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Two types of Science
Induction and Hypothesis based science
Induction Based Science
A predictive generalization Ex. Cell theory - generalizations about cells
Hypothesis Based Science
Deductive Reasoning Hypothesis - explanation for an observations
Occam's Razor
If several explanation work with your evidence, then go for the simplest one. The razor shaves off unnecessary details.
What happens if there is no control in an experiment
No support for hypothesis
Negative Control
Did nothing
Positive Control
A known characterized treatment. It will give a well known effect that is no surprise
Progress in Science
Explanatory power New ideas are formed, and the old rejected
Need a huge amount of evidence Ex. Theory of natural selection Theories are excepted only because of the evidence behind them.
Sample size does not equal 1 Has a greater chance of convincing results with replicates Did all results do the same thing ?
Can others do your experiment? The same results should be from the same experiment, regardless of where and when.
Composition of an Atom
Nucleus has protons (1+) and neutrons (0) Electrons (1-) are in orbitals around nucleus
What defines an atom
The number of protons and the number of neutrons
Have the same atomic number, but a different number of neutrons
What are bonds based on
How many bonds does Carbon have
How many bonds does Hydrogen have
How many bonds does Oxygen have
Smallest atom H+ are important for cellular metabolism
What is left over if Hydrogen loses an electron
Only a proton
positively charged ion
a negatively charged ion
Second smallest atom Two protons atom is mostly empty space Noble gas
What does a chemical bond require
one pair of electrons each atom providing one electron
What type of bond is N
Non polar
no partial charge on atoms Share equal
Bonds are shared
Electronegativity (EN)
The ability of some atoms to attract electrons to itself
Polar Covalent Bonds
Shared unequally in a covalent bonds - if moderate difference
Refers to the fact that partial charges due to unequal sharing
What is water held together by
two polar bonds - example of a polar molecule
Examples of Non polar covalent bonds
O-H, N-H, 0-C, N-C
Ionic Bonds
No sharing Taking electrons (higher EN) Ex. Salts Form between between atoms with different EN
Hydrogen Bonds
Constantly breaking and reforming (transient) Consequence of polar covalent bonds containing hydrogen Water molecules stick together due to hydrogen bonds
Cells are 80% water Water is the solvent of life
Universal Solvent
Does not exist
What does water exhibit
Water liking Polar/Charged
Water fearing Non polar covalent bonds not soluble in water
What is water attracted to
Large polar/ charged molecules Ex. Sugars
What is more soluble
Small hydrophilic molecules
Large polar molecule solubility
They are also hydrophilic But can be too big to be soluble
What are Hydrophobic molecules composed of
Non polar covalent bonds Ex. C-C, C-H Fats are hydrophobic
What can water do
Reverse disassociate
Strong acid
Complete dissociation unlike equilibrium for water dissociation HCl-->H+ +Cl-
protons (H+) More than High acidity
Measure of acidity -log[H+]
What is pH 7
Higher than 7 pH
Lower than 7 pH
What makes water pH lower
The atmosphere
What is carbon based
Life ;)
What roles do Carbon molecules play
1) Structural Role 2) Metabolic Role
Why is carbon a Lego block
Will form non polar covalent bonds with C+H Form polar covalent bonds with O or N
How many types of isomerism
Double Bonds (Planar)
cannot rotate
Structural Isomerism
Same molecular formula, but differ in how carbons are arranged Different covalent arrangements of atoms
Cis/Trans isomerism
Different molecules have the same formula, but different on how parts of molecules are based around carbon
Enantiomer Isomerism
Called asymmetrical Same 4 things attached but in different ways Mirror images not equivalent
How to read organic Chemistry
C and H are implied Every angle has Carbon unless differently shown Carbon has 4 bonds if not Hydrogen is attached
Very large Polymer Many monomer subunits Ex. Carbon molecules Condensation synthesis
Large Biological Molecules
Not a big as macromolecules Ex. Lipids Still big tho
Can exist on their own Also building blocks Ex. Glucose
Linked monomers from covalent bonds Ex. Polytrene
Condensation Reaction/ Dehydration
Formation of covalent bond Loss of water molecules H20 is product
Condensation Synthesis
Several to many rounds of condensation reaction Leading to large biological macro molecules
Break apart using water Opposite of condensation release monomer Water is reactant
Hydrolysis of macromolecules
Remove damaged macro molecules Monomer subunits can be recycled
Monomer/small polymer Carbs that are larger than monomers are monosaccharide Simple sugars or polymer of sugar unit May contain 3-7 carbon atoms
polymers of amino acids (Amino acids are monomer sub units
Large biological molecule (not a macro molecule) Have C-C/C-H (non polar covalent)
Nucleic Acid
DNA and RNA Nucleic acid are polymers of nucleotides
Two Major Roles of Monosaccharides
1) Form parts of other molecules 2) Energy metabolism Ex. glucose is blood sugar
Short Chain 2 or more sugar monomer (not macro or large) Chain is formed by condensation synthesis
2 subunits
3 subunits
True macromolecule Many rounds of condensation synthesis Cannot dissolve well 100-1000 monomer subunits Ex. starch, glycogen, cellulose
Glucose polymer Cellulose is not a good energy for humans (dietary fiber in human diets) Cant access glucose in digestive system
Sub Groups of Lipids
Fats Phospholipids Steroids
Don't dissolve in water Can dissolve in less polar solvent (acetone) Fats have greater density than terms
How to Build a Fat
Glycerol and three fatty acid join H and OH and palmitic acid 3 condensation reactions 3 H20 are released in the process
Saturated Fatty Acid
C-C single bond, straight
Unsaturated Fatty Acid
C=C double bond, causes kink in chain Trans (H on different side) or Cis (H on same side)
What is Saturated Fat at room temp?
What is Poly Saturated Fat at room temp
3 carbon back bone 2 fatty acids and a head group Structural molecules
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Is a head group hydrophilic or hydrophobic
Both ! It is Amphipathic (has polar and non polar regions)
Hydrophobic, non fatty acid lipids All have four C- based rings
What Two Major Roles do Steroids Play?
1) Hormones Ex. estrogen, testosterone 2) Structural - components of bio membrane (influence fluidity of membrane)
Basic Steroid Structure
Steroids are like cholesterol They are made from 4 fused hydrogen rings
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Proteins are Macromolecules
Amino acids are the monomer subunits They are a linear sequence they don't branch
Protein Amino Acids
There are 20 Plants have the ability to produce/synthesize all of them Humans cant synthesize all of them Essential amino acids must be provided in the diet
Amino acids have a central asymmetric (chiral carbon)
An amino group Carboxyl group Hydrogen atom and a side chain
What are proteins held together by
Peptide bonds
What are Peptide bonds
Condensation /Dehydration synthesis reaction
What are the Levels of Protein Structure?
All have primary, secondary, and tertiary Some have quaternary
Primary Structure
Linear sequences of amino acids
Secondary Structure
Alpha helices, and Beta pleaded sheets Due to H between H-O in amino acids
Tertiary Structure
4 chemical bonds between R groups Vanity of chemical interactions determine the proteins tertiary structure Includes hydrophobic, ionic bond, H bond
Quaternary Structure
From 2+ polypeptide units - string of amino acids Also has 1,2,3 in it as well as 4
Example of Quaternary Structure
O2 carrying pigment/molecule in red blood cell 4 separate polypeptides come together to make
a peptide containing 10 to more than 100 amino acids Subunit of protein with 4 structure
What happens if You Sub in One Amino Acid in a Protein
May change the shape of the protein
String of 10+ amino acids Oligo=few
Protein Denaturation
A change in conformation away from the native conformation May not be reversible
Proteins have Native Conformation
3 dimensional shape - function protein not 1 structure Requires protein in proper environment
Change in 3 dimensional structure of protein Ex. High temp is an irreversible denaturation
Nucleic Acid
Genetic info central to cell
Info intermediate (messenger) Structural role in ribosome Amino acid arrangement (transfer) Single strand mRNA, rRNA, tRNAr
1) 1 structure (=amino acid sequence) proteins/polypeptides 2) nucleotide sequence of RNA (rRNA, tRNA)
DNA Sequence
DNA ---->mRNA--->Protein/polypeptide
A phosphate group 5C sugar Nitrogenous base
RNA Possible nitrogenous base
DNA Possible nitrogenous base
What is Nucleic Acid linked together by
Phosphate and 5C sugar Nitrogenous base does not take part in the bonding Alternating sugar phosphate backbone
What is DNA Organized into
A double Helix Two helixes that face each other Nitrogenous bases face inwards in the double helix
What type of bonding is between DNA bases on opposite strands
H- bonding A=T and C=G
Are DNA and RNA Complementary
History of Cells
First escribed in 1665 Cells were not initially excepted Old idea of spontaneous generation
Spontaneous Generation
Idea that living organisms could be generated from non-living matter Eventually in the mid 1800s it was found that organisms came from organisms, and cells came from cells
1600s light microscope work started and it showed the importance of cells New types of microscopes were invented after Ex. electron microscope (1950s)
What is Cell Theory
An example of inductive reasoning 1) All organisms are composed of one or more cells 2) The cell is the basic unit of life 3) All cells come from other cells
Recent Findings about Cells
1) Cells are surrounded by a cell membrane 2) Cells contain DNA 3) There are two types: Eukaryotic/Prokaryotic
Can You Culture Multicellular Organisms?
Yes Although nothing smaller than a cell
Cells with Nucleus and membrane oriented organelle Compartmentalized
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What Does Domain Eukarya Include
Algae Amoebae Plants Fungi Animals
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Terminology for Organelle
1) Membrane delimited subcellular department 2) Any subcellular structure (membrane not required)
Protein building machines that don't have a membrane Eukaryotes and prokaryotes have them Sometimes ribosomes are organelles and sometimes not
Don't have membrane delimited subcellular compartments
Water based gel-like fluid that surrounds the organelles
All the material inside the plasma membrane Except for the nucleus Includes cytosol and ribosomes
What is the nuclear envelope
A double membrane the nucleus is delimited by
The protein in it plays a structural role into organizing chromosomes DNA is presented as a part of it which is a protein DNA complex
How are Chromosomes Presented?
A non condensed state
What is needed in the Cytosol?
Information needed in the cytosol
What is the Molecule that Transfers Info to the Cytosol?
Messenger mRNA
What are Ribosomes Comprised of?
A combo of rRNA and protein
What does a functional Ribosome Contain?
Subunits and a piece of mRNA
Where are Ribosomal Subunits assembled?
In the nucleus
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Endomembrane System
Linked by membrane flow membranes are fluid
Endomembrane System Includes:
Nuclear envelope ER Golgi bodies Lysosomes Plasma membrane Various small vacuoles
Not Part of the Endomembrane System:
Mitochondria Peroxisomes Chloroplasts
Endoplasmic Reticulum
Runs through cytosol Major site of membrane synthesis for endomembrane system Lumen space
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Rough ER
Protein Synthesis
Smooth ER
Golgi Bodies/Apparatus Functions:
1) Protein modification 2) Protein Sorting
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Where does Protein go if its from Rough ER?
It goes to the lumen