Bio mid term 1 :(

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

Theories

Need a huge amount of evidence
Ex. Theory of natural selection
Theories are excepted only because of the evidence behind them.

Replication

Sample size does not equal 1
Has a greater chance of convincing results with replicates
Did all results do the same thing ?

Reproducibility

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

Isotopes

Have the same atomic number, but a different number of neutrons

What are bonds based on

Electrons

How many bonds does Carbon have

4

How many bonds does Hydrogen have

1

How many bonds does Oxygen have

2

Hydrogen

Smallest atom
H+ are important for cellular metabolism

What is left over if Hydrogen loses an electron

Only a proton

Cations

positively charged ion

Anion

a negatively charged ion

Helium

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

3

Non polar

no partial charge on atoms
Share equal

Covalent

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

Polar

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

Water

Cells are 80% water
Water is the solvent of life

Universal Solvent

Does not exist

What does water exhibit

Cohesion

Hydrophilic

Water liking
Polar/Charged

Hydrophobic

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-

Acidity

protons (H+)
More than High acidity

pH

Measure of acidity
-log[H+]

What is pH 7

Neutral/water

Higher than 7 pH

Acidic

Lower than 7 pH

Basic

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

3

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

Macromolecules

Very large
Polymer
Many monomer subunits
Ex. Carbon molecules
Condensation synthesis

Large Biological Molecules

Not a big as macromolecules
Ex. Lipids
Still big tho

Monomers

Can exist on their own
Also building blocks
Ex. Glucose

Polymer

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

Hydrolysis

Break apart using water
Opposite of condensation
release monomer
Water is reactant

Hydrolysis of macromolecules

Remove damaged macro molecules
Monomer subunits can be recycled

Carbs

Monomer/small polymer
Carbs that are larger than monomers are monosaccharide
Simple sugars or polymer of sugar unit
May contain 3-7 carbon atoms

Proteins

polymers of amino acids
(Amino acids are monomer sub units

Lipids

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

Oligosaccharides

Short Chain 2 or more sugar monomer (not macro or large)
Chain is formed by condensation synthesis

Disaccharides

2 subunits

Trisaccharides

3 subunits

Polysaccharide

True macromolecule
Many rounds of condensation synthesis
Cannot dissolve well
100-1000 monomer subunits
Ex. starch, glycogen, cellulose

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

Fats

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?

Solid

What is Poly Saturated Fat at room temp

Liquid

Phospholipids

3 carbon back bone
2 fatty acids and a head group
Structural molecules

Is a head group hydrophilic or hydrophobic

Both ! It is Amphipathic (has polar and non polar regions)

Steroids

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

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