1. Ch. 3 Biochemistry

2. Ch. 3-1 WATER

3. Polarity Water has chemical properties
These have to do with the structure of water molecules
Recall: H2O is covalently bonded
Although they share the electrons, they DO NOT share them evenly
The oxygen pulls the shared electron more strongly towards itself
Therefore the electrical charge is unevenly distributed: this is POLARITY
Oxygen has a slightly more negative charge & hydrogens have a slightly more positive charge - O + + H H

4. Hydrogen Bonding
The polar nature of water cause H2O molecules to be attracted to one another
This attraction is what holds two water molecules together is called: Hydrogen bonding
Caused by positive region of one water molecule attracted to negative region of another water molecule
Very weak bonds BUT still attractive enough to cause water molecules to cling to each other

5. Cohesion and Adhesion
Cohesion: attractive force between particles of the same kind
Ex. Water molecules attracted to one another
This allows for surface tension of water
Adhesion: attractive force between unlike substances
Example:
Cohesion

6. Capillary Action .
Due to adhesion, the ability of water to move upward through narrow tubes against the force of gravity = Capillarity

7. Temperature Moderation
In order for the temperature of water to change, it must gain or lose a large amount of energy
When water it heated, the majority of the thermal energy (heat) is used to break the hydrogen bonds between the molecules
Why is this important to living things?
Living things contain a lot of water
This water needs to remain at a relatively constant temperature in order to maintain HOMEOSTASIS!

8. Review Questions Describe the structure of a water molecule.
How do molecules of a polar compound differ from those of a nonpolar compound?
What happens when ionic compounds are mixed with water?
What are two properties of water that result from water’s tendency to form hydrogen bonds?
What is capillarity?
Most automobiles have water-cooled engines. What must be true about a solution that can replace water in the cooling system, such as antifreeze?

9. Review Questions: Answers
Describe the structure of a water molecule: What is composed of two hydrogen atoms covalently bonded to one oxygen atom. Water is polar, with the oxygen atom slightly positively charged and the hydrogen atoms slightly negatively charged.
How do molecules of a polar compound differ from those of a nonpolar compound? Polar molecules have slightly differing charges on different regions, while nonpolar molecules have a uniform charge.
What happens when ionic compounds are mixed with water? Ionic compounds dissociate when they are dissolved in water.
What are two properties of water that result from water’s tendency to form hydrogen bonds? Two properties of water that arise from hydrogen bonding are adhesion and cohesion, capillarity.
What is capillarity? It is the ability of water to move up the sides of a narrow tube as a result of water’s properties of adhesion and cohesion
Most automobiles have water-cooled engines. What must be true about a solution that can replace water in the cooling system, such as antifreeze? Solutions that can replace water as a coolant in automobile engines must have the ability to absorb large quantities of heat withou easily changing temperature.

10. CH. 3-2 CARBON COMPOUNDS

11. Carbon Bonding
Carbon has 4 electrons in outermost energy level: it wants 8 electrons
Because of this, carbon readily forms 4 covalent bonds with other elements
Carbon also readily forms bonds with other carbon atoms forming:
Straight chains
Branched chains
Rings

12. Carbon Chains
STRAIGHT CHAIN BRANCHED CHAIN RING

13. Covalent Bonds
Single covalent bond: bond formed when two atoms share a pair (2) electrons
C C
Double covalent bond: bond formed when two atoms share two pairs (4) of electrons
Triple covalent bond: bond formed when two atoms share three pairs (6) of electrons

14. Functional Groups
Clusters of atoms in organic compounds that influence the properties of the molecules in which they are located
Functional groups determine the characteristics of the compound
Ex: hydroxyl group (-OH)
Important to living things

15. Hydroxyl Group (-OH)
Alcohol-organic compound-with hydroxyl group attached to one of its carbon atoms
Some common alcohols:
Ethanol
In alcoholic beverages
Causes cell death in liver and brain
Methanol AKA Wood alcohol
Causes blindness or death when consumed
Glycerol
IMPORTANT FOR LIVING ORGANISMS
Assembles certain molecules within the body

16. Alcohols

17. Large Carbon Molecules
Monomers: simple molecules used to build large carbon molecules
This is done by bonding to each other to form complex molecules: Polymers
MONOMER + MONOMER + MONOMER (etc) = POLYMER
Large polymers = Macromolecules

18. Macromolecules
The process of building a polymer is called Dehydration synthesis or Condensation Reaction
This is the taking away of a water molecule in order to bond monomers with each other forming a polymer
The process of breaking apart a polymer is called Hydrolysis
This is the reversal of dehydration synthesis
Hydrolysis is the addition of a water molecule to a polymer which breaks it apart

19. Dehydration Synthesis
Building a Polymer
Hydrolysis Reaction
Breaking apart of Polymer

20. Energy Currency Life processes require constant supply of energy
Adenosine Triphosphate (ATP): compound that contains a large amount of energy in the structure
Part of the structure of ATP is a phosphate group
Each phosphate is bonded to each other by a covalent bond
When a phosphate is taken away, this covalent bond is broken releasing a lot of energy

21. COVALENT BOND
When one of the phosphate group bonds in broken, a large amount of energy is released.
ATP  ADP
adenosine TRIphosphate  adenosine DIphosphate

22. Review Questions What is an organic compound?
What property allows carbon compounds to exist in a number of forms?
Define functional group and give an example:
How does a polymer form?
How does a polymer break down?
Scientists can determine the age of a substance using a method that compares the amounts of different forms of carbon atoms present in the substance. Is this method more useful for organic substances or inorganic substances?

23. Review Questions: Answers
What is an organic compound? With few exceptions, organic compounds contain carbon covalently bonded to itself and other atoms (carbon backbone)
What property allows carbon compounds to exist in a number of forms? Carbon can form four covalent bonds with any number of atoms, including other carbon atoms. This allows it to form molecules of different shapes.
Define functional group and give an example: Functional groups are clusters of atoms that influence the properties of the molecules they compose. For example, the hydroxyl group is a functional group.
How does a polymer form?
How does a polymer break down?
Scientists can determine the age of a substance using a method that compares the amounts of different forms of carbon atoms present in the substance. Is this method more useful for organic substances or inorganic substances?

24. Ch. 3-3 MOLECULES OF LIFE

25. Carbohydrates Organic compounds composed of: Carbon, Hydrogen, Oxygen
In ratio of 2:1 (2 hydrogen: 1 oxygen)
Number of carbon atoms varies
Carbohydrates exist as:
Monosaccharides
Disaccharides
Polysaccharides

26. Carbohydrates: Monosaccharides
A monomer of a carbohydrate
Monosaccharide = simple sugar
Carbon: Hydrogen: Oxygen
1 : :
Common monosaccharides:
Glucose, fructose, galactose
Glucose = main source of energy for cells
Fructose = found in fruits; sweetest of all monosaccharides
Galactose = found in milk
Glucose, fructose, galactose are all isomers: Compounds with a single chemical formula but different forms
All have chemical formula = C6H12O6

27. Isomers

28. Carbohydrates: Disaccharides
Disaccharide = double sugar
Disaccharide is made up of monosaccharide + monosaccharide
This process is also through the dehydration synthesis AKA condensation reaction

29. Carbohydrates: Polysaccharides
Complex molecules composed of three or more monosaccharides
Ex: Glycogen
Consists of hundreds of glucose molecules strung together
Glycogen is “stored sugar” and located in liver and muscles
Ready to be used for quick energy

30. Carbohydrates

31. Proteins Organic compounds made of: Carbon, hydrogen, oxygen, nitrogen
Formed from linkage of monomers
Catalysts are made of proteins
Muscle and skin made of proteins

32. Proteins: Amino Acids 20 different amino acids (AA)
AA are monomer building blocks of proteins
All share basic structure: 4 main parts
Hydrogen atom
Carboxyl group (-COOH)
Amino group (-NH2)
R group
Differences btwn AA located in R group  Difference causes each protein to be a different shape  Different shapes allow proteins to perform many different roles/functions

33. Amino Acid R H N C OH O H H C AMINO GROUP CARBOXYL GROUP R GROUP
HYDROGEN C R H N C OH O H H

34. Proteins: Peptides
Peptide bond: two amino acids bonded by a covalent bond
Dipeptide: two amino acids bonded
This bonding results from Dehydration reaction (condensation reaction)
Polypeptide: many amino acids bonded together forming a long chain of AA
Proteins are made of one or more polypeptides
Some proteins are very large molecules
These are bent and folded upon themselves due to:
Hydrogen bonding
Temperature
Example: cooking an egg: this heat changes the shape of the proteins in the egg  went from clear, runny liquid to a solid white solid

36. Proteins: Enzymes Act as catalysts Essential for cell functioning
Enzyme reactions depend on physical fit between enzyme & substrate: reactant being catalyzed
“Lock & Key” mechanism
The linkage of enzyme & substrate changes the enzyme’s shape slightly
Conforms to substrate’s shape
Weakens bonds in substrate which lowers activation energy
***AFTER REACTION, ENZYME RELEASES PRODUCTS & ENZYME ITSELF IS UNCHANGED THEREFORE CAN BE USED AGAIN!

37. Enzymes in Action

38. What do enzymes have to do with homeostasis?
Enzymes may fail to work in the wrong conditions
For example
Change in temperature
Change in pH
These can change the shape of the enzyme causing it not to work properly it will not fit into the substrate therefore the reaction it would have catalyzed will not happen! 
DENATURATION

39. Lipids
Large, non-polar organic molecules that DO NOT dissolve in water
Store energy efficiently
Have many hydrogen-carbon bonds which store more energy than carbon-oxygen bonds common in other organic compounds
Made up of fatty-acids

40. Lipids: Fatty Acids
Fatty acids: un-branched carbon chains that make up most lipids
Contain long, straight carbon chain with a carboxyl group –COOH attached at one end
Each end of a fatty acid has very different properties
Carboxyl group end:
Polar-attracted to water molecules  Hydrophilic: “water-loving”
Hydrocarbon end:
Nonpolar-not attracted to water molecules Hydrophobic: “water-fearing”

41. Fatty acids are made up of two parts:
Carboxyl End: -COOH
Hydrocarbon Chain: made of only hydrogen & carbons!

42. Fatty Acid Structure

43. Fatty Acids: two main types
SATURATED: all carbon atoms are single-bonded to hydrogen atoms
UNSATURATED: some carbon atoms have formed double-covalent bonds to each other

44. Complex Lipids
Lipids are divided into categories according to their structure
Three classes are:
1) Triglycerides
Composed of 3 molecules of fatty acid joined to 1 molecule of glycerol
Can be saturated or unsaturated
Saturated Triglycerides: solid at room temp., high melting points, EX. Shortening & animal fats
Unsaturated Triglycerides: liquid at room temp., EX. Plant seeds & fruits

45. Complex Lipids Cont.
2) Phospholipids: composed of 2 fatty acids joined to 1 molecule of glycerol
Cell membrane is composed of two layers of phospholipids = phospholipid bilayer
Lipids do not dissolve in water which is important for the cell because it forms a barrier between the inside and outside of the cell

46. Complex Lipids Cont.
3) Waxes: consists of long fatty-acid chain joined to a long alcohol chain
Highly waterproof
Plants have protective coating on outer surfaces made of wax
We have ear wax for prevention of microorganisms from entering

47. Lipids: Steroids NOT composed of fatty acids
Composed of four fused carbon rings with functional groups attached to them
Many hormones are steroid compounds
Most familiar in humans: Cholesterol

48. Nucleic Acids
Very large and complex organic molecules that store important information
Use system of four compounds to store hereditary information in cells
Deoxyribonucleic acid (DNA): contains information essential for all cell activities
Ribonucleic acid (RNA): stores & transfers info essential for making proteins
Both DNA & RNA are composed of monomers called nucleotides

49. Nucleotides Each made of three main components: Phosphate group
Five-carbon sugar backbone
Ring-shaped nitrogen base- there are 4 different bases

50. Review Questions
Define monosaccharide, disaccharide, and polysaccharide
Describe the structure of amino acids and proteins
Explain the relationship between an enzyme and its substrate
How do the two ends of a fatty acid differ?
Name the two types of nucleic acids, and describe their functions.
High temperatures can weaken bonds between different parts of a protein molecule, thus changing its shape. How might this change alter the effectiveness of an enzyme?

51. Review Questions: Answers
Define monosaccharide, disaccharide, and polysaccharide: A monosaccharide is a simple sugar that contains carbon, hydrogen, and oxygen in the ratio of 1:2:1. A disaccharide is composed of two monosaccharides. A polysaccharide is a complex carbohydrate composed of three or more monosaccharides.
Describe the structure of amino acids and proteins: An amino acid consists of a central carbon atom bonded to a hydrogen atom, an amino group, a carboxyl group, and a variable R group. Proteins are polymers of amino acids.
Explain the relationship between an enzyme and its substrate: An enzyme attaches physically to the substrate and catalyzes the reaction. The enzyme molecule then releases the resulting products and can be used again.
How do the two ends of a fatty acid differ? The carboxyl end is polar and therefore hydrophilic. The hydrocarbon end is nonpolar and therefore hydrophobic.

52. Review Questions: Answers
Name the two types of nucleic acids, and describe their functions: DNA stores information essential for almost all cellular activities. RNA stores and transfers information essential for the manufacture of proteins.
High temperatures can weaken bonds between different parts of a protein molecule, thus changing its shape. How might this change alter the effectiveness of an enzyme? Changing the shape of an enzyme may affect its ability to function because the enzyme may no longer physically interact appropriately with its substrate.