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

Example of Quaternary Structure

O2 carrying pigment/molecule in red blood cell 4 separate polypeptides come together to make

Polypeptide

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

Oligopeptide

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

Denaturation

Change in 3 dimensional structure of protein Ex. High temp is an irreversible denaturation

Nucleic Acid

Genetic info central to cell

RNA

Info intermediate (messenger) Structural role in ribosome Amino acid arrangement (transfer) Single strand mRNA, rRNA, tRNAr

DNA

1) 1 structure (=amino acid sequence) proteins/polypeptides 2) nucleotide sequence of RNA (rRNA, tRNA)

DNA Sequence

DNA ---->mRNA--->Protein/polypeptide

Nucleotide

A phosphate group 5C sugar Nitrogenous base

RNA Possible nitrogenous base

AUCG

DNA Possible nitrogenous base

ATCG

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

Yes DNA - TTGCACC RNA - AACGUAGG

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

Microscopes

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

Eukaryotic

Cells with Nucleus and membrane oriented organelle Compartmentalized

What Does Domain Eukarya Include

Algae Amoebae Plants Fungi Animals

Terminology for Organelle

1) Membrane delimited subcellular department 2) Any subcellular structure (membrane not required)

Ribosomes

Protein building machines that don't have a membrane Eukaryotes and prokaryotes have them Sometimes ribosomes are organelles and sometimes not

Eukaryotes

Don't have membrane delimited subcellular compartments

Cytosol

Water based gel-like fluid that surrounds the organelles

Cytoplasm

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

Chromatin

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

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

Rough ER

Protein Synthesis

Smooth ER

Tubules

Golgi Bodies/Apparatus Functions:

1) Protein modification 2) Protein Sorting

Where does Protein go if its from Rough ER?

It goes to the lumen