Unit 2: Chemistry of Life

acid

a substance that donates hydrogen ions and therefore lowers pH

adhesion

the attraction between water molecules and molecules of a different substance

amino acid

a monomer of a protein

anion

a negative ion formed by gaining electrons

base

a substance that absorbs hydrogen ions and therefore raises pH

buffer

a solution that resists a change in pH by absorbing or releasing hydrogen or hydroxide ions

carbohydrate

a biological macromolecule in which the ratio of carbon to hydrogen to oxygen is 1:2:1; carbohydrates serve as energy sources and structural support in cells

cation

a positive ion formed by losing electrons

cellulose

a polysaccharide that makes up the cell walls of plants and provides structural support to the cell

chemical bond

an interaction between two or more of the same or different elements that results in the formation of molecules

chitin

a type of carbohydrate that forms the outer skeleton of arthropods, such as insects and crustaceans, and the cell walls of fungi

cohesion

the intermolecular forces between water molecules caused by the polar nature of water; creates surface tension

covalent bond

a type of strong bond between two or more of the same or different elements; forms when electrons are shared between elements

denaturation

the loss of shape in a protein as a result of changes in temperature, pH, or exposure to chemicals

deoxyribonucleic acid (DNA)

a double-stranded polymer of nucleotides that carries the hereditary information of the cell

disaccharide

two sugar monomers that are linked together by a glycodsidic bond

electron

a negatively charged particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a charge of -1

electron transfer

the movement of electrons from one element to another

element

one of 118 unique substances that cannot be broken down into smaller substances and retain the characteristic of that substance; each element has a specified number of protons and unique properties

enzyme

a catalyst in a biochemical reaction that is usually a complex or conjugated protein

evaporation

the release of water molecules from liquid water to form water vapor

fat

a lipid molecule composed of three fatty acids and a glycerol (triglyceride) that typically exists in a solid form at room temperature

glycogen

a storage carbohydrate in animals

hormone

a chemical signaling molecule, usually a protein or steroid, secreted by an endocrine gland or group of endocrine cells; acts to control or regulate specific physiological processes

matter

occupies space and has matter, all mass is composed of elements

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atom

the smallest component of an element that retains all of the chemical properties of an element 

Ex. One hydrogen has all properties of the element hydrogen, such as it exists as a gas at room temperature, and it bonds with oxygen to create a water molecule

• Hydrogen atoms cannot be broken down into anything smaller, while still having the 

properties of hydrogen (like subatomic particles)

proton

positively charged particles that reside in the nucleus (core of an atom) of an atom and has mass of 1 and charge of +1.

Neutrons

 like protons, reside in the nucleus of an atom. They have a mass of 1 and no charge. The protons and electrons charges balance its  charge, (zero charge)

Atomic Mass

number of protons and neutrons of an element 

Atomic number

number of protons in an element 

Periodic table of elements

a chart of elements that include the atomic number and atomic mass

• Provides key information about elements, often indicated by color-coding 

• Arrangement of the table shows how the electrons in each element are organized and provides how atoms will react with each other to form molecules. 

Isotopes

different forms of the same element that have the same number of protons, but a different number of neutrons

Radioactive isotopes

are unstable, losing protons, subatomic particles, or energy to form more stable elements. 

Chemical Bonds

Interactions between two or more of the same or different that result in the formation of molecules. 

• To gain greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by sharing electrons, accepting electrons from another atom, or donating electrons to another atom

Octet Rule

an element can donate, accept, or share electrons with other elements to fill its outer shell 

Ion

atoms that does not contain equal numbers of protons and electrons 

Each has a net charge:

• Positive ions- formed by losing electrons called cations 

Negative ions- formed by gaining electrons, called anions

Electron Transfer

movement of electrons from one element to another

Ionic Bond

positive and negative charges attract, these ions stay together by bonding over the electron from one element staying predominantly with the other element.

Covalent Bond

-formed when an electron is shared between two elements and is the strongest and most common form of chemical bond in living organisms.

-Forms between the elements that make up the biological molecules in our cells.

Covalent vs Ionic

Covalent bonds do not dissociate in water

Non-Polar

form between two atoms of the same element or between different elements that share the electrons equally. 

Ex. Oxygen-Oxygen = covalent bond (2 electrons) to fill outer shell

Nitrogen-Nitrogen=Triple covalent bond (3 electrons)

Polar Covalent

electrons shared by atoms spend more time close to one nucleus than to the other nucleus

• Unequal distribution between different nuclei causes a slightly positive or slightly negative charge.

Ex. Covalent bonds between oxygen and hydrogen atoms in water are polar covalent bonds. The shared electrons spend more time near oxygen nucleus, small negative charge, then they spend near hydrogen nuclei, giving these molecules a small positive charge

Hydrogen Bonds

 two weak bonds that occur frequently

• Attractions between positive and negative charges that do not require much energy to break 

EX. Hydrogen Bond- when polar covalent bonds contain a hydrogen atom form, the hydrogen atom in the bond has a slightly positive charge.(The shared electrons are pulled more strongly to the binding of S+ charge of the hydrogen atom of one molecule and S- of another molecule. (without hydrogen bonding, water would be has and not liquid at room temperature)

• Can form between different molecules and they do not always have to include a water molecule.

• Hydrogen atoms in polar bonds within any molecule can form bonds with adjacent molecules 

• Hydrogen bonds can hold together 2 long strands of DNA, giving double standard structure. Hydrogen is also responsible for proteins' three-dimensional structure.

Van der Waals Interactions

weak attractions between molecules 

• They occur between polar, covalently bonded, atoms in different molecules. 

• Some of these weak attractions are caused by temporary partial changes formed when electrons move around a nucleus. 

• Some of these weak attractions are caused by temporary partial changes formed when electrons move around a nucleus (Important in biological systems 

what bond does hydrogen and oxygen within water form?

polar covalent bonds

• he shared electrons spend more time with oxygen atoms than hydrogen atoms. This creates S+ (H) and S- (O).

• S+ (H) repel each other 

• Each water molecule attracts other water molecules because of the S+ and S- charges in different parts of a molecule. 

Hydrophillic

“water loving”

When a substance readily forms hydrogen bonds with water, it can dissolve in water and it is referred to as hydrophilic. (water loving)

hydrophobic 

When a substance is not readily formed with nonpolar substances like oils and fats

Why does water stabilize temperature?

The hydrogen bonds in water allow it to absorb and release heat energy more slowly than many other substances.

What is the measure of motion within molecules?

Temperature

• As the motion increases, energy is higher, temperature is higher, this disrupts the hydrogen bonds between water molecules. 

• Because these bonds can be created and disrupted rapidly, water absorbs an increase in energy, temperature changes only minimally (water molecules temperature changes in the environment and within organisms)

Evaporation

as energy input continues, the balance between hydrogen-bond formation and destruction, swings more towards the destruction side.

• More bonds are broken than formed, this results in the release of individual water molecules at the surface of the liquid

Ex. Evaporation of sweat, allows cooling of an organism 

If the molecule decreases and temperatures drop, less energy is present to break the hydrogen bonds between water molecules. 

• When bonds remain intact and form a rigid, lattice-like structure, ice forms 

Ex. Ice acts like insulation for animals and plant life in water 

Solvent

a substance capable of dissolving another substance 

• The charged particles will form hydrogen bonds with a surrounding layer of water molecules, referred to as a sphere of hydration, keeping particles separated or dispersed in the water.

**water is an excellent solvent

Cohesion

water molecules are attracted to each other (due to hydrogen bonding), keeping molecules together at gas interface.

Surface Tension

the capacity of a substance to withstand rupture when placed under tension or stress

Adhesion

attraction between water molecules and other molecules

pH

the measure of acidity or basicity 

pH test

measures the amount of hydrogen ions that exists in a given solution 

• High concentration ions yield low pH, low levels of hydrogen ions yield high pH

pH scale

0-14, a change in one unit is a factor of 10, 2 units = 100, etc 

• Pure water is neutral, pH of 7

Acids

substances that provide hydrogen ions and lower pH

Bases

provided hydroxide ions, raise pH

Buffers

absorb excess H+ or OH-, maintaining the body in the right pH range 

• Ex.Carbon Dioxide 

What are the four types of biological compounds?

carbohydrates, nucleic acids, lipids, and proteins

• All of these compounds are composed of different monomers, which can be combined to form unique polymers.

• Ex. protein= amino acid (monomer),when a specific number of them are combined in a certain order, a unique protein is made.

Carbon backbone

the series of carbon atoms bonded together that forms the main structural chain of an organic molecule

Hydroxyl organic compound

•  a hydrogen bound to an oxygen on the carbon backbone 

Carbonyl organic compound

a carbon linked by a double bond to an oxygen

Carboxyl organic compound

a carbon double-bonded to both an oxygen and hydroxyl group.

Amino organic compound

a nitrogen bonded to two hydrogen atoms.

Phosphate organic compound

phosphorus bonded to three oxygen atoms

Simple carbohydrates

compounds containing carbon, hydrogen, and oxygen in exact ratios (CnH2nOn), referred to monosaccharides

Monosaccharides can be combined to form other carbohydrates such as disaccharides, oligosaccharides, and polysaccharides.

what are the three types of monosaccharides?

glucose, fructose, galactose, all with formula C6H12O6, isomers of each other ( no one can be converted into another), They are primarily used as a source of energy production in cells.

Short chain carbohydrates

two classes: disaccharides and oligosaccharides  

All disaccharides are composed of glucose, but each are unique due to the second monosaccharide added to it:

• Lactose (glucose + galactose) present in milk 

• Sucrose (glucose + fructose) transport form of sugar used in plants and harvested by humans for food

• Maltose (two glucose) present in germinating seeds

An oligosaccharide

a short chain of three or more glucose monomers 

• Ex. Raffinose and Stachyose, found in beans

Complex Carbohydrates

long chains of glucose, these chains may be branded or unbranded in their configuration 

1. Polysaccharide- straight or branched chain of hundreds or thousands of sugar monomers. 

2. Starch- plant storage form of energym arranged as un-branched coiled chains, easily hydrolyzed to glucose units. 

3. Cellulose- source of dietary fiber-tough, insoluble-used in plant cell walls. 

4. Pectin- source of dietary fiber, insoluble, used in plant cell walls 

5. Glycogen- a highly branched chain, used by animals to store energy in muscles and liver. 

6. Chitin- specialized polysaccharide with nitrogen attached to glucose units, used as structural material in arthropod exoskeletons and fungal cell walls.

Lipids

greasy/oily compounds with little tendency to dissolve in water (non-polar/hydrophobic) 

• They can be broken down by hydrolysis reactions and created by condensation reactions. 

• Functions in energy storage, membrane structure, and coatings.

Triglycerides

a fatty acid, a long chain of mostly carbon and hydrogen atoms with a carboxyl group at one end.

Saturated (triglycerides) fatty acids

have only single c-c bonds in their fatty acid tails

Fats are formed by the attachment of one (mono), two (di-) or three (tri-) fatty acids to a glycerol.

Unsaturation fatty acids

liquids (oils) at room temperature because one or more double bonds between the carbons in the fatty acids permit “kinks” in the tails. 

It can also have a cis or trans configuration: the double bond in a cis fatty acid can cause the fatty acid to bend, whereas the bond in a trans fatty acid enables the fatty acid to maintain a linear (non-bent) configuration.

what has a rich source of energy, yielding more than twice the per weight basis as carbohydrates + provides an insulation blanket for animals that must endure cold, harsh temperatures. 

Saturated and Unsaturated fatty acids

Phospholipids

composed of two fatty acids and a phosphate group; both bound a carbon backbone referred to as a glycerol. They are the main structural material of cell membranes, arranged in bilayers.

Sterols and their Derivatives

sterols have a backbone of four carbon rings but no fatty acid tails are considered a subgroup of steroids.

Ex. Cholesterol is a sterol and found in plants and animals.

Waxes

 formed by attachment of long-chain fatty acids to long-chain alcohols or carbon rings and serve as coatings for plant parts and as animal coverings.

Proteins

most diverse of all biological molecules 

What are the functions of proteins?

catalysts (enzymes), cell movement, storage and transport agents, hormones, antibodies, structural material

What is the monomer unit of proteins?

amino acid, contains central carbon that binds a hydrogen, an amino group, a carboxyl group, and one of twenty varying R groups.

Polypeptides

polymers of amino acids, reflect special peptide bonds that form between the amino acids.

What are the four levels of organization?

1. Primary structure- ordered sequences of amino acids each linked together by peptide bonds to form polypeptide chains. 

2. Secondary Structure- helical coil (hemoglobin) or sheet-like array (as in silk) that results from hydrogen bonding of side groups on the amino acid chains. 

3. Tertiary Structure- result of folding due to interactions among R groups along the polypeptide chain, sometimes called “supercoiling”

4. Quaternary Structure- describes the twisting of two or more polypeptide chains. 

Denaturation

process of changing protein three-dimensional structure due to changes in protein’s biochemical and thermal environment.

Nucleic Acids

DNA (Deoxyribonucleic acid) and RNA (Ribonucleic Acid) are polymers of nucleotides, which are composed of three units:

• 5- carbon sugar (ribose or deoxyribose)

• A nitrogen-containing base 

• A phosphate group

What are the four bases in DNA

Adenine

Cytosine 

Guanine 

Thymine (RNA uses Uracil)

What gives DNA’s helical shape?

two polynucleotide chains that are hydrogen bonded together

• Hydrogen bonding occurs as a result of specific complementary pairing of nucleotide bases.