fields of chemistry inorganic organic all molecules in organic chemistry must contain carbon – in...
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Fields of Chemistry
Inorganic Organic
• All molecules in organic chemistry must contain carbon – in an organified manner – which basically says you need some hydrogens- thus organic chemistry is a “Hydrocarbon” chemistry
• CO2 contains carbon – but since it does not contain hydrogen – it is inorganic
Biochemistry
Animal Plant
Human Other Animals
Since our focus is on human biochemistry – we will discuss the major biochemical molecules
carbohydrates, lipids, proteins and nucleic acids
The Carbohydrates, Lipids, Nucleic Acids have two main commonalities
(1) a monomer to polymer relationship(2) Interaction of Water into the chemical
reactions
Organic Chemistry is a covalently bonded chemistry – thus all the chemical bonds joining monomers are covalent bonds
Monomer to Polymer Relationship• A monomer is as individual unit capable of
repeat• The individual unit is a molecule itself• The monomers chemically bond together to
form “polymers” – the repeated unit• Monomer of carbohydrate is termed a
monosaccharide (glucose is an example)• Monomer Chemical Bond• Polymer •
Interaction (Insertion) of Water into the chemical reactions
H HO • H20 Inserted -- result water molecule splits and
one molecule gets the H and other the OH
• If a molecule of water is introduced into the chemical bond it will split it apart (hydration decomposition or hydrolysis decomposition)
Interaction (Removal) of Water into the chemical reactions
H HO • result H20 removed
• -- result water molecule reformed and chemical bond reformed between the monomers. This is called dehydration (remove water) synthesis (anabolic process)
Carbohydrates• Carbon, hydrogen, and oxygen are in 1:2:1 ratio.• Most important as source of energy.• Monosaccharide – simple sugar. 3-7 carbon atoms.
– Triose – 3 carbons– Tetrose – 4 carbons– Pentose – 5 carbons– Hexose – 6 carbons– Heptose – 7 carbons
• Glucose is a hexose
Glucose
• May form straight chain or a ring structure.• Ring is more common in human body.
Carbon – Why for life?• Carbon has an atomic number of 6 – with 4
electrons in is outer energy level – thus it needs four more electrons. Carbon can combine covalently with 4 atoms to give it its 4 electrons. The fact that one carbon atom can combine with so many atoms – gives it tremendous diversity – thus the basis of life on this planet. x2
• x1 C x3
• x4
Carbon likes to bond to CarbonCarbon Backbone
• Though carbon can bond to 4 different atoms – it generally likes to bond to itself forming a “carbon backbone”
C C C C C C
When I quickly draw a ring structure – the corners always mean carbon unless I put some other atom
there.
Nomenclature Naming of Organic Compounds• In an organic chemistry course this subject would be,
in detail, discussed – but it is beyond the scope of this course.
• Just for example• How many carbons? Prefix - meth 1 eth 2 prop 3 but
4 pent 5 hex 6• Do you have double covalent bonds present in the
molecule? Suffix – ane if no double bonds, ene if double bonds
• C C C versus C C C• Propane Propene
Isomers• Molecules with the same molecular formula but
a change in structural formula
• C6H12O6 is the formula for glucose, fructose and galactose – the atoms are arranged differently in 3 –D space for each of those molecules
• Just like in our large world – shape makes a difference – so is the case in the molecular world – the arrangement of atoms in 3 –D space defines the molecule – switch the atoms around in the molecule and you form a new molecule
ISOMERS
• The body usually treats different isomers as distinct (different) molecules.
• Simple sugars such as glucose and fructose are isomers.
• Fructose is a hexose found in most fruits and in secretions of the male reproductive tract.
• So, separate enzymes and reaction sequences control its breakdown and synthesis.
Types of Isomers
• Structural Isomers• Geometric Isomers (Cis-Trans)• Optical Isomers
Monosaccharide
• The monomer (individual molecule capable of repeat) of a carbohydrate is termed a
“Monosaccharide”• Its empirical formula is CH2O• The most notable monosaccharides
glyceraldehyde (3-carbon carbohydrate), ribose and deoxyribose (5-carbon carbohydrate, glucose, galactose and fructose (6-carbon carbohydrate)
Bonding Carbohydrate monomers together• Monosaccharides bond together by the
removal of a water molecule (dehydration synthesis) to form a covalent bond between the two monosaccharides known as a “glycosidic bond”
• When bond two monosaccharides together termed a disaccharide, when join 3 – 10 together termed an Oligosaccharide – more than 10 together – termed a polysaccharide
Common Disaccharides• Sucrose – table sugar (glucose alpha 1,2 to
fructose)• Maltose – in beer (glucose alpha 1,4 to glucose)• Lactose – in milk (galactose beta 1, 4 to glucose)
Disaccharides
• Most foods contain disaccharides, but all carbohydrates except simple sugars must be broken down by hydrolysis before they can provide useful energy.
• Most commonly used in junk foods and candies, sodas.
Oligosaccharides• Carbohydrates with 3 – 10 monosaccharides bonded
together
• Oligosaccharides are often found as a component of glycoproteins or glycolipids and as such are often used as chemical markers, often for cell recognition.
• An example is ABO blood type specificity. A and B blood types have two different oligosaccharide glycolipids embedded in the cell membranes of the red blood cells, AB-type blood has both, while O blood type has neither.
Polysaccharides• Carbohydrates consisting of greater than 10
monosaccharides bonded together• Food wise some are termed the “starches”
and one is termed “fiber”• Their purposes are either for (1) Storage of energy (glycogen, amylose,
amylopectin) or (2) Structure (Cellulose, chitin)
Polysaccharides
• Can be straight chained or highly branched.• Starches are glucose-based polysaccharides.• Most starches manufactured by plants.• Most starches can be broken down by human
digestive tract.• Cellulose is a polysaccharide that humans
cannot break down.• Provide bulk for digestive purposes.
STARCH
Glycogen
• Animal starch• Branched polysaccharide composed of
interconnected glucose molecules.• Does not dissolve in water.• Liver and muscles manufacture and store
glycogen.
Lipids• Contain carbon, hydrogen, and oxygen, but not in
same ratio as carbohydrates.• In general, contains much less oxygen.• May also contain phosphorous, nitrogen, or
sulfur.• Most lipids are insoluble in water, so there are
special transport mechanisms to carry them in the blood.
Lipids
• Form structural components of all cells.• Important as energy reserves.• Lipids provide twice the energy gram for gram
as carbohydrates.• Fat: 1 gram = 9 calories • Carbohydrates: 1 gram = 4 calories
Lipids
• Account for 10 – 12 percent of body weight (normal or average),
• We will consider 5 types of lipids:• 1. fatty acids• 2. eicosanoids• 3. glycerides• 4. steroids• 5. phospholipids and glycolipids
Unsaturated Fat
Solid Fat versus Liquid Fat at Room Temperature
Fatty acids
• Long carbon chains with hydrogens attached.• One end of the chain ALWAYS has a carboxylic
acid group attached to it.
Typical fatty acids. Note the carboxylic acid end.
Carboxylic acid: CO2H
Fatty acids
• The name carboxyl should help you remember that a carbon and hydoxyl (-OH) group are in it.
• The end opposite the carboxylic acid end is the hydrocarbon “tail”.
• When a fatty acid is placed in solution, only the hydrophilic carboxyl end associates with water molecules.
• The rest of the chain is hydrophobic.
Fatty acids
• Saturated – each carbon atom has four single covalent bonds.
• Unsaturated – Some of the carbon – carbon bonds are double bonds, thus reducing the number of hydrogens.
• Monounsaturated – one double bond in the molecule.
• Polyunsaturated – numerous double bonds in the molecule.
Fatty acids and Health
• Both saturated and unsaturated fats can be broken down for energy.
• Large amounts of saturated fats increases risk of heart disease.
• Current research suggests monounsaturated fats may be more effective than polyunsaturated fats in lowering risk of heart disease.
Fatty acids and Health
• When margarine and vegetable shortening (CRISCO) are manufactured from polyunsaturated fats.
• Hydrogen is added to break double bonds to make the fat more solid (for baking, palatability, etc.), trans fatty acids are produced, which increase risk of heart disease.
Fatty acids and Health
• A carbon in a fatty acid molecule is numbered beginning at the carboxylic acid end.
• The last carbon in the chain is called the “omega” carbon.
• So, if you have a double bond three carbons before the omega carbon, you have an “Omega-3 fatty acid”
Cis versus Trans Fatty Acids
Eicosanoids
• Lipids derived from arichidonic acid.• Arachidonic acid cannot be synthesized by the
body, so we have to get it through diet.• Two major classes of eicosanoids:
– Prostaglandins– Leukotrienes
Virtually all tissues synthesize and respond to prostaglandins, so lekotrienes will be talked about later.
Prostaglandins
• Short chained fatty acids that have 5 of their carbon atoms arranged in rings.
• Coordinate and direct cell activities.• Powerful and effective in small quantities.• Examples: released by damaged tissue to
stimulate pain receptors.• Start uterine contractions in birthing process.
Prostaglandins
Prostaglandins
• Usually do not travel through circulatory system to reach target cell.
• So prostaglandins are called local hormones.
Glycerides
• Individual fatty acids cannot be strung together in a chain like the simple sugars.
• They can be attached to another compound called glycerol.
• The result is a lipid call a glyceride.• A dehydration synthesis can produce a
monoglyceride which is glycerol plus one fatty acid.
Glycerides
• Each additional reaction can produce a diglyceride (glycerol plus two fatty acids) or a triglyceride (glycerol plus three fatty acids).
Triglycerides
• Known as neutral fats.• Have 3 important functions:
Triglyceride function 1
• Fatty deposits in body are energy reserves.• In times of need, the triglycerides are
disassembled to yield fatty acids that can be broken down to form energy.
Triglyceride function 2
• Fat deposits under skin serve as insulation.• Heat loss through a layer of lipids is about
one-third that of other tissues.
Triglyceride function 3
• Fat deposits around organs provide cushioning and protection.
Triglycerides
• Stored in body as lipid droplets within cells.• These absorb and accumulate lipid-soluble
drugs, vitamins, or toxins.• Good and bad: Store vitamins A, D, E and K• Store pesticides such as DDT.• Marijuana Is A Fat Soluble Substance
Function of Cholesterol and other Steroids1. Cholesterol is required to build and maintain cell
membranes.2. Within the cell membrane, cholesterol also
functions in intracellular transport, cell signalling and nerve conduction.
3. Cholesterol is an important precursor molecule for the synthesis of Vitamin D and the steroid hormones, including the adrenal gland hormones cortisol and aldosterone as well as the sex hormones progesterone, estrogens, and testosterone and their derivatives.
Cholesterol StructureCholesterol is a sterol type steroid - are also known as steroid alcohol. When a steroid has an OH (hydroxyl) group at the 3-position of the A-ring – it is termed a
sterol.
Cholesterol
Where does cholesterol come from?
• Obtained from 2 sources:– Absorption from animal products in diet.– Synthesis within the body.
There is a strong link between high cholesterol intake and heart disease.
Sice body makes cholesterol, it is sometimes difficult to lower cholesterol levels only with diet.
Types of cholesterol
• There are two types of cholesterol: "good" and "bad." It's important to understand the difference, and to know the levels of "good" and "bad" cholesterol in your blood. Too much of one type — or not enough of another — can put you at risk for coronary heart disease, heart attack or stroke.
Types of cholesterol
• HDL is the "good" cholesterol which helps keep the LDL (bad) cholesterol from getting lodged into your artery walls. A healthy level of HDL may also protect against heart attack and stroke, while low levels of HDL (less than 40 mg/dL for men and less than 50 mg/dL for women) have been shown to increase the risk of heart disease.
Types of cholesterol
• The 4-ring region of cholesterol is the signature of all steroid hormones (such as testosterone and estrogen). All steroids are made from cholesterol.
• The combination of the steroid ring structure and the hydroxyl (alcohol) group classifies cholesterol as a "sterol." Cholesterol is the animal sterol. Plants only make trace amounts of cholesterol, but make other sterols in larger amounts.
Types of cholesterol
• Because cholesterol contains both a water-soluble region and a fat-soluble region, it is called amphipathic.
• Cholesterol, however, is not water-soluble enough to dissolve in the blood. Along with fats and fat-soluble nutrients, therefore, it travels in the blood through lipoproteins such as LDL and HDL.
Types of cholesterol
• HDL and LDL stand for "high-density lipoprotein" and "low-density lipoprotein." VLDL stands for "very low-density lipoprotein," IDL stands for "intermediate-density lipoprotein" and Lp(a) stands for "lipoprotein (a)."
LDL
• LDL that does not get taken up into cells tends to oxidize. The polyunsaturated fatty acids (PUFA) in its membrane get damaged by free radicals, and then they proceed to damage the protein in the surface, and finally the fatty acids and cholesterol in the core.
• Once LDL oxidizes, it can invade the arterial wall in areas that experience disturbed blood flow, like the points were arteries curve or branch.
LDL
• These areas, especially in people who do not exercise enough, are permeable to large molecules. Oxidized lipids cause them to attract white blood cells and initiate an inflammatory cascade that produces arterial plaque.
HDL
• HDL particles can extract free cholesterol from cell membranes and attach it to fatty acids, producing cholesterol esters. They generally pass this off to LDL and other apoB-containing proteins in exchange for fats, also called triglycerides, and fat-soluble vitamins such as vitamin E. The result is that, over time, HDL tends to be rich in fats and vitamin E, while the other lipoproteins, especially LDL, are rich in cholesterol.
HDL
• HDL delivers vitamin E to the endothelial cells that line the blood vessel wall.
• Both HDL and isolated Vitamin E suppress the ability of these cells to oxidize LDL with free radical-generating enzymes and also suppress their production of inflammatory molecules that attract the white blood cells that invade the arterial wall to form arterial plaques.
Steroids
• Large lipid molecules that share a common, distinctive carbon framework.
Steroid functions
• Regulation of sexual function. Testosterone and Estrogen.
• Regulation of tissue metabolism and mineral balance. Adrenal cortex hormones corticosteroids and calcitrol.
• Derivatives called bile salts required for normal processing and breakdown of dietary fats. Produced in liver and store/secreted by gall bladder.
Phospholipids and glycolipids
• Structurally related.• Body can produce both of them.• Phospholipid – phosphate group links a
diglyceride to a nonlipid group.• Glycolipid – carbohydrate is linked to a
glyceride.
GLYCOLIPID
Protein• A Protein is a polymer made up of monomers
termed “amino acids”
Protein functions
1. Support: structural proteins create a three-dimensional framework for the body and cells.
2. Movement: contractile proteins responsible for muscle contraction. Related proteins responsible for movement of individual cells.
3. Transport: lipids, respiratory gases, minerals, and hormones are bound to transport proteins.
Protein functions
4. Buffering: prevent dangerous changes in pH.5. Metabolic regulation: Enzymes accelerate
chemical reactions in living cells. Enzymes are very sensitive to environmental conditions such as pH and temperature. Control pace and direction of metabolic pathways.
6. Coordination and control: Influence metabolic activities of every cell in body. Can affect a specific function of specific organs or organ systems.
7. Defense: Waterproof proteins of skin, hair, and nails.
• Antibodies- protect from disease• Clotting proteins – restrict bleeding
Proteins are made-up of monomers called “amino acids. There 20 naturally occurring amino acids.
Structure of proteins
• Long chains of amino acids.• Typical protein has about 1000 amino acids.• Largest proteins may have 100,000 or more.• Each amino acid composed of a central carbon
atom to which four groups are attached:– Hydrogen atom– Amino group (-NH2)
– Carboxylic acid group (-COOH)– Variable group known as R or side chain.
Structure of proteins
• Different R groups distinguish one amino acid from another, giving each its unique chemical properties.
• The name amino acid refers to the presence of the amino group and the carboxylic acid group.
• AAs are relatively small, water soluble molecules.
POLYPEPTIDES
Figure 2.17
Amino acids join together by performing dehydration synthesis
Peptide bonds
• Two amino acids can be linked together by dehydration synthesis.
• This creates a covalent bond between the carboxylic acid group of one amino acid and the amino group of another.
• This bond is known as a peptide bond.• Two amino acids joined together would be a
dipeptide.
Peptides
• 2 AA = dipeptide• 3 AA = tripeptide• Tripeptides and larger are called polypeptides• If have more than 100 AA, it is called a
protein.
Charge of a protein
• At pH of body, carboxylic acid groups of AA give up their hydrogens.
• When the carboxylic acid group changes from –COOH to –COO- , they become negatively charged.
• So an entire protein always has a negative charge and is sometimes abbreviated as Pr-
R group still free
Structure of proteins
• The primary structure of proteins:– the order of the amino acids joined together to
make the protein. – Using three letter abbreviations, a bit of a protein
chain might be represented by, for example:• gly-gly-ser-ala is the primary structure for a polypeptide
composed of , glycine, glycine, serine, and alanine, in that order, from the N-terminal amino acid (glycine) to the C-terminal amino acid (alanine).
Structure of proteins
• The secondary structure of proteins:• Within the long protein chains there are regions in
which the chains are organized into regular structures known as alpha-helices (alpha-helixes) and beta-pleated sheets. These are the secondary structures in proteins.
• These secondary structures are held together by hydrogen bonds. These form as shown in the diagram between one of the lone pairs on an oxygen atom and the hydrogen attached to a nitrogen atom:
Structure of proteins
• The tertiary structure of proteins– The tertiary structure of a protein is a description
of the way the whole chain (including the secondary structures) folds itself into its final 3-dimensional shape.
– The tertiary structure of a protein is held together by interactions between the the side chains - the "R" groups.
Structure of proteins
• Quaternary Structure:– refers to the regular association of two or more
polypeptide chains to form a complex.– Multimeric proteins contain two or more
polypeptide chains, or subunits, held together by noncovalent bonds. Quaternary structure describes the number (stoichiometry) and relative positions of the subunits in a multimeric protein.
– There are two major categories of proteins with quaternary structure - fibrous and globular.
Fibrous Proteins:
• fibrous proteins such as the keratins in wool and hair are composed of coiled alpha helical protein chains with other various coils analogous to those found in a rope.
Globular Proteins:
• globular proteins may have a combination of the above types of structures and are mostly clumped into a shape of a ball. Major examples include insulin, hemoglobin, and most enzymes.
Primary Structure – linear sequence of Amino Acids (the only thing DNA codes for directly)
Secondary Structure – does the Polypeptide or protein have repeating regions (alpha helix or beta pleated sheet). Secondary structuring is held together by
hydrogen bonds
Tertiary Structure – describe the 3-D fold of the single stranded Polypeptide or Protein (held together
by different types of chemical bonds depending on location and AA
Quaternary structure – if the protein is made-up of more than one polypeptide chain (strand) – the
quaternary structure is the shape of the entire protein (inclusive of all its strands)
Fibrous Protein (L) Globular Protein (R)
Shape and Function
• The shape of a protein determines its functional properties.
• Then shape is determined by the sequence of the amino acids.
• If one amino acid is changed in a protein consisting of 10,000 or more AA , the shape and function are altered.
Shape and Function
• Several cancers and sickle cell anemia are the result of a sigle change in the AA sequence of a protein.
• Tertiary and quaternary structures depend on the amino acid sequence and also the local environment characteristics.
• If temperature or pH of the surroundings change, it can affect the function of a protein.
Shape and Function
• Protein shape can also be affected by hydrogen bonding to other molecules in solution.
• This is significant especially when considering the functions of the proteins called enzymes.
Enzymes(a Biologic catalyst)
• A catalyst is a chemical additive that accelerates a chemical reaction without itself being consumed in the reaction.
• By the catalyst not being consumed in the chemical reaction – it is capable on working over-and-over again on several reactions of the same kind
• An enzyme is a biologic catalyst- thus it is a biochemical additive that accelerates a biochemical reaction without itself being consumed in the reaction
What does an enzyme do to the energy of activation?
• It lowers the energy of activation• Key issue: An enzyme lowers the energy of
reaction – but it in no way donates any energy to the reaction.
• If an enzyme donated energy to a reaction – it would slowly but surely become consumed in the reaction - REMEMBER THE DEFINITION
Figure 2.20
An enzyme lowers the energy of activation
How does an enzyme lower the energy of activation?
• Before an enzyme can function as a catalyst, the substrates in the reaction must bind to a specific region of the enzyme called the active site.
• The tertiary or quaternary structure determines the shape of the active site, typically a groove or pocket where the substrates can nestle.
• There are two active site shape models – – Lock and Key– Induced Fit
Lock and Key model
Lock and Key model
• In this model, the amino acids that make up an enzyme's active site in the unbound state are said to form a shape that exactly matches the shape of the substrate. Thus, the substrate fits into this active site, just as a key fits into a lock whose shape is designed to match the key.
Lock and Key
• However, the active sites of many enzymes do not have a shape in the unbound form that exactly matches the shape of the substrate. The shape of the active site changes when the substrate binds to the enzyme, creating a shape into which the substrate fits.
• This is known as induced fit model.
Induced fit model
All enzymes share three basic characteristics
• 1. Specificity – each enzyme catalyzes only one type of reaction and can accommodate only one type of substrate molecule.
• 2. Saturation limits – the rate of reaction is directly proportional to the concentration of substrate and enzymes. When substrate molecules are high enough in concentration that all enzymes are being used, further increases in substrate concentration will not increase the reaction rate.
Enzyme characteristics
• Saturation limit cont. – the substrate concentration required for the maximum reaction rate is called the saturation limit.
• An enzyme reaching the saturation limit is saturated.
Enzyme characteristics
• Regulation – a variety of factors can turn enzymes off or on in a cell in order to control reaction rates.
• One example is the presence of cofactors.• Every cell has lots of enzymes, so inactivation
and activation of these enzymes is important for control of cellular activities.
• The activation/deactivation is immediate.
Cofactors
• Ions or molecules that must bind to the enzyme before the enzyme can bind the substrate.
• Calcium, magnesium are examples
Coenzymes
• Non-protein organic molecules.• Vitamins are common cofactors.
Apoenzymes and Holoenzymes
• Apoenzyme- An enzyme that requires a cofactor but does not have one bound. An apoenzyme is an inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor.
• Holoenzyme- An apoenzyme together with its cofactor. A holoenzyme is complete and catalytically active.
The ImpostersWhat are the inhibitors?
• Enzyme inhibitors are molecules that bind to enzymes and decrease their activity (slow down the reaction).
• The imposter (inhibitor) molecule has a shape similar to the real substrate - remember in the induced fit model -the active site does not exactly fit the substrates – like in the old Lock and Key model – thus look-alike imposters could enter the active site
• Enzyme inhibitors can be bad – like taking a poison
• Enzyme inhibitors can be good – for example some of the antibiotics – they block a vitally needed enzyme in the pathogen’s biochemistry – but we don’t have the same enzyme -so it kills the pathogen but does not bother us.
Types of InhibitorsCompetitive (attached to the active site) • Reversible (transiently attaches to AS)• Non-reversible (permanently attaches to AS)
Non-competitive (Attaches to other sites on the enzyme)
Competitive Inhibition
Non-reversible (Irreversible) Inhibition
Note how the irreversible inhibitor locks onby strong covalent bonding.
Non-competitive Inhibition
Active SiteSubstrate
Allosteric site whereNon-competitive Inhibitor binds
Enzyme Involvement in DiseaseVirtually every chemical step of metabolism is catalyzed by an enzyme. Disorders of these enzymes that result from abnormalities in their genes are known as inborn errors of metabolism.
Phenylketonuria (PKU) is the most common disorder of amino acid metabolism, and it is a paradigm for effective newborn screening. Phenylalanine is an essential amino acid (meaning that it cannot be synthesized but must be taken in through the diet). The first step to its breakdown is the phenylalanine hydroxylase reaction, which converts phenylalanine to another amino acid, tyrosine. A genetic defect in the phenylalanine hydroxylase enzyme is the basis for classical PKU. Untreated PKU results in severe mental retardation, but PKU can be detected by screening newborn blood spots, and the classical form can be very effectively treated by using medical formulas that are limited in their phenylalanine content.
Enzymes and disease
• Alkaptonuria is a disorder of tyrosine breakdown. The intermediate that accumulates, called homogentisic acid, can polymerize to form pigment that binds to cartilage and causes progressive arthritis and bone disease and that also is excreted to darken the urine.
Enzymes and disease
• Tay-Sachs disease is due to a defect in the beta-hexosaminidase A enzyme, which removes a sugar from certain lipids called gangliosides, which build up in the lysosome. The disease causes neurological symptoms, an enlarged head, and death in early childhood.
Enzyme denaturation
• Every enzyme works best at a narrow pH and temp. range.
• If temp. increases, proteins change shape and function deteriorates.
• Body temp. above 110 degrees F causes death because proteins denature (permanent change in tertiary or quaternary structure).
• Denatured proteins are non-functional.
Enzyme denaturation
• Enzymes also sensitive to pH changes:– Pepsin breaks down proteins in stomach and
works at pH of 2.0– Trypsin also breaks down proteins in small
intestine but works at pH of 7.7
The Nucleic Acids (DNA and RNA)
• DNA is a polymer and is our genetic material• RNA is a polymer and assists our genetic
material
Nucleic acids
• Large organic molecules composed of carbon, hydrogen, oxygen, nitrogen, and phosphorous.
• DNA = deoxyribonucleic acid• RNA = ribonucleic acid
DNA
• Determines inherited characteristics• Encodes information to make all proteins
needed by body
RNA
• Cooperate to make proteins using information from DNA.
Structure of nucleic acids
• Nucleic acid is series of nucleotides linked through dehydration synthesis.
• Nucleotide has three basic components– Sugar (ribose or deoxyribose)– Phosphate group– Nitrogenous base (adenine, guanine, cytosisne,
thymine, uracil)
Fig. 5-27c-1
(c) Nucleoside components: nitrogenous bases
Purines
Guanine (G)Adenine (A)
Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)
Nitrogenous bases
PyrimidinesEach nucleotide contains one of these 5 NBs!
DNA has cytosine , adenine, guanineand thymine (DNA has no uracil)
RNA has cytosine , adenine, guanineand uracil (RNA has no thymine)
Fig. 5-27c-2
Ribose (in RNA)Deoxyribose (in DNA)
Sugars
(c) Nucleoside components: sugars
A nucleotide has one of these two sugars – in DNA the nucleotidecontains Deoxyribose as the sugar ( thus Deoxyribonucleic acid )and in RNA the nucleotide contains ribose (thus Ribonucleic Acid)
Ribose has a oxygen at the second carbon andDeoxyribose does not – thus deoxy
Fig. 5-27
5 end
Nucleoside
Nitrogenousbase
Phosphategroup Sugar
(pentose)
(b) Nucleotide
(a) Polynucleotide, or nucleic acid
3 end
3C
3C
5C
5C
Nitrogenous bases
Pyrimidines
Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)
Purines
Adenine (A) Guanine (G)
Sugars
Deoxyribose (in DNA) Ribose (in RNA)
(c) Nucleoside components: sugars
The third component of the nucleotide isthe phosphate group
Nucleic Acid Structure
• Adenine and Guanine are double ring structures and called purines.
• Others are single ring and called pyrimidines.• Uracil found only in RNA, thymine only in
DNA.• Easy to remember that uracil “replaces”
thymine in RNA.
Nucleic Acid Structure
• The nucleic acids are very large molecules that have two main parts. The backbone of a nucleic acid is made of alternating sugar and phosphate molecules bonded together.
• When a nitrogenous base attaches to a pentose (ribose or deoxyribose) sugar, a nucleoside is formed. Nucleoside is named after the nitrogenous base.
Nucleotide
• When a nucleoside combines with a phosphate group.
• To make a nucleic acid, dehydration synthesis attaches the phosphate group of one nucleotide to the sugar of another.
• The “backbone” of a nucleic acid is a linear sugar to phosphate to sugar sequence with the nitrogenous bases projecting to one side.
Nitrogenous BaseSugar Phosphate group Nitrogenous Base
Single Strand Design of Nucleic Acid Design
Fig. 5-27ab5' end
5'C
3'C
5'C
3'C
3' end
(a) Polynucleotide, or nucleic acid
(b) Nucleotide
Nucleoside
Nitrogenousbase
3'C
5'C
Phosphategroup Sugar
(pentose)
DNA Special Bonding of Nitrogenous Bases
• The DNA code (Chargaff’s rule) a purine on one side hydrogen bonds to a pyrimidine on the other side
• More specifically if Adenine is on one side it will hydrogen bond to Thymine on the other side
• If Cytosine is on one side it will hydrogen bond to Guanine on the other side - so
A TG C
Figure 2.22a, b
Figure 2.22a
RNA
• Single strand of nucleotides• Three types:
– Messenger (mRNA)– Transfer (tRNA)– Ribosomal (rRNA)
• Each has different shape and function, but all 3 required for protein synthesis.
DNA
• Double strand of nucleotide chains.• Complementary base pairing:
– Purine bonds with opposing pyrimidine– Adenine:Thymine– Guanine:Cytosine
DNA
• The two strands of DNA are anti-parallel• If one strand is in the 3’ 5’ direction – the
other side is in the 5’ 3’ direction
High energy compounds
• Energy in cells obtained from enzymatic catabolism of organic substrates.
• The energy somehow has to be “captured” so it can be transferred from one molecule to another or from one part of the cell to another.
• Usual method of transfer involves creation of high-energy bonds.
High energy compounds
• High-energy bond – covalent bond. When broken down releases energy that can be used by the cell.
• Humans: phosphate group connected to an organic molecule.
High energy compounds
• Phosphorylation – attachment of phosphate group to another molecule.
• High-energy compound requires:– Phosphate group– Appropriate enzymes– Suitable organic substrates
High energy compounds
• Most important substrate is adenosine.• Adenosine monophosphate (AMP) is
phosphorylated to Adenosine diphosphate (ADP). This requires significant energy expenditure.
• Adenosine diphosphate (ADP) is then phosphorylate to Adenosine triphosphate (ATP). More energy required at this stage also.
Energy conversion in cells
• ADP converted to ATP and then reverted to ADP.– ADP + phosphate group + energy ↔ ATP + H2O
• Human cells are constantly using this energy for metabolism, protein synthesis, and contraction of muscles.
• ATP is most abundant energy source in body.
Other energy sources
• Guanosine triphosphate (GTP)• Uridine triphosphate (UTP)• Used in specific enzyme reactions.
Quiz
• 1. Carbohydrates, lipids, and proteins are formed from their basic building blocks by the:
• A. removal of a water molecule between the building blocks
• B. addition of a water molecule between the building blocks
• C. addition of carbon to each molecule• D. addition of oxygen to each molecule
2.
• Complementary base pairing in DNA includes• A. adenine-uracil; cytosine-guanine• B. adenine-thymine; cytosine-guanine• C. adenine-guanine; cytosine-thymine• D. guanine-uracil; cytosine-thymine
3
• What is the role of enzymes in chemical reactions?
4
• List three important functions of triglycerides in the human body.
5
• List seven major functions performed by proteins.
Review
• P. 67: 21 – 31• P. 68: 6 and 7
• When finished, continue with tissue and cell slides. Look at them many times so you can recognize the different cell and tissue types.
