AP BIO Unit 2: The Chemistry of Life

Evolution

the process of change that has transformed life on Earth

Adaptation

A trait or feature which helps an organism survive in a certain enviorment; genetic, change takes a long time.

Acclimation

An organisms short term behavorial changes made to help it thrive in a new enviorment; short window of change.

What determines function?

Structure

Cells & Shared Characteristics

Smallest unit of life that can perform all the required activities; All enclosed by membrane, all contain DNA.

Eukaryotic Cells

Contains membrane-enclosed organelles, including a DNA-containing nucleus (Building blocks of a lifeform)

Prokrayotic cells

Lacks a nucleus or other membrane-bound organelles and are generally smaller than eukaryotic cells: still has DNA, older then Eukaryotic, mostly bacteria, very simple, they are each their own lifeform.

Characteristics of Life

1. Living things are complex, well organized (made of cells)

2. Living things must obtain and use energy (Metabolism)

3. Maintain internal enviorment (Homeostasis)

4. Grow

5. Respond to Stimuli

6. Reproduce

7. Evolve as a species

Endosymbiotic Theory

complex eukaryotic cells evolved from simpler prokaryotic cells through a symbiotic relationship where one cell engulfed another.

Matter

Anything that occupies space and has mass (quantity); is made up of elements

Element

Substance that cannot be broken down to other substances by chemical reactions

Compound

A substance consisting of two or more elements in a fixed ratio

Elements of life

CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur); make up 99% of life

Detoxifying

When plants which have adapted to enviorments containing elements that are usually toxic are used to remove toxicity from an area.

Electronegativity

An atoms attraction for the electrons in a covalant bond

Nonpolar covalant bond

the atoms share electrons equally; net nuetral charge

Polar covalant bond

one atom is more electronegative, and the atoms do not share the electrons equally; creates partial negative and partial positive areas within each atom or molecule.

Polar

Opposite: dissolves in water, most of what is in our bodies.

Bonds strength ranked

1. Bonds within molecules (induce chemical change; make new things)

1a. Covalant Bonds (strong)

1b. Ionic Bonds (strong when dry)

2. Bonds between molecules (weaker)

2a. Hydrogen bonds (weak)

2b. VDW interactions (weak)

Hydrogen Bond

Hydrogen of a polar molecule bonding with something in another polar molecule. (Bond formed when a hydrogen atom is covalantly bonded to one electronegative atom and is also attracted to another electronegative atom.)

Van der waals interactions

attractions between molecules that are close together as a result of charges: weak, only occur when atoms/molecules are very close, can be strong collectively.

Molecular Mimic

Science mimicing naturally occuring molecules to create artifical results. (key and receptor) Ex: Morphine

Properties of Water

Cohesive behavior, Ability to moderate temperature, Expansion upon freezing, Versatility as a solvent. (All comes from hydrogen bonding between molecules)

Cohesion

Water molecules linked by hydrgen bonds stay close together. (Water sticks to itself) Allows for Evapotranspiration and surface tension.

Adhesion

Waters polarity results in it sticking to other things.

Moderation of temp

Water absorbs hear from warm air and releases stored heat to cooler air. Water can absorb or release large amounts of heat without changing its own temp much. Water has a very high specific heat. Ocean moderates temp in coastal areas.

Temparture

Average kinetic energy of molecules

Thermal Energy

Measure of the total amount of kinetic energy due to molecular motion.

Heat

transfer of thermal energy.

Calories

amount of heat required to raise the tempature of 1g of water by 1 C

Joule

unit of measurment for energy

Kilocalories

Kcal=1,000 cal, Calories which are displayed on food packaging

Specific Heat

amount of heat that must be absorbed or lost for 1g of a substance to change its tempature by 1 C. Specific heat of water is 1 cal/g/C. Water has high specific heat due to H-Bonds

Evaporation Cooling

Transformation of a substance from liquid to a gas at the surface, keeping the surface cool.

Expansion of a Solid

Ice is less dense then water, therfore it floats on water.

The Solvent of life

Water is a versatile solvent due to its polarity, dissolves lots of things, keeps life alive

Solution

Liquid that is a homogenous mixture of substances

Solvent

the dissolving agent of a solution

Solute

the substance that is dissolved

Aqueous solution

A solution in which water is the solvent

Hydration Shell

forms around ionic compounds dissolved in water.

Hydrophobic vs. Hydrophilic

Hydrophobic- water fearing (typicallly nonpolar) Hydrophilic- water loving (typically polar)

Acids

have high amounts of H ions. Low pH. Increases H concentration in water.

Bases (alkaline)

Have high amounts of OH ions. High pH. Takes things off of a surface. Decreases H concentration in water.

Neutral

pH ~ 7, most things found in our bodies are close to neutral

Buffers

substances that minimize changes in concentrations of H and OH in a solution. Something that makes pH change difficult

Ccean Acidification

Ocean holds way more C then the atmosphere, massive C sink, pulls in C.

Organic

related to carbon, related to life.

Carbon

All major molecules of life are heavily carbon, makes up most of living organisms, can form large complex bonds with a variety of atoms (due to 4 valence electrons) can bond with four other things at once. "social & flexible"

Testosterone & Estrogen

Sex hormones, have a lot in common but subtle differences make them behave very differently, not about presence about amount.

Carbon Chains

Form skeletons of most organic molecules, vary in length and shape

Hydroxl Group

-OH

Carbonyl Group

C=O

Carboxyl Group

-COOH

Amino Group

-NH2

Sulfhydrl Group

-SH

Phosophate Group

-OPO3^-2

Methyl Group

-CH3

ATP

Important energy molecule created by the mitochondria, primary energy-transferring molecule in the cell, consists of adenosine attached to a string of three phosphate groups, energy becomes avalible when on phosophate is broken off.(polymer) (like an energy packet or a battery)

Polymer

long molecule consiting of many similar building blocks (monomers)

Monomers

Small building blocks

Hydrolysis

Addition of water. Dissasembles polymers into monomers.

Dehydration Reaction

Removing water to come together. Occurs when two monomers bond together through the loss of a water molecule. H & OH are both removed creating a bond.

Enzymes

Catalysts for chemical reactions in living things, proteins which speed up chemical reactions

Carbohydrates

sugars and the polymers of sugars. Great short term energy source.

Monosaccharides

monomer of carbs, different rations of CH2O, building blocks of carbs, EX: Glucose. Classified by number of Carbons in Carbon Skeleton and placment of Carbonyl group. Fish Scale like shape. Short term energy source, think sweet.

Monosaccharide Examples

glucose, fructose, galactose, ribose

Disaccharides

two monosacchrides joined together by dehydration. EX: Sucrose (Glucose bonded to Fructose)

Glucose

Most common Monosaccharide, ideal energy source for creating ATP.

Polysaccharides

Polymers of sugars, have storage and structural roles, longer term more complex carbs, have to be broken down into glucose for ATP, storage of glucose (glycogen and starch)

Starch

A storage of polysaccharide of plants, consists only of glucose monomers.

Glycogen

storage of polysaccharide in animals, short term energy storage

Cellulose

plant cell wall, polymer of glucose, different glycosidic linkages every other glucose is inverted (Beta-beta-beta linkages, starch and glycogen has Alpha-alpha-alpha linkages)

Starch linkages vs. Cellulose linkages

Starch, chain of alpha glucose 1-4 glycocitic likage.

Cellulose, 1-4 linkage of beta glucose flipped every other time.

Fat

excess energy stored for long term

Chitin

Polysaccharide, cell wall for fungus cells, containts a singular N, exception to CHO pattern across carbs.

Lipids

Not a true polymer, marcomolecules with unique identities, made primarily of CHO, very hydrophobic (made of mostly hydrocarbons, which form nonpolar covalant bonds) Most important lipids: Fats, Phospholipids, Steroids. Breaks into completely unique parts. As a group very hydrophobic.

Fats

Long term energy storage constructed from two types of smaller molecules: Fatty acids, and glycerol (both nothing like fat on their own, not monomers). Energy in fat is acsessed by enzymes breaking up bonds

Saturated fatty acids

Have the maximum number of hydrogen bonds possible, no bending, no double bonds, easily become solids

Unsaturated fatty acids

have one or more double bonds, less hydrogen, creates bends, harder to become solid, healthy/good for you.

Phospholipids

two fatty acids and a phosphate group are attached to a glycerol. Physical things that make up cell membrane. Have a hydrophillic head and a hydrophobic tail that determine its structure in different enviorments.

Steroids

Lipids characterized by a carbon skeleton consisting of four fused rings. Generally slow down the immune system.

Amphiphatic

Consisting of hydrophobic and hydrophillic components.

Cholesterol

import steroid, is a component in cell membrane, essential in animals, high levels in the blood may lead to cardiovascular diseases.

Proteins

molecular workers inside the body which preform many jobs.

Have specific shapes, jobs, & functions

Accounts for more than 50% of the dry mass of most cells

Biologically functional molecule that consists of one or more polypeptides

Enzymatic Proteins

Selective acceleration of chemical reactions

Defensive proteins

Provide protection against disease

Storage proteins

storage of amino acids

Transport proteins

Transport of substances

Hormonal proteins

Coordination of an organism's activities

Receptor Proteins

Response of a cell to chemical stimuli

Contractile and Motor proteins

Movement

Structural Proteins

Support

Polypeptides

unbranched polymers built from the same set of 20 amino acids linked by covalant peptide bonds.

Range in length

Each polypeptide has a unique sequence of amino acids

Functional proteins contain one or more polypeptides

Don't have jobs, not yet uniquely folded

Amino acids

Organic molecules with carboxyl and amino groups

Monomers of proteins

20 different kinds

Similar/Universal structure (all have amino groups, carboxyl groups, and lone H) with differing R groups or side chains (can be hydrophobic or hydrophillic, acidix or basic, etc.)

Ribosomes

Organelles which create proteins

Primary structure

First level of protein structure.

Unique sequence/chain of amino acids held together by peptide bonds created by dehydration reactions.

Secondary structure

Second levle of protein structure; H-bonds between amino acids cause the polypeptide to take on either the shape of an alpha helix or a beta pleated sheet.

Tertiary Structure

The third level of protein structure.

Goes from a polypeptide to a protein.

Becomes uniquely folded by interactions between amino acids R groups (disulfide interactions, ionic bonds, hydrophobic interations, VDW interactions, hydrogen bonds) Has a unique job, can be a fuctioning protein in this state.

Quarternary structure

More complex protein consisting of multiple tertiary structure protiens bonded together. Also a function protein uniquely folded to have a unique job, just a bit more advanced.