 O C H H3N C + O CH2 O H3N + C O Electrically charged H3N+

O NH3+ O CH2 C CH2 CH2 CH2 CH2 CH2 CH2 CH2 O C H3N + C O CH2 C H O H3N+ C

H Aspartic acid (Asp) O C O C O H Glutamine (Gln) NH2 C H H3N C Asparagine (Asn) C O CH2 + Basic O C CH2

O H Acidic C O H Tyrosine (Tyr) Cysteine (Cys) Threonine (Thr) C NH2 O C SH CH3 OH NH2 O Glutamic acid (Glu) NH2+ C Lysine (Lys) H3N+

C H C H CH2 NH CH2 H3N+ CH2 O O NH+ O C O O C O Arginine (Arg) Histidine (His) AMINO ACID POLYMERS Amino acids OH Peptide bond OH Are linked by peptide bonds

CH2 H SH CH2 H N CH2 H C C H N C C OH H N C H O H O H (a) C OH O DESMOSOMES H2O OH DESMOSOMES DESMOSOMES SH Peptide CH2 bond CH2 OH CH2 H H N C C

H O Figure 5.17 (b) Amino end (N-terminus) H H N C C H O N C C OH H O Carboxyl end (C-terminus) Side chains Backbone PROTEIN CONFORMATION AND FUNCTION A proteins specific conformation determines how it functions Two models of protein conformation: Groove (a) A ribbon model Groove

Figure 5.18 (b) A space-filling model FOUR LEVELS OF PROTEIN STRUCTURE Primary structure Is the unique sequence of amino acids in a polypeptide H3N Amino end Gly ProThr Gly Thr Gly + Amino acid subunits Glu CysLysSeu LeuPro Met Val Lys Val Leu Asp AlaVal ArgGly Ser Pro Ala Glu Lle Asp Thr

Lys Ser Lys Trp Tyr Leu Ala Gly lle Ser ProPheHis Glu Ala Thr PheVal Asn His Ala Glu Val Thr Asp Tyr Arg Ser Arg Gly Pro Thr Ser Tyr lle Ala Ala Leu Leu Ser Pro SerTyr Thr Ala Val

Val Glu ThrAsnProLys Figure 5.20 c o o Carboxyl end Secondary structure Is the folding or coiling of the polypeptide into a repeating configuration Includes the helix and the pleated sheet pleated sheet O H H C C N Amino acid subunits C N H R R O H H C C N CC N O H H

R R C H R O C O C N H N H N H O C O C H C R H C R H C R H C R N H O C N H O C O C H C O N H N C C H R H R Figure 5.20 C C N OH H R O C

C H H helix R O H H C C N C C N OH H R O C H H H C N HC C N HC N C N H H C O C C O R R O H O H H C C N R

R N R O C H H NH C N C H O C R R C C O R H C N HC N H O C Tertiary structure Is the overall three-dimensional shape of a polypeptide Results from interactions between amino acids and R groups Hyrdogen bond CH2 CH 2

O H O H3C CH CH3 H3C CH3 CH Hydrophobic interactions and van der Waals interactions Polypeptide backbone HO C CH2 CH2 S S CH2 Disulfide bridge O CH2 NH3+ -O C CH2 Ionic bond Quaternary structure Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen Chains

Iron Heme Chains Hemoglobin SICKLE-CELL DISEASE: A SIMPLE CHANGE IN PRIMARY STRUCTURE Sickle-cell disease Results from a single amino acid substitution in the protein hemoglobin WHAT DETERMINES PROTEIN CONFORMATION? Protein conformation Depends on the physical and chemical conditions of the proteins environment Denaturation Is when a protein unravels and loses its native conformation Denaturation Normal protein Figure 5.22 Denatured protein Renaturation Chaperonins

Are protein molecules that assist in the proper folding of other proteins Polypeptide Cap Correctly folded protein Hollow cylinder Chaperonin (fully assembled) Figure 5.23 2 The cap attaches, causing 3 The cap comes Steps of Chaperonin the cylinder to change shape in off, and the properly Action: such a way that it creates a folded protein is 1 An unfolded polyhydrophilic environment for the released. peptide enters the cylinder from one end. folding of the polypeptide. DETERMINING STRUCTURE X-ray crystallography Is used to determine a proteins three-dimensional structure X-ray diffraction pattern Photographic film Diffracted X-rays X-ray X-ray

beam source Crystal Nucleic acid Protein Figure 5.24 (a) X-ray diffraction pattern (b) 3D computer model 5.4 THINK ABOUT IT Why does a denatured protein no longer function normally? 5.5 NUCLEIC ACIDS STORE, TRANSMIT, AND EXPRESS HEREDITY INFORMATION Amino acid = monomers important for the formation of nucleic acids. All amino acids are made from an amine group (-NH2), a carboxylic group (COOH), and an amino acid specific side group (-R). Polypeptide = long chains of amino acids bound with peptide bonds, covalent bonds between the carboxyl group of one amino and the amine group of another. The sequence of a polypeptide is programmed by a gene, the unit of inheritance found in DNA. TWO TYPES OF NUCLEIC ACIDS DNA = deoxyribonucleic acid and RNA = ribonucleic acid.

Both provide organisms the ability to copy their own complex makeup and pass it to each generation. There are some major differences. Structural Jobs THE CENTRAL DOGMA: STEP 1 DNA RNA proteins The entirety of genetics boils down to this. DNA directs it own replication as well as RNA replication and protein synthesis. DNA molecules are hugely long and complex, made up of hundreds of thousands of genes. Before a cell undergoes mitosis (cell division), the entire DNA sequence is copied and the copy is passed on to the daughter cells. IMPORTANT: DNA may run the show with giving out instructions, but DNA has very little to do with the daily cellular operations DNA makes proteins which carry out all instructions.

FROM DNA TO RNA Each gene is made of a particular sequence of nucleotide bases, and each gene is responsible for the synthesis of a specific type of messenger RNA molecule (mRNA). The mRNA molecules take their information and interact with the cellular machinery that synthesize proteins (called ribosomes). In particular they direct the order of amino acids in a new polypeptide chain. In eukaryotes, DNA is located in the nucleus of cells, but the ribosomes are outside the nucleus in the cytoplasm. DNA cannot travel outside the nucleus, so the mRNA acts as the go-between. Prokaryotic cells dont have nuclei, but they still use mRNA as a middle man NUCLEIC ACID STRANDS Nucleic acid = polymer made of nucleotide monomers. 3 parts: Nitrogenous base Pentose sugar Phosphate group

NITROGENOUS BASES These are rings of C and N that are separated into two more groups: purines and pyrimidines. Purines: 6-membered ring joined to a 5membered ring. 2 purines: adenine and guanine Pyrimidines: single 6-membered ring. 3 pyrimidines: cytosine, thymine, and uracil. All the nucleotides are abbreviated by the first letter of their name. DNA and RNA share three bases, cytosine, guanine, and adenine, but thymine is only found in DNA while uracil is only found in RNA. PENTOSE SUGARS Both DNA and RNA have a 5 ringed sugar joined to the nitrogen base, but in DNA the sugar is called deoxyribose while RNA uses ribose. The main difference between the sugars is the placement of oxygen on the second carbon.

The atoms in the nitrogenous base and the sugar are numbered, meaning the carbon that may or may not have an oxygen is called 2 (2 prime). Its missing in deoxyribose, hence the name. The carbon that is not part of the ring is carbon 5, so 5 carbon. Pentose + nitrogenous base = nucleoside. PHOSPHATES Adding the third piece, the phosphate group, made a nucleoside monophosphate, or nucleotide. Polynucleotides are created with adjacent nucleotides form covalent bonds between the OH on the 3 of one and the phosphate on the 5 of the next. This makes a repeating sugar phosphate backbone. The nitrogenous bases extend off the backbone. One end of the chain is called the 3 end because there is no phosphate bound the OH on the 3 carbon. The other end is the 5 end because that carbon is free. INHERITANCE IS BASED ON REPLICATION OF THE DNA DOUBLE HELIX

DNA is made of two strands that bond together and twist while RNA is a single strand. There is such a thing as a quadruple helix: http://www.huffingtonpost.com/2013/01/23/quadruple-helix-dna_n_252788 2.html?utm_hp_ref=science 1953 James Watson and Francis Crick first proposed the double helix structure of DNA. Other scientists supported their proposal with work of their own, but Watson and Crick tend to get most of the credit. The sugar-phosphate backbone is on the outside and the two backbones run in opposite directions. One runs 5-3 the other runs 3-5. This arrangement is called antiparallel. COMPLEMENTS The nitrogenous bases form pairs on the inside of the sugar-phosphate backbone in DNA. We saw the shapes of the bases before, and because of the shape only certain bases can bond with other certain bases. Adenine ALWAYS with thymine, cytosine ALWAYS with guanine. A-T and C-G. Because of this complementary bonding, we know what one strands sequence is if we have its complement.

During cell division, each strand serves as a template to order the nucleotides into a new complementary strand. GENES AND EVOLUTION DNA, RNA and proteins keep track of the ancestry of an organism. Therefore, scientists can develop a molecular genealogy in order to compare the similarity and heredity lines of species. DNA molecules are passed from parent to offspring, usually without any significant changes. The main reasoning is that is two species appear similar in fossil record and molecular evidence, then the DNA and protein sequences should also be similar. This can be used to compare an entire set of DNA or a specific molecule sequence. Hemoglobin polypeptide: 146 amino acids, humans and gorillas differ by just 1 amino acid, while humans and frogs differ by 67 amino acids. NERD ALERT! http://safeshare.tv/w/xZqeJNUYyx

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