Chapter 3 Biochemistry

Water Water has 4 important properties. Water has 4 important properties. Water is polar. Water is polar. Water has hydrogen bonding. Water has hydrogen bonding. Water is cohesive. Water is cohesive. Water is adhesive. Water is adhesive.

Polarity Many of water’s biological functions stem from its chemical structure. Many of water’s biological functions stem from its chemical structure. The hydrogen and oxygen in water share electrons with covalent bonds. The hydrogen and oxygen in water share electrons with covalent bonds. These atoms do not share the electrons equally. These atoms do not share the electrons equally. Since the oxygen atom is bigger than the hydrogen atoms, the electrons tend to hang around the oxygen atom more often. Since the oxygen atom is bigger than the hydrogen atoms, the electrons tend to hang around the oxygen atom more often. This gives oxygen a small negative charge and the hydrogen a small positive charge. This gives oxygen a small negative charge and the hydrogen a small positive charge.

A polar molecule is when opposite ends have opposite charges. Not charges like ionic bonds but smaller attractions that sometimes only water has. A polar molecule is when opposite ends have opposite charges. Not charges like ionic bonds but smaller attractions that sometimes only water has.

Being polar leads to other things like……… Hydrogen bonds Hydrogen bonds This occurs when the slightly positive hydrogen atom is attracted to a slightly negative oxygen atom of another water molecule, it is a very weak attraction. This occurs when the slightly positive hydrogen atom is attracted to a slightly negative oxygen atom of another water molecule, it is a very weak attraction. hydrogen oxygen

Cohesion This occurs when molecules of the same kind stick to one another This occurs when molecules of the same kind stick to one another

Cohesion creates surface tension. Water is very sticky!

Adhesion This is when molecules that are not alike are attracted, example, water to walls of a test tube, or plant walls This is when molecules that are not alike are attracted, example, water to walls of a test tube, or plant walls When you see adhesion, think adhesive, sticky. When you see adhesion, think adhesive, sticky.

Capillarity This is when water goes up a small, narrow tube like a plant stem or paper towel. This is when water goes up a small, narrow tube like a plant stem or paper towel. Adhesion makes this possible. Adhesion makes this possible.

Water’s Unique Properties Water has 4 unique properties. Water has 4 unique properties. 1 Water is polar. 2 Water makes hydrogen bonds. 3 Water is cohesive. 4 Water is adhesive.

Density of Water is Special!

Water is one of the only substances on Earth in which the solid phase is less dense than the liquid phase! Water is one of the only substances on Earth in which the solid phase is less dense than the liquid phase! Because of this, life can exist in many places. Because of this, life can exist in many places.

When winter comes, the ice floats and keeps fish safe. ICE Ouch!

If ice was actually denser than water……. I wish I could get to safer water below!

Temperature Moderation Water must gain or lose a relatively large amount of energy for its temperature to change. Water must gain or lose a relatively large amount of energy for its temperature to change. When water is heated, most of the thermal energy that the water initially absorbs breaks the hydrogen bonds between the molecules. When water is heated, most of the thermal energy that the water initially absorbs breaks the hydrogen bonds between the molecules. When the bonds are broken, the thermal energy is released and increases the motion of the molecules. When the bonds are broken, the thermal energy is released and increases the motion of the molecules. Water’s ability to absorb large amounts of energy helps keep cells at an even temperature despite temperature changes in the environment. Water’s ability to absorb large amounts of energy helps keep cells at an even temperature despite temperature changes in the environment.

Carbon Compounds A carbon atom has 4 electrons in its outer level which means it can create 4 bonds with any other atoms including itself. A carbon atom has 4 electrons in its outer level which means it can create 4 bonds with any other atoms including itself. This makes carbon an excellent backbone for many organic molecules. This makes carbon an excellent backbone for many organic molecules. Carbon can even form rings and double and triple bonds! Carbon can even form rings and double and triple bonds!

Functional Groups A functional group is a group of atoms that influence the properties of the molecules they compose. A functional group is a group of atoms that influence the properties of the molecules they compose. Alcohol is a functional group that has oxygen and hydrogen attached. Alcohol is a functional group that has oxygen and hydrogen attached. Alcohols can cause blindness or even death when consumed. Alcohols can cause blindness or even death when consumed. Some alcohols are important to assemble certain molecules in the body. Some alcohols are important to assemble certain molecules in the body.

Large Carbon Molecules In large carbon compounds, the molecules are built up from smaller, simpler molecules called monomers. In large carbon compounds, the molecules are built up from smaller, simpler molecules called monomers. Monomers can bind together to create larger, more complex molecules called polymers. Monomers can bind together to create larger, more complex molecules called polymers. Large polymers are called macromolecules. Large polymers are called macromolecules.

How are polymers made and broken? Monomers link together in a condensation reaction. Monomers link together in a condensation reaction. When two monomers combine, water is released. When two monomers combine, water is released. When polymers are broken, it is called a hydrolysis reaction. When polymers are broken, it is called a hydrolysis reaction. Water is broken into two parts and breaks the bonds that holds the monomers together. Water is broken into two parts and breaks the bonds that holds the monomers together.

Energy Currency Life processes require energy. Life processes require energy. This energy is available to life in the form of a compound called ATP. This energy is available to life in the form of a compound called ATP. ATP has three phosphates on the molecule and when one phosphate is broken off, energy is released. ATP has three phosphates on the molecule and when one phosphate is broken off, energy is released.

Carbohydrates A monomer of a carbohydrate is called monosaccharide. A monomer of a carbohydrate is called monosaccharide. A monosaccharide is a simple sugar. A monosaccharide is a simple sugar. Two monosaccharides form a disaccharide. Two monosaccharides form a disaccharide. A polysaccharide is a complex molecule composed of three or more monosaccharides. A polysaccharide is a complex molecule composed of three or more monosaccharides. What are some carbs? What are some carbs?

Proteins Proteins are organic compounds made from monomers called amino acids. Proteins are organic compounds made from monomers called amino acids. There are 20 different amino acids. There are 20 different amino acids. The differences between the amino acids are their R groups. The differences between the amino acids are their R groups. Two amino acids bond to form a dipeptide. Two amino acids bond to form a dipeptide. In a condensation reaction, two amino acids form a covalent bond called a peptide bond. In a condensation reaction, two amino acids form a covalent bond called a peptide bond. Long chains of amino acids are called polypeptides. Long chains of amino acids are called polypeptides. What are some proteins? What are some proteins?

Enzymes are a special kind of protein. Enzymes are proteins that are important catalysts for chemical reactions. Enzymes are proteins that are important catalysts for chemical reactions. Enzyme reactions depend on the physical fit between the enzyme and the substrate. Enzyme reactions depend on the physical fit between the enzyme and the substrate. The substrate is the reactant being catalyzed. The substrate is the reactant being catalyzed. Enzymes may fail to work when the temperature isn’t correct. Enzymes may fail to work when the temperature isn’t correct. Other chemicals and pH are also a factor. Other chemicals and pH are also a factor.

Affects on Enzymes Temperature-raising of lowering temperature can cause an enzyme to malfunction Temperature-raising of lowering temperature can cause an enzyme to malfunction Denature-a protein unravels when it gets too hot Denature-a protein unravels when it gets too hot A change in pH can decrease the ability of an enzyme to function. A change in pH can decrease the ability of an enzyme to function. A foreign chemical or metal can decrease the ability of an enzyme to function. A foreign chemical or metal can decrease the ability of an enzyme to function.

Lipids Lipids are large, non polar molecules that do not dissolve in water. Lipids are large, non polar molecules that do not dissolve in water. Fatty acids are unbranched carbon chains that make up most lipids. Fatty acids are unbranched carbon chains that make up most lipids. Hydrophilic-water-loving, molecules dissolve in water Hydrophilic-water-loving, molecules dissolve in water Hydrophobic-water-fearing, molecules do not dissolve in water Hydrophobic-water-fearing, molecules do not dissolve in water

Types of Lipids A triglyceride is composed of three molecules of fatty acids joined to an alcohol called glycerol. A triglyceride is composed of three molecules of fatty acids joined to an alcohol called glycerol. Phospholipids have two fatty acids joined with glycerol. Phospholipids have two fatty acids joined with glycerol. Phospholipids are contained in the cell membrane and form a double layer to create a barrier between the inside and outside of cell. Phospholipids are contained in the cell membrane and form a double layer to create a barrier between the inside and outside of cell. A wax is a type of structural lipid. A wax is a type of structural lipid. A steroid has 4 carbon rings. Cholesterol is an example. Steroids are also hormones and very important for life. A steroid has 4 carbon rings. Cholesterol is an example. Steroids are also hormones and very important for life.

Types of Fats(Lipids) A saturated fat has all available bonds used by hydrogen. A saturated fat has all available bonds used by hydrogen. Saturated fats are solid at room temperature and are all single bonded, straight chains Saturated fats are solid at room temperature and are all single bonded, straight chains Unsaturated fats have a double bond which means not all available bonds are taken by hydrogen. Unsaturated fats have a double bond which means not all available bonds are taken by hydrogen. Unsaturated fats are generally liquid at room temperature and are healthier. Unsaturated fats are generally liquid at room temperature and are healthier.

Nucleic Acids Nucleic acids are large and complex organic molecules that store important information in the cell. Nucleic acids are large and complex organic molecules that store important information in the cell. RNA stores and transfers information to make proteins. RNA stores and transfers information to make proteins. DNA contains information that is essential for cell activities. DNA contains information that is essential for cell activities. Both RNA and DNA are composed of monomers called nucleotides. Both RNA and DNA are composed of monomers called nucleotides. A nucleotide has 3 components: a phosphate group, a sugar and a nitrogen base. A nucleotide has 3 components: a phosphate group, a sugar and a nitrogen base.

Nucleotide

DNA

Essential Questions 1. Describe the structure of the water molecule. 1. Describe the structure of the water molecule. 2. What are two properties of water that are caused by hydrogen bonding? 2. What are two properties of water that are caused by hydrogen bonding? 3. What is an organic compound? 3. What is an organic compound? 4. Define functional group and give an example. 4. Define functional group and give an example.

Essential Questions 5. How does a polymer form? 5. How does a polymer form? 6. How does a polymer break down? 6. How does a polymer break down? 7. What are the 4 classes of organic compounds? Give an example of each. 7. What are the 4 classes of organic compounds? Give an example of each. 8. Explain the relationship between enzyme and substrate. 8. Explain the relationship between enzyme and substrate. 9. What affects the ability of enzymes to work? 9. What affects the ability of enzymes to work?