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