Atoms and Molecules

• Chapter 2 focuses on atoms, molecules, and their importance in living organisms

Matter and Atoms

• Matter includes tangible substances in solid, liquid, and gaseous states
• Atoms are the fundamental units of matter, serving as the building blocks of all living and non-living things
• Atoms are extremely small spheres, about 10 million times smaller than a typical object

The Atom

• The nucleus is the central core of an atom
• A nucleus contains positively charged protons and neutral neutrons
• Negatively charged electrons surround the nucleus, traveling in defined paths or shells
• Electrons orbit the nucleus in multiple shells
• An atom typically has no net charge due to an equal number of electrons and protons

Electrons

• Electrons have a negative charge and orbit the nucleus
• Electrons are involved in forming molecules by joining atoms together

Protons

• Protons have a positive charge and reside within the nucleus
• The number of protons determines the characteristics and behavior of an atom, defining its element

Elements

• Elements are types of atoms
• There are approximately 100 different types of atoms, corresponding to 100 different elements
• Atoms with the same number of protons share the same characteristics and belong to the same element
• Carbon atoms contain 6 protons
• Hydrogen atoms have 1 proton
• Each element has a 1- or 2-letter abbreviation

Elements of Life

• Elements are atoms with the same characteristics
• All atoms within the same element share the same number of protons
• There are over 100 known elements
• Hydrogen (H), carbon (C), nitrogen (N), and oxygen (O) are the most abundant chemical elements in living organisms

Molecules and Bonds

• Atoms combine to form molecules
• A molecule consists of two or more atoms bonded
• Atoms can bond with other atoms of the same element or different elements to form molecules
• A compound is a molecule composed of different elements
• C6H12O6 (glucose), H2O (water), and H2SO4 (sulfuric acid) are compounds, while O2 (oxygen gas) is not

Bonds

• Bonds are forces that join atoms to form molecules

Matter and Molecules

• References to matter often pertain to molecules rather than individual atoms
• Water (H2O) consists of one oxygen atom bonded with two hydrogen atoms
• Oxygen gas (O2) consists of two oxygen atoms bonded
• Table salt (NaCl) is made of one sodium atom bonded with one chlorine atom
• Sugar (C6H12O6) consists of 6 carbon, 12 hydrogen, and 6 oxygen atoms bonded

Ionic Bonds

• Ionic bonds join oppositely charged atoms (ions) together
• These bonds form through the attraction between ions of opposite charges
• Atoms gain or lose electrons to become ions
• Oppositely charged ions attract and bond to each other
• Compounds formed by ionic bonds are known as salts

Covalent Bonds

• Covalent bonds form when two atoms share electrons
• Atoms forming covalent bonds do not become charged

Covalent Bonds: Sharing Electrons

• Atoms can share electrons with one or more atoms, for example, H2 or CH4 and H2O
• Each atom contributes at least one electron to be shared, resulting in atoms being held together

Types of Covalent Bonds

• A single bond involves 2 shared electrons, exemplified by H2 and CH4
• A double bond involves 4 shared electrons, like in O2 represented structurally as O=O
• A triple bond involves 6 shared electrons
• Covalent bonds are stronger than ionic bonds

Chemical Notation/Formula

• Chemical formulas are abbreviated names for molecules
• Chemical formulas indicate the types of elements present in a compound
• Elements are represented by their chemical symbols/abbreviations, e.g., carbon=C, hydrogen=H, oxygen=O
• They indicate the number of atoms of each element in a molecule using subscripts; if only one atom of an element is present, no subscript is used
• Examples of chemical formulas are H2O, CH4, C6H12O6, and H2SO4

Structural Formula

• Chemical notation does not indicate the arrangement of atoms in a molecule
• Structural formulas illustrate the arrangement of atoms, indicating which atoms are connected
• Each atom is represented by its abbreviation, and lines are drawn between atoms to show covalent bonds
• One line represents a single bond, and two lines represent a double bond
• The structural formula for water (H2O) is H-O-H, and for oxygen (O2) it's O=O

Molecular Interactions

• Chemical reactions are an example of molecules interacting with each other
• Polar molecules can form hydrogen bonds with each other
• Salt molecules pack together into crystals

Bonds and Chemistry

• Chemical reactions entail the transformation of one molecule into another
• These reactions involve dismantling existing bonds between atoms and creating new ones
• Chemical reactions consist of atom formation and bond-breaking, which results in either the synthesis or decomposition of molecules

Reactants and Products

• Chemical reactions convert molecules into other molecules through the making and breaking of bonds
• Chemical reactions involve breaking existing bonds and forming new ones, depicted by reactants converting into products
• Reactions entail rearranging elements, such as breaking bonds between H atoms and O atoms to form water molecules H20

Chemical Reactions

• Chemical reactions involve forming or breaking bonds between atoms
• Life depends on these reactions; cells and organisms must conduct chemistry to survive
• Reactants are the starting materials and are on the left side of the arrow
• Products are what the reactants become and are on the right side of the arrow

Polar Molecules

• Polar molecules contain a hydrogen atom covalently bonded to oxygen, sulfur, or nitrogen
• A polar molecule has slightly positive and slightly negative regions

Water: A Polar Molecule

• Oxygen atoms share e- with 2 H atoms
• Oxygen attracts electrons more strongly due to more protons causing O atoms to have slightly negative charge and H atoms a slightly positive charge

Hydrogen Bonds

• Hydrogen bonds are weak forces of attraction between polar molecules
• Individual polar molecules attract each other weakly through hydrogen bonds
• Water molecules can form hydrogen bonds with each other
• Hydrogen bonds can also form between a polar molecule and an ion
• Hydrogen bonds do not join atoms to form molecules

Forming Hydrogen Bonds

• Hydrogen bonds occur between a positive portion (H atom) of one polar molecule and the negative portion of another polar molecule
• Hydrogen atoms of one water molecule form hydrogen bonds with the oxygen atom of another water molecule
• A water molecule can form up to 4 hydrogen bonds with other water molecules
• Polar molecules forming hydrogen bonds are involved in mixing and rinsing

Intramolecular Hydrogen Bonds

• Hydrogen bonds can also form within the same large molecule
• Hydrogen atoms covalently bonded to O, N, or S can form hydrogen bonds with another O, N, or S atom within the same molecule
• In large molecules, hydrogen atoms connected to oxygen atoms can form hydrogen bonds with nitrogen atoms
• Hydrogen bonds forming within a molecule aid in maintaining the molecule's shape

Hydrogen Bonds and Polarity

• Hydrogen bonds enable polar molecules to drag each other
• Polar molecules forming hydrogen bonds can attract another polar molecule or a charged item (like an ion)
• Water forming hydrogen bonds with ions or other alcohols or sugar can drag these items
• Rinsing and mixing things into water is made possible

Molecules Essential for Life

• Organic molecules contain carbon and hydrogen atoms, such as carbohydrates, lipids, proteins, and nucleic acids
• Inorganic molecules, like water salts and acids/bases, lack either carbon or hydrogen

Organic Compounds

• Organic compounds contain carbon and hydrogen, and may contain other elements
• Organic compounds consist of a carbon skeleton/backbone (all organic molecules) and functional groups

Carbon Skeleton

• Portions of molecules which contain only carbon and hydrogen atoms
• Carbon atoms in organic molecules join in various ways, defining molecule shape
• They may join in straight chains, chains with branches, rings, or combinations thereof
• Most carbon atoms in the skeleton are also bonded to hydrogen atoms

Functional Group

• Functional groups are portions of organic molecules that contain elements other than C and H
• Functional groups are attached to carbon skeleton and are responsible for chemical properties of a particular organic compound
• Organic molecules can have one or more functional groups, or none at all (only C and H)

Diversity of organic Molecules

• Organic molecules must have C and H, and can have other elements.
• Other elements may be part of a functional group
• C and H portion is the "skeleton", abbreviated as “R”
• Organic molecules are very diverse in groups, shapes and sizes

Organic Compound Sizes

• Small organic molecules can combine into a large organic molecule (macromolecule)
• A polymer is a large organic molecule composed of smaller organic molecules joined end to end
• Most macromolecules are polymers (chainlike form)
• Each molecule in polymer/chain is called a monomer
• Linking sugar molecules to create a long chain, with each sugar is a monomer

Dehydration synthesis

• Smaller molecules joining together to make it bigger through dehydration synthesis. H and OH are removed to combine and form H20.

Hydrolysis

• Big molecule breaking into smaller ones with use of water.

Major Organic Molecules in the Cell

• Carbohydrates (sugar)
• Lipids (fats)
• Proteins ("meat")
• Nucleic acids (DNA/genes)

Carbohydrates

• Carbohydrates provide structure and act as energy sources
• Carbohydrates are molecules that have a starchy texture or a sweet taste
• Carbohydrates consist of C, H, and O, with a formula of (CH2O)n where n is the number of carbons above 3
• The number of C and O atoms must be equal, and there must be twice as many H atoms

Types of Carbohydrates

• Monosaccharides, Disaccharides and Polysaccharides
• Monosaccharides are the simplest of carbohydrates (aka "simple" sugars)
• Monosaccharides contain 3 to 7 carbon atoms
• Monosaccharides act as monomers, forming larger sugars
• Monosaccharides are for cell energy
• Most monosacchrides take on a ring-like shape when placed into an environment that's very watery

Disaccharides and Carbohydrates

• Disaccharides form when two monosaccharides join by dehydration synthesis
• Lactose and sucrose are disaccharides
• Disaccharides break down into component monosaccharides by hydrolysis

Polysaccharides

• Polysaccharides are the largest type of carbohydrates
• Formed through joining a number of saccharides with dehydration synthesis
• Monosacchriding is stored through polysaccharides
• Polysaccharides are the building materials of fuel stroinf molecules

Examples of Polysaccharides

• Starch: a straight chain found in many monosaccharides that stores glucose in plants
• Glycogen: chain with branches that chain stores glucose in animal cells
• Cellulose: building material unique to plant cells
• Peptidoglycan: chain of many disaccharides that is unique to bacteria

Lipids

• Lipids consist of carbon, hydrogen, and oxygen
• Lipids are largely nonpolar due to no hydrogen atoms covalently bonded to an oxygen atom
• Lipids aren't able to form hydrogen bonds
• Lipids don't mix well with water
• Lipids act as the primary element of plasma membranes and are unused for energy
• Three Lipid Subtypes: triglyceride (fat), phospho-lipids, steroids

Triglycerides

• Triglycerides are simple fats consisting of one glycerol molecule with three alcohol functional groups, and three fatty acid molecules

Fatty Acids

• Fatty acids are long chains of carbon atoms, typically 15-25, covalently bonded to each other with a carboxyl group at one end
• Each fatty acid, or FAT, molecule is joined to glycerol through dehydration synthesis,
• Fat can be split into one glycerol and three FAs by hydrolysis

Additional Points on Fatty Acids

• Saturated fat: contains straight FAT joined by only single bonds
• Unsaturated fat: One or more bent fatty acids, with double bonds
• Bacteria stores unused energy as deposits aka spare-tires

Phospholipids

• A glycerol molecule is attached to a two fatty acid to act as a functional group
• Head regions consists of glycerol portion (charged) and tails are non-polar

Arrangement

• They has a distinct arrangement.
• Heads and tails can interact with water
• Phospholipids make up membranes

Steroids

• Steroids consist of four carbon rings
• Cholesterol, for example

Cholesterol

• Part of cell membrane
• Act as signalling hormines knowns as testosterone and estradiol

Proteins

• Proteins are universal structural and support of organisms
• Proteins are necessary for the cell structure and function
• Many structural cells are made by proteins
• Transporters are made of proteins
• Enzymes speed up the process

Polymer

• Polymers are made up of chained amnio acids
• Proteins are also known as ploy peptides

Protein Composition

• Made of amino acides that are bonded together through "peptide" bonds through a chain

Residue

• A residue is anny AA that is part of chain

Amino Acids

• They have the alpha Carbon bonded to four items
• Amino Group
• Carboxyl Group
• H Atoms
• Sid Chain

Sid Chain Properties

• determines chemical properties
• There are 20 AA with own set Sid chains

Structure of Protein

• Amino acids forming polypeptides of dehydration synthesis
• The peptide binds when joined together due to water

Diversity of Proteins

• Consists of 60000 diverse groups, each with unique function

Diversity of Amino Acids

• Varied sequence from how amino acids combine together
• Some contain chains and function for some others with 3D functions for H bonds.

Protein Structure

• The structure or shape is vital for protein to operate
• Terminology of protein structure happens with chain like movements/ order.
• A Specific order for all

Secondary Structure

• Occurs in specific regions of the polypeptide • alpha helix: coil • Beta sheet/pleats: polypep chain folds on itself like a hairpin • 2ndary structure maintained by H bonds

Tertiary Structures

• 3D shape of polypep
• Formed by bending .Maintained by various interactions

Structures of bonds associated

• hydrogen
• disulfide bridge molecules
• ionic

Structures in 3D order

• 1st structure: amino acid
• 2nd structure: Beta sheets pleated with chain like bonds
• 3rd folding shape to create polypeptide bonds
• 4th: Applies when made out monomers

Chain bond features

• They are linked together with chain like hydrogen atoms.
• They bond side ways

Diverse Folding bonds

• They contains H bonds when folded
• disfuldide bonds of 2-

Protein shapes

• Compact 3D
• The fibers have chain like compacts

Protein bond disruptions

• Disrupt structures, disrupt or destroy protein

Denaturation

• Disruption happens with water.

Nucleic Acids

• Nucleic acids are polymers/chains of nucleotides, also known as "strand"

Nucleotides

• Nucleotides consist of a sugar , phosphate group, and base
• 2 nucleotides: DNA at and RNA at

DNA: Nucleobases

• 2 polymers or dna nucleotides
• contains deoxy-ribose
• Exists as double helix

Bonding Properties

• Adenine bonds with Thymine
• Cytosin Bonds with Guanine
• Genetic Blueprint material for storing memory

One Chain RNA

• Contains ribose
• Single stranded bonds with U
• It binds and holds the chain
• They carry proteins

ATP

• Modified nucleotide with base A
• Stores energy that get from food
• The usable "form" in the cell
• It uses " energy from ATP,ADP

Additional Information that binds with Electrolytes

• It is helpful with withlysis bond to libarate energy
• The Phosphate and dehydration synthesis happen with ADP.

Other facts

• Closer to an a protein and nucleus

Importance of water

• Consist of 85%-95% within organisms.
• Cell can use water to work.
• water is a good environment

Maintain the liquid

• Is easy to with maintainance.
• Is helpful for constant envirment.
• Works hand and hand with organisms.

Molecules, with good solvent quality

• Many and with salt and good qualitiy
• molecules run into one each other easily
• It does so with chain
• Fats dissolve easily thanks to the liquid state

Ionic mix quality

• They contain chain of billions of chains or items
• H bonds can carry to each
• Crystalline will desolve

Electrolytes

• H20 will help form with electrolytes. That will create and overide to function. When combined salt, all the Ions desolve easuly.

Important of liquid water

• Cells/organism contain Electrolyes
• Molecules move when slosh.
• solids move much less than liquids for moving

Bases and Acids

Made with H+ solutions. They can also be liquid that release ions. A good example of Acid is HCL.

• Bases also contain a good compound OH-Ions. Such as Water that release good fluid. NAOH also releases good.
• All the component increase

Exchange reactions

They will also combine and balance when mixed together

• They both will balance + and - when bonded

Properties are determined

• Acidity come from many H+ Ions
• The balance comes from HO-and balance.
• PH is used for a measurable level
• Electrolyes in the long rung =H balance for body/

PH is a measurable scale.

• PH scales reads as 0-14 .
• Small equal bigger
• 7 can be equal, and higher/ lower are acidic
• H bond is a measurables scale for that balance
• Cells function with PH due to balance and proteins Reatcion often happen and have protein usage.

Balance of Cells

• Cells function and have constant acid levels
• Microbes can have ranges that are higher. Reactions have PH balance depending on the type. To reach stable PH the needs something in return.