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Unit 2: Biochemistry

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Casey Brennan

on 13 September 2016

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Transcript of Unit 2: Biochemistry

Unit 2 - Biochemistry
Matter: Atoms and Molecules
Chemical Notation
Chemical Reactions
Inorganic Compounds
Organic Compounds
Chemicals & Cells
Anything that occupies
space
and has
mass
Types of Matter
Composition of Matter
Elements
fundamental units of matter
made of only 1 kind of atom
Each element is designated by a one or two letter abbreviation called an
atomic symbol
Common Elements Making Up the Body
Major Elements (96.1%)
Minor Elements (3.9%)
Trace Elements (< 0.01%)
Carbon (C)
Oxygen (O)
Hydrogen (H)
Nitrogen (N)
Calcium (Ca)
Phosphorus (P)
Potassium (K)
Sulfur (S)
Sodium (Na)
Chlorine (Cl)
Magnesium (Mg)
Iodine (I)
Iron (Fe)
Chromium (Cr), Cobalt (Co), Copper (Cu), Fluorine (F), Manganese (Mn), Molybdenum (Mo), Selenium (Se), Silicon (Si), Tin (Sn), Vanadium (V), Zinc (Zn)
Smallest
unit of an element
Subatomic
Particles:
Protons
(
+
) charge found in
nucleus
Neutrons
(
0
) charge found in
nucleus
Electrons
(
-
) charge found in
motion around the nucleus
(not in nucleus)
Shows electrons orbiting the nucleus like planets
Ions
atoms that have wither gained or lost electrons
and now carry a positive or negative charge
Anions
Cations
(-) atoms
(+) atoms
C
C
p+ = 6
e- = 7
p+ = 6
e- = 5
extra e-
extra p+
Two or more
atoms joined together
Can be made of
the same atoms
or of
different atoms
Compound
= two or more atoms of
different
elements are joined together
Complex chemical compounds and reactions are most easily described with a simple form of chemical shorthand.
example: sugar
C
6
H
12
O
6
Ex: Carbon (
C
), Oxygen (
O
), Iron (
Fe
), Aluminum (
Al
)
Ex: O
2
H O
2
Ex: C H O
6
Role of electrons in bond formation
Electrons occupy energy levels called
electron shells
Only electrons in the
outermost
shell are important to consider in bonding behavior
The outer electron shell is called the
valence shell
Octet Rule (rule of 8s)
Shell 1 holds 2 e-
Shell 2 holds 8 e-
When the valence shell holds less than 3, it
gives up
or
loses
electrons
When the valence shell holds more than 6, it
gains
electrons
Reactive elements - valence shells are not full and are unstable; they will react to try to get 8 e- in the outer valence shell. These reactions will lead to
chemical bonds
When the valence shell holds 8 electrons, it is
stable
6
12
Three Types of Chemical Bonds
Ionic
Bond

Covalent
Bond

Hydrogen
Bond

attraction between oppositely charged ions
usually occurs between metals & nonmetals (salts)
when 2 atoms share electrons
usually occurs between like atoms and between nonmetals
Polar
Covalent Bond
Nonpolar Covalent Bond
even sharing of electrons
uneven
sharing of electrons
weak electrical attractions between neighboring polar molecules
contain
Carbon
and often Hydrogen and Oxygen

do
not contain Carbon
; tend to be simple compounds

Water properties
Acids / Bases
1. High heat capacity
2. Polarity/solvent properties
3. Density
will absorb and release a lot of heat before temperature changes
lots of chemicals dissolve easily in it
water becomes less dense when is freezes causing ice to float
When acids and bases are dissolved in water, they dissociate (separate) into ions.
Acid
- compound that has a
higher
concentration of H3O+ (H+) compared to OH- in solutions
pH between 1 and 6.9
concentration of H+
increases
as the pH
decrease
s
Base
- compound that has a
lower
concentration of H3O+ (H+) compared to OH-
pH between 7.1 and 14
concentration of H+
decreases
as the pH
increases
Just a slight change in pH can be harmful to an organism because the molecules in cells are extremely sensitive to H+ and OH-
Buffers
- compounds that
resist change
in pH; make the pH move closer to 7
accept H+ ions if the environment is too
acidic
bond with OH- if the environment is too
basic
Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbohydrates contain C, H, and O with a 1:2:1 ratio of C:H:O
Building blocks - sugars
Carbs are hydrophilic - "water loving" - dissolve easily in water
Function of carbs:
1. Main energy source
2. Structural component in plant cells
Categorized based on size of molecules:
1. Monosaccharide - one sugar molecule
2. Disaccharide - two sugar molecules
3. Polysaccharide - Many sugars
a. Glucose - main energy source; used to build other molecules
b. Fructose - fruit sugar; sweeter than glucose
c. Galactose - found in dairy products and synthesized in the body where it forms part of glycolipids and glycoproteins in several tissues
d. Ribose - sugar in RNA
e. Deoxyribose - sugar in DNA
a. Sucrose - table sugar; glucose + fructose
b. Lactose - milk sugar; glucose + galactose
c. Maltose - malt sugar; glucose + glucose
a. Cellulose - structural carbohydrate in plant cells;
most abundant carbohydrate;
composed of thousands of glucose units;
nondigestable - known as a dietary fiber
c. Glycogen - stored glucose
2 main reactions:
1. Dehydration
2. Hydrolysis
links molecules together by removing water
the process of breaking down polymers by adding HOH molecules, thus splitting the polymers
b. Starch - energy storage carbohydrate formed in plants
composed of thousands of glucose units;
dietary staple of almost every society
Lipids contain carbon, hydrogen, and oxygen
Carbon and hydrogen outnumber oxygen
Building blocks - fats (glycerol & fatty acids)
Hydrophobic - "water fearing"; do not dissolve in water; think about oil and water
Fat is stored in the body in adipose tissue
Function of Lipids:
1. long-term energy storage
2. insulation
3. protective cushion
4. basis of many steroids
Types of Lipids:
1. Triglycerides - main component of fats;
made up of a glycerol molecule jointed with 3 fatty acid chains
2. Phospholipids - composed of a polar head and 2 nonpolar tails
form cell membranes
1. Fat (saturated) - solid at room temperature
2. Oil (unsaturated) - liquid at room temperature
3. Steroids - compound that forms the basis of many hormones, vitamin D, and bile salts
Cholesterol - single most important steroid molecule
Contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur
Building blocks: Amino acids
There are 20 different amino acids.
A different sequence of amino acids = a different protein, thus protein possibilities are almost endless.
Functions of Proteins:
1. Structure - construction materials
a. Collagen - most common protein
forms cartilage, ligaments, and extracellular matrix
b. Keratin - protein in hair and fingernails
2. Cell function - found embedded in cell membranes and determine the function of the cell and provide identification of the cell
3. Enzymes - catalysts that speed up or start chemical reactions without being changes
Types of Proteins:
Classification of proteins based on shape and structure
a. Fibrous - proteins that function in structure (collagen, keratin)
b. Globular - functional proteins that are mobile and play crucial roles in all biological processes (antibodies, hormones, enzymes)
Enzyme Action
During an enzyme induced reaction, the enzyme structure is not changed; therefore the same enzyme molecule is used in repeated reactions
The body only requires a small amount of any one enzyme
Substrate - molecule that binds to an enzyme
Shape specific - only 1 type of enzyme will fit to 1 type of substrate - think lock and key
Active site - the region on the enzyme that fits to the substrate
After the reaction takes place, the enzyme is free to bind to another substrate remaining unchanged
While the substrate that has undergone the chemical reaction is changed.
An enzyme must have the correct 3 dimensional shape to be functional. If the shape changes, then the enzyme cannot complete the reaction
A protein's shape can be changed by environmental factors
a. temperature
b. pH
c. salinity
Denature - when the enzyme shape has been changed due to environmental factors and is no longer functional
How many words can you make out of 29 alphabets?
Contain carbon, oxygen, hydrogen, phosphorus, and nitrogen
Nucleic acids - provide the blueprint of life; determines cell function
Building blocks - nucleic acids
Nucleotides consist of 3 parts:
1. Sugar - deoxyribose/ribose
2. Phosphate
3. Base
There are 5 nucleotide bases:
1. Adenine (A)
2. Guanine (G)
3. Cytosine (C)
4. Thymine (T)
5. Uracil (U)
DNA Bases: A, T, C, G
RNA Bases: A, U, C, G
The sequence of nucleotides indicates the sequence of amino acids in a protein.
Function of Nucleic Acids - information storage molecules that provide the directions for building proteins
Nucleic acids are located in the nucleus of cells
2 types of nucleic acids:
1. DNA - deoxyribonucleic acid - a gigantic polymer that contains codes for telling cells how to assemble proteins; it is a double helix capable of making exact copies of itself
2. RNA - ribonucleic acid - much smaller than DNA; it is single stranded; acts as a messenger between DNA in the nucleus and site of protein production in the cytoplasm
Amino acids bonded by peptide bond
Identify the differences between RNA and DNA
How do cell use energy?
Cells store energy in high-energy compounds called ATP
ATP - adenosine triphosphate - provides energy for all cells
The phosphate bonds of ATP are high energy bonds.
Energy is released when the outermost phosphate bond is broken
When phosphate bond is broken, this forms ADP - adenosine diphosphate
ATP is reformed when energy and a phosphate is added back
3 Uses of ATP:
1. Transport - used to carry molecules across cell membranes
2. Mechanical - muscle contraction
3. Chemical - provides energy for chemical reactions
EX: Water
http://learn.genetics.utah.edu/content/begin/cells/scale/
How can you tell if a substance is polar or non-polar?
TRY TO DISSOLVE IT IN WATER
Salt
Oil
SOLVENT-
does the dissolving
SOLUTE-
is being dissolved
So is salt hydrophobic or hydrophilic?

What about oil? Hydrophobic or Hydrophilic?
Water is composed of
2
hydrogen +
1
oxygen atoms
Hydrogen bonds
hold
water molecules together
Cohesion is the attraction
between two
like
things.
Cohesion is caused because water molecules are attracted to each other because of their polarity. Hydrogen bonds then hold them together.
Adhesion is the attraction between two
different
substances.
Capillary action
is where water moves up a tube.
Water is attracted to the sides of the tube.
Water molecules are still attracted to each other.
Solvents are good at
dissolving other substances
Substances that dissolve in water are called HYDROPHILIC because they are all
polar
molecules.
Salt dissoves in water because the polarity of water breaks apart the ions that make up salt (Na+ and Cl-)
HYDROPHOBIC (water fearing) substances lack charged poles making them non-polar.
They can't break the hydrogen bonds that hold water together.
Density of Ice
Ice floats on water because as water freeze the molecules move farther apart from each other because they move into a crystalline structure.
Why is this important?
Heat Capacity
Water can absorb and release a lot of heat before the temperature changes.
the amount of energy needed to raise the temperature of a system 1 degree
This is important because it means that the oceans do not heat up and cool down very fast. The temperature remains fairly constant.
When water evaporates, the water molecule takes the heat with it causing the temperature to drop. This is why sweating and the evaporation of sweat cools a person down.
pH
Concentration of H3O+
0
14
7
pH
- a measurement of the concentration of
hydrogen
ions in a solution (H3O+) --> Also called Hydronium Ions
Strong Acid
Strong Base
Neutral
Weak Acid
Weak Base
pH scale
Mr. Anderson talks about pH
Mixtures
Mixtures
are substances that are made of two or more elements or compounds that are physically mixed together.
All parts of a mixture maintain their original
physical properties
.
Examples:


Mixtures that are made with water:
SOLUTIONS
SUSPENSIONS
SOLUTIONS
Parts of solutions are
evenly mixed
There are two parts to a solution:
SOLUTE
and
SOLVENT
Solute
- part that is dissolved
Solvent
- does the dissolving

Examples:
Suspensions
Suspensions are mixtures of
water
and
non-dissolved
substances where the non-dissolved parts can settle out
Why do you think some substances don't dissolve in water?
Colloids
are a type of mixture made of
two phases of matter
where there is not settling out of particles.
Heterogenous
mixture- the parts of the mixture are not uniform, you can see the different substances
Homogenous
mixture- the parts of the mixture are uniform and you cannot see the different
contain
CARBON
Why are life-forms carbon based?
Carbon has
4 valence electrons
Each electron can join with another electron to form a strong
covalent bond
This allows carbon to bond with
many other elements
and other
carbon atoms
Carbon bonding can create
long chains
Macromolecules
"Giant molecules"
Made of thousands of smaller molecules
Monomers
join together to make
polymers
Ex: They are like Legos
There are
FOUR
macromolecules important for life
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic Acids
Carbohydrates (a.k.a
Saccharides
)
Composed of the elements:
Carbon
Hydrogen
Oxygen
Main functions include:
1)
Energy
2)
Structure
Examples of carbohydrates include:
1)
Sugar
2)
Starches
3)
Cellulose
4)
Chitin
Monosaccharides:
Made of a
single
sugar molecule
They are the building blocks of larger carbohydrates
Ex:
Glucose
- MAIN source of energy
Fructose- fruit sugar
Galactose- found in dairy
Ribose
- sugar in RNA
Deoxyribose
- sugar in DNA
Disaccharides:
Made of
two
sugar molecules bonded together
Must be
broken apart
for the body to be able to use them
Ex:
Table sugar
(
sucrose
)- made of glucose + fructose
Milk sugar (
lactose
)- made of glucose + galactose
Malt sugar (
maltose
)- made of glucose + glucose
Oligosaccharides:
Made of
3-10
sugar monosaccharides
Found as important components of glycoproteins and glycolipids (structures that are found in
cell membranes
)
Ratio for Carbohydrates
C:H:O = 1:2:1
Polysaccharides
Made of
hundreds to thousands
of monosaccharides
Used for:
Starch-
energy storage in plants, dietary staple for most civilizations (potatoes are high in starch)
Glycogen
- stored in the liver of animals and used for energy
Cellulose
- most ABUNDANT carbohydrate, used for structural purposed in plant cells (wood), undigestible
Hydrolysis
-
breaks apart
sugars
Water is added and enzymes are used to break the bonds holding the sugars together
Dehydration
-
builds
sugars
Water is removed (hence 'dehydration')
Lipids (a.k.a.
Triglycerides)

Composed of the elements:
Carbon
Hydrogen
Oxygen
Main functions include:
1)
Energy storage
2)
Main parts of cell membranes
Examples:
Fats
Oils
Waxes
Made up of:
glycerol
3 fatty acid tails
Saturated Fats vs. Unsaturated Fats
Saturated- has hydrogen bonded all the way around the outside of the tails
- All three tails are straight
- Is solid at room temperature
EX: Butter
Unsaturated- does not have hydrogen bonded at all places around the tails
- Tails are crooked/bent
- Is a liquid at room temperature
EX: oils (olive oil, vegetable oil)
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