Organic Chemistry

Organic Chemistry Organic molecules  contain at least Carbon and Hydrogen Hydrocarbons  contain ONLY Carbon and Hydrogen Inorganic molecules may have Carbon OR Hydrogen, but not both!

Practice Identify the following molecules as: Organic, Inorganic, Hydrocarbon CH4 C6H12O6 H20 CO2 C2H5OH

Why is carbon so nifty? Has 4 valence electrons, meaning it can form 4 covalent bonds! It can form single, double, even triple bonds!

Bonding Characteristics of Elements Different numbers of valence electrons  each element will make different numbers of covalent bonds Carbon  4 Oxygen  2 Nitrogen  3

So what are cells made of? Water  human body approx. 65-75% Functions Solvent, temp regulation, transportation, cushion, etc. Minerals  (Fe, Ca, P, Cl, Na, I……..) Function: help maintain fluid balance; act as a pH buffer aid in structure of cells (body) allow nervous system to work

What are cells made of? (cont) Organic Macromolecules are the major organic components of the cell Macro  Big Organic  Contains carbon and hydrogen Molecules  Bonded together

4 classes of Organic Macromolecules Carbohydrates Sugars, starches, plant fiber (cellulose) Lipids fats, oils, waxes Proteins Muscle tissue, enzymes Nucleic Acids DNA, RNA

BIG IDEAS The cells of organisms are ALL made of the same 4 types of macromolecules. AT THE CELLULAR LEVEL, LIFE IS PRETTY MUCH ALL THE SAME! Organisms are constantly BUILDING UP and BREAKING DOWN organic molecules

How to Build a Macromolecule Start with a small single molecule  MONOMER Linking many monomers together  POLYMER

Monomer Polymer Figure 2-27 Essential Cell Biology (© Garland Science 2010)

How we BUILD –UP and BREAK DOWN Building Up Use DEHYDRATION SYNTHESIS Dehydration – removing water Synthesis – Building - up Breaking Down Use HYDROLYSIS Hydro – water Lysis – splitting apart

Dehydration Synthesis Monomers are linked together by the removal of an OH from one side and an H from another to make WATER

Hydrolysis Opposite of Dehydration Synthesis Water molecule is put back in, which results in polymers separating into monomers

Remember, this whole unit is going to focus on how we BUILD UP and BREAK DOWN the four major building blocks of macromolecules Monomers Polymers MONOSACCHARIDES Figure 2-15 Essential Cell Biology (© Garland Science 2010)

CARBOHYDRATES Monomer of carbs: monosaccharide - means “one sugar” - these are the simple sugars (taste sweet!) - made of C, H and O in a 1:2:1 ratio

Simple vs. Complex Carbs Glucose (monosaccharide) Starch (polysaccharide)

Types of Carbohydrates MONOSACCHARIDES ONE SUGAR Ex GLUCOSE, FRUCTOSE, GALACTOSE DISACCHARIDES TWO SUGARS EX LACTOSE (Dairy), SUCROSE (sugar in bowl) POLYSACCHARIDES – MANY SUGARS STARCH – storage in plants GLYCOGEN – storage in animals CELLULOSE – plant cell walls

Monosaccharides Called simple sugars (one unit) Three simple sugars are absorbed with no digestion (meaning….?) glucose found syrup or honey fructose found in fruit - sweetest galactose found in dairy products ISOMERS!!!!!!!

Disaccharides Two monosaccharides are joined together to build disaccharides sucrose (a sugar) can be produced by dehydration synthesis of glucose and fructose. Lactose = Disaccharide formed by joining glucose and galactose.

Polysaccharides Long chains of monosaccharides! Glycogen (animal starch) Short term energy storage in animals (fat is what we use for long-term) Plant starch stores excess sugar in a plant. Cellulose provides strength and rigidity in plants We cannot digest!

Polysaccharides as Energy Storage Molecules (cont.)

Polysaccharides as Energy Storage Molecules (cont.)

Polysaccharides as Energy Storage Molecules (cont.)

Polysaccharides and YOU! You eat starch from plants and break it down into glucose (monosaccharide) Your cells take the glucose from your blood and A. Use it right away for cell energy B. Save it for later by linking them together into large molecules of glycogen (pasta party anyone?) The other polysaccharide plants make, cellulose, is NOT DIGESTABLE by you. So, it is what we call dietary fiber……..hmmmm…..?

Cellulose and our ecosystem Plants = Structurally made of cellulose We (animals) cannot break it down when we eat it So, what happens to all those leaves, grass clippings, banana peels etc? DECOMPOSITION! BACTERIA AND FUNGI CAN BREAK DOWN PLANT CELLULOSE

Lipids • Lipids are a diverse group of macromolecules that are insoluble in water. • Fats and oils are well-known lipids used for energy storage and other purposes. • Phospholipids are components of the membranes that surround cells. • Steroids, which have a different structure from most lipids, are used as hormones and for other purposes.

Fats and Oils: Long-term Energy Storage Fats and oils contain two subunits. – Glycerol is a compound with three polar –OH groups. – Fatty acids are long chain hydrocarbons. A fat or oil is formed when a dehydration reaction adds fatty acids to the –OH groups of glycerol and broken down by hydrolysis reactions. Since three fatty acids are attached to a glycerol, fats and oils are often called triglycerides.

Triglycerides (large lipid molecule) Composed of fatty acids and glycerol

Building a triglyceride Triglyceride formation animation How would we break one down????

Fatty Acids Have a long hydrocarbon (carbon and hydrogen) chain with a carboxyl group. Chains usually contain 16-18 carbons

SATURATED VS. UNSATURATED FATTY ACIDS HAVE ONLY SINGLE BONDS FORM STRAIGHT CHAINS – COMPACT AT ROOM TEMP. (solid fats) UNSATURATED FA’S HAVE ONE OR MORE DOUBLE BONDS  KINK – LIQUID AT ROOM TEMP. (oils) Polyunsaturated – More than one double bond in the carbon chain.

Fatty Acids (cont.)

Fatty Acids (cont.)

Fatty Acids (cont.)

Saturated vs. Unsaturated Fatty Acids See your Lipids reading/questions for info on these. You are responsible for structural differences between each of the following and the effect of those differences: Saturated Unsaturated (polyunsaturated) Hydrogenated Trans

LIPIDS: LONG TERM ENERGY STORAGE STORED IN ADIPOSE (fat) TISSUE FUNCTIONS LONG TERM ENERGY STORAGE STORED IN ADIPOSE (fat) TISSUE More energy per gram than glycogen STRUCTURAL CELL MEMBRANES] HYDROPHOBIC – “dislikes” water (repels water) http://micro.magnet.fsu.edu/cells/plasmamembrane/images/plasmamembranefigure1.jpg

Fat vs. Carbs for energy storage?

Phospholipids: Membrane Components • Phospholipids are lipids that contain a polar, hydrophilic phosphate group (instead of a third phosphate group.) In watery media, the hydrophilic phosphate groups are oriented towards the water. Phospholipids can form bilayers that separate two compartments of water. Phospholipids comprise the membranes that surround cells and internal structures within cells.

Phospholipids: Membrane Components (cont.)

Steroids: Four Fused Rings • Steroids are lipids that have four fused hydrocarbon rings with different functional groups attached. • Cholesterol, found in animal cell membranes, and the sex hormones testosterone and estrogen are steroids. An anabolic steroid is a synthetic testosterone.

Steroids: Four Fused Rings (cont.)

PROTEINS IMPORTANCE!?!?! Some important functions of proteins are listed below. enzymes (chemical reactions) hormones storage (egg whites of birds, reptiles; seeds) transport (hemoglobin) contractile (muscle) protective (antibodies) membrane proteins (receptors, membrane transport, antigens) structural toxins (botulism, diphtheria

Protein monomers  Amino Acids Twenty different amino acids are used to make protein. Each has a carboxyl group (COOH) and an amino group (NH2).

Amino Acids: Subunits of Proteins (cont.)

Proteins There are 20 different amino acids - all have same amino end, carboxyl end and central carbon - EACH has a different R group Amino acids are made of: C, H, O, N, and S (in R group of some)

Amino Acid Bonding Amino acids are joined together by a peptide bond. Formed as a result of a dehydration synthesis reaction

Peptide Bond Animation

Peptide Bond How is it different than the dehydration reaction we looked at with carbs and lipids?

BUILDING A PROTEIN Amino acids are linked together to form polypeptides To become a “protein” a polypeptide must be folded into a unique 3D shape Only proteins have a “job”. Polypeptides don’t “work” until folded into a specific shape

4 LEVELS OF PROTEIN STRUCTURE PRIMARY – AMINO ACID SEQUENCE [CODED BY YOUR GENES] SECONDARY – PLEATED SHEET OR HELIX TERTIARY – GLOB QUATERNARY – 2 OR MORE GLOBS TOGETHER Not all proteins go to this level!

DENATURATION LOSS OF SHAPE  LOSS OF FUNCTION. http://whatscookingamerica.net/Eggs/EggDone2.jpg DENATURATION LOSS OF SHAPE  LOSS OF FUNCTION. CAUSED BY HIGH TEMPRATURES, SALT, OR pH CHANGES. http://www.aeb.org/KidsAndFamily/images/color-broken-egg.gif

NUCLEIC ACIDS: Examples FUNCTIONS DNA [DEOXYRIBONUCLEIC ACID] – RING OR HELIX, DOUBLE STRANDED RNA [RIBONUCLEIC ACID] – SINGLE STRANDED. FUNCTIONS INFORMATION STORAGE DIRECTIONS FOR HOW TO BUILD PROTEINS  YOU!

NUCLEIC ACIDS: MONOMER  NUCLEOTIDE SUGARS – DEOXYRIBOSE OR RIBOSE 5-Carbon Sugar + Nitrogenous Base Phosphate Group SUGARS – DEOXYRIBOSE OR RIBOSE

Elements of NA: C,H,O,N and P Structure of Nucleotide Elements of NA: C,H,O,N and P Base P o CH2 H OH H H H P = Phosphate = H2PO3

NUCLEIC ACIDS: NITROGEN BASES make the nucleotides different DNA Adenine (A) Guanine (G) Cytosine (C) Thymine (T)

Structure of DNA Two long chains of nucleotides Connected between ribose groups by phosphates Paired nitrogen bases (A-T; C-G) Forms a double helix with H bonds

o = Phosphate = H2PO3 Structure of Nucleic Acids - Build/broken down using same reactions!! Base P o CH2 H OH H H H P = Phosphate = H2PO3

Base o P CH2 H H H H OH H20 o H OH Base CH2 P P = H2PO3

Base o P CH2 H H H H o H OH Base CH2 P

Forms Phosphate-sugar backbone o Chain forms by connecting the sugar of one NT to the Phosphate of the next Forms Phosphate-sugar backbone o H Base CH2 OH P

DNA structure Two long chains of nucleotides Connected between ribose groups by phosphates Paired nitrogen bases (A-T; C-G) Forms a double helix with H bonds Forms genes – units of genetic information p s s p s c p a t g g a t a c c g t

RNA Contains ribose instead of deoxyribose sugar Uracil instead of thymine A-U; C-G Single strand, highly folded Three types of RNA t-RNA, m-RNA, r-RNA Each performs a different role in protein synthesis

Relationship Between Proteins and Nucleic Acids The order of amino acids in a protein determines its shape and function. The DNA contains the instructions for the sequence of amino acids in each protein. Errors or faults in the DNA can change the function of the encoded protein.

Relationship Between Proteins and Nucleic Acids (cont.)