College Biology - Biochemistry Unit

Test 2

Elements

Substances that can no longer be broken down into other substances and keep their characteristic properties

CHNOPS - what is it

An acronym for the 6 essential elements to life (99%)

CHNOPS - what they stand for

C - Carbon

H - Hydrogen

N - Nitrogen

O - Oxygen

P - Phosphorus

S - Sulfer

Valance Electron - what is it

Electrons found only on the outside layer

Valance Electron - how to find

# of electrons - 10

Lewis Dot Structure

The amount of electrons in an element

Focus on Valence Electrons in drawing

• Go around until all sides have 1 before moving to doubling up

Subatomic Particles

Neutron (0), Electron (-), and Proton (+)

Atomic Number - where it is found

Top right corner of element

Atomic Mass - where it is found

Bottom of the element

Proton

Atomic #

Electron

Atomic #

Neutron

Atomic Mass - Atomic #

Isotope

Element with a different atomic mass

Orbitals

The undefined path an electron travels in

How Orbitals Work

• Move to lowest energy level possible (close to nucleus)

• If energy is added, electrons move/jump to higher levels

• Energy is given off when electrons move back to lower levels

Ionic Bonds - weak

One atom gains electrons & one atom loses electrons

• The two atoms become charged and are called ions

Ionic Bond Example

1. Make sure to draw arrows

2. The + and - are opposite of what you think

Covalent Bonds - strong

The sharing of electrons

• Can be polar or non-polar

Polar

Electrons are pulled more towards one nuclei than another, the molecule is charged

Non-polar

Electrons are pulled equally towards nuclei and there is no charge

Covalent Bond Example

• Remember to add charges

• Circle covalent bonds

Hydrogen Bond - weakest

Form between compounds, these bonds break and reform easy

Hydrogen Bond Example

• Covalent bonds that connect in a larger form

Super Solvent - Importance of Water

Dissolves more compounds in greater amounts than any other liquid

Example of Super Solvent

Breaks things down in the body

Solute

Getting dissolved

Solvent

Doing the dissolving

Solid is less dense than liquid - Importance of Water

Solid has more H bonds (water molecules spread out)

Liquid is moving and H bonds are breaking and reforming quickly

Example of Solid is less dense than liquid

Only top of lake freezes

High Specific Heat - Importance of Water

• It takes a lot of energy to raise water temp

• Water absorbs heat

• When the environment around water cools off, water releases heat

High Specific Heat

The amount of energy it takes to raise the temp 1 degree C

Example of High Specific Heat

Stable environments and bodies

Cohesion - Importance of Water

• Water is attracted to water

Surface Tension

Molecules are not attracted to the air above, pulled towards water below

Example of Cohesion

Trees get water into roots

Hydrophobic

Doesn’t mix well with water

Hydrophilic

Does mix well with water

pH Scale

Membranes and Enzymes require a specific pH

• 0 - very acidic

• 7 - neutral 

• 14 - not acidic

  • 0 - 7: acid

  • 7 - 14: base

Carbon (life is based on)

• 4 valence electrons

• Great bonding

• Covalent bonds (strong)

• Atoms attach to a carbon compound, giving it a special property / shape

  • Most are polar (+) (-)

General composition of any carbohydrate

C_xH_2xO_x

Carboxyl (COOH)

Found in fatty acids / amino acids

• Remember to have constant at the beginning (C with 3 H bonds)

Hydroxyl (OH)

Found in alcohol / carbohydrates

• Remember to have constant at the beginning (C with 3 H bonds)

Amino (NH₂)

Found in amino acids

• Remember to have constant at the beginning (C with 3 H bonds)

Phosphates (PO₄)

Found in DNA / ATP

• Remember to have constant at the beginning (C with 3 H bonds)

Monomer

Small molecule that can be combined w/ others to make a polymer

Polymer

Large molecule made up of similar sub units (monomers)

Monosaccharides - Carbohydrates

One carbohydrate - monomers: glucose, fructose, deoxyribose 

Disaccharides - Carbohydrates

Two carbohydrates - maltose, sucrose, lactose, dehydration / condensation reactions, glycosidic bonds

Glycosidic

The bond between 2 glucose molecules

Polysaccharides - Carbohydrates

Complex carbs

Starch - polysaccharides

Carb storage in plants

Gycogen - polysaccharides

Carb storage in animals (muscle and liver cells)

Cellulose - polysaccharides

Structure to plants — insoluble fiber for animals (Dense and rigid)

Chitin - polysaccharides

Exoskeleton structure of arthopods / animals

Lipid Properties

• Insolubility in water (hydrophobic)

• Form internal containers for living things

• Store energy 

• Insulation

• Not a polymer - has blobs :)

Glyceride

Triglycerides make up most of lipid weight in food

• Glycerol plus three fatty acids

Saturated Fat

Saturated fatty acids have as many H atoms bonded to it as possible

Unsaturated Fat

Unsaturated fatty acids have one or more double bonds (room for more H)

Saturated Fat Drawing

Molecule is flat, stack up close: forms solids

• Remember carbon base in front

Unsaturated Fat Drawing

Molecule bends: forms liquids

• Remember carbon base in front

Steroid Traits (reminder: it is also a lipid)

• 4 carbon rings: all points are considered carbon

• Cholesterol

  • found in cell membrane of animals

• Testosterone / Estrogen

Cholesterol

HDL, LDL are 2 types of this molecule that is used to maintain membrane stability

***Phospholipids (unique, do not follow pattern of lipids)

• Glycerol, 2 fatty acids, phosphate group

• Fatty acid tails are hydrophobic

• Phosphate head is hydrophilic

Protein Monomer

Amino Acid

Polypeptide - protein

Linear chain of amino acids

• When the polypeptide folds up 3-D, it is called a protein

What combines with an amino group to make a polypeptide chain?

Carboxyl 

Amino Acid & Protein Traits

All have carboxyl, amino, and H on top

• Order of amino acids determines the protein

• All amino acids have 1 carboxyl and 1 amino group

• Carboxyl group of one amino acid bonds with the amino group of another

Protein Drawing

• Called a peptide bond between proteins

• R - The variant group in protein that ultimately determines the shape

Protein Structure - how it works

THE SHAPE IS CRUCIAL

• Puzzle / Lock & Key

Primary Structure - protein

Sequence of amino acids

Secondary Structure - protein

Coils created by bonds between amino acids

• Helix or B Pleated Sheet

Tertiary Structure - protein

Larger 3-D shapes

Quaternary Structure - protein

Several polypeptides linked

Dehydration

Type of reaction that is used in forming carbohydrates, lipids and proteins

Protein Molecule Diagram Characteristics

• Begins with NH₂ or NH₃

• Has a Carboxyl

• Amino Acid

• R group

Carbohydrates Molecule Diagram Characteristics

ONLY carbon, hydrogen, and oxygen throughout

Nucleic Acids Molecule Diagram Characteristics

Have nitrogen or N in the rings ONLY (no other N in any chains)

Lipids Molecule Diagram Characteristics

Have carbon and hydrogen BUT very few oxygens

• Most likely one at the beginning or a couple throughout

Enzyme

A protein that speeds up chemical reactions

Example of an enzyme

Lactase

• -ASE = enzyme

How do enzymes work?

Either split OR combine molecules (build OR break down)

Substrate

The substance an enzyme works on

Enzyme Shape

Stays the same

Substrate Shape

Changes shape

Metabolic Pathway (simple terms)

• Most large scale activities involve multiple enzymes

• Set of enzyme steps

Enzymes lower what?

Enzymes lower the activation energy

Enzyme Characteristics

Proteins with a Tertiary and Quaternary structure

Only a few of the amino acids are involved in binding the substrate

Active Site

Active Site

Where the substrate binds

Reactant

A substance that takes part in and undergoes change during a reaction

Product

Substances generated by living organisms during metabolic or biochemical processes

What affects the amount of product?

• Amount of substrate

• If the active site is occupied by a molecule that is not a substrate

  • Competitive Inhibition

Competitive Inhibition

Blocked off

Negative Allosteric Regulation

On/Off Enzyme

Enzyme Lab - Ezyme?

Catalase

Enzyme Lab - Substrate?

Hydrogen Peroxide (H₂O₂)

Enzyme Lab - Formula?

H₂O₂ — H₂O + O₂

• H₂O_{2 = Reactant}

• _{— = Catalase}

• H₂O + O_{2 = Product}

Enzyme Lab - Balanced Formula?

2 H₂O₂ — 2 H₂O + O₂