Missing Pieces:Dipoles (Polar molecules)Cohesion

Biochemistry and Cell Compounds  we will now look at biologically important molecules that are

based around carbon atoms. It is said that life on Earth is "Carbon Based..."

Biochemistry: the chemicals of life and their study. Organic chemistry is the study of carbon compounds. As

will see, a lot of biochemistry revolves around organic chemistry.

Why Carbon?1.has four available covalent bonds -- allows for other atoms to

bind.2.capable of forming strong bonds with itself therefore can form long chains -- can be straight or branched

--> great VARIETY of possible combinations.carbon atoms in chains can rotate, forming single, double, and

multiple ring structures (e.g. glucose, nucleotides, lipids, proteins)

MacromoleculesThe next slides will examine the four major

molecules of life and the process by which they are combined and separated.

Two terms to be familiar with: Polymer: Monomer

Polymer and monomerLook at the term: polymer, Poly- means

"many.”So what does polymer mean?Polymer means many monomers. Sometimes

polymers are also known as macromolecules or large-sized molecules. A monomer is a molecule that is able to bond in long chains.Here is a monomer:     Here is a polymer:     

Large Organic Molecules Have Monomers1. Each small organic molecule can be a unit of a large

organic molecule called a macromolecule.2. Small organic molecules (e.g., monosaccharides,

glycerol and fatty acid, amino acids, and nucleotides) that can serve as monomers, the subunits of polymers.

3. Polymers are the large macromolecules composed of three to millions of monomer subunits.

4. Four classes of macromolecules (polysaccharides or carbohydrates, triglycerides or lipids, polypeptides or proteins, & nucleic acids such as DNA & RNA) provide great diversity.

Dehydration Synthesis and Hydrolysis

• a POLYMER is a large molecule formed from repeating subunits of smaller molecules (e.g. proteins, starch, DNA are all polymers).

• DEHYDRATION SYNTHESIS: forms large molecules (polymers) from small molecules. (Dehydration = to remove water) In the process water is produced. (Also called condensation)

• HYDROLYSIS (hydro = water, lysis = to split): is the opposite reaction. Water breaks up another molecule. The addition of water leads to the disruption of the bonds linking the unit molecules together.

Details, details….

DEHYDRATION SYNTHESIS: one molecule loses an H+, one molecule loses an OH-. Amino acids can continue to be added to either end of the dipeptide to form polypeptides. Large polypetides are called proteins.

• HYDROLYSIS: One molecule takes on H+ and the other takes an OH-. This also requires the action of helping molecules called enzymes. Enzymes that do this are called hydrolytic enzymes.

Dehydration:

CarbohydratesCarbohydrates contain the elements carbon,

hydrogen, and oxygen in the ratio of 1C:2H:1O. The building blocks or monomers that make up

more complex carbohydrate polymers are called monosaccharides and have a ring structure with five or six sides. Examples of monosaccharides are glucose and fructose. Two monosaccharides can be combined to produce disaccharides such as sucrose (table sugar) and maltose. The large complex carbohydrate polymers that are produced include starch, glycogen, and cellulose. (Polysaccarides)

Carb Functions:used for ENERGY, FOOD STORAGE, & STRUCTURAL

SUPPORT in plants and animals. Carbohydrates are very important in living systems for the following functions:

1. Short-term energy supply (e.g. glucose is used by all cells to produce ATP energy)

2. Energy storage (e.g. glycogen is stored in liver and muscles and can be rapidly converted to glucose: starch has a similar role in plants)

3. Cell membrane markers (receptors & “identification tags”)

4. As structural material (e.g. plant cell walls are made of cellulose, insect exoskeletons are make of the carbohydrate chitin)

Starch

Carb Structure

Lipids: Fats, oils and waxesinclude fats oils (neutral fats),phospholipids, & steroids.Fats and oils, called neutral fats, are composed of a glycerol

backbone and three fatty acids. Glycerol is a 3-carbon molecule. Fatty acids are long carbon chains with an acid group at the end. Fatty acids can be saturated or unsaturated with hydrogen atoms.

Phospholipids are similar in structure to neutral fats but have one of the fatty acid molecules replaced with a phosphate group. They are the main component of cell membranes.

Steroids are easily recognized by a backbone of four fused carbon rings. Cholesterol found in cell membranes can be transformed into common steroid hormones such as testosterone and estrogen.

THE MAIN TYPES OF LIPIDS: Fatty Acidsi. Fatty Acids: a long chain of carbons with hydrogens attached,

ending in an acid group (-COOH). There are two main types:• Saturated fatty acids - no double bonds between

carbons. All carbons are "saturated" with hydrogens. Saturated fats tend to be solid at room temp. These are the "bad" dietary fats (e.g. butter, lard, meat fat), which are known to contribute to heart disease, strokes, and cancer.

• Unsaturated fatty acids - have one (monounsaturated) or more (polyunsaturated) double bonds between carbons in chain. That means that the carbons are not “saturated” with hydrogens.

• Unsaturated fats tend to be liquid at room temperature. e.g. vegetable oils, Omega-3 unsaturated fatty acids. Are thought to be better for your heart than saturated fats.

Continued: Neutral/Triglyceridesii. NEUTRAL FATS: (also called

TRIGLYCERIDES)formed by dehydration synthesis reaction

between glycerol (a molecule of 3 hydrated carbons and 3 fatty acids.

continued• All triglycerides are non-charged, non-

polar molecules. • They do not mix with water. This

property of not mixing with water is called “hydrophobic” which literally means “water-fearing.” This is the opposite of polar molecules, which mix readily with water and are called “hydrophilic” which means “water-loving.”

STEROIDS: a different type of lipid

They are multi-ringed structures, all derived from CHOLESTEROL

essential molecule found in every cell in your body (it forms parts of cell membranes, for example).

Steroids can function as chemical messengers, and form many important HORMONES (e.g. testosterone, estrogen, aldosterone, cortisol) that have a wide variety of effects on cells, tissues, and organs.

Lipid Function1. Long-Term Energy storage: (fat is excellent

for storing energy in the least amount of space, and packs 9.1 calories of energy per gram, versus 4.4 for carbohydrates and proteins).

2. Insulation ("blubber")3. Padding of vital organs4. Structural (e.g.cell membranes are mostly

composed of phospholipids, white matter of brain contains a high proportion of lipid material)

5. Chemical messengers (e.g. steroid hormones like testosterone, estrogen, prostaglandins).

Short Hand: Triglyceride

Proteinspolymers constructed from amino acid monomers. Amino acids have a central carbon atom. This central

carbon is bonded to a hydrogen atom and three groups. An amino group (-NH2), an acid Carboxyl group (COOH), and an R-group. The R-group is unique to an amino acid and determines its identity. When amino acids bond together to form proteins the amino group of one combines with the acid group of another producing a (C-N) or peptide bond. This peptide bond is easily seen in a dipeptide containing two amino acids.

There are 20 different amino acids in living things. Our bodies can make 12 of these. The other 8, which we must get from food, are called “Essential Amino Acids.”

Identify: Amino Group, Carboxyl Acid, Central Carbon and R-Group.

Peptide bonds through Dehydration Synthesis.

Protein Functionsprovide STRUCTURAL SUPPORT (e.g. elastin, collagen in

cartilage and bone, muscle cells)MOVEMENT (actin and myosin etc. in muscle cells)METABOLIC FUNCTIONS: ENZYMES (biochemical catalysts that speed up biochemical

reactions). Crucial to life. ANTIBODIES: proteins of your immune system that fight disease.Transport: HEMOGLOBIN is a protein that transports oxygen in

your blood. Proteins in cell membranes act as channels for molecules entering or leaving the cell.

Hormones: many hormones, like insulin, are proteins. Hormones control many aspects of homeostasis.

Protein Structureii. Dipeptide: two amino acids joined

togetheriii. Polypeptide (abreviation = ppt): >2

amino acids joined together. Usually short: less than 20 amino acids or so.

iv. Protein: a polypeptide chain is called a protein when it gets large (usually ~75 or more amino acids in length – though there is no absolute rule here)

Structure continuedPrimary, secondary, tertiary, quatrenary

DENATURING PROTEINprotein shape is critical to its functionchanges in temperature or pH, or the presence of certain

chemicals or heavy metals, can disrupt the bonds that hold a protein together in its particular shape.

If a protein is DENATURED, it has lost normal structure/shape because normal bonding between -R groups has been disturbed.

heating an egg white (raising the temperature above 50°C will reliably denature most animal enzymes)

adding vinegar to milk (this is the same thing as changing the pH, since vinegar is an acid)

adding heavy metals such as lead and mercury also denature proteins

Nucleic AcidsNucleic Acids are double-stranded DNA

(Deoxyribonucleic Acid) and a single-stranded cousin RNA (Ribonucleic Acid). Both of these polymers are built from nucleotides.

Nucleotides are composed of three parts; a sugar, a phosphate, and a nitrogenous base.

There are four different nucleotides found in DNA (adenine, thymine, guanine, and cytosine). In RNA the thymine nucleotide is replaced with a uracil nucleotide. If a polymer is made from nucleotides it is a nucleic acid.

Nucleic Acid

From Nucleotides to Chromosomes.• Sections of DNA form functional units

called GENES. A gene is one instruction for making one polypeptide (protein), and is about 1000 nucleotides long, on average.

• DNA is packaged into chromosomes, and is located in the nucleus. You have about 4 billion nucleotide pairs in each of your cells. Each of your 46 chromosomes (23 from mom, 23 from dad) contains one very long polymer of DNA around 85,000,000 nucleotides long!

http://www.biologyjunction.com/biochemistry_notes_bi_ch3.htm

http://www.chemistrypictures.org/v/cell_structure/cell_structure.jpg.html

Acid, acid (carboxyl) group, adenine, adenosine triphosphate (ATP), alpha helix, amine group, amino acid, base, beta pleated sheet, bonding, buffer, carbohydrate, cellulose, complementary base pairing, cytosine, dehydration synthesis, deoxyribonucleic acid (DNA), deoxyribose, dipeptide, disaccharide, double helix, glucose, glycerol, guanine, glycogen, hemoglobin, hydrogen bonding, hydrolysis, lipid, lubricant, maltose, monomer, monosaccharide, neutral fat, nitrogenous base, nucleic acids, nucleotide, organic, peptide bond, pH, phosphate, phospholipid, polarity, polymer, polypeptide, polysaccharide, primary structure, protein, quaternary structure, R-group, ribonucleic acid (RNA), ribose, saturated fatty acid, secondary structure, solvent, starch, steroid, sugar-phosphate backbone, temperature regulator, tertiary structure, thymine, unsaturated fatty acid, uracil