unit 1.1

Topic: The smallest unit of matter biochemists care about is the atom.
Definition: The smallest stable unit of matter that has the characteristics of its specific element.
Structure:
- Nucleus contains protons and neutrons.
- Electron orbitals surround the nucleus.
- Protons are positively charged.
- Neutrons are neutral and have no charge.
- Electrons are negatively charged and occupy orbitals.
Energy levels:
- Each orbital has a different amount of energy.
- Closer to the nucleus = lower energy level.
- Farther from the nucleus = higher energy level.
Valence electrons:
- Found in the outermost orbital.
- Used for making different types of bonds.
- Most elements want $8$ electrons in their valence shell (octet rule).

Ions: atoms with a net electric charge due to unequal numbers of electrons and protons.
Anions (negative ions):
- Have more electrons than protons.
- Carry a negative charge.
Cations (positive ions):
- Have more protons than electrons or lose electrons.
- Carry a positive charge.
Neutral atoms: #electrons = #protons.

Main elements of life: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N) – CHON.
All other elements are trace elements:
- Found in small (trace) amounts in the body.
- Critical to maintaining homeostasis.
- Without them, organisms would quickly die.

Carbon is the basis of organic life forms.
Inorganic carbon is fixed from the atmosphere by plants during photosynthesis.
Carbon is incorporated into carbohydrates and is a main source of biomass in ecosystems.
Organisms utilize carbon to produce every biomolecule: carbohydrates, proteins, nucleic acids, and lipids.
When organisms die, decomposers recycle carbon back into the environment.
Carbon-depleted areas lead to organism death because biological molecules cannot be made.

Inorganic nitrogen is fixed from the atmosphere by bacteria and other decomposers and absorbed by plants to enter the food web.
Organisms utilize nitrogen to produce proteins and nucleic acids.
Nitrogen is recycled into the environment by decomposers.
Nitrogen-depleted areas lead to organism death because proteins or nucleic acids cannot be made.

Phosphorus is used to build nucleic acids and certain types of lipids (phospholipids).
Organisms in phosphorus-depleted areas will die because they cannot make nucleic acids or phospholipids (major component of cell membranes).

Think: How are the chemicals secreted by the fish being used by the plant in this aquarium?
Pair: Share answers with your partner.
Share: Deschamps will call on students to share their answers.

Which of the following statements best describes how molecules released by the fish become nutrients for the plants?
A. The carbon dioxide molecules released by the fish are converted by the bacteria to oxygen atoms, which are used by the plants to make water molecules.
B. The oxygen molecules released by the fish are converted by the bacteria to ammonia molecules, which are used by the plants to make lipids and fatty acids.
C. The nitrites released by the fish are converted by the bacteria to carbon dioxide molecules, which are used by the plants to make carbohydrates.
D. The ammonia molecules released by the fish are converted by the bacteria to nitrates, which are used by the plants to make proteins and nucleic acids.
Correct answer: D. Ammonia is oxidized by bacteria to nitrates, which plants use to synthesize proteins and nucleic acids.
The model shows exchange of matter between plants, fish, and bacteria, with bacteria in the gravel at the bottom of the aquarium.

Definition: Electronegativity is the measure of how strongly atoms attract bonding electrons to themselves.
- It indicates how much an atom will pull electrons toward itself.
Determinants:
- Electronegativity is influenced by the number of electrons in the valence shell.
- The closer an element is to having $8$ electrons in its valence shell, the more electronegative it is.
Significance: Electronegativity helps explain bond type, polarity, and molecule behavior.

Order among common biologically relevant nonmetals:
- Fluorine > Oxygen > Nitrogen (in terms of electronegativity).
Note from the slides: Fluorine is the most electronegative element, not common in biology, but important to know; Oxygen is highly electronegative; Nitrogen is also very electronegative but slightly less than Oxygen.

Definition: A measure of the ability of elements to donate electrons and form positive ions.
Characteristics:
- Typically have 1 or 2 electrons in their valence shells.
- They are not very electronegative.

Overview: How electrons are arranged and shared determines bond types and molecule properties.

Covalent Bonds:
- Occur when two atoms share electrons.
- Energy is stored in covalent bonds and is released when the bond is broken.
Ionic Bonds:
- Weaker than covalent bonds.
- Result from transfer of valence electrons from a metal to a non-metal.
- Tend to dissociate in water, so they are less common in biology.

Description: A direct consequence of electronegativity that is crucial for life.
Polar molecules:
- Occur when there is unequal sharing of electrons across a covalent bond.
- Happen when a very electronegative element is bonded to a very small or very electropositive element.
Charge distribution:
- Overall neutral, but with partial charges on the poles.
- The electronegative element becomes partially negative; the electropositive element becomes partially positive.

Definition: Weak attraction between a hydrogen atom bonded to an electronegative atom (O, N, or F) and another O, N, or F atom.
Why O, N, F?: They are highly electronegative; hydrogens bonded to them carry a partial positive charge, and the other electronegative atoms have partial negative charges.
Consequence: Opposite charges attract, forming hydrogen bonds.

Key idea: How atoms are bonded together determines the molecule’s shape.
Importance:
- The structure, shape, and chemical properties of a molecule determine its function.
- This concept recurs across biology and chemistry.

Energy conservation:
- Energy is ALWAYS conserved in a reaction.
- Energy that appears lost is usually released as heat.
Conservation of atoms:
- The amount and types of atoms are conserved in a reaction.
- If you start with two oxygens and four hydrogens, you must end with the same atoms (unless more are added).
Conservation of bonds:
- The number of bonds in a chemical reaction is conserved.
- If you start with four bonds, you end with four bonds.

Understanding atoms and their electrons underpins all of biochemistry: bonding types, polarity, and molecular shapes drive biomolecule function.
Carbon, nitrogen, and phosphorus are central to biological macromolecules (nucleic acids, proteins, lipids, carbohydrates).
Humans rely on microbial recycling (decomposers) to return essential elements to the environment.
The interplay of electronegativity, bond type, and polarity explains how biomolecules interact with water and other molecules in living systems.