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Chapter 3-2 & 3-3 Biochemistry

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1 Chapter 3-2 & 3-3 Biochemistry
Carbon Compounds Organic compounds, Molecules of Life Macromolecules Why do they matter? Because what goes on at this small scale which I might add has an entirely different set of rules from the large scale, has a huge impact. And with so many billions of atoms having to be in the right place in the right time it’s a miracle we manage to keep this bucket of bolts together. We’ll start small and work our way up.

2 Objectives Define organic compound, name 3 elements commonly found in organic compounds Explain why carbon forms so many different compounds Define functional group and explain its significance Compare condensation reaction with hydrolysis Define monosaccharide, disaccharide, polysaccharide & discuss their significance Relate the sequence of amino acids to the structure of proteins. Relate the structure of lipids to their functions List 2 essential functions of nucleic acids

3 Structural Isomers Molecular formulae are identical, but the structures and chemical properties are different Ethanol: Flammable; colorless; found in alcoholic beverages Ethyl ether is an anesthetic, and starting fluid for diesel engines You can get the most information from the structural, but it takes up space.

4 Metabolism All the chemical reactions of the body Catabolism Anabolism
energy releasing (exergonic) decomposition reactions Anabolism energy releasing (endergonic) synthesis reactions

5 Organic Molecules Carbon compounds and functional groups carbohydrates
lipids proteins nucleotides and nucleic acids

6 Organic Molecules: Carbon
Bonds readily with other carbon atoms, hydrogen, oxygen, nitrogen, sulfur needs 4 more valence electrons Can form rings or long carbon chains that serve as the backbone for organic molecules What is it about carbon that makes it such a good element of compounds found in living things? What alternatives might there be? It’s shape, ability to bond to four things. It can make these great polymer’s that organize and store energy easily. Silicon: So there’s theory that Silicon based life exists

7 Functional Groups Groups of atoms attach to carbon backbone
Determine the properties of organic molecules

8 Monomers and Polymers Monomers Polymers Polymerization
subunits of macromolecules DNA has 4 different monomers (nucleotides) proteins have 20 different monomers (amino acids) Polymers series of monomers bonded together Polymerization the bonding of monomers together to form a polymer caused by a reaction called dehydration synthesis Remember your prefixes: Mono = 1, Poly = many What are some example words? Monotheism, Polytheism,

9 Dehydration Synthesis
Monomers bond together to form a polymer (synthesis), with the removal of a water molecule (dehydration)

10 Hydrolysis Splitting a polymer (lysis) by the addition of a water molecule (hydro) Digestion consists of hydrolysis reactions This reaction is thermodynamically irreversible, so the body uses it in many of its metabolic pathways, Its great for breaking up proteins.

11 Organic Molecules: Carbohydrates
Hydrophilic organic molecule General formula (CH2O)n , n = number of carbon atoms for glucose, n = 6, so formula is C6H12O6 Names of carbohydrates word root sacchar- or the suffix -ose often used monosaccharide or glucose They’ll often going to end in OSE

12 Monosaccharides Three major monosaccharides Simplest carbohydrates
General formula is C6H12O6 structural isomers Three major monosaccharides glucose, galactose and fructose mainly produced by digestion of complex carbohydrates

13 Disaccharides Pairs of monosaccharides Three major disaccharides
sucrose glucose + fructose lactose glucose + galactose maltose glucose + glucose When fruits are frozen just a little the water comes out of them as ice leaving behind more of the sugar making them sweeter.

14 Polysaccharides Starch, cellulose and glycogen
long chains of glucose form these polysaccharides Starch produced by plants is digested by amylase Cellulose gives structure to plants, fiber to our diet Cellulose is great because it is the most abundant biomolecule on the planet. Its in every blade of grass, and tree. And we can’t eat it. Certain microorganisms can, some animals like cows and termites have made a home for these microorganisms in their gut so they can eat grass. Imagine if you were the bioengineer who figured out how to enable people to get their energy from yard grass or trees, you’d solve world hunger.

15 Polysaccharides Glycogen is an energy storage polysaccharide produced by animals Liver cells synthesize glycogen after a meal to maintain blood glucose levels When you have diabetes you can’t process this glycogen correctly. The assembly line backs up, the liver might get too much, and the blood too little.

16 Carbohydrate Functions
Source of energy Conjugated carbohydrates glycolipids external surface of cell membrane glycoproteins mucus of respiratory and digestive tracts proteoglycans carbohydrate component dominant cell adhesion, gelatinous filler of tissues (eye) and lubricates joints

17 Organic Molecules: Lipids
Hydrophobic organic molecule Less oxidized than carbohydrates, have more calories per gram Five primary types fatty acids triglycerides phospholipids eicosanoids steroids

18 Fatty Acids Chain of usually 4 to 24 carbon atoms Carboxyl (acid) group on one end and a methyl group on the other Polymers of two-carbon acetyl groups

19 Fatty Acids Saturated fatty acid - carbon atoms saturated with hydrogen Unsaturated fatty acid - contains C=C bonds that could bond more hydrogen

20 Triglyceride Synthesis (1)
Three fatty acids bonded to glycerol by dehydration synthesis

21 Triglyceride Synthesis (2)
Triglycerides called neutral fats fatty acids bond with their carboxyl ends, therefore no longer acidic

22 Triglycerides Hydrolysis of fats occurs by lipase enzyme
Triglycerides at room temperature liquid called oils, often polyunsaturated fats from plants solid called fat, saturated fats from animals Function - energy storage also insulation and shock absorption for organs

23 Cholesterol All steroids have this 4 ringed structure with variations in the functional groups and location of double bonds The name originates from the Greek chole- (bile) and stereos (solid), as researchers first identified cholesterol in solid form in gallstones.

24 The good, the bad, and the cholesterol
LDL: “Bad” cholesterol Low-density Lipoprotein Builds up as plaques in arteries. Causing Heart Attacks  Hydrogenated oils & trans fatty acids are sources HDL: “Good” cholesterol High-density Lipoprotein Removes LDL cholesterol back to the liver

25 Phospholipids Amphiphilic character
Hydrophobic “tails” similar to neutral fats with two fatty acids attached to glycerol Hydrophilic “head” differs from neutral fat with the third fatty acid replaced with a phosphate group attached to other functional groups

26 A Phospholipid - Lecithin

27 Steroids Cholesterol other steroids derive from cholesterol
cortisol, progesterone, estrogens, testosterone and bile acids required for proper nervous system function and is an important component of cell membranes produced only by animals 85% naturally produced by our body only 15% derived from our diet


29 Organic Molecules: Proteins
Polymer of amino acids 20 amino acids identical except for -R group attached to central carbon amino acid properties determined by -R group The amino acids in a protein determine its structure and function

30 Amino Acids Nonpolar -R groups are hydrophobic
Polar -R groups are hydrophilic Proteins contain many amino acids and are often amphiphilic

31 Peptides A polymer of 2 or more amino acids
Named for the number of amino acids they contain dipeptides have 2, tripeptides have 3 oligopeptides have fewer than 10 to 15 polypeptides have more than 15 proteins have more than 100 Dehydration synthesis creates a peptide bond that joins amino acids

32 Dipeptide Synthesis

33 Protein Structure Secondary structure Tertiary structure
Primary structure determined by amino acid sequence (as the sequence of letters of our alphabet make up different words) Secondary structure α helix (coiled), β-pleated sheet (folded) shapes held together by hydrogen bonds between nearby groups Tertiary structure interaction of large segments to each other and surrounding water Quaternary structure two or more separate polypeptide chains interacting


35 Primary Structure of Insulin
Composed of two polypeptide chains joined by disulfide bridges

36 Conjugated Proteins Contain a non-amino acid moiety called a prosthetic group Hemoglobin has 4 polypeptide chains, each chain has a complex iron containing ring called a heme moiety

37 Hemoglobin

38 Sickle Cell Caused by one different ammino acid in hemoglobin Genetic
Pain in joints No cure at present Strangely Sickle Cell raises resistance to Malaria

39 Protein Conformation and Denaturation
Conformation - overall 3-D shape is crucial to function important property of proteins is the ability to change their conformation opening and closing of cell membrane pores Denaturation drastic conformational change that destroys protein function as occurs with extreme heat or pH often permanent

40 Protein Functions Structure Communication Membrane Transport Catalysis
collagen, keratin Communication some hormones, cell receptors ligand - molecule that reversibly binds to a protein Membrane Transport form channels, carriers (for solute across membranes) Catalysis enzymes are proteins Rollie Fingers Rollie Fingers

41 Protein Functions 2 Recognition and protection Movement Cell adhesion
glycoprotein antigens, antibodies and clotting proteins Movement muscle contraction Cell adhesion proteins bind cells together

42 Enzymes Function as catalysts
promote rapid reaction rates Substrate - the substance an enzyme acts upon Naming Convention enzymes now named for their substrate with -ase as the suffix amylase enzyme digests starch (amylose) Lower activation energy energy needed to get reaction started is lowered enzymes facilitate molecular interaction

43 Enzymes and Activation Energy

44 Enzyme Structure and Action
Active sites area on enzyme that attracts and binds a substrate Enzyme-substrate complex temporarily changes a substrates conformation, promoting reactions to occur Reusability of enzymes enzymes are unchanged by reactions and repeat process Enzyme-substrate specificity active site is specific for a particular substrate Effects of temperature and pH change reaction rate by altering enzyme shape optimum: temp = body temp, pH = location of enzyme

45 Enzymatic Reaction Steps

46 Cofactors and Coenzymes
nonprotein partners, (like iron, copper, zinc, magnesium or calcium ions) may bind to an enzyme and change its shape, creating an active site many enzymes cannot function without cofactors Coenzymes organic cofactors usually derive from water-soluble vitamins pantothenic acid in coenzyme A (required for synthesis of triglycerides and ATP), niacin in NAD+ and riboflavin (B2) in FAD (transfer electrons as H)

47 Coenzyme Action NAD+ involved in ATP synthesis
transfers electrons and energy review redox reactions next

48 Oxidation - Reduction Reactions
molecule releases electrons and energy, often on hydrogen atoms Reduction (negative e- reduces charge) molecule accepts electrons, gains chemical energy (E) AH NAD+  A NADH high E low E low E high E reduced oxidized oxidized reduced state state state state

49 Metabolic Pathways Chain of reactions, each catalyzed by an enzyme
   A  B  C  D A is initial reactant, B+C are intermediates and D is the end product , ,  represent enzymes Regulation of metabolic pathways activation or deactivation of the enzymes in a pathway regulates that pathway end product D may inhibit  or  enzymes cofactors

50 Organic Molecules: Nucleotides
3 principle components nitrogenous base single or double carbon-nitrogen ring sugar (monosaccharide) one or more phosphate groups ATP contains adenine ribose 3 phosphate groups ATP is the universal energy carrying molecule

51 ATP High energy bonds second and third phosphate groups are attached by high energy covalent bonds phosphate groups are negatively charged and naturally repel each other ATPases hydrolyze the 3rd high energy phosphate bond of ATP producing ADP + Pi + energy Kinases (phosphokinases) enzymes that phosphorylate (add the Pi released from ATP to) other enzymes or molecules to activate them

52 ATP

53 Production and Uses of ATP

54 ATP Production - Glycolysis
splits one 6 carbon glucose into two 3 carbon pyruvic acid molecules yield 2 net ATP’s

55 ATP Production - Anaerobic Fermentation
If no oxygen is available pyruvic acid is converted to lactic acid (build up causes muscle soreness) No ATP produced Allows glycolysis to start over (regenerates NAD+)

56 ATP Production - Aerobic Respiration
If oxygen is available pyruvic acid is efficiently consumed yielding 36 more ATP molecules (from the original glucose) Aerobic respiration occurs in mitochondrion

57 Overview of ATP Production

58 Other Nucleotides Guanosine triphosphate (GTP)
may donate a phosphate group (Pi) to other molecules or to ADP Cyclic adenosine monophosphate (cAMP) formed after removal of both high energy Pi’s after chemical signal (first messenger) binds to cell surface, it triggers the conversion of ATP to cAMP (second messenger) to activate effects inside cell Nucleic acids are polymers of nucleotides

59 cAMP

60 Nucleic Acids DNA (deoxyribonucleic acid) RNA (ribonucleic acid)
100 million to 1 billion nucleotides long contains the genetic code for cell division, sexual reproduction, the instructions for protein synthesis RNA (ribonucleic acid) 3 forms of RNA range from 70 to 10,000 nucleotides long carries out instructions given by DNA synthesizes the proteins coded for by DNA

61 1. What is an organic compound?
Carbon covalently bonded to carbon and other elements 2. What property allows carbon compounds to exist in a number of forms? A carbon atom has 4 valence electrons so it can form 4 bonds with other atoms

62 Define functional group and give an example.
Clusters of atoms that influence the moiety of the molecules they make up. 4. How does a polymer form? Condensation reactions between monomers

63 5. How does a polymer break down?
Hydrolysis 6. Comparing the different forms of carbon in a substance allows you to tell how old it is. Is this more useful for organic substances or inorganic substances?

64 Define monosaccharide, disaccharide, polysaccharide
Describe the structure of amino acids and proteins Explain the relationship between an enzyme and its substrate

65 How are the ends of phospholipids different?
Name 2 types of nucleic acids and describe their substances High temperatures or changes can weaken bonds between different parts of a protein changing its shape. How might this change the effectiveness of an enzyme?

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