Chemistry of Life (Ware)

Scientific Method

Scientific Method

Process of systematic observation, measurement, and experimentation to test a hypothesis

Hypothesis

A proposed explanation requiring further investigation

• "If (independent variable)....then (dependent variable)"

Independent Variable

• 1 variable that is changed in experiment

• the "cause"

• x-axis

• isn't changed by the other variables you are trying to measure

Dependent Variable

• dependent on the independent variable

• the "effect"

• y axis

Controlled Variable

• Variables that stay CONSISTENT to ensure it doesn't influence results

Control

Without the independent/manipulated variable

Scientific Theory

• throughly tested

• reasoning that groups many different observation

• unlike scientific hypothesis (not fully tested yet)

Steps of Origin of Life

1. formation of the earth (4.5 billion), acquired organic chemicals by the collision with other comets/meteorites

2. Prebiotic synthesis & Accumulation of amino acids, sugars, lipids, etc in the environment

3. Prebiotic condensation & reactions with polymers of proteins and nucleic acids (RNA)

4. Synthesis of lipids - self-assembly into membranes/liposome capturing prebiotic molecules

5. Protobiont Formation- first living systems with cooperative interactions

Early Atmosphere Gases

Hydrogen sulfide (toxic gas) and carbon dioxide

Common Elements of Life

Hydrogen, oxygen, carbon, nitrogen, sulfur

Chemosynthesis

• bacteria use hydrogen sulfide to make sugar (early life in deep ocean vents)

Life Moving to Earth's Surface

• energy = sun

• chlorophyll - traps sunlight, turns co2 and oxygen into food

• PHOTOSYNTHESIS CAUSES LIFE TO SPREAD

Stromatolites (Cyanobacteria on Top)

• oldest fossil

• bacteria's waste gas with iron to ocean floor: rusts earth, makes iron ore

• cynaobacteria makes oxygen, got rid of toxic gases - made ozone layer

Microbes

Ruled earth for 3 billion years

RNA

• ribonucleic acid

• contains sugar ribose

• solves "chicken and egg" problem" (genes need enzymes to form, enzymes need genes to form)

• RNA acts both as genes and enzymes

DNA

• deoxyribonucleic acid

• contains sugar deoxyribose

A) Ocean Surface

• began near tide pool, pond, moist clay

• gas from volcano mixed with UV light/electric discharges makes PREBIOTIC MOLECULES

B) Panspermia

• comets and meteors carried living organisms onto earth when it landed

• organisms will need to survive the heat of landing

C) Undersea Thermal Vents

• life have survived and arises from ancient volcanic vents

• needs gases, energy, catalysts (metal sulfides)

Miller-Urey Experiment

• 1950s, to recreate conditions of primitive earth to see what might given rise to molecules of first organisms

• created amino acids, nucleic acids, sugars, lipids, adenine, ATP

Endosymbiosis Theory

Origin of Eukaryotes:

• large prokaryote cells ingest free-floating prokaryotes

• organelles: mitochondria and chloroplast- dependent on the nucleus to direct metabolic processes

Origin of Mitochondria

prokaryote cells engulfing purple bacteria

Origin of Chloroplasts

prokaryote cells engulfing cyanobacteria (already capable of photosynthesis)

2 Sequence of Evolutionary Change

1. Animal Cells diverged before leading to plant cells

2. Plant Cells to Animal Cells (plant cell evolved from plant cells and lost chloroplast)

Buildup of Free Oxygen In Atmosphere

Allows animals to develop features to turn oxygen into energy (ex photosynthesizing)

First Appearances

Primitive Cells: 3500 mya Invertebrates: 550 mya Fish (ray-finned): 400 mya Land Plants: 375 mya Reptiles: 260 mya Mammals: 200 mya Birds: 180 mya

Significance of Mass Extinctions to Biodiversity

• causes living things to compete for living resources

• most adaptable types can live

• stimulation for more complex organisms

One or More Cells

All living things are made up of... (unicellular/multicellular)

Reproduce

All living things...

sexual = two sex cells required asexual= no gameates/sex cells used (only needs 1 parent cell)

Genetic Code

All living things contain a....

(univeral, passes down to offspring, starts as RNA but DNA rules because more stable)

Grow and Develop

All living things 1 and 2_...

1. Increases in size (divides repeadly)

2. Change/performs different functions

Metabolism

All living things have a....

Combination of chemical reactions when organisms makes/breaks molecules (etc obtain and use material/energy)

Autotroph

Organisms obtains energy from sun/inorganic compound (photosynthesis)

etc: the grass

Heterotroph

Organism obtains energy from consuming nutrients (organic molecules) from environment

etc: cow

Respond

All living things ________ to their environment.

Stimulus

• a signal from the environment that causes internal/external reaction

Behavior

a complex response to stimulus

Homeostasis

All living this maintain....

Maintaining stable internal conditions (body tempt, blood sugar levels,etc) despite external environment changes

Evolve

As a group, all living things....

• adapt to environment to survive

• small changes over millions years to big changes

Water

All living things need _____ to survive.

For metabolic processes, homeostasis, chemical reactions

Hierarchy

Structural Organization of cellular organisms

Each level is part of next, higher level

Carbon

• #6, solid at room temp

• found everywhere (atmosphere oceans, living things/ores, minerals)

• oxygen for photosynthesis, energy production

• gas absorbed by organism

Oxygen

• #8, gas at room temp

• found in atmosphere/waters

• absorbed through lungs/gills

• ozone layer - protects organism, cellular respiration

Hydrogen

• #1, gas in room temp

• gases, stars, water, microorganisms

• absorbed mainly through water

• producing energy, fuels sun, main part of water

Nitrogen

• #7, commonly a gas, very stable

• soil/plants, water, amino acids/proteins

• bacteria convert it to ammonia - absorbed

• animo acids - proteins, nucleic acid

Sulfur

#16, commonly a solid

• volcanic areas/ hot springs/underground

• plants get it from soil, animals from eating plant

• growth of plants, metabolism, photosynthesis, builds and fixes DNA

Phosphorus

#15, mostly as a solid, flammable when exposed to air

• erosion from rocks, soil

• eating plants, or plant-eating animals

• holds dna together

Calcium

• #20, solid at room temp

• limestone deposit

• muscle contraction, human skeleton, good for shells

Sodium

#11, solid when pure, highly reactive

• seawater, earths crust consume sodium (salt) plants get from roots (not required to live)

• holds water in blood/helps blood pressure

Potassium

#19, solid when pure

• earth's crust, salty water, foods

• plants get it, animals eat these plants

• normal levels of fluid in living cells

Magnesium

#12, commonly solid

• minerals (magnesite/dolomite), in the sea, foods

• chlorophyll in plants, nerve/muscle function, steady heartbeat

Chlorine

#17, commonly a gas

• salt, ocean algae

• acquired by touching, eating, breathing

• concentrates in chloroplasts, excretion, acid balance of body

Iron

#26, solid in pure state

• in many stars, earth's core, ores

• acquired through food

• transports oxygen, produces energy

Atoms

• basic building blocks of life

• incredibly small

• electrically neutral (same # of proton/electron)

• of protons is atom's number

Isotopes

• forms of the same element that contain equal numbers of protons but DIFFERENT numbers of NEUTRONS in their nuclei

• different in relative atomic mass but not in chemical properties (same number of electrons)

• radioactive isotopes: unstable nuclei that break down at a constant rate

Ions

• when atoms gain/lose electrons

• positively or negatively charged

• different # of protons/electrons

Ionic Bonds

• formed when one or more electrons are transferred from one atom to another.

Covalent Bonds

• forms when electrons are shared between atoms

Protons

• positively charged particles (+)

• about same mass as neutrons

Neutrons

• carry no charge

• protons and neutrons together form the nucleus

Electrons

• negatively charged particle

• atoms have same number of protons electrons so atoms do not have a charge

Molecules

the structure that results when atoms are joined together by covalent bonds

• unequal electron sharing = regions of positive/negative charges

van der Waals forces

• Slight attraction between the oppositely Charged regions of nearby molecules

Elements, Compounds, Mixtures

1. pure substance that consists entirely of one type of atom

2. a substance formed by the chemical combination of two or more elements in definite proportions

3. material composed of two or more elements or compounds that are PHYSICALLY mixed together (NOT chemically)

Solution

mixture in which all the components are evenly distributed throughout the mixture

solute = (like salt) solvent = (like water)

Acid

• compound that forms H+ HYDROGEN ions in solution

• lower than 7 on pH scale

Bases

• compound that produces OH- HYDROXIDE ions in solution

• higher than 7 on pH scale

Valance Electrons

• electrons at the highest level for that element (non full levels will bond with other elements)

first level = 2 second level = 8

HYDROGEN VALENCE: 2-1=1 CARBON VALENCE: 6-2=4 NITROGEN VALENCE: 7-2=5 OXYGEN VALENCE: 8-2=6

Water Molecule

• consists of 2 hydrogens, 1 oxygen

• neutral

• oxygen end has slight - charge, hydrogen end has slight + charge

Hydrogen Bonding

• the attraction between the hydrogen atom on one water molecule and the oxygen atom on another water molecule

• affected by polarity

• water molecule: 4 hydrogen bonds

Adhesion

• attraction between molecules of different substances

• etc: water molecules attached to tube - meniscus

Cohesion

• attraction between molecules of the same substance

• etc: surface tension of water

Surface Tension

• created by hydrogen bonds/property of cohesion

• allows insects to walk on water

High Specific Heat

Specific heat: amount of energy required to change 1 gram of a substance 1 C

Water RESISTS change in temperature (thermal inertia) because of hydrogen bonds

Moderates Earth's climate/ocean temperature - sweat to cool down skin from overheating

Less Dense as a solid

Water is......

density because of hydrogen bonds

Many substances

Water dissolves...

Water is polar molecule - can dissolve ionic compounds/polar molecules

Capillary Action

• liquid can flow through narrow spaces from cohesion (water attracted to each other) and adhesion (water attracted to walls of the tube)

• etc: plant absorbing water in soil up its roots vessels thinner - stick to the wall better

Polar Molecules

• A molecule in which the charges are unevenly distributed

• 1 atom is not shared equally with another atom "hogging the electrons" (partial negative)

• can attract each other

Boiling Water

• heated water molecules break free from the hydrogen bonds

• liquid to gas

• as gas leaves, it remove thermal energy from the liquid with it SO temperature of the liquid remains CONSTANT during boiling

Carbohydrate

Macromolecule

C,H,O in a carbon-ring form

General Formula: (CH2O)x

Role: short/ long term energy, fuel for cellular respiration (glucose), component of cells

Monomer: monosaccharide (simple sugar): glucose, fructose

Polymer: polysaccharides (starches like glycogen for animal, cellulose)

Lipid

Macromolecule

Glycerol with 3 fatty acid tails lots of C, lot ofs H, some O

General Formula: CH3(CH2)nCOOH

• HYDROPHOBIC so waterproofing of surfaces, insulation in animals, steroid hormones, long-term energy storage

Saturated: carbons in chain have 4 single bonds ("saturated" with H) Unsaturated: some carbon atoms in bond has double bonds, less H

Nucleic Acid

Macromolecule

Made of C, H, O, N and P (5 c sugar, nitrogenous base a,t,g,c,u, phosphate group)

Monomers: nucleotides Polymers: nucleic acid (DNA/RNA)

control and regulate life’s processes; transcribes & translates genetic information into proteins.

Amino Acids/Proteins

Macromolecule

Made of C, H, O and N

Monomer: Amino Acids Polymers: Polypeptides (2 amino acids bonded by PEPTIDE BOND) Protein is 1+ polypeptide strand is folded/coiled/arranged into shape

Amino acids:

• Carboxyl group

• Amino group

• R group (different) 20 different types - forms shape

Major structural component in body part, regulate body proccesses, aid in movement, transports molecules

Monomer

• smaller units that joins together to form polymers/macromolecules

Polymer

a naturally occurring or synthetic compound consisting of large molecules made up of a linked series of repeated simple monomers

Dehydration Synthesis

a chemical reaction that BONDS two monomers together by removing 2H and 1O (1 H2O) in the process

Absorbs energy

Hydrolysis

A chemical reaction in which a bond between two monomers is BROKEN by using a water molecule (1 H2O)

Release energy

Four Levels of Protein

Primary: long single strand of a.a.'s (polypeptide)

• not yet a protein

Secondary: Alpha Helix and beta pleated sheet (back and forth)

Tertiary: has many interactions (H-bonds, Disulfide bridges, Ionic bonds, Hydrophobic interactions) between R-groups along the same polypeptide chain, forming a unique globular shape

Quaternary: More than 1 polypeptide chain interacting together in any way (mentioned previously) to make one protein molecule

Chemical Reaction

Turns Substrates into Products (one set of chemicals into another) mass/energy is CONSERVED

Enzymes

proteins that act as biological CATALYST - lower's reaction activation energy to speed up rate of chemical reaction

reactants= substrates - binds with enzyme at the activation site

• either tertiary or quaternary

Activation Energy

energy needed to get every chemical reaction started

• enzymes lowers

Enzyme activity influences

• Environmental conditions (temp., pH, ionic concentrations such as NaCl)

• Cofactors and coenzymes: inorganic or organic compounds needed (ex., vitamins) for proper enzyme activity

• Enzyme inhibitors: molecules that either

1. mimic the substrate SO it blocks the active site

2. bond to the enzyme so that it changes the shape of the active site

Catabolic Enzyme Reaction

• takes larger structures (like proteins, fats or tissues) and breaks them down into smaller units (such as cells or fatty acid)

(digesting food)

BREAKING

Anabolic Enzyme Reaction

creating bigger, complex molecules from smaller, simpler molecules for future use

BONDING