Thursday, September 19, y

Unit 1 Chemistry of Life Summary

- Organisms are made of matter, anything that has mass.

- Matter is made up of multiple elements, there are 92 elements.
- About 20% of elements are “essential” which means organisms need them
to live.
- Humans need more essential elements than plants.
- Oxygen, Carbon, Nitrogen, and Hydrogen make up a lot of the living uni-
verse.
- Trace Elements are elements that organisms need and use very small
amounts.
- There are some elements like Arsenic that are actually toxic to some or-
ganisms.
- Some species have developed tolerance to toxic elements.
- An element’s properties depend on the structure of its atoms.
- There are subatomic particles called protons, neutrons, and electrons.
- Elements have atomic numbers and atomic masses, an atomic number is
the amount of protons in the nucleus.
- The atomic mass is the total number of protons and neutrons.
- There are isotopes of elements that have the same number of electrons
and protons, but different amounts of neutrons. This creates variants like
carbon 12.
- There are stable isotopes and radioactive isotopes.
- EX: Carbon-14 can have neutrons that decay into protons, creating Nitro-
gen-14
- Radioactive isotopes can be used as tracers to track metabolism of biologi-
cal processes. This is relatively safe, but can be hazardous at a larger scale
- Scientists can measure the exact age of biological components like fossils
by using radioactive dating, which utilizes a half life between a parent and
daughter isotope to track age.

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- We use daltons to more easily track atomic mass.
- Energy is defined as the capacity to change.
- Electrons are found in different shells at set distances from the nucleus.
- Electrons outside the shell have more energy and are less stable.
- The outer shell is called the valence shell and the outermost electrons are
called valence electrons.
- The three dimensional space an electron shell inhabits is called an orbital.
- Covalent bonds are when both atoms are sort of sharing a dedicated pool
of electrons.
- EX: 2 Hydrogens can each share their one valence electron to make a pair
for each.
- EX b.: H-H, Single Bond
- Covalent bonds can form with more than two electrons. They can form
with 3+ and fill each other out in a unique way.
- Electrons shared equally are due to the same electronegativity, this is
called a non polar covalent bond
- Electrons of a bond that aren’t shared equally are due to different elec-
tronegativity, this is called a polar covalent bond.
- In a bond where the electronegativity is so powerful between two ele-
ments, One will actually steal an electron for itself forming an ionic bond.
- EX: Na and Cl, they bond to form Na+, and Cl-. This is because the protons
outweigh the electrons in the Na molecule, and they are outweighed by
the electrons in the Cl molecule. This forms an anion and a cation.
- t=+
- n = negative
- A hydrogen bond is a bond between two molecules where a partial nega-
tive and partial positive attract.
- Van der Waals interactions are made from very slight positive and nega-
tive charges on opposite ends of a covalent bond.
- The point where interactions balance completely is called chemical equilib-
rium.

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- H20 Molecules are very polar, so one’s end constantly bonds to another’s
- The water molecules are rapidly shifting where these hydrogen bonds are
occurring.
- When water freezes the molecules drift further apart and become still,
making it less dense and allowing it to float.
- The weird V shape’s unevenness makes it a polar molecule.
- Water has 2 main properties, Cohesion & Adhesion
- Water also can effectively transfer heat from warm air to cool air without
heating itself.
- Thermal energy is basically just average kinetic energy.
- So yeah water basically just stores and moderates temperature without
changing itself.
- When water heats up it moves faster. This causes the bonds to stop form-
ing and the water transfers to its gas state. This is called evaporation.
- Heat of vaporization is basically a term for how much energy is required to
convert 1 gram of liquid to a gas state.
- Evaporative cooling is basically just saying the water left over will be
cooler after boiling.
- If a school transferred its 100 fastest runners to another school, the aver-
age running speed of the students at the school would decrease.
- So basically the freezing of water is locking in the hydrogen bonds further
apart. Making it less dense, but also a crystalline solid.
- Hydrophilic substances have an affinity for water.
- Hydrophobic substances hate water.
- Most bio chem reactions involve solutes dissolved in water.
- Sometimes, a water molecule steals a hydrogen from another molecule,
forming an H3O+ ion and an OH- ion.
- Concentrations of this are even in pure water, but other solutes solutes
can change the balance, we use a pH scale to describe this.
- An acid added to the solvent reduces the H+ and imbalances it.
- Other solutes might be added that reduce the OH- and make it a basic so-
lution.
- pH scale ranges from 0-7 (Acidic), 7 Water, and 7-14 (Basic)
- 7 is basically the balance for living things.

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- Compounds with Carbon relate to organic chemistry.

- Carbon is very versatile, 4 valence electrons means lots of potential.
- O, H, & N, are common to bond with carbon. These are the “partners”
- Most organic compounds also contain hydrogen.
- Carbon is found in 4 macro molecules.
- Vitalism is the idea that organic compounds can only come to be in organ-
isms, this was disproved.
- Mechanism is the view that all natural phenomena are governed by physi-
cal and chemical laws.
- Life could have formed abiotically near volcanoes.
- Carbon bonded to four other atoms has tetrahedral shape.
- Carbon bonded to three other atoms has a trigonal planar shape.
- Hydrocarbons are compounds with only carbon and hydrogen.
- Fats have many hydrocarbon components.
- Hydrocarbon reactions = a lot of energy
- Isomers are different forms of the same compound.
- Structural isomers have the same quantities, but different arrangements.
- Cis-trans isomers have the same covalent bonds but differ in spatial ar-
rangements.
- Enantiomers are isomers that are mirror images of each other.
- Enantiomers are important with pharmaceuticals.
- Two enantiomers might have different effects.
- Usually only one isomer is biologically active.
- Distinctive properties of organic compounds depend on carbon skeleton
and molecular components.
- There are a lot of “groups” that attach to the carbon.
- These are called functional groups.
- The number and arrangement of the functional groups make them distinct.
- Hydroxyl group: written as -OH or HO-
- Hydroxyl is a type of alcohol (ol/yl endings)
- Found in ethanol, attached instead of a hydrogen on one end.

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- Carbonyl, at its root, C=O, with 2 other single bonds off of the C.
- Called ketones if within the group
- Aldehydes if at the end of the skeleton.
- Carboxyl, basically a Carbonyl, but one of the other single bonds is con-
nected to an OH hydroxyl group.
- Typically carboxylic acids/organic acids
- Can ionize as an acid by giving away its H in the hydroxyl part and creat-
ing an O- and an H+
- Amino group, 2 hydrogens bonded to a nitrogen,
which is all single bonded through the nitrogen to
the skeleton.
- The amino group can pick up an H+, making a posi-
tively charged N with three hydrogen.
- Sulfhydryl, -SH or HS-
- Cross linking can stabilize protein structure.
- Phosphate groups, too hard to describe so here’s a picture
- Phosphates are part of nucleic acids.
- Contributes a negative charge to the molecule.
- Able to react with water and release energy
- Methyls are carbons attached to 3 hydrogen atoms.
- Has an impact on female and male sex hormones.
- ATP is basically energy currency in the cell.
- ATP is just three phosphate groups combined and attached to adenosine.
- Adenosine Triphosphate
- Primary energy transferring molecule.
- Variation at molecular level is the foundation of biodiversity.

- All living things are made of 4 macromolecules.

- Carbohydrates, Lipids, Proteins, and Nucleic Acids.
- Macromolecules are large molecules with lots of small parts.
- Basically Polymers made of small Monomers

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- Structure and function work hand in hand.
- Polymers are long molecules made up of small molecule building blocks
called monomers.
- 3/4 classes of the organic molecules are polymers: Carbs, Proteins, Nucleic
Acids.
- A dehydration reaction is when 2 monomers bond together through loss of
water molecule.
- Polymers are disassembled to monomers by hydrolysis, basically the re-
verse of dehydration.
- Carbohydrates/sugars are basically energy/food.
- Carbohydrates can be monosaccharides, disaccharides, or polysaccha-
rides.
- Polysaccharides are bigger and “healthier.”
- Monosaccharides are smaller, simpler, and “less healthy.”
- Monosaccharides have molecules that are usually multiples of CH2O
- Glucose is the most common monosaccharide.
- Monosaccharides are classified by:
- The location of the carbonyl group.
- The number of carbons in the skeleton.
- Often drawn as linear, in aqueous solutions sugars form rings.
- Serve as major fuel for cells and raw material for building molecules.
- Linear and Ring forms are structural isomers.
- You can have sugars with many numbers of sugars.
- Disaccharides form when a dehydration reaction joins two monosaccha-
rides.
- This covalent bond is called a glycosidic linkage.
- Polysaccharides are polymers of sugars.
- Usually have structural and storage roles.
- Structure and function are determined by sugar monomers and the posi-
tions of glycosidic linkages.
- Storage polysaccharides are also known as starches. How plants are able
to store energy.

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- Glycogen is the storage in animals, we store this in liver and muscles. Al-
pha glucose points upwards.
- Cellulose is a structural polysaccharide in plant cells. Beta glucose mole-
cules are pointing upwards.
- Our body doesn’t produce enzymes to digest beta glucose like we do alpha
glucose.
- Examples of this are the strings on celery.
- Made of microfibrils that link as a strong unit.
- Chitin is a structural polysaccharide.
- It has a nitrogen on its base monomer.
- This lets it provide support in exoskeletons and the cell walls of fungi.
- Used in surgical thread.
- Lipids
- Fats
- Hydrophobic
- Doesn’t form as a polymer.
- Has little or no affinity for water.
- Fats, phospholipids, and steroids.
- Fats are glycerol and fatty acids.
- 3 carbons with a hydroxyl group.
- Fatty acid is a carboxyl group with a long carbon skeleton.
- To form a fat, 3 fatty acids, are joined to a glycerol and create a triacyl-
glycerol.
- Different types of fatty acids.
- Vary in length and number of double bonds.
- Saturated fatty acids have the maximum number of hydrogen atoms and
no double bonds.
- Unsaturated fatty acids have one or more double bonds.
- Energy Storage and Insulation, Cushioning.
- Phospholipid
- 2 fatty acids attached to a glycerol.

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- 2 tails are hydrophobic, but the attaches and phosphate group are hy-
drophilic.
- When added to water the phospholipids form a bilayer with hydrophobic
tails pointed to the interior.
- This is a major component of cell membranes.
- Steroids
- Lipids characterized by a carbon skeleton consisting of four fused rings.
- Cholesterol, important steroid, component in animal cell membranes.
- Cholesterol is essential to animals, but too much in blood is bad for you
and can contribute to heart disease.
- Proteins
- Make up most of the dry mass.
- Structural support, storage, transport, communication, movement, de-
fense.
- Enzymatic proteins
- speed up chemical reactions.
- catalyze stuff
- Defensive proteins
- protection against disease
- antibodies
- Storage proteins
- store amino acids
- Transport Proteins
- transport of substances like hemoglobin
- Hormonal Proteins
- coordination of an organisms activities.
- Receptor Proteins
- response to stimulation from cells and stuff
- Contractile and motor proteins
- made for movement, cilia and flagella
- Structural proteins
- made for support

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- keratin and stuff like that
- Enzymes
- A type of protein that acts as a catalyst to speed up reactions
- Perform functions repeatedly, workhorses that carry out the processes of
life.
- Polypeptides are unbranched polymers made from the same set of 20
amino acids.
- A protein is a biologically functioning molecule that consists of one or more
polypeptides.
- Amino Acids
- Organic Molecules with carboxyl and amino groups
- Differ in properties due to differing side chains called R groups.
- Forming polypeptides
- Amino acids are linked by peptide bonds
- A polypeptide is a polymer of amino acids.
- Polypeptides range in length from a few to more than 1000 monomers.
- Each polypeptide has a unique amino acid chain with a carboxyl end and
an amino end.
- Protein Structure and Function
- One or more polypeptides precisely twisted, folded and coiled.
- Structure determines function
- Primary structure is the sequence of amino acids in protein.
- Primary structure determined by genetic info.
- Secondary structure is the coils and folds from repeating hydrogen bonds.
- Coil called alpha helix and folded structure called beta pleaded sheet.
- Tertiary Structure
- I’m tired so like its just more ways to define it with R groups.
- Quaternary structure is when more chains form a macromolecule like colla-
gen or hemoglobin
- Lots of environmental factors can effect structure making it a denturation
and biologically inactive.
- Nucleic Acids

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- Sequence of amino acids are programmed by nucleic acids.
- Nucleic acids store genetic info
- 2 types
- DNA
- RNA
- DNA directs it’s own replication into RNA to eventually form protein and
this is called protein synthesis.
- Protein synthesis occurs in ribosomes.
- Nucleic acids are polymers called polynucleotides and each one is made of
monomers called nucleotides.
- Each nucleotide consists of a nitrogenous base, a pentose sugar - deoxyri-
bose/ribose, and 1+ phosphate groups.
- portion without the phosphate group is called a nucleoside.
- Nucleotide polymers join together to make a polynucleotide.
- Adjacent nucleotides joined by covalent bonds that form between the -OH
group on the 3’ carbon one one nucleotide and the phosphate on the adja-
cent 5’ carbon.
- Links create a backbone of units with nitrogenous bases as appendages.
- Sequence of bases is unique for each gene.
- Bases pair accordingly A-T and G-C and T is replaced by U in RNA
- Closely related species have similar DNA

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