Intro: Answer the best you can. We will learn all this and much more this unit. 1.What are proteins?...

Intro: Answer the best you can. We will learn all this and much more this unit.

1. What are proteins?

2. Why do we need proteins?

3. What are lipids (fats)?

4. Why do we need lipids?

5. What are carbohydrates?

6. Why do we need carbohydrates?

7. What are nucleic acids?

8. Why do we need nucleic acids?

Biochemistry Day 1

Elements• Cannot be broken down into a simpler

substance

• 90 occur naturally; the rest are synthetic or radioactive

• # of Protons gives characteristic nature – state, reactivity, etc

• Many are needed by Living Orgs. for 8 characteristics….

Periodic Table of Elements

A. Human Body Composition

Biochemistry• Most of the human body is made up of water, H2O, with

cells consisting of 65-90% water by weight. Therefore, it isn't surprising that most of a human body's mass is oxygen. Carbon, the basic unit for organic molecules, comes in second. 99% of the mass of the human body is made up of just six elements: oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus.

• Oxygen (65%) • Carbon (18%) • Hydrogen (10%) • Nitrogen (3%) • Calcium (1.5%) • Phosphorus (1.0%)

96% Living things are made up of the elements C,H,N,O

(Carbon, Hydrogen, Nitrogen, and Oxygen)

Elements: ~25 elements are essential to life

Found in the body in very small amounts, yet play vital roles!

What are trace elements?

B. Basic Atom

The Atom• The charge of a proton = +1 (positive 1)

• The charge of an electron = -1 (negative 1)

• The charge of a neutron = 0 (neutral)

• The mass of a proton = about 1 amu

• The mass of a neutron = about 1 amu

• The mass of an electron is close to zero in comparison to protons and neutrons

• Protons and neutrons are found in the nucleus

• Electrons are found in orbitals outside the nucleus

Atomic Number

Mass Number

The Atom• atomic number = The number of protons

• The Atomic Mass = The mass of all protons, neutrons, and electrons.

• Number of neutrons = The atomic mass rounded – The Atomic number

• Or since the electrons weigh near zero

• Number of Neutrons = Number of protons and neutrons – the number of protons

• The number of neutrons in Helium =

4 - 2 = 2

Activity 1

• How many protons neutrons and electrons in the following atoms:

a. Carbon

b. Oxygen

c. Iron

Activity 2: Carbon

• Draw an atom of Carbon. Identify the parts of the atom

Carbon

• Draw an atom of Carbon. Identify the parts of the atom

• Number of Protons 6 • Number of Electrons 6• Number of Neutrons = 12 - 6 = 6

• If there is no charge the number of protons = the number of electrons

6P6N

-

-

- -

-

-

C. Atoms vs. Ions

• What is the difference between an atom and an ion?

• An ion is a atom that has lost or gained an electron.

• Ions have a different number of electrons than protons and therefore have a charge

• An atom that looses a(n) electron(s) becomes a cation or positively charged ion

• An atom that gains a(n) electron(s) becomes a anion or negatively charged ion

D. Isotopes

• How are isotopes different?

• How are isotopes different?

• Isotopes have the same number of protons but different numbers of neutrons

• In carbon-13, the 13 stands for the number of protons plus neutrons

E. Atoms, Elements, Molecules, and Compounds

• Example Atoms: H, He, Li, Be, B, C, N, O, F, Ne

• Example Molecules: O2 , H2O, CO2 NH3

• How is an atom different than a molecule?

• Molecules are made up of more than one atom covalently bonded

• Example Elements: O2, H2, He, N2

• Example Compounds: H2O, CO2 NH3

• How is an element different than a compound?

• Isomer = Same chemical composition but different arrangement

• Example Elements: O2, H2, He, N2

• Example Compounds: H2O, CO2 NH3

• How is an element different than a compound?

• Elements have only one type of atom

• Compounds have more than one type of atom

F. Chemical Formulas

• Subscripts are used to tell you how many of that atom are present

• Ex. CO2 is composed of one carbon and 2 oxygen atoms

• Coefficients tell you how many molecules are present

• 2(CO2) is telling you that there are two entire carbon dioxide molecules

• A missing subscript or superscript means that there are only 1

• What atoms are present and how many are in each compound?

• O2 = Oxygen

• H2O = Water

• CO2 = Carbon dioxide

• What atoms are present and how many are in each compound?

• O2 is Oxygen

• 2 Oxygen atoms

• What atoms are present and how many are in each compound?

• H2O is Water

• 2 Hydrogen atoms

• 1 Oxygen atom

• What atoms are present and how many are in each compound?

• CO2 = Carbon dioxide

• 1 Cabon atom

• 2 Oxygen atoms

G. Covalent, Ionic, and Hydrogen Bonds

In covalent bonding the electrons are _shared__ between the atoms. In Ionic bonding atoms are ____transferred____ from one atom to another. Covalent bonding forms ____molecules______. Ionic bonding forms __ions___.

Electrons are constantly in motion around the Electrons are constantly in motion around the nucleusnucleus• Electrons are attracted to the positive Electrons are attracted to the positive charges in the nucleus (protons) so they charges in the nucleus (protons) so they remain in orbit around the nucleusremain in orbit around the nucleus• Electrons move around in energy levels Electrons move around in energy levels called called electron cloudselectron clouds• Each can hold a Each can hold a certain number of certain number of electronselectrons

--firstfirst level can hold up to level can hold up to 2 e2 e--

--second second level can hold up to level can hold up to 8 e8 e--

--thirdthird level can hold up to level can hold up to 8 e8 e--

-- 4th4th level – 18e- level – 18e-

The Atom:Electron clouds & “dot” diagrams

Electron Cloud Can hold a max of ___ e-’s

1 2

2 8

3 8

4 18

Look at the periodic table to clear up any confusion…

2

8

8

18

The Atom:Electron clouds

• EXAMPLE: Carbon has 6 electrons

• They are arranged as:– 2 in the first e- cloud– 4 in the second e- cloud

• Electrons in the outer orbital are called valence electrons.– Valence electrons determine an elements

bonding potential (or reactivity)– An atoms outer orbital must be filled to be stable

• Example:– How many valence e-’s does carbon have?– How many does it “want” to be stable?

Valence Electrons

Chemical bonds:Forming a compound

• Bond – to join together atoms using electron energy/force

• Atoms are most stable when their outer e- cloud is full

• Elements can share electrons to fill their outer (valence) e- cloud

• This causes stability

1. Covalent bonds

Figure 6.6

EXAMPLE:

Oxygen alone only has 6 electrons in its outer E level

If it shares 2 more it would have 8 in its outer E level and be stable

”CO” = share

Single, Double and Triple Covalent Bonds

• 1 electron shared = single bond

• Ex: C - H

• 2 electrons shared = double bond

• Ex: O = O

Write this on your notes somewhere

• Organic means something is based on carbon

Why is carbon important to life?• Carbon has the ability to form four covalent

bonds. It can bond on all sides.

• This allows it to form complex structures like proteins, lipids, carbohydrates, and nucleic acids

2. Ionic bonds

Figure 6.7

• When atoms give or take electrons; not sharing

• The atoms with extra (or less) e- are now not neutral = ION = bond forms

Bond Strengths

• How much energy is stored bond/How much energy it takes to break the bond

1. Triple Covalent

2. Double Covalent

3. Covalent Single

4. Ionic

5. Hydrogen*

Chemical Reactions• Bonds of atoms are broken and re-formed

into new substances• Reactions are written as “chemical equations”

which show reactants and products• All reactions in an organism = Metabolism

What does balanced mean?

Chemical Reactions

• EXAMPLE – Photosynthesis

6CO2 + 6H2O C6H12O6 + 6O2

Elements in water become the elements in glucose!

Reactants Products

End Day 1

• Work on page 1 of the study guide and the first question on page 2

(5. BONDING: Compare and contrast “Ionic” and “Covalent” bonds.)

Day 2 Notes: Water

Hydrophilic vs. Hydrophobic

• Hydrophilic – substances have affinity water

• Hydrophobic – substances that repel water; form clusters called hydrophobic interactions. – Ex: Oil and H2O

• Like dissolves like – Polar dissolves polar– Non-polar dissolves non-polar

Intro• Place the following bonds based on strength in the

correct order• (Hydrogen Bond, Triple Covalent Bond, Double Covalent

Bond, Ionic Bond, Single Covalent Bond)• Write down the following with the bonds in the right place

Strongest Bond

1.

2.

3.

4.

5.

Weakest Bond

• What is polarity in a molecule?

• Polarity is when there are charged sides in an overall neutral molecule. Larger atoms tend to hog electrons and become slightly negative

Oxygen is a neutral molecule but the oxygen side is slightly negative and the hydrogen side is slightly positive.

What is a hydrogen bond?

• A hydrogen bond is a polar bond where hydrogen is involved.

• There is an intermolecular attraction between positive and negatively charged sides of different molecules

Hydrogen bonds in water

Properties of Water

If there are other beings who have seen Earth, he said, they must surely call it “the blue planet.” The astronaut

was referring to the blue appearance of the water in the oceans, which cover three fourths of Earth’s surface. Water is also the single most abundant

compound in most living things.

Things to know

• Hydrogen bond – Because of positive and negative charges of water (polarity).

• Water attracts other water molecules.

• Cohesion- attraction between molecules of the same substance.

• Adhesion- attraction between molecules of different substances Adhesion- Substance to

glass (capillary action)

9 properties of water

1. is a powerful solvent – can dissolve things2. is very cohesive (due to H bonds holding water

together)3. Is very adhesive (due to H bonds with other

things)4.Has capillary action5.has high surface tension6.has high specific heat7.has a high boiling point – a high heat of

vaporization8. is a good evaporative coolant9.has a high freezing point and lower density as a

solid than a liquid (density anomaly)

Water Properties

1. Powerful, versatile solvent – due to polarity. Called the universal solvent

Water Properties

2. Very Cohesive behavior (due to H bonds holding water together)

Water Properties

3. Very Adhesive behavior (due to H bonds with other things)

Water Properties

4. Has capillary action

Water Properties

5. High Surface Tension

Water Properties

6. High Specific Heat

• Specific heat: The amount of energy needed to raise the temperature of one gram 1°C

• Water is high vs. most moleculesSome common specific heats and heat capacities:

Substance S (J/g 0C)

Air 1.01Aluminum 0.902Copper 0.385Gold 0.129Iron 0.450Mercury 0.140NaCl 0.864Ice 2..03Water 4.179

Water Properties

7. High Boiling Point – High Heat of Vaporization

Water Properties

8. Good evaporative coolant

Water Properties

9. High freezing point and lower density as a solid than a liquid (density anomaly)– Water is less dense in a frozen state

Water Benzene

This is unusual for most substances

Why is waters lower density as a solid than a liquid important

for life?

• When water freezes it does not fall to the bottom of a lake. It stays up top allowing for life to continue below.

Mixtures

• Solutions vs. Suspensions

How is a solution different than a suspension?

• A solution is homogeneous meaning that the parts dissolve and the mixture looks all the same throughout

How is a solution different than a suspension?

• A suspension is heterogeneous meaning that the parts do not dissolve and you can see different particles in the mixture

What are the parts of a solution

• What are the parts of a solution:

• The solvent is the substance being dissolved in

• The solute is the substance being dissolved

Creamer- solute

Coffee- solvent

Worksheet

• Biochem Review and Practice

Water Lab Day

Day 3 Notes: Acids vs. Bases• It is the presence of hydrogen ions(H+)

relative to hydroxide(OH-) that determines a solution's pH.

• hydrogen ions(H+) are not usually found alone, instead they have a tendency to attract to a H2O and become hydronium ions (H3O)+

Acids vs. Bases

• The molecules in pure water auto-dissociate into hydronium and hydroxide ions in the following equilibrium:

2H2O ↔ OH− + H3O+

hydroxide hydronium ions

• Acids have a high concentration of H+ ions (called hydrogen ions or protons)

• Bases have a high concentration of OH- ion (called hydroxide ions)

• In pure water, there is an equal number of hydroxide and hydrogen ions, so it has a neutral pH of 7.

• A pH value less than 7 indicates an acidic solution, and a pH value more than 7 indicates a basic solution or “alkaline”.

pH: a measurement of

hydrogen ions

Figure 2.10

Acids = forms hydrogen (H+) ions in water

Bases = forms hydroxide (OH-) ions in water

Neutral substances have a pH of 7

Acid and Base Strength

• Acid and Base STRENGTH is based on how many H+ are given up (acids) or attracted to (bases) OH-

• Water can’t equalize strong acids/bases

• bases and acids are used to neutralize each other

• Neutralization reaction – acid + base water + salt (pH 7)

• NaOH (strong base) + HCl (strong acid) NaCl (salt) + H2O (water)

Measuring pH• There are several

INDICATORS to measure pH:– pH paper– litmus paper– pH meter

Acids in the Biology

• HCl in stomach – involved in digestion

• Acidic blood – too much CO2 in body causes brain to speed up respiration (CO2 out and O2 in) blood more basic

• Lactic acid build up – not enough O2 in muscles for aerobic respiration (soreness)

• Most food – slightly acidic

Bases in Biology

• Neutralize stomach acids (antacids)

• Bile salts – liver, pancreas – emulsify lipids (fats) in body for digestion

• Blood buffers - Blood has a pH of 7.4; bicarbonate keeps blood slightly basic

• Many poisons are basic…are foods?

• Many cleaners are basic…why?

Intro Quiz1. What is a ion?

2. What is a isotope?

3. Acids have a lot of what ion?

4. Bases have a lot of what ion?

5. What is the pH of a neutral ion?

6. Draw a pH scale labeling the neutral, the acid side, the base side.

7. Place the materials we tested in yesterdays lab on this scale

8. What is a heterogeneous mixture?

Macromolecules

Life molecules are base on big (Macro) carbon based (organic)

molecules

Polymers are made of monomers

• All macromolecules

• Have monomers (mono means one- a single units)

• Polymers are large chains of these monomers

Monomer

Monomer

Monomer

Monomer

Monomer

• Monomers are put together by dehydration synthesis

Monomer

Monomer

• Monomers are put together by dehydration synthesis

• Gives off water (H2O)

Monomer

Monomer

H2O

• Monomers are broken apart by hydrolysis

• Takes water (H2O)

• Hydro (water) Lysis (destroying)

Monomer

Monomer

H2O

• Monomers are broken apart by hydrolysis

• Takes water (H2O)

• Hydro (water) Lysis (destroying)

Monomer

Monomer

4 life macromolecules

• Carbohydrate

• Lipid (Fat)

• Protein

• Nucleic Acid

Carbohydrates

•Elements that make carbohydrates

•Carbon (C)

•Hydrogen (H)

•Oxygen (O)

•1:2:1 ration of C:H:O

•Two H for every C and O

• Monomer

• Monosaccharide– Ex. Glucose and Fructose are isomers– Have Same formula but different

configuration

– Both C6H12O6 1:2:1 ratio

Carbohydrate- Function(s) in the cell

•1. Quick Energy

•2. Building Block– Plant Cells have cell walls made of Cellulose

(a polysaccharide)

Cellulose Cell Wall

• SPECIFIC Examples

• Types of carbohydrates (the shorter the quicker energy)

• Monosaccharide: ex. glucose and fructose

• Disaccharide (double monomer): ex. Sucrose (table sugar), Lactose (milk sugar)

• Polysaccharide (multiple monomers: ex. Starch, cellulose (plant cell walls)

monosaccharide

Lipids

•Elements that make Lipids

•Mainly C and H

•Sometimes O, P, N , and S

• Monomer(s)– Fatty acid– Sometimes glycerol

Fatty Acids

• Lipids function(s) in the cell– 1. Long Term Storage– 2. Cell Membranes– 3. Protection (padding)

Fatty Acids

• SPECIFIC Examples

• Unsaturated (Commonly called oils)– Liquid at room temperature– Have double bonds

Double Bonds bend molecule

• Saturated (Commonly called Fats)– Solid at room temperature– Have only single bonds

No Double Bonds

Flat Molecules that melt at a higher temperature

• Other lipids– Cholesterol– Steroids

Proteins

•Elements that make Proteins

•N,H,C,O

• Monomer(s)– Amino Acid – Four levels of structure (very complex)– Start with amino acids bonded together by

peptide bonds– 20 types of amino acids commonly found

• Monomer(s)– Amino Acid – Four levels of structure

(very complex)– Start with amino acids

bonded together by peptide bonds

– 20 types of amino acids commonly found

Called Primary Structure (first level of four)

• Monomer(s)– Amino Acid – Four levels of structure (very complex)– Amino Acids are bonded together by peptide

bonds– 20 types of amino acids commonly found

Protein function(s) in the cell1. Building blocks (provide the structure of

living things)

2. Catalyze reactions (make them occur easier)enzymes are proteins that serve this

purpose

• SPECIFIC Examples– Enzymes- Catalyze reactions– structural proteins- hair, nails, horns, and

hooves– muscles (all meats are protein)

Nucleic Acids

•Elements that make nucleic acids

•O,H,C,N,P

• Monomer(s)

• Nucleotides: Made of a base, sugar, and phosphate

Nucleic Acid Function in the cell

•1. Transmit genetic material (heredity)

• SPECIFIC Examples– DNA- deoxyribonucleic acid– RNA- ribonucleic acid

Energy & Reactions

ENZYMES!

Chemical Reactions and Enzymes

• Enzymes are special proteins • Usually end in the suffix –ase• They speed up (also called catalyze) reactions

Chemical Reactions

•Reactants- react•Products- produced

•Activation energy- energy needed to get a reaction started

•Energy can be gained or lost in a reaction

Reactants ProductsA + B C

Types of reactions:

•exergonic reaction gives off energy (Ex for energy exits)

•endergonic reaction takes in energy (En for sounds like in)

Endergonic Reaction Exergonic Reaction

• An enzyme is a (protein) catalyst • A catalyzed reaction is aided by an enzyme• speeds up the reaction by lowering the activation

energy (energy needed to get it started)• reactions involving enzymes will conserve energy

because the enzyme helps lower the activation energy

• lower the _______energy. Activation energy (Uncatalyzed)

Activation energy (Catalyzed)

Normal Reaction

Catalyzed Reaction

Product

Reactant

Active Site

Substrate

EnzymeEnzyme-Substrate Complex

Products

Enzymes are specific to certain substrate

An enzyme like amylase only breaks down amylose (starch)

Enzyme at Work1. Substrate binds at active site2. Enzyme breaks the substrate (reactant) down3. Products are released4. The enzyme is unchanged (not used up and can be used again)

Active Site

Substrate

EnzymeEnzyme-Substrate Complex

Products

Other Terms

• Metabolism: The sum of all chemical processes in cells

• Enzymes Help Metabolism

The Body Can Regulating Enzymes:

• Competitive Inhibitors: Bind to enzymes active site and block their intended activity

• Denaturing- changing shape of enzyme stops it from working

Active Site

Substrate

EnzymeEnzyme-Substrate Complex

Products

Competitive inhibitor: Stops the enzyme from working since the substrate no longer fits

Competitive inhibitors can be used by the body to stop an enzyme from working