NMAT Biochem

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• The chemistry of living organisms is called biochemistry. • Biochemical molecules tend to be very large and difficult

to synthesize.

• Living organisms are highly ordered. Therefore, living organisms have very low entropy.

• Most biologically important molecules are polymers, called biopolymers.

• Biopolymers fall into three classes: proteins, polysaccharides (carbohydrates), and nucleic acids.

Introduction to

Biochemistry

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Amino Acids

• Proteins are large molecules present in all cells. • They are made up of -amino acids.

• There are two forms of an amino acid: one that is neutral (with -NH₂ and -OH groups) and one that is zwitterionic (with -NH₃+ and -O- groups).

• A zwitterion has both positive and negative charge in one molecule.

• There are about 20 amino acids found in most proteins. • Each amino acid is assigned a three-letter abbreviation.

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Proteins

Amino acids are the basic structural units of proteins. An

amino acid is a compound that contains at least one amino group (-NH₂) and at least one carboxyl group (-COOH)

+_H 3N C C N C C O- + H2O H R₁ H R₂ O O H +_H 3N C C O- + +H3N C C O -H R₁ H R₂ O O Peptide bond 25.3

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Amino Acids

• Our bodies can synthesize about 10 amino acids.

• Essential amino acids are the other 10 amino acids, which have to be ingested.

• The -carbon in all amino acids except glycine is chiral (has 4 different groups attached to it).

• Chiral molecules exist as two nonsuperimposable mirror images.

• The two mirror images are called enantiomers.

• Chiral molecules can rotate the plane of polarized light.

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Amino Acids

• The enantiomer that rotates the plane of polarized light to the left is called L- (laevus = “left”) and the other

enantiomer is called D- (dexter = right).

• Enantiomers have identical physical and chemical properties. They only differ in their interaction with other enantiomers.

• Most amino acids in proteins exist in the L-form.

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Amino Acids

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Polypeptides and Proteins

• Proteins are polyamides.

• When formed by amino acids, each amide group is called a peptide bond.

• Peptides are formed by condensation of the -COOH group of one amino acid and the NH group of another amino acid.

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Polypeptides and Proteins

• The acid forming the peptide bond is named first. Example: if a dipeptide is formed from alanine and

glycine so that the COOH group of glycine reacts with the NH group of alanine, then the dipeptide is called glycylalanine.

• Glycylalanine is abbreviated gly-ala.

• Polypeptides are formed with a large number of amino acids (usually result in proteins with molecular weights between 6000 and 50 million amu).

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Protein Structure

• Primary structure is the sequence of the amino acids in the protein.

• A change in one amino acid can alter the biochemical behavior of the protein.

• Secondary structure is the regular arrangement of segments of protein.

• One common secondary structure is the -helix.

• Hydrogen bonds between N-H bonds and carbonyl groups hold the helix in place.

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Protein Structure

• Pitch is the distance between coils.

• The pitch and diameter ensure no bond angles are strained and the N-H and carbonyl

functional groups are

optimized for H-bonding.

• Tertiary structure is the three dimensional structure of the protein.

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Protein Structure 25.3 Carbon Nitrogen Oxygen R group Hydrogen The structure is held in position by intramolecular hydrogen bonds (………)

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Protein Structure

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Protein Structure

25.3

Intermolecular Forces in a Protein Molecule

ionic forces ionic forces hydrogen bonds _dispersion forces dispersion forces dispersion forces dipole-dipole forces

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Hydrogen Bonds in Parallel and Antiparallel b-pleated Sheets

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• Enzymes are biological catalysts.

• Most enzymes are protein molecules with large molecular masses (10,000 to 106 amu).

• Enzymes have very specific shapes.

• Most enzymes catalyze very specific reactions.

• Substrates undergo reaction at the active site of an enzyme.

• A substrate locks into an enzyme and a fast reaction occurs.

• The products then move away from the enzyme.

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Enzymes

• Only substrates that fit into the enzyme lock can be involved in the reaction.

• If a molecule binds tightly to an enzyme so that another substrate cannot displace it, then the active site is blocked and the catalyst is inhibited (enzyme inhibitors).

• The number of events (turnover number) catalyzed is large for enzymes (103 - 107 per second).

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Enzymes

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Enzyme Catalysis

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• Carbohydrates have empirical formula C_x(H₂O)_y. • Carbohydrate means hydrate of carbon.

• Most abundant carbohydrate is glucose, C₆H₁₂O₆.

• Carbohydrates are polyhydroxy aldehydes and ketones. • Glucose is a 6 carbon aldehyde sugar and fructose 6

carbon ketone sugar.

• The alcohol side of glucose can react with the aldehyde side to form a six-membered ring.

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• Most glucose molecules are in the ring form. • Note the six-membered rings are not planar.

• Focus on carbon atoms 1 and 5: if the OH groups are on opposite sides of the ring, then we have -glucose; if they are on the same side of the ring, then we have -glucose.

• The - and - forms of glucose form very different compounds.

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Disaccharides

• Glucose and fructose are monosaccharides.

• Monosaccharides: simple sugars that cannot be broken down by hydrolysis with aqueous acids.

• Disaccharides are sugars formed by the condensation of two monosaccharides. Examples: sucrose (table sugar) and lactose (milk sugar).

• Sucrose is formed by the condensation of -glucose and fructose.

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Disaccharides

• Lactose is formed from galactose and -glucose.

• Sucrose is about six times sweeter than lactose, a little sweeter than glucose and about half as sweet as fructose. • Disaccharides can be converted into monosaccharides by

treatment with acid in aqueous solution.

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Polysaccharides

• Polysaccharides are formed by condensation of several monosaccharide units.

• There are several different types. Example: starches can be derived from corn, potatoes, wheat or rice.

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Polysaccharides

• Starch is not a pure substance.

• Enzymes catalyze the conversion of starch to glucose. • Starch is poly glucose whereas cellulose is poly

-glucose.

• Enzymes that hydrolyze starch do not hydrolyze cellulose because of the different shapes of the polymers.

• Ingested cellulose is recovered unmetabolized.

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Polysaccharides

• Bacteria in the stomach of animals contain cellulases, which are enzymes that enable animals to use cellulose for food.

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• Nucleic acids carry genetic information.

• DNA (deoxyribonucleic acids) have molecular weights around 6 - 16 106 amu and are found inside the nucleus of the cell.

• RNA (ribonucleic acids) have molecular weights around 20,000 to 40,000 amu and are found in the cytoplasm outside the nucleus of the cell.

• Nucleic acids are made up of nucleotides.

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Nucleic Acids

Nucleic acids are high molar mass polymers that play an

essential role in protein synthesis.

1. Deoxyribonucleic acid (DNA) 2. Ribonucleic acid (RNA)

DNA molecule has 2 helical strands. Each strand is made up of nucleotides.

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• There are three important parts to a nucleic acid: – phosphoric acid unit,

– five carbon sugar (e.g. deoxyribose), and

– nitrogen containing organic base (e.g. adenine).

• DNA and RNA have different sugars (dexoyribose vs. ribose).

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• There are only five bases found in DNA and RNA: – adenine (A),

– guanine (G), – cytosine (C),

– thymine (T found in DNA only), and – uracil (U found in RNA only).

• Nucleic acids are formed by condensing two nucleotides (the phosphoric acid condenses with the O-H group of the sugar).

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The Components of the Nucleic Acids DNA and RNA

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• DNA consists of two deoxyribonucleic acid strands wound together in a double helix.

• The phosphate chains are wrapped around the outside of the DNA molecule.

• Complementary base pairs are formed from bases which optimize H-bonding: T and A or C and G.

• The complementary base pairs are held together by hydrogen bonding.

• During cell division, the DNA double helix unwinds.

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Base-Pair Formation by Adenine and Thymine and by Cytosine and Guanine

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• A new strand is formed when bases attach to each strand of the unwinding double helix.

• Because of the optimized hydrogen bonding, there is only one location for each base.

• Therefore, the order of bases in the new strand is the same as the order of bases in the original strand.

• This is how genetic information is preserved during cell division.

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• DNA structure provides us with the understanding of how protein synthesis occurs, how viruses infect cells, and

Lipids

• Lipids: a heterogeneous class of naturally occurring organic compounds classified together on the basis of common solubility properties.

– insoluble in water, but soluble in organic solvents including diethyl ether, dichloromethane, and acetone

• Lipids include:

– fatty acids, triglycerides, sphingolipids, phosphoacylglycerols, and glycolipids.

– lipid-soluble vitamins.

– prostaglandins, leukotrienes, and thromboxanes. – cholesterol, steroid hormones, and bile acids.

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Protein Synthesis

• The central dogma of molecular biology

– Information contained in DNA molecules is expressed in the structure of proteins.

prote in Transcription Translation DNA re plication DNA mRNA Reverse transcriptase RNA re plication

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Transcription

• Replication involves separation of the two original

strands and synthesis of two new daughter strands using the original strands as templates.

• Transcription: the process by which information encoded in a DNA molecule is copied into an mRNA molecule.

• Translation: the process whereby a base sequence of mRNA is used to create a protein.

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• Metabolism: the sum of all chemical reactions involved in maintaining the dynamic state of a cell or organism.

Pathway: a series of biochemical reactions.

– Catabolism: the biochemical pathways that are involved in generating energy by breaking down large nutrient

molecules into smaller molecules with the concurrent production of energy.

– Anabolism: the pathways by which biomolecules are synthesized.

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