Chapter 2- Chemical level of organization Flashcards
Matter
Anything that occupies space and has mass
-The substance of the universe -from a grain of sand to a star
Element
A pure substance that is distinguished from all other matter by the fact that it cannot be created or broken down by ordinary chemical means
-All matter in the natural world is composed of one or more of the 92 fundamental substances called elements
Compound
A substance composed of two or more elements joined by chemical bonds
-Elements combine to form compounds
ex: the compound glucose is composed of carbon, hydrogen, and oxygen
Atom
The smallest quantity of an element that retains the unique properties of that element
ex: An atom of hydrogen is a unit of hydrogen
What are atoms made up of?
Three subatomic particles:
proton
neutron
electron
What gives mass to the atom?
The number of positively- charged protons and non-charged (neutral) neutrons
What equals the number of protons?
The number of negatively-charged electrons that “spin” around the nucleus at close to the speed of light
An electron has about _____ the mass of a proton or neutron
1/2000th
(An element’s) Atomic number
The number of protons in the nucleus of the atom, identifies the element
(An element’s) Mass number
The sum of the number of protons and neutrons in the nucleus
Periodic table of elements
A chart identifying the 92 elements found in nature, as well as several larger, unstable elements discovered experimentally
Istotope
One of the different forms of an element, distinguished from one another by different number of neutrons
Electron shell
A layer of electrons that encircle the nucleus at a distinct energy level
Valence shell
An atom’s outermost electron shell
-If the v shell is full, the atom is stable; its electrons are unlikely to be pulled away from the nucleus by the electrical charge of other atoms
-If the v shell is not full the atom is reactive; it will tend to react with other atoms in ways that make the v shell full
ex: hydrogen with its one electron only half-filling its v shell. This single electron is likely to be drawn into relatiosnhips w the atoms of other elemtns, so that hydrogen’s single v shell can be stabilized
Chemical bond
Atoms link by forming a chemical bond
A bond is a weak or strong electrical attraction that holds atoms in the same vicinity
Ion
An atom that has an electrical charge - whether positive or negative
Cation
A positively charged ion
Anion
A negatively charged ion
Ionic bond
An ongoing, close association betweens ions of opposite charge
-Formed by the attraction between a cation’s positive chargr and an anion’s negative charge
Covalent bond
Molecules formed by a CB share electrons in a mutually stabilizing relationship
ex: The atoms do not lose or gain electrons permanently, instead the electrons move back and forth between the elements
Why are covalent bonds stronger than ionic bonds?
Because of the close sharing of pairs of electrons (one electron from each of two atoms)
Nonpolar covalent bond
Covalently bonded molecules that are electrically balanced. No region of the molecule is either more positive or more negative than any other
Nonpolar molecules
Molecules that do not have any electrical charges or partial charges
-Made of atoms that have a similar value of electronegativity (the tendency of an atom to attract electrons)
Polar covalent bond
Exists when atoms with different electronegativities share electrons in a covalent bond
Polar molecule
A molecule that contains regions that have opposite electrical charges
-Occurs when atoms share electrons unequally, in polar covalent bonds
Hydrogen bond
Formed when a weakly positive hydrogen atom already bonded to one electronegative atom ( ex: the o2 in the water molecule) is attracted to another electronegative atom from another molecule
-In other words, hydrogen bonds always include hydrogen that is already part of a polar molecule
Kinetic energy
Is the form of energy powering any type of matter in motion
ex: You are building a brick wall. The energy it takes to lift and place one brick atop the other is KE- the energy matter possesses because of its motion…..once the wall is in place it starts potential energy….
Potential energy
The energy of position, or the energy matter possesses because of the positioning or structure of its components
-If the brick wall collapses, the stored potential energy is released as kinetic energy as the bricks fall
Chemical energy
The form of potential energy in which energy is stored in chemical bonds
Reactant
All chemical reactions begin with a reactant, the general term for the one or more substances that enter into the reaction
ex: sodium and chloride ions are the reactants in the production of table salt
Product
The one or more substances produced by a chemical reaction
Synthesis reaction
A chemical reaction that results in the synthesis (joining) of components that were formerly seperate
-Two components bond to make a larger molecule
Energy is required and is stored in the bond
ex: A+B—–> AB
ex: NOTE + BOOK —–> NOTEBOOK
Decomposition reaction
A chemical reaction that breaks down or “de-composes” something larger into its consituent parts.
Bonds between components of a larger molecule are broken, resulting in smaller products
Ex: AB—-> A + B
ex: BOOKWORM —–> BOOK + WORM
In this example, ammonia is catabolized into its smaller components , and the potential energy that had been stored in its bond is released
Exchange reaction
A chemical reaction in which both synthesis and decomposition occur, chemical bonds are both formed and broken, and chemical energy is absorbed, stored, and released.
- Bonds are both formed and broken such that the components of the reactants are rearranged
NOTEBOOK+ WORM—–> NOTE + BOOKWORM
The simplest form of an exchange reaction might be: A + BC—-> AB + C
Notice that to produce these products, B and C had to break apart in a decomposition reaction, whereas A and B had to bond in a synthesis reaction
A more complex exchange reaction might be AB+CD—> AC + BD or AB+CD —> AD+BC
Reactant concentration
Chemists can speed up chemical reactions not only by increasing the concentration of particles- the number of particles in the space- but also by decreasing the volume of the space, which would correspondingly increase the pressure.
ex: If there were 100 dancersin that club, and the manager abruptly moved the party to a room half the size, the concentration of the dancers would double in new space, and the likelihood of conditions would increase accordingly
Catalyst
A substance that increases the rate of a chemical reaction without itself undergoing any change
-Think of a catalyst as a chemical change agent
-They help increase the the rate and force at which atoms, ions, and molecules collide, thereby increasing the probability that their valence shell electrons will interact
Enzyme
A catalyst composed of protein or ribonucleic acid (RNA)
-The most important catalysts in the human body
-Like all catalysts, enzymes work by lowering the level of energy that needs to be invested in a chemical reaction
Activation energy
A chemical reaction’s activation energy is the “threshold” level of energy needed to break the bonds in the reactants.
-Once those bonds are broken, new arrangements can form. Without an enzyme to act as a catalyst, a much larger investment of energy is needed to ignite a cheical reaction
Inorganic compound
A substance that does not contain both carbon and hydrogen.
Organic compound
A substance that contains both carbon and hydrogen
-Synthesized via covalent bonds within living organisms, including the human body
Solution
For cells in the body to survuve, they must be kept moist in a water-based liquid called a solution
Consists of a solvent that dissolves a substance called a solute
Solvent
Able to dissolve other substances
The liquid in which a solute is dissolved to form a solution
Solute
The minor component in a solution, dissolved in the solvent
Colloid
A mixture that is somewhat like a heavy solution.
The solute particles consist of tiny clumps of molecules large enough to make the liquid texture opaque (because the particles are large enough to scatter light).
Ex: Familiar examples of colloids are milk and cream.
Ex: In the thyroid glands, the thyroid harmone is stored as a thick protein mixture also called a colloid
Suspension
A liquid mixture in which a heavier substance is suspended temporarily in liquid, but over time, settles out.
Sedimentation
The seperation of particles from a suspension
Salts
Formed when ions form ionic bonds
Acid
A substance that releases hydrogen ions (H+) in solution
Base
A substance that releases hydroxyl ions (OH-) in solution, or one that accepts H+ already present in solution
pH
The negative, base-10 logarithm of the hydrogen ion (H+) concentration of the solution
-The relative acidity or alkalinity of a solution can be indicated by its pH
Buffer
A solution of a weak acid and its conjugate base
-Can neutralize small amounts of acids or bases in bodily fluids
Functional group (of an organic compound)
A group of atoms linked by strong covalent bonds and tending to function in chemical reactions as a single unit
Ex: Tightly knit “cliques” whose members are unlikely to be parted
What are the 5 functional groups in human physiology?
Hydroxyl
Carboxyl
Amino
Methyl
Phosphate
Hydroxyl Group
Polar.
Components of all 4 types of organic compounds discussed in this chapter.
They are involved in dehydration synthesis and hydrolysis reactions
-O-H
Carboxyl Group
Found within fatty acids, amino acids, and many other acids
Check book for structural formula
Amino Group
Found within amino acids, the building blocks of proteins
-N-H2 (lowercase 2)
Methyl Group
Found within amino acids
-C-H3 (lowercase 3)
Phosphate Group
Found within phopholipids and nucleotides
Check book for structural formula
Macromolecule
Any large molecule`
Monomer
Macromolecules made up of several copies of single units
Polymers
Monomers link by covalent bonds to form polymers
Monomers form polymers by?
Engaging in dehydrated synthesis
Polymers are split into monomers by
Hydrolysis
Dehydration synthesis
Monomers form polymers.
This reaction results in the release of a molecule of water
Each monomer contributes: One gives up a hydrogen atom and the other gives up a hydroxyl group
Hydrolysis
Polymers are split into monomers
The bonds between the monomers are broken, via the donation of a molecule of water, which contributes a hydrogen atom to one monomer and one hydroxyl group to the other
Carbohydrate
A molecule composed of carbon, hydrogen, and oxygen; in most carbohydrates, hydrogen and oxygen are found in the same two-to-one relative proportions they have in water
Three kinds of carbohydrates “saccharides” (“sugars”)
Monosaccharides
Disaccharides
Polysaccharides
Monosaccharides
Monomers of carbohydrates
Disaccharides
A pair of monosaccharides
Made up of two monomers
Formed via dehydration synthesis, and the bond linking them is referred to as a glycosidic bond.
Polysaccharides
The polymers and can consist of hundreds to thousands of monomers
Adenosine triphosphate (ATP)
Composed of a ribose sugar, an adenine base, and three phosphate groups
Releases free energy when its phophate bonds are broken, and thus supplies ready energy to the cell
Lipid
One of the highly diverse groups of compounds made up mostly of hydrocarbons
Triglyceride
One of the most common dietary lipid groups, and the type found most abundantly in body tissues.
This compound, referred to as fat, is formed from the synthesis of two types of molecules
Glycerol
A glycerol backbone at the core of triglycerides, consists of three carbon atoms
Fatty Acid
Three fatty acids, long chains of hydrocarbons with a carboxyl group and a methyl group at opposite ends, extend from each of the carbons of the glycerol
Phospholipid
A bond between the glycerol component of a lipid and a phosphorus molecule.
Prostaglandin
One of a group of signaling molecules, but prostaglandins are derived from unsaturated fatty acids.
Protein
An organic molecule composed of amino acids linked by peptide bonds
Critical components of all tissues and organs
Amino Acid
A molecule composed of an amino group and a carboxyl group, together with a variable side chain
20 different amino acids contribute to nearly all of the thousands of different proteins important in human structure and function
Peptide bond
A covalent bond between two amino acids that forms by dehydration synthesis
A peptide is a very short chain of amino acids
Polypeptide
Strands containing fewer than about 100 amino acids are generally referred to as polypeptides rather than proteins
Denaturation
A change in the structure of a molecule through physical or chemical means
When they are exposed to heat, acids, bases, and certain other substances, proteins will denature
Example of protein denaturation: The curdling of milk when acidic lemon juice is added
Substrate
A reactant in an enzymatic reaction. This occurs on regions of the enzyme known as active sites.
Enzyme-substrate complex
Binding of a substrate produces an enxyme-substrate complex
Nucleotide
The fourth type of organic compound important to human structure and function
A nucleotide is one of a class of organic compounds composed of three subunits
Can be assembled into nucleic acids (DNA or RNA) or the energy compound adenosine triphosphate
A nucleotide is one of a class of organic compounds composed of what three units?
- One or more phosphate groups
- A pentose sugar: either deoxyribose or ribose
-A nitrogen-containing base: adenine, cytosine, guanine, thymine, or uracil
Deoxyribonucleic acid (DNA)
Is nucleotide that stores genetic information
Contains deoxyribose (so-called because it has one less atom of oxygen than ribose) plus one phosphate group and one nitrogen-containing base
The nucleic acids differ in their type of ____ _____
Pentose sugar
The building blocks of all nucleotides are________
One or more phosphate groups
A pentose sugaar
A nitrogen containing base
Ribonucleic acid (RNA)
A ribose- containing nucleotide that helps manifest the genetic codes as protein
RNA contians ribose, one phosphate group, and one nitrogen containing base, but the “choices” of base for RNA are adenine, cytosine, guanine, and uracil
Purine
A nitrogen-containing molecule with a double ring structure, which accommodates several nitrogen atoms
The nitrogen-containing bases adenine and guanine are classified as purines
Pyramidine
A nitrogen-containing base with a single ring structure
The bases cytosine, thymine (found in DNA only) and uracil (found in RNA only) are pyramidines
Phosphorylation
The addition of a phosphate group to an organic compound, in this case, resulting in ATP
Mass
The quantity of matter in an
object
On Earth, mass = weight
Solid
Maintain volume and shape at ordinary temp and pressure
Liquid
Maintain volume, but not fixed shape
Gas
Does NOT maintain volume or shape
What are chemicals composed of?
Atoms
Atom
Smallest stable unit of matter
Composed of subatomic particles
Water
Only substance that exists in all three states of matter
at temperatures compatible with life
-Solid (ice)
- Liquid (water)
Exists over a broad range of temperatures due to interactions among the
polar water molecules
-Gas (water vapor)
Nucleus
The nucleus of an atom lies at its center.
Contains one or more protons and it may contain neutrons as well.
The mass of the atom is primarily determined by the numbers of protons and neutrons in the nucleus
Electron Cloud
The electrons in the atom whirl around the nucleus, creating an electron cloud
Molecule
When atoms interact, they
produce larger, more
complex structures called
molecules
All matter composed of
varying arrangements of
atoms
Variation in matter
characteristics results from
types of atoms and ways
they interact
4 categories of organic compounds important to the human body
Carbohydrates
Lipids
Proteins
Nucleic Acids
Metabolic pathway
Series of complex reactions occurring in the body
Each reaction interlocking with next
step
Each reaction controlled by specific
enzyme
May absorb or release energy on
completion (exergonic or endergonic)
