BiochemistryBiochemistry

Chapter 3 NotesChapter 3 Notes

What are Organic Molecules?What are Organic Molecules? Most of the substances that make up cells Most of the substances that make up cells

contain carboncontain carbon They are called organic compounds.They are called organic compounds. Most inorganic compounds do not contain carbon.Most inorganic compounds do not contain carbon. Two different molecules can have the exact same Two different molecules can have the exact same

number and kind of elements in it, but they are number and kind of elements in it, but they are different because they are put together differently.different because they are put together differently.

Rings form when carbons form double bondsRings form when carbons form double bonds Each carbon atom can form a total of 4 bonds with other Each carbon atom can form a total of 4 bonds with other

atoms.atoms.

A functional group is a group of atoms that bond A functional group is a group of atoms that bond to C (carbon) and give it a particular function.to C (carbon) and give it a particular function.

There are 4 functional groups:There are 4 functional groups: 1. Hydroxyl = OH1. Hydroxyl = OH

Found in sugars & alcoholsFound in sugars & alcohols Makes them attract to/dissolve in waterMakes them attract to/dissolve in water

2. Carbonyl = CO2. Carbonyl = CO Found in sugarsFound in sugars

3. Amino = NH3. Amino = NH22 Found in proteins Found in proteins

4. Carboxyl = COOH4. Carboxyl = COOH Found in proteins, organic acids Found in proteins, organic acids

Hydrocarbons are molecules of C (carbon) and Hydrocarbons are molecules of C (carbon) and H (hydrogen). Ex = methane: CHH (hydrogen). Ex = methane: CH44

““Macromolecules” are large molecules made Macromolecules” are large molecules made up of hundreds or thousands of atoms.up of hundreds or thousands of atoms. ““monomers” are individual molecules that make monomers” are individual molecules that make

up macromoleculesup macromolecules ““dimers” are groups of 2 monomersdimers” are groups of 2 monomers ““polymers” are groups of 3 or more monomerspolymers” are groups of 3 or more monomers

Examples: food molecules (lipids, carbs and proteins) Examples: food molecules (lipids, carbs and proteins)

HydrocarbonsHydrocarbons

Macromolecules are created by a process Macromolecules are created by a process called dehydration synthesis or a condensation called dehydration synthesis or a condensation reaction reaction the removal of water to join 2 the removal of water to join 2 molecules.molecules.

http://nhscience.lonestar.edu/biol/dehydrat/dehydrat.html

HydrocarbonsHydrocarbons

HydrocarbonsHydrocarbons

Macromolecules (from your food) are broken Macromolecules (from your food) are broken down in your cells by a process called down in your cells by a process called hydrolysis hydrolysis breaking bonds between food breaking bonds between food molecules by adding water.molecules by adding water.

http://nhscience.lonestar.edu/biol/dehydrat/dehydrat.html

““Energy Currency”Energy Currency”

ATP = Adenosine Triphosphate ATP = Adenosine Triphosphate Energy storage molecule that provides the energy Energy storage molecule that provides the energy

your cells need to carry on life processes.your cells need to carry on life processes. When your body metabolizes food, it is When your body metabolizes food, it is

“harvesting” ATP from the chemical bonds “harvesting” ATP from the chemical bonds between food molecules.between food molecules.

4 major classes of biomolecules (or 4 major classes of biomolecules (or “macromolecules”):“macromolecules”): 1. Protein1. Protein

Made up of (their monomers are calledMade up of (their monomers are called) amino acids Examples/Function: meats, fish, oatmeal; build body

parts and to repair the body.

2. Lipid2. Lipid Made up of (their monomers are called) fatty acidsMade up of (their monomers are called) fatty acids Examples/Functions: butter, oil, lard; provides energy Examples/Functions: butter, oil, lard; provides energy

for the bodyfor the body

33. Carbohydrates Made up of (their monomers are called)

monosaccharides – most common = glucose Examples/Function: sugar, pasta; gives energy

4. Nucleic Acids4. Nucleic Acids Made up of (their monomers are called) nucleotidesMade up of (their monomers are called) nucleotides Examples/Function: DNA & RNA; contains the cell’s Examples/Function: DNA & RNA; contains the cell’s

genetic informationgenetic information

CarbohydratesCarbohydrates

““saccharide” refers to saccharide” refers to sugar units

Mono, di, poly = the number of sugar units

mono = 1; di = 2; poly = many

Contain carbon, hydrogen and oxygen in the ratio of 1 C:2 H:1 O (C6H12O6 = glucose)

Common examples:Common examples: Monosaccharides:Monosaccharides:

Fructose = fruit sugar & honey

Glucose = source of energy for cells

Fructose & glucose are ISOMERS = they have the same chemical formula but different structures.

Fructose

Glucose

Disaccharides:Disaccharides: Maltose = 2 glucoseMaltose = 2 glucose Lactose = milk sugarLactose = milk sugar Sucrose = table sugar (glucose & Sucrose = table sugar (glucose &

fructose)fructose)

Polysaccharides:Polysaccharides: Starch = energy Starch = energy

storage storage carbohydrate in carbohydrate in plantsplants

Cellulose = HUGE Cellulose = HUGE structural support structural support molecule in plantsmolecule in plants

Glycogen = Glycogen = energy storage energy storage carbohydrate in carbohydrate in the liver of the liver of animals.animals.

Importance of CarbsImportance of Carbs

Provide us with energy – pasta, fruits, breads Provide us with energy – pasta, fruits, breads (sugars & starches)(sugars & starches)

Cellulose:Cellulose: Plants – found in cell walls – allows them to grow Plants – found in cell walls – allows them to grow

tall; used to make paper.tall; used to make paper. Animals – animals can use it for energy; humans Animals – animals can use it for energy; humans

can only use it as “roughage” or fiber . . .can only use it as “roughage” or fiber . . .

Carbs in our dietsCarbs in our diets Low carb diets are not good for the body. Disrupts Low carb diets are not good for the body. Disrupts

the amount of nitrogen in the body – causes the the amount of nitrogen in the body – causes the body to break down its own proteins.body to break down its own proteins.

Foods high in carbs: bread, rice, potatoes, pasta, Foods high in carbs: bread, rice, potatoes, pasta, fruits, veggies, baked goodsfruits, veggies, baked goods

Recommended daily intake of carbs: 40% - 60% Recommended daily intake of carbs: 40% - 60% of daily food intake (most should be GOOD carbs of daily food intake (most should be GOOD carbs like whole grains, veggies, fruits, etc.)like whole grains, veggies, fruits, etc.)

LipidsLipids Triglycerides are Triglycerides are fats – DO NOT dissolve in

water because they are nonpolar. Examples:

Fats – made by animals; solid at room temperature (“bad” for the body)

Oils – made by plants; liquid at room temperature (most are “good” for the body)

““Saturated” fats have Saturated” fats have no double bonds; they are “straight” molecules with the maximum number of H possible. Examples: lard, butter – solids at room temp.

““Unsaturated” fats have a double or triple Unsaturated” fats have a double or triple bond; they are “bent” molecules with fewer bond; they are “bent” molecules with fewer than maximum number of H possiblethan maximum number of H possible Examples: vegetable oils – liquid at room tempExamples: vegetable oils – liquid at room temp.

Saturated

““Polyunsaturated” fats Polyunsaturated” fats have many double or triple bonds; bent with many fewer H atoms

“Trans fats” are unsaturated fats that are changed into saturated fats by adding H-atoms (oil changed to a solid) Examples: shortening, margarine & packaged

baked goods (“partially hydrogenated” on label.) “trans fats” increase the “long life” of foods

Phospholipids are found Phospholipids are found in in the cell membrane in 2 layers. They form a water-proof barrier around cells.

Steroids Steroids Examples in the human Examples in the human

body: body: cholesterol, vitamin D and hormones. They contain rings of carbon.

Anabolic steroids . . .

(EEWWWW!!!!!)

ProteinProtein

They consist of two or more amino acids They consist of two or more amino acids joined by joined by peptide bonds.peptide bonds. Peptide bonds form between the carbon and Peptide bonds form between the carbon and

nitrogen of the neighboring amino acids. (proteins nitrogen of the neighboring amino acids. (proteins = “polypeptides”)= “polypeptides”)

Protein StructureProtein Structure

There are 20 different amino acids:There are 20 different amino acids: How can there be so many different types of How can there be so many different types of

protein? protein? They are arranged in different combinations. (Think of They are arranged in different combinations. (Think of

26 letters of alphabet making thousands of words.)26 letters of alphabet making thousands of words.) Amino acid structure: central Amino acid structure: central C-atomC-atom, , amino groupamino group, , a a

carboxyl groupcarboxyl group, , an H-atom an H-atom, and , and an R-groupan R-group The “R-group” is significant because it gives each The “R-group” is significant because it gives each

amino acids its unique properties….there are 20 amino acids its unique properties….there are 20 different R-groups.different R-groups.

Protein StructureProtein Structure

Polypeptides fold/cluster into a particular shape. The Polypeptides fold/cluster into a particular shape. The way a protein folds is determined by the interactions way a protein folds is determined by the interactions among the R-groups of its amino acids.among the R-groups of its amino acids.

All proteins/polypeptides have 3 structures to their All proteins/polypeptides have 3 structures to their shape (some have 4):shape (some have 4): Primary = sequence of amino acidsPrimary = sequence of amino acids Secondary = coiling of the a.a. chainSecondary = coiling of the a.a. chain Tertiary = folding of the coiled a.a. chain (this is when it Tertiary = folding of the coiled a.a. chain (this is when it

has a 3-D shape and “gets” its function.)has a 3-D shape and “gets” its function.) Quaternary = groups of tertiary proteins clustered togetherQuaternary = groups of tertiary proteins clustered together

Protein functions:Protein functions: Structure: Make up hair, feathers, hooves, Structure: Make up hair, feathers, hooves,

ligaments, spider webs.ligaments, spider webs. Storage: seeds & eggsStorage: seeds & eggs ““Contractile” functions: can become shorter or Contractile” functions: can become shorter or

longer – muscle cellslonger – muscle cells

Digestion & regulation: Digestion & regulation: enzymes (biological enzymes (biological catalysts) control digestion catalysts) control digestion and other chemical reactions and other chemical reactions in the body.in the body. Factors like temperature Factors like temperature

and pH can destroy or and pH can destroy or “denature” the enzyme “denature” the enzyme and ruin the active site’s and ruin the active site’s shape.shape.

HIGH fever!!!!!HIGH fever!!!!!

Each type of food we take in (substrate) has Each type of food we take in (substrate) has one type of enzyme to break it down.one type of enzyme to break it down. Each enzyme contains an active site where it can Each enzyme contains an active site where it can

bond with the substratebond with the substrate An active site and a substrate are like a lock and a An active site and a substrate are like a lock and a

key; only ONE substrate type will fit into ONE key; only ONE substrate type will fit into ONE shape of active site. shape of active site.

If the shapes don’t match, the substrate is not broken If the shapes don’t match, the substrate is not broken down by the enzyme. down by the enzyme.

Our bodies are made mostly of protein; we Our bodies are made mostly of protein; we need it to:need it to: Build and repair body partsBuild and repair body parts Assist with immune functionsAssist with immune functions Break down food (enzymes)Break down food (enzymes)

Nucleic AcidsNucleic Acids Function: Information storage (genetic Function: Information storage (genetic

information)information) Examples: DNA = Examples: DNA = DDeoxyriboeoxyriboNNucleic ucleic AAcid – cid –

it it containscontains the information; RNA = the information; RNA = RRiboiboNNucleic ucleic AAcid – it cid – it translatestranslates information information

Each nucleotide is made up of 3 basic partsEach nucleotide is made up of 3 basic parts 1. Phosphate1. Phosphate 2. Sugar2. Sugar

Difference between RNA & DNADifference between RNA & DNA: RNA has ribose sugar, DNA has deoxyribose

3. Nitrogen base – adenine, thymine, cytosine, & guanine