Chapter 3 Biochemistry
Organic Molecules- The Building Blocks of Life
I.Whatis anOrganic Compound?
- Contains carbon atoms
- Built from carbon (C), hydrogen (H) and nitrogen (N)- Covalently Bonded
Where is Carbon on the Periodic Table?
It forms4 covalent bonds
Carbon has 4 electrons in its outmost electron shell.
Carbon bonds: Chains, Branched, RingsEach line represents a single covalent bond
Carbon also forms double & triple bonds
A good site for more explanation:
Methane- the simplest carbon compound- 1 Carbon & 4 hydrogen atoms
Other simple organic molecules
B. Functional groups
- A specific group of atoms that gives a known type of behavior to molecules
– changes the characteristics of the compound-
(See page 52 in your textbook for more on functional groups)
Hydrocarbons - C and H only
Alcohols - OH
Acids - COOH
Amines - NH2
Example -adding a hydroxyl group – makes ethane into an alcohol-
Example - adding an amino group
- makes methane or ethane into- an amine
C. Sizes of Molecules
1. Monomers-small simple molecules
2. Polymers-big molecules formed when monomers bonded to each other
3. Reactions to build or break down molecules
- Condensation Reaction
- Hydrolysis Reaction
- polymers are broken back down- they need a wateradded.
Hydrolysis of sucrose
D. Energy from ATP
- Life needs a constant supply of energy
- Chemical bonds store energy.
- One molecule that living things use to store energy is in the bonds of the ATP molecule
- Adenosine Triphosphate
Blue = ribose (a 5-carbon sugar)Green = adenine (a nitrogenous base)
Yellow = phosphate groups
Energy is stored in bonds joining thephosphate groups
Energy is stored in ATP (ADP + P)
Energy is used as needed & ATP is
converted back to ADP + phosphate.
4 Classes of Organic Molecules
- Nucleic Acids
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Monomers & Polymers
- single sugar unitsglucose
- twomonosaccharides. Lactose, maltose
- linking many sugar units together
Examples: starch, glycogen, cellulose
- General formula [CH2O]n
- where n is a number between 3 and 6.
- Ex- glucose= C6H12O6
What does it mean to be
Got Milk?- milk’ssugar is lactose
- Infant mammals are fed on milk from mom
- Enzyme lactase digests
the molecule into its two
subunits for absorption.
- in most species, including humans,
the production of lactase gradually
ceases with maturity, & they are
then unable to metabolize lactose…
becoming “Lactose intolerant”
Lots of monomers linked together
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An Amino Acid
- an amino end(NH2)
- a carboxyl end (COOH).
- R is the variable (R-group) of each amino acid.
*Amino acids are linked together by joining the amino end of one molecule to the carboxyl end of another. *Removal of water (condensation reaction) links amino acids with a peptide bond.
2. PEPTIDE BONDS
Some examples of proteins
- Antibodies: they recognize molecules of invading organisms.
- Receptors: part of the cell membrane, they recognize other proteins, or chemicals, and inform the cell... 'The Door Bell'.
- Enzymes: assemble or digest.
- Neurotransmitters and some hormones: Trigger the receptors... (the finger on the door bell...)
- Channels, and pores:holes in the cell membrane (with or without a gate). Usually, filter the flow...
- Organic molecules that act as catalysts
- Enzymes & substrates (the reactants) fit together like a “lock & key”
- This fit weaken bonds so thatless energy is needed for reaction.
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Structure of Fatty Acids
- The carboxyl head is polar- therefore it is HYDROPHILIC – water loving
- The hydrocarbon CH2 units are HYDROPHOBIC- water fearing
(not water soluble).
- Can be saturated (meaning they have as many hydrogens bonded to their carbons as possible)
- Unsaturated (with one or more double bonds connecting their carbons, hence fewer hydrogens).
- A fat is solid at room temperature, while an oil is a liquid under the same conditions. The fatty acids in oils are mostly unsaturated, while those in fats are mostly saturated.
- Triglycerides are composed of three fatty acids (usually) covalently bonded to a 3-carbon glycerol.
Fats and oils function in energy storage.
- Animals convert excess sugars into fats.
- Most plants store excess sugars as starch, although some seeds and fruits have energy stored as oils (e.g. corn oil, peanut oil, palm oil, canola oil, and sunflower oil).
- Fats yield 9.3 Kcal/gm, while carbohydrates yield 3.79 Kcal/gm. Fats store six times as much energy as glycogen.
Diets & Fat Intake
- Attempts to reduce the amount of fats present in specialized cells known as adipose cells that accumulate in certain areas of the human body.
- By restricting the intakes of carbohydrates and fats, the body is forced to draw on its own stores to makeup the energy debt.
- The body responds to this by lowering its metabolic rate, often resulting in a drop of "energy level."
- Successful diets usually involve three things: decreasing the amounts of carbohydrates and fats; exercise; and behavior modification
- One fatty acid is
replaced with a
- The negative charge(s) of the phosphate makes the “head” of the phospholipid hydrophilic. The long, hydrocarbon tail is non-polar and, therefore, hydrophobic.
*The water loving edge of the molecule orients toward water- the inside and outside of the cell.
*The water fearing edges of the molecule orient toward each other to make a lipid “bilayer”
- the construction of the cell membrane.
4. Cholesterol and steroids:
- Structure is a lipid with 4 carbon rings with various functional groups attached
- Cholesterol has many biological uses, such as its occurrence in the cell membranes, and its role in forming the sheath of some neurons. Excess cholesterol in the blood has been linked to atherosclerosis, hardening of the arteries.
- Steroids are mainly used as hormones in living things
- Structure of four steroids. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.
D. Nucleic Acids
- Function - informational molecules – heredity/genetic, protein synthesis, and energy
- A nucleotide is formed from a 5 carbon sugar, a phosphate and a nitrogen base.
- Polymers formed by linking together long chains of nucleotide monomers.
- 3 Nucleic Acids
- DNA-deoxyribonucleic acid
- Double strand of nucleotides
- Double Helix shape
- RNA-ribonucleic acid
- Single strand nucleotides
- ATP -Adenosine Triphosphate
Structure of DNA Structure of tRNA -double strand of nucleotides -single strand of nucleotides
RNA differs from DNA in the following ways:
- RNA is single stranded while DNA is double stranded.
- RNA has a sugar called ribose while DNA has a sugar called deoxyribose.
- RNA has the base uracil while DNA has the base thymine.
How DNA & RNA work together
- DNA(deoxyribonucleic acid) is the genetic material.
- It functions by storing information regarding the sequence of amino acids in each of the body’s proteins.
- This "list" of amino acid sequences is needed when proteins are synthesized.
- Before protein can be synthesized, the instructions in DNA must first be copied to another type of nucleic acid called messenger RNA.
3 types RNA
- Messenger RNA, or mRNA.
- carries the code for building a protein from the nucleus to the ribosomes in the cytoplasm. It acts as a messenger.
- Transfer RNA or tRNA.
- picks up specific amino acids in the cytoplasm & brings them into position on ribosome where they are joined together in specific order to make a specific protein.
- Ribosomal RNA or rRNA –place for protein synthesis
How a protein is built