Ch 4: Carbon ChemistryCh 5: Macromolecules

2016

Chapter 4 and 5From Topic 2.1Essential idea: Living organisms control their composition by a complex web of chemical reactions.Nature of science: Falsification of theories—the artificial synthesis of urea helped to falsify vitalism. (1.9)Understandings:• Molecular biology explains living processes in terms of the chemical substances involved.• Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.• Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.• Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensationreactions.• Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.Applications and skills:• Application: Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.• Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.• Skill: Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

Guidance:• Only the ring forms of D-ribose, alpha–D-glucose and beta-D-glucose are expected in drawings.• Sugars include monosaccharides and disaccharides.• Only one saturated fat is expected and its specific name is not necessary.• The variable radical of amino acids can be shown as R. The structure of individual R-groups does not need to be memorized.• Students should be able to recognize from molecular diagrams that triglycerides, phospholipids and steroids are lipids. Drawings of steroids are not expected.• Proteins or parts of polypeptides should be recognized from molecular diagrams showing amino acids linked by peptide bonds.Aims:• Aim 7: ICT can be used for molecular visualization of carbohydrates, lipids and proteins in this sub-topic and in 2.3 and 2.4.• Aim 6: Food tests such as the use of iodine to identify starch or Benedict’s reagent to identify reducing sugars could be carried out.

Carbon Chemistry

• Organic Chemistry – branch of chemistry dealing with carbon.

• Organic Molecules- Molecules that have carbon.

CrashCourse: Carbon Intro*:http://www.youtube.com/watch?v=QnQe0xW_JY4

CarbonUnderstanding: Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.

• Carbon forms four bonds– Why?

• Can effect three dimensional shape of molecules.

• Variations on carbon skeletons– Length– Shape– Number and location of

bonds– Other elements

Methane, CH4

Functional Groups• See separate notes or

Figure 4.10 of Campbell 7th edition textbook*

Intro to MacromoleculesUnderstanding:• Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

• There are four main large organic polymers1) Carbohydrates2) Lipids3) Proteins4) Nucleic Acids

• Polymers are long molecules consisting of many similar or identical building blocks connected by covalent bonds. These repeating subunits are called monomers, also known as the building blocks.

Synthesis and Breakdown of Polymers• Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensationreactions.• Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

• Synthesis (making of) polymers from monomers occurs in dehydration reaction or condensation reaction.

• Disassembly of polymers into monomers occurs in hydrolysis.• Base on the IB standards above, match the terms.*

Dehydration Reaction• AKA dehydration synthesis and condensation reactions

- Linking molecules by the removal of water.

Dehydration Reaction and Hydrolysis Animation: http://resource.rockyview.ab.ca/t4t/bio20/mm/m7/hydrolysis/Bio20_Hydrolysis_Final.swf

Hydrolysis• Hydrolysis: “hydro” means water; “lysis” means to break;

this is the process of breaking polymers with the addition of water to break the covalent bonds found in a polymer molecule.

• Hydrolytic enzymes are enzymes that work by reversing the condensation reactions, breaking polymers into monomers.

• Examples of hydrolytic enzymes are digestive enzymes which break down the food you eat.

Chapter 5: CarbohydratesFrom Topic 2.1Guidance: • Only the ring forms of D-ribose, alpha–D-glucose and beta-D-glucose are expected in drawings.• Sugars include monosaccharides and disaccharides. From Topic 2.3Essential idea: Compounds of carbon, hydrogen and oxygen are used to supply and store energyUnderstanding: Monosaccharide monomers are linked together by condensation reactions to form disaccharides and polysaccharide polymers.Application & Skills: • Application: Structure and function of cellulose and starch in plants and glycogen in humans.• Skill: Use of molecular visualization software to compare cellulose, starch and glycogen.Guidance: • The structure of starch should include amylose and amylopectin.• Sucrose, lactose and maltose should be included as examples of disaccharides produced by combining monosaccharides.Utilization: Potatoes have been genetically modified to reduce the level of amylose to produce a more effective adhesive. From Topic 6.1 (introduced in HL 1 but reinforced in HL 2)Utilization: • Some hydrolytic enzymes have economic importance, for example amylase in production of sugars from starch and in the brewing of beer.

Chapter 5: Carbohydrates• Sugars include monosaccharides and disaccharides.

• Carbohydrates: Organic molecules made of sugars and their polymers.• Its monomers are simple sugars called

monosaccharides; “mono” mean one “saccharides” means sugar

Monosaccharides• Only the ring forms of D-ribose, alpha–D-glucose and beta-D-glucose are expected in drawings.

• Are single sugars • Empirical formula is CH2O • Can be made into more complex structures• Ex: Glucose, Galactose, Fructose.

- Glucose can be produced by photosynthesis with the use of CO2, light, and H2O

Alpha glucose Galactose

Disaccharides• Sugars include monosaccharides and disaccharides.Understanding: Monosaccharide monomers are linked together by condensation reactions to form disaccharides and polysaccharide polymers.

• Disaccharide: two monosaccharides linked together by glycosidic linkage during dehydration reaction

• Ex: Maltose, lactose, and sucrose

Types of Disaccharides• Sucrose, lactose and maltose should be included as examples of disaccharides produced by combining monosaccharides.

• Maltose: Use in brewing• Glucose and Glucose

• Lactose: Transport Sugar in Milk• Glucose and Galactose

• Sucrose: Transport Sugar in Plants• Glucose and Fructose

PolysaccharidesUnderstanding: Monosaccharide monomers are linked together by condensation reactions to form disaccharides and polysaccharide polymers.Application & Skills: • Application: Structure and function of cellulose and starch in plants and glycogen in humans.• Skill: Use of molecular visualization software to compare cellulose, starch and glycogen.Guidance: • The structure of starch should include amylose and amylopectin.Utilization: Potatoes have been genetically modified to reduce the level of amylose to produce a more effective adhesive.

• Polysaccharides: Are macromolecules, made of a few hundred or thousand monosaccharides.

• Functions• Act as energy storage

• Ex: Starch, Glycogen• Act as structural support

• Ex: Cellulose and Chitin

Storage PolysaccharidesUtilization: Potatoes have been genetically modified to reduce the level of amylose to produce a more effective adhesive.*• Some hydrolytic enzymes have economic importance, for example amylase in production of sugars from starch and in the brewing of beer.**

Starch: storage polysaccharide of plants- made of only α-glucose monomers- Has two components: amylose

(unbranched) and amylopectin (branched with 1-6 glycosidic linkages)

Glycogen: storage polysaccharide of animals- made of only α-glucose monomers- Similar to amylopectin but more

branched - stored in muscle and liver

Structural Support PolysaccharidesCellulose: structural support in plants- Found in cell walls - Made of β-glucose monomers- Straight molecule (unbranched)- Only certain enzymes can breakdown the

β linkages of cellulose; therefore, not all organisms can breakdown cellulose

Chitin: structural support in athropods- Made of acetylglucosamine monomers,

amino sugar- Forms exoskeleton- Also found in fungi- Similar to cellulose but contains nitrogen

appendage on carbon #2

Starch vs. Cellulose

Starch vs. Cellulose vs. Glycogen Skill: Use of molecular visualization software to compare cellulose, starch and glycogen.

Chapter 5: Lipids From Topic 2.1

Guidance: • Only one saturated fat is expected and its specific name is not necessary.• Students should be able to recognize from molecular diagrams that triglycerides, phospholipids and steroids are lipids. Drawings of steroids are not expected. From Topic 2.3Essential idea: Compounds of carbon, hydrogen and oxygen are used to supply and store energy.Nature of science: Evaluating claims—health claims made about lipids in diets need to be assessed (5.2).Understandings: • Fatty acids can be saturated, monounsaturated or polyunsaturated.• Unsaturated fatty acids can be cis or trans isomers.• Triglycerides are formed by condensation from three fatty acids and one glycerol.Application & Skills: • Application: Scientific evidence for health risks of trans fats and saturated fatty acids.• Application: Lipids are more suitable for long-term energy storage in humans than carbohydrates.• Application: Evaluation of evidence and the methods used to obtain the evidence for health claims made about lipids.• Skill: Determination of body mass index by calculation or use of a monogram.Guidance: • Named examples of fatty acids are not required.International-mindedness: Variation in the prevalence of different health problems around the world could be discussed including obesity, dietary energy deficiency, kwashiorkor, anorexia nervosa and coronary heart disease.Aim 8: There are social implications of obesity.

• Students should be able to recognize from molecular diagrams that triglycerides, phospholipids and steroids are lipids. Drawings of steroids are not expected.Essential idea: Compounds of carbon, hydrogen and oxygen are used to supply and store energy.

• Lipids: diverse group of organic compounds that are insoluble in water, but will dissolve in non-polar solvents.

Examples:(1) Fats/oils(2) phospholipids(3) steroids

Lipids

• Triglycerides are formed by condensation from three fatty acids and one glycerol.• Named examples of fatty acids are not required.

• Fats store large amounts of energy• Made of glycerol backbone and 3 fatty acids chains• Connected by ester linkages• Forming a triglyceride molecule (aka fat molecule,

triacylglycerol)

(1) Fats/Oils

Characteristics of Fats/Oils• Not soluable in water• Source of variation is the fatty acids

– Can all be same– Or all three different– Vary in length– Vary in number and location of double bonds.

Saturated vs. Unsaturated Fats

• No double bonds • Carbon has max number of

hydrogens, therefore, “saturated”

• Usually solid at room temp• Most animal fats, such as

bacon grease, lard, butter

• One or more double bond(s) present

• Double bonds can be either cis or trans*

• Tails kink at double bonds; Can’t pack close enough to solidify at room temp

• Usually liquid at room temp

• Most plant fats, such as corn oil, olive oil, peanut oil

• Fatty acids can be saturated, monounsaturated or polyunsaturated.• Unsaturated fatty acids can be cis or trans isomers.

Function of Fats• Application: Lipids are more suitable for long-term energy storage in humans than carbohydrates.

1) Long-term energy storage- More energy less weight than other molecules

2) Cushions vital organs3) Act as insulation

Phospholipids• Glycerol and two fatty acids with a

phosphate on the third. They usually have a third group as well.

• Make up the major component of cell membrane.

• Show differing interaction with water due to its polar, hydrophilic head and nonpolar, hydrophobic tails.

• Micelle Intro Video: http://www.uic.edu/classes/bios/bios100/lectures/membranes01.htm

• Micelle Formation Video*: https://www.youtube.com/watch?v=boRRoAwjyjI

Steroids• Steroids: lipids that have four fused carbon

rings with various functional groups.• Cholesterol is an important steroid

• Precursor to many other steroid molecules such as…

• testosterone, estrogen, etc…• major component of cell membranes• contributes to atherosclerosis

Fat TransportNature of science: Evaluating claims—health claims made about lipids in diets need to be assessed (5.2).• Application: Scientific evidence for health risks of trans fats and saturated fatty acids.• Application: Evaluation of evidence and the methods used to obtain the evidence for health claims made about lipids.• Skill: Determination of body mass index by calculation or use of a monogram.***

• Chylomicrons: A small fat globule composed of protein and lipid; found in the blood and lymphatic fluid where they serve to transport fat from its port of entry in the intestine to the liver and to adipose tissue.

• LDL (bad) vs HDL (good)*: low density lipoprotein vs. high density lipoproteinLDL cholesterol- contribute to plaque, causing atherosclerosisHDL cholesterol- removes LDL cholesterol from arterieshttp://www.wiley.com/college/pratt/0471393878/instructor/animations/lipoproteins/index.html**

Chapter 5: ProteinsFrom Topic 2.1 Guidance:• The variable radical of amino acids can be shown as R. The structure of individual R-groups does not need to be memorized.• Proteins or parts of polypeptides should be recognized from molecular diagrams showing amino acids linked by peptide bonds. From Topic 2.4Essential idea: Proteins have a very wide range of functions in living organisms.Nature of science: Looking for patterns, trends and discrepancies—most but not all organisms assemble proteins from the same amino acids (3.1).Understandings:• Amino acids are linked together by condensation to form polypeptides.• There are 20 different amino acids in polypeptides synthesized on ribosomes.• Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.• The amino acid sequence of polypeptides is coded for by genes.• A protein may consist of a single polypeptide or more than one polypeptide linked together.• The amino acid sequence determines the three-dimensional conformation of a protein.• Living organisms synthesize many different proteins with a wide range of functions.• Every individual has a unique proteome.

Applications and skills:• Application: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.• Application: Denaturation of proteins by heat or by deviation of pH from the optimum.• Skill: Drawing molecular diagrams to show the formation of a peptide bond. Guidance:• The detailed structure of the six proteins selected to illustrate the functions of proteins is not needed.• Egg white or albumin solutions can be used in denaturation experiments.• Students should know that most organisms use the same 20 amino acids in the same genetic code although there are some exceptions. Specific examples could be used for illustration.Utilization:• Proteomics and the production of proteins by cells cultured in fermenters offer many opportunities for the food, pharmaceutical and other industries.Aims:• Aim 7: ICT can be used for molecular visualization of the structure of proteins.• Aim 8: Obtaining samples of human blood for immunological, pharmaceutical and anthropological studies is an international endeavor with many ethical issues.

From 3.1 Applications and skills:• Application: The causes of sickle cell anemia, including a base substitution mutation, a change to the base sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.Guidance: • Students should be able to recall one specific base substitution that causes glutamic acid to be substituted by valine as the sixth amino acid in the hemoglobin polypeptide. From Topic 2.7 (further discussed in Protein Synthesis Unit of HL 1)Essential idea: Genetic information in DNA can be accurately copied and can be translated to make the proteins needed by the cell.• Aim 8: There are ethical implications in altering the genome of an organism in order to produce proteins for medical use in humans. From Topic 7.1 (further discussed in Protein Synthesis Unit of HL 1)Understandings:• Some regions of DNA do not code for proteins but have other important functions.

From Topic 7.2 (further discussed in Protein Synthesis Unit of HL 1)Understandings:• Gene expression is regulated by proteins that bind to specific base sequences in DNA.

From Topic 7.3 (further discussed in Protein Synthesis Unit of HL 1)Understandings:• Free ribosomes synthesize proteins for use primarily within the cell.• Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes.• The sequence and number of amino acids in the polypeptide is the primary structure.• The secondary structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen bonding.• The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups.• The quaternary structure exists in proteins with more than one polypeptide chain.Guidance:• Polar and non-polar amino acids are relevant to the bonds formed between R groups.• Quaternary structure may involve the binding of a prosthetic group to form a conjugated protein. From Topic 11.2 (introduced in HL 1 but reinforced in HL 2)Guidance:• Calcium ions and the proteins tropomyosin and troponin control muscle contractions.

Chapter 5: Proteins Continue

Proteins• Amino acids are linked together by condensation to form polypeptides.• The amino acid sequence of polypeptides is coded for by genes.• Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.

• Proteins are polypeptide chains made of amino acids by condensation reactions.• One of the four macromolecules consisting of one or

more polypeptide chains folded into a specific conformation.

Nature of science: Looking for patterns, trends and discrepancies—most but not all organisms assemble proteins from the same amino acids (3.1).• There are 20 different amino acids in polypeptides synthesized on ribosomes.• The amino acid sequence of polypeptides is coded for by genes.• Polar and non-polar amino acids are relevant to the bonds formed between R groups.• Students should know that most organisms use the same 20 amino acids in the same genetic code although there are some exceptions. Specific examples could be used for illustration.

• Amino acids are the monomers of proteins.• Are coded by genes (DNA).• There are 20 common amino acids are grouped by their

properties– Hydrophobic, acids, bases…– Polar and Non-polar help proteins stay oriented in

membranes, create channels, and active site binding.

Amino Acids

Functions of ProteinsEssential idea: Proteins have a very wide range of functions in living organisms.• Living organisms synthesize many different proteins with a wide range of functions.• Application: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.• The detailed structure of the six proteins selected to illustrate the functions of proteins is not needed.

• Functions… there are too many:• Structural support (Keratin, collagen)• Transport• Storage• Signaling (insulin, rhodopsin)• Movement (Actin, Myosin)• Defense (Immunoglobulins)• Catalysts (Rubisco, Lactase)• Made of 20 amino acid monomers

Polar Amino Acids

Nonpolar Amino Acids

Electrically Charged Amino Acids

How Peptide Bond Forms• The variable radical of amino acids can be shown as R. The structure of individual R-groups does not need to be memorized.• Proteins or parts of polypeptides should be recognized from molecular diagrams showing amino acids linked by peptide bonds.

Protein Conformation• The shape determines function• The native conformation is found

under normal biological conditions.

• Four Levels of Protein Structure: • Primary, Secondary, Tertiary,

and Quaternary

Primary Structure• The sequence and number of amino acids in the polypeptide is the primary structure.• The amino acid sequence determines the three-dimensional conformation of a protein.

Change in Primary Structure• Application: The causes of sickle cell anemia, including a base substitution mutation, a change to the base sequence of mRNA transcribed from it and a change to the sequence of a polypeptide in hemoglobin.• Students should be able to recall one specific base substitution that causes glutamic acid to be substituted by valine as the sixth amino acid in the hemoglobin polypeptide.

Secondary Structure• The secondary structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen bonding.

• Hydrogen bonds dictate the alpha-helix coils or beta-pleated sheets

Tertiary Structure• The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups.

• Dominant interactions: • Hydrophobic interactions• Ionic bonds (salt bridges)• Disulfide bridges b/w

cysteines only

Quaternary Structure• A protein may consist of a single polypeptide or more than one polypeptide linked together.• The quaternary structure exists in proteins with more than one polypeptide chain. • Quaternary structure may involve the binding of a prosthetic group to form a conjugated protein.

• When more than one polypeptide chain (multiple subunits) combined

• Subunits can be the same or different

Protein Structure Review: http://www.bcconline.com/biol10rs/Pearson-Animations/protein_structure.swf

• Fibrous:– Keratin- hair and feathers– Elastin- ligaments and blood vessels– Collagen- Most abundant in body. Connective tissue and

cartilage. • Globular:

– Enzymes- Catalyze reactions– Hormones- signal (insulin)– Antibodies- bind/recognize invaders

Shape leads to Function

Denaturation• Application: Denaturation of proteins by heat or by deviation of pH from the optimum.• Egg white or albumin solutions can be used in denaturation experiments.

• Denaturation: loss of protein confirmation (loss of shape)• hydrophobic vs Hydrophilic solvent• chemical agents• pH• heat• Ionic strength Frying an Egg: http://www.sumanasinc.com/webcontent/animations/content/proteinstructure.html

Proteome• Every individual has a unique proteome.• Proteomics and the production of proteins by cells cultured in fermenters offer many opportunities for the food, pharmaceutical and other industries.• Aim 7: ICT can be used for molecular visualization of the structure of proteins.• Aim 8: Obtaining samples of human blood for immunological, pharmaceutical and anthropological studies is an international endeavor with many ethical issues.

• Proteome: entire set of proteins coded by the genomeProteomics: http://www.dnaftb.org/41/animation.html

Chapter 5: Nucleic AcidsFrom Topic 2.6Essential idea: The structure of DNA allows efficient storage of genetic information.Nature of science: Using models as representation of the real world—Crick and Watson used model making to discover the structure of DNA (1.10).Understandings:• The nucleic acids DNA and RNA are polymers of nucleotides.• DNA differs from RNA in the number of strands present, the base composition and the type of pentose.• DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs (further discussed in the DNA Unit of HL 1).Applications and skills:• Application: Crick and Watson’s elucidation of the structure of DNA using model making.• Skill: Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentoses and bases.

Nucleic Acids• Application: Crick and Watson’s elucidation of the structure of DNA using model making.Nature of science: Using models as representation of the real world—Crick and Watson used model making to discover the structure of DNA (1.10).

• Nucleic Acids: transmit hereditary information• Protein conformation is determined by the primary structure. Primary

structure is determined by genes. Genes consist of segments of DNA that code for a particular series of amino acids.

DNA vs. RNA• Functions in protein synthesis• Sites of protein synthesis is on the

ribosomes (made of RNA and protein)• mRNA carries coded info from nucleus

to cytoplasm (in eukaryotes).• Flow of genetic information

DNA RNA Protein

• The nucleic acids DNA and RNA are polymers of nucleotides.• DNA differs from RNA in the number of strands present, the base composition and the type of pentose.• DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs (further discussed in the DNA Unit of HL 1).

• Contains coded information• Directs its own replication• Passed on from one

generation to another• Found primarily in the nucleus• Makes up genes• Codes for the production of

proteins with RNA intermediate.

DNA to Protein

Nucleus

Genetic message is transcribed from DNA into mRNA.

mRNA-------------->

Moves into cytoplasm.

Cytoplasm

Genetic message translated into a protein.

Nucleotide Structure• Skill: Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentoses and bases.

• Nucleotide• Sugar• Phosphate• Nitrogenous bases

• Adenine = Purine• Guanine = Purine• Cytosine = Pyrimidine• Thymine = Pyrimidine

Pentose Sugar in DNA and RNA• DNA contains deoxyribose in its nucleotide while RNA

contains ribose

Which nucleotide is this? DNA or RNA?

Polymerization of DNA

Biotechnology: A Laboratory Skills Course

Adding Nucleotides

Phosphodiester Link

Using dntps