Organic Molecules of Life

Organic molecules : are compounds created by living organisms contain the elements carbon and hydrogen

Carbon atoms: need four electrons to fill their outer electron shell Must form four bonds with other elements. These are covalent bonds. Most often bond with Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur, and other Carbon atoms 6 P 6 N

These can include: Single bonds (one electron shared) Double bonds (two electrons shared) Or triple bonds (three electrons shared)

Carbon Atoms: Can bond with other atoms of carbon to form long chains These chains can be: Straight Branched Rings

Isomers Molecules with the same formula Atoms are arranged differently Carbons are branched in various ways

Functional groups: Are special groups of atoms that stay together and act as a single unit can bond with the carbon chains determine how the entire molecule will react.

The functional groups you need to know are:

Hydroxyl Group one oxygen and one hydrogen usually written as -OH

Carboxyl Group one carbon with a double bond to an oxygen AND a single bond to a hydroxyl group usually written as COOH or O=C–OH Creates an organic acid (carboxylic) Oxygen Carbon Oxygen Hydrogen

Amino Group one nitrogen bonded to two hydrogen usually written as NH2 or H–N–H Hydrogen Nitrogen Hydrogen

Phosphate Group: One phosphorus bonded to two hydroxyl groups, and two other oxygens (one has a double bond) Usually written as –P or OH O P O Phosphorus

Biological molecules can be made up of thousands of atoms

These large molecules are built from basic units called monomers. One monomer

The monomers are linked together to form the large molecules called polymers. Polymer – chain of repeating monomer units

Making and Breaking Polymer Bonds Monomers When two monomers are put together to form larger molecules, a water molecule is created. Polymer

This process is called: Dehydration Synthesis. (Dehydration means to lose water Synthesis means to build or put things together)

When polymers are broken apart, it is done by adding a water molecule.

(hydro- for water, -lysis for breaking apart) This is called Hydrolysis (hydro- for water, -lysis for breaking apart)

Types of Organic Molecules There are four categories of organic molecules in organisms: Carbohydrates Lipids Proteins Nucleic acids

Carbohydrates

What are Carbohydrates? Organic compounds Commonly called starches and sugars Used as: An energy source Energy storage Cellular structures

Chemical Composition Contains only three elements: Carbon Hydrogen Oxygen Ratio of hydrogen to oxygen is 2:1 (just like water) Example: C6H12O6 Basic Unit is called a saccharide

Types of Carbohydrates Monosaccharides Simple, single (mono-) sugar unit Building block of all other carbohydrates Name usually ends in –ose Used as energy source

Examples of Monosaccharides Glucose – blood sugar Fructose – fruit sugar Galactose – one monomer in lactose (milk) Isomers of C6H12O6

Examples of Monosaccharides Ribose and Deoxyribose 5 - Carbon sugars in RNA and DNA

Types of Carbohydrates Disaccharides Double sugar units synthesized from monosaccharides All are isomers of C12H22O11 Formed by dehydration synthesis (requires enzymes)

Examples of Disaccharides Sucrose – table sugar Glucose + Fructose Maltose – seed sugar Glucose + Glucose Lactose – milk sugar Glucose + Galactose

Types of Carbohydrates Polysaccharides Large, complex chains of many (poly-) repeating sugar units Polymers Bonded together by dehydration synthesis Used by living things as a sugar storage or for structures

Examples of Polysaccharides Amylose – plant starch Used as sugar storage in seeds, roots, stems Glycogen – animal starch Used as sugar storage by humans in the liver Cellulose Very tough polymer Used as a main component of cell walls Indigestible by humans Chitin Used in exoskeletons (crab shells, insects)

Digesting Polysaccharides Broken apart by hydrolysis with the help of enzymes

Lipids

What are Lipids? Three elements: Carbon Hydrogen Oxygen Ratio of H:O much greater than 2:1 Example: Oleic acid C18H34O3 Insoluble in water Greasy, slippery texture Three main groups: Fats oils and waxes At room temperature: Liquid – oils/Solid – fats and waxes Phospholipids Steroids

What are the Functions of Lipids? Fats, Oils and Waxes: Long term energy storage More than twice as much energy stored than carbohydrates fats- 9 Calories/gram; carbohydrates- 4 Cal/g In plants: stored in and around seeds Peanut oil, corn oil, olive oil In animals: stored under the skin and around internal organs Used as insulation and shock absorber

What are the Functions of Lipids? Phospholipids Structural Part of Cell membranes Steroids Part of cell membranes, transport of lipids, regulate body functions (hormones)

Chemical Composition Fats Oils, Waxes Fatty Acid Glycerol One or more fatty acids attached to a Glycerol backbone Fatty Acids: Long chains of carbon with a carboxyl group at the end Glycerol: C3H8O3 Formed by dehydration synthesis NOT a polymer Glycerol Lipid

Formation of a Triglyceride:

Types of Fats Saturated All carbons of the fatty acid have single bonds All carbons are “filled” with hydrogen Solid at room temperature Associated with heart disease risk Examples: Bacon grease, butter

Types of Fats Unsaturated Carbons share one or more double or triple bonds with other carbons Monounsaturated – only one double bond Polyunsaturated – many double or triple bonds Liquid at room temperature Examples: corn oil, olive oil

Phospholipids Phosphate group replaces fatty acid on one end Used as the main component of cellular membranes

Steroids: Four Fused Rings lipids with four fused hydrocarbon rings Includes: Cholesterol - found in animal cell membranes Testosterone, estrogen, progesterone - sex hormones Vitamin D An anabolic steroid is a synthetic testosterone.

Proteins

Protein Functions Structural parts Carriers Regulators cell membrane, muscles, hair, nails, pigments Regulators Hormones, enzymes Carriers Transport materials in, out and around cells Identification Allow cells to recognize each other Immune system antibodies

Composition of Proteins Elements: carbon, hydrogen, oxygen and NITROGEN Very large, complex Hemoglobin: C3032H4816O872N780S8Fe4 Monomers (building blocks) are amino acids 20 common amino acids 9 are essential 11 are non essential

The R group is different for each of the twenty amino acids

Peptide Bonds Chains of amino acids are called peptides Amino acids are joined by dehydration synthesis This occurs between the carboxyl end of one amino acid and the amino end of another amino acid. The resulting bond is called a Peptide bond

Primary Structure The sequence of amino acids in a protein is called the Primary Structure The sequence is unique for each protein and is determined by the DNA

Secondary Structure Hydrogen bonds are formed between the chains of amino acids causing different shapes.

Secondary Structure Two shapes are common – a helix and a sheet. Sheet and Helix

Tertiary Structure The 3-D arrangement of the molecule caused by weak bonds between the R groups The most important structure format Determines the function of the protein

Quaternary Structure More than one protein molecule can combine to create a macromolecule This is the quaternary structure of the protein This creates either globular (hemoglobin) or fibrous (collagen) proteins

Nucleic Acids

Nucleic Acids are: The largest molecules in living things The DNA of humans has about 6 billion monomers Some reptiles have 20 times more units The largest DNA known is a flower with 5 trillion units

The two most important Nucleic Acids: DNA (deoxyribonucleic acid) RNA (ribonucleic acid)

Functions of Nucleic Acids DNA make up chromosomes and their genes that carry hereditary information found in the nucleus, mitochondria and chloroplasts (plants) RNA functions in the synthesis of proteins for the cell found in cell parts: nucleoli, ribosomes, and throughout the cytoplasm

General Structure of Nucleic Acids Polymers, with many repeating units called nucleotides Nucleotides have three subunits: a five carbon sugar a phosphate group a nitrogenous base (a base that contains nitrogen) Phosphate group Nitrogenous Base Five Carbon Sugar

Structure of DNA The sugar backbone is deoxyribose

Structure of DNA The base can be one of four: Adenine Guanine Thymine Cytosine

Structure of DNA The bases pair up – A (adenine) always pairs with T (thymine) G (guanine) always pairs with C (cytosine)

Structure of DNA

Structure of DNA Two polymer chains of nucleotides are connected by weak hydrogen bonds and are twisted into a double helix

Structure of DNA Sequence of nitrogenous bases codes for specific amino acids Amino acid sequence determines the protein made in the cell and the cellular activity

Relationship Between Proteins and Nucleic Acids

Structure of RNA Ribose is its sugar backbone

Structure of RNA The base can be one of four: Adenine Guanine Cytosine Uracil Thymine is replaced by Uracil

Structure of RNA Only a single polymer chain is created in RNA, but strands of RNA have complex, folded structures that compliment their function.

Enzymes

What are Enzymes? Large, Complex Proteins Function as Organic Catalysts Allow reactions to occur at lower temperatures ( 37° C) Used temporarily Unchanged by the reaction Can be reused Specific to one reaction

What are Enzymes? Bind to reactants called substrates Enzyme names usually end in –ase and can be named for their substrate: Protease – proteins Lipase – lipids Maltase – maltose ATPase – ATP Acetylcholinesterase - acetylcholine

How Do Enzymes Work? Reduces energy needed to begin reaction (Activation energy) Without catalyst With catalyst Activation Energy Energy Energy Time Time

How Do Enzymes Work? Lock and Key Model Products Substrate Active Site Substrate attaches to enzyme at active site Enzyme Substrate Complex Formed Reaction takes place and products are released

How Do Enzymes Work? Induced Fit Model Product Enzyme substrate complex formed Substrate Enzyme Enzyme Enzyme Substrate attaches to active site Enzyme changes shape to match substrate – Stressed molecule may help to weaken bonds Enzyme resumes original shape after product formed

How Do Enzymes Work? Coenzymes sometimes needed Non proteins – minerals, vitamins Smaller molecules Part of the enzyme structure or work along side the enzyme Enzyme and substrate do not match Coenzyme fills in needed shape Coenzyme

Denaturation: If the shape changes, the enzyme cannot function properly

Factors Affecting Enzymes Temperature Enzyme activity increases with temperature Optimum temperature for each enzyme Higher temperatures denature (change the shape) of the enzyme’s active site Rate of reaction decreases quickly after optimum temperature Optimum temperature 10 20 30 40 50

Factors Affecting Enzymes pH Enzymes are pH dependent Some work at low pH (acid) Some at high pH (basic) Surrounding solutions will activate or deactivate enzyme by changing the shape of the active site Extremely high or low pH values generally result in complete loss of activity for most enzymes pH for Optimum Activity Enzyme pH Optimum Lipase (pancreas) 8.0 Lipase (stomach) 4.0 - 5.0 Lipase (castor oil) 4.7 Pepsin 1.5 - 1.6 Trypsin 7.8 - 8.7 Urease 7.0 Invertase 4.5 Maltase 6.1 - 6.8 Amylase (pancreas) 6.7 - 7.0 Amylase (malt) 4.6 - 5.2 Catalase

Factors Affecting Enzymes Concentration: Increasing amount of enzyme: rate increases then levels off substrate levels fall and reduces efficiency Increasing amount of substrate: enzyme is saturated and no additional reactions can occur Presence of Inhibitors Bind to enzyme and change shape or compete with the substrate