Solutions with dissolved substances such as glucose, CO2, O2, ect.
takes cells apart and separates the major organelles from one another
-centrifuges and enables scientists to determine the functions of organelles
the shape dictates the function
Order and work requires energy
external energy must be converted into usable forms
Central DOgma of Molecule Biology
Plasma Membrane Comp and Func:
Phospholipid bilayer with embedded proteins
Selective passage of molecules into and out of cell
Nucleus comp and func:
Nuclear envelope surrounding nucleoplasm, chromatin, and nucleolus
Storage of genetic information
Nucleolus comp and func:
Located within nucleus
Concentrated area of chromatin, RNA, and proteins
Site for ribosome synthesis
Ribosome comp and func:
Protein and RNA in two subunits
Endoplasmic reticulum comp and func:
Membranous saccules and canals
Synthesis and/or modification of proteins and other substances, and transport by vesicle formation
Smooth ER comp and func:
Having no ribosomes
Various; lipid synthesis in some cells
Golgi apparatus comp and func:
Stack of membranous saccules
Processing, packaging, and distribution of molecules
Vacuole and vesicle comp and func:
Storage and transport of substances
Lysosome comp and func:
Membranous vesicle containing digestive enzymes
Mitochondrion comp and func:
Inner membrane(with cristae) within outer membrane
Cytoskeleton comp and func:
Microtubules, actin filaments, and intermediate filaments
Shape of cell and movement of its parts
Cilia and flagella comp and func:
pattern of microtubules
Movement of cell
Centriole comp and func:
pattern of microtubules
Formation of basal bodies
the ratio of an object's image size to its real size
The measure of the clarity of the image or the minimum distance of two distinguishable points
Visible differences in parts of the sample
Total surface area equation:
(height x width) x sides x number of boxes
Total volume equation:
Height x width x length x number of boxes
Surface to volume ratio equation
surface area / volume
Differential Interference Contrast
Who came up with the term cells and when?
Robert Hook 1665
First person to see "animalcules" under the microscope and when?
Van Leeuwennhoek, 1674
A molecule that releases a proton when dissolved in water; this dissociation generates hydronium(H30+) ions, thereby lowering the pH.
Functional group (-NH2)
Can accept a proton and carry a positive charge in aqueous solution.
The smallest particle of an element that still retains its distinctive chemical properties; consists of a positively charged nucleus surrounded by a cloud of negatively charged electrons
Molecule that serves as the principal carrier of energy in cells; this nucleoside triphosphate is composed of adenine, ribose, and three phosphate groups
The number of molecules in a mole, the quantity of a substance equal to its molecular weight in grams; approximately 6x10^23
Molecule that accepts a proton when dissolved in water; also used to refer to the nitrogen-containing purines or pyrimidine's in DNA and RNA
Mixture of weak acids and bases that maintains the pH of a solution by releasing and taking up protons
An exchange of electrons that holds two atoms together. Types found in living cells include ionic bonds, covalent bonds, and hydrogen bonds.
Combination of atoms, such as a hydroxyl group (-OH) or an amino group (-NH2), with distinct chemical and physical properties that influences the behavior of the molecule in which it resides
Chemical reaction in which a covalent bond is formed between two molecules as water is expelled; used to build polymers, such as proteins, polysaccharides, and nucleic acids.
Precise, three-dimensional shape of a protein or other macromoluecule, based on the spatial location of its atoms in relation to one another
Stable chemical link between two atoms produced by sharing one or more pairs of electrons
Double-stranded polynucleotide formed from two separate chains of covalently linked deoxyribonucleotide units. It serves as the cell's store of genetic information that is transmitted from generation to generation.
Negatively charged subatomic particle that occupies space around an atomic nucleus
Force that draws together oppositely charged atoms. Examples include ionic bonds and the attractions between molecules containing polar covalent bonds
Molecule that consists of a carboxylic acid attached to a long hydrocarbon chain. Used as a major source of energy during metabolism and as a starting point for the synthesis of phospholipids.
A weak noncovalent interaction between a positively charged hydrogen atom in one molecule and a negatively charged atom, such as nitrogen or oxygen, in another; these interactions are key to the structure and properties of water
Chemical rxn that involves cleavage of a covalent bond with the accompanying consumption of water
The form taken by a proton (H+) in aqueous solution
Molecule or part of a molecule that readily forms hydrogen bonds with water, allowing it to dissolve; literally, "water loving"
Nonpolar, uncharged molecule or part of a molecule that forms few or no hydrogen bonds with water molecules and therefore does not dissolve; "water fearing"
Type of noncovalent bond that forces together the hydrophobic portions of dissolved molecules to minimize their disruption of the hydrogen-bonded network of water; helps push together membrane phospholipids and fold proteins into a compact, globular shape
Not composed of carbon and hydrogen
An atom carrying an electrical charge, either positive or negative
Interaction formed when one atom donates electrons to another; this transfer of electrons causes both atoms to become electrically charged
Organic molecule that is insoluble in water but dissolves readily in nonpolar organic solvents; typically contains long hydrocarbon chains or multiple rings.
Thin pair of closely juxtaposed sheets, composed mainly of phospholipid molecules, that forms the structural basis for all cell membranes
Polymer built from covalently linked subunits; includes proteins, nucleic acids, and polysaccharides with a molecular mass greater than a few thousand daltons
Group of atoms joined together by covalent bonds
Sum of the atomic weights of the atoms in a molecule; as a ratio of molecular masses, it is a number without units.
Small molecule that can be linked to others of a similar type to form a larger molecule (polymer)
Chemical association that does not involve th sharing of electrons; singly are relatively weak, but can sum together to produce strong, highly specific interactions between molecules. Examples are hydrogen bonds and van der Waals attractions
Basic building block of the nucleic acids, DNA and RNA; includes a nucleoside with a series of one or more phosphate groups linked to its sugar
Chemical compound that contains carbon and hydrogen
Concentration of hydrogen ions in a solution, expressed as a logarithm. Thus, an acidic solution with pH3 will contain 10^-3 M hydrogen ions
In chemistry, describes a molecule or bond in which electrons are distributed unevenly
Long molecule made by covalently linking multiple identical or similar subunits (monomers).
Polymer built from amino acids that provides cells with their shape and structure and performs most of their activities
Positively charged particle found in the nucleus of every atom; also, another name for a hydrogen ion (H+)
Molecule produced by the transcription of DNA
usually single-stranded, it is a poluculeotide composed of covalently linked ribonucleotide subunits.
The linear order of monomers in a large molecule, for example amino acids in a protein or nucleotides in DNA; encodes info that specifies a macromolecules's precise biological func.
A monomer that forms par of a larger molecule, such as an amino acid residue in a protein or a nucleotide residue in a nucleic acid.
A substance made of carbon, hydrogen, and oxygen with a general formula(CH20)n.
van der Waals attractions
Weak noncovalent interaction, due to fluctuating electrical charges, that comes into play between two atoms within a short distance of each other
Activated carrier that donates the carbon atoms in its readily transferable acetyl group to many metabolic rxns, including the citric acid cycle and fatty acid biosynthesis; the acetyl group is linked to coenzyme A by a thioester bond that releases a large amount of energy when hydrolyzed
A small molecule that stores energy or chemical groups in a form that can be donated to many different metabolic rxns.
The energy that must be acquired by a molecule to undergo a chemical rxn
Set of metabolic pathways by which large molecules are made from smaller ones
An enzyme-catalyzed process by which complex molecules are formed from simple substances by living cells; also called anabolism
Set of enzyme-catalyzed reactions by which complex molecules are degraded to simpler ones with release of energy.
Substance that accelerates a chemical rxn brought about by the action of a catalyst; virtually all rxns in a cell require such assistance to occur under conditions present in living organisms
Substance that accelerates a chemical rxn by lowering its activation energy; enzymes perform this role in cells
Chemical reaction in which a covalent bond is formed between two molecules as water is expelled; used to build polymers, such as proteins, polysaccharides, and nucleic acids
Linked pair of chemical rxns in which free energy released by one rxn serves to drive the other rxn
Process by which molecules and small particles move from one location to another by random, thermally driven motion
Thermodynamic quantity that measures the degree of disorder in a system
All transfers increase disorder to the universe
A protein that catalyzes a specific chemical rxn
State in which the forward and reverse rates of a chemical rxn are equal so that no net chemical change occurs
Equilibrium constant, K
For a reversible chemical rxn, the ratio of substrate to product when the rates of the forward and reverse rxns are equal
Free energy, G
Energy that can be harnessed to do work, such as driving a chemical rxn
free-energy change, changeG
in a chemical rxn, the difference in free energy between reactant and product molecules.
Large neg vaule of G = strong tendency to occur
Measurement of concentration, temperature and pressure
Chemical rxn that involves cleavage of a covalent bond with the accompanying consumption of water
The sum total of the chemical rxns that take place in the cells of a living organism
Concentration of substrate at which an enzyme works at half its maximum velocity; serves as a measure of how tightly the substrate is bound
Removal of electrons from an atom, as occurs during the addition of oxygen to a carbon atom or when a hydrogen is removed from a carbon atom
The process by which plants, algae, and some bacteria use the energy of sunlight to drive the synthesis of organic molecules from carbon dioxide and water
Addition of electrons to an atom, as occurs during the addition of hydrogen to a carbon atom or the removal of oxygen from it
General term for any process in a cell in which the uptake of molecular oxygen is coupled to the production of CO2
Standard free-energy change
A molecule on which an enzyme acts
The number of substrate molecules an enzyme can convert into product per second
The process of making polymers
what creates order to the universe?
What do you call a polysaccharide linkage?
Amino Acids make?
Simple Sugars make:
Fatty acids make:
What is a lipid linkage called?
What is the special bond in phospholipids?
What are the two ways a phospholipid form?
Name for when something is both hydrophobic and hydrophilic
What prevents our cells from freezing in the winter?
monosaturated fatty acid
Special structure of steriods
4 fused rings
Why is ATP such a great energy source?
Because it has 3 negative energies, readily wants to repel them
Nonpolar Amino acids
Uncharged polar amino acids
Positively charged amino acids
Negatively charged amino acids
Amino acids form what type of bond?
Amino acid functions
* Peptide bonds
* Bacterial cell walls
* Signal molecule in brain
Amino Acids Bond Types:
Amino Acid structure
Amino Acids Polymer
Nucleotides Bond Types
Monosaccharides bonding type
Production & storage of energy
Plant cell walls
slime & mucus
Fatty Acids polymers, but not a polymer
Fatty Acids function
primary building block of all membranes
Fatty acids bond type
Composed of Carbohydrates: cellulose or chitin
Involved in hydrogen peroxide synthesis and degradation
site of photosynthesis
Series of chemical rxns involved in storing (anabolism) or releasing (catabolism) energy
Anaerobic process in cytoplasm in which glucose, a 6 carbon compound, is oxidized to two pyruvates, which are both three carbon chains
Aerobic process that oxidizes pyruvates to CO2
1. to be preserved and transmitted
2. to control various biological functions through the production of proteins and RNA
the components of nucleic acids, three subunits
3. Nitrogenous base
How many different proteins are there?
an enzyme that oxidizes a substrate by a reduction rxn that transfers one or more hydrides (H-) to an electron acceptor
a physical system which doesn't exchange any matter with its surroundings, and isn't subject to any force whose source is external to the system
a system which continuously interacts with its environment or surroundings
the study of how organisms manage their energy resources
The Chemistry of Lie is organized into Metabolic Pathways
Metabolism: totality of an organisms chem rxns
Metabolic Pathway: begins w/a specific molecule and ends w/a product
3 kinds of kinetic energy
the capacity to cause change
Potential energy is:
energy that matter possesses because of its location or structure
Types of potential energy:
The 5 Laws of Energy Transformation
2. Isolated system
3. Open system
4. Organisms are open systems
5. These laws apply to the universe as a whole
2 Laws of Thermodynamics
1. Law of Conservation of Energy
Law of Conservation of Energy
1. The energy of the universe is constant
-energy can be transferred and transformed from one form to another, cannot be created or destroyed
2. Implication-must account for source and fate of all energy in biological systems
Law of Entropy
During every energy transfer or transformation, some energy becomes unusable, often lost as heat.
-Every transfer or transformation increases disorder(entropy)
-Entropy tends to increase in closed systems
-for a process to occur spontaneously, it must increase the entropy of the universe
Energy flows into an ___________ in the form of _________ and exits in the form of _________
Cells create ordered __________ from less ordered ______
Organisms replace ordered forms of ________ and _______ with less ordered forms
The evolution of more complex organisms does not violate the ____ ___ __ ___________
second law of thermodynamics
Oxidation/Reduction Rxn Definition:
The transfer of partial transfer of an electron from one atom to another
Photosynthesis energy input and output
Cellular Respirations energy inputs and outputs
Glucose->CO2 & heat
What does ATP do after created from cellular respiration?
Cellular work and heat
What products become oxidized and reduced in this equation:
CH4 + 2O2 = CO2 + energy + 2H2O
Oxidized: CH4 -> CO2
Reduced: 2O2 ->2 H2O
2 of the most stable molecules(as in oxidization/reduction)
How does a exergonic rxn proceed?
with a net release of free energy and is spontaneous
How does an endergonic rxn proceed?
absorbs free energy from its surroundings and is nonspontaneous
Free energy chemical rxns proceed.....
in direction that causes a loss in free energy which increases in net disorder
Gibbs Free energy is
a measure of a system's total energy available to do work, w/o reference to the surroundings
Endergonic=positive G=is the rxn spontaneous or not
Exergonic=negative G=is the rxn spontaneous or not
When the net change of G is negative, the rxns are spontaneous
In a Na Cl rxn what gets oxidized and what gets reduced. Also which is negative ion and which is the positive ion?
Na+ is the positive ion that gets oxidized
Cl- is the negative ion that gets reduced
Rxns in a ______ system eventually reach _______ and then do _ _____
Cells are ___ in ________; they are ____ systems experiencing a constant flow of materials
not in equilibrium
A defining feature of life is that ________ is never at __________
A ________ pathway in a cell releases ______ _______ in a series of rxns
ATP powers cellular work by coupling __________ rxns to __________ rxns
3 main kinds of work a cell does
To do work, cells manage energy resources by ________ _________
Most energy coupling in cells is mediated by ___
Why is there so much energy in ATP?
the negative charges don't like being so close
What can break the phosphate bonds in ATP?
WHen is energy released from ATP?
when the terminal phosphate bond is broken
Where does the energy come from when the phosphate bond in ATP is broken?
chemical change to a state of lower free energy
What happens when change in G=0?
3 high energy electron carriers:
1. NAD+ -> NADH
2. NADP+ -> NADPH
3. FAD -> FADH2
________ speed up metabolic rxns by __________ energy barriers
A chemical agent that speeds up a reaction without being consumed by the reaction
A catalytic protein
The initial energy needed to start a chemical rxn is called:
__________ ___________ is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings
Nonprotein enzyme helpers
An organic cofactor is called a:
What randomness does coenzymes include?
What binds to the active site of an enzyme, competing with the substrate?
What binds to ANOTHER part of an enzyme to change shape and make the active site less effective?
What are some examples of inhibitors?
toxin, poisons, pesticides and antibiotics
________ _____ store, transmit, and help express hereditary information
The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a:
______ are made of DNA
Nucleic acid made of monomers called:
_____ provides directions for its own replication
DNA directs synthesis of ______ and through _____ controls protein synthesis
What do nucleic acids do?
store & transmit hereditary information
regulate gene expression
What are the two super charged molecules in DNA & RNA that repel each other?
Phosphate group & Nitrogenous base
Enzymatic Protein func and ex
Selective acceleration of chem rxns
EX: digestive enzymes catalyze the hydrolysis of bonds in food molecules
Defensive proteins func & ex
Protection against disease
ex: antibodies inactivate and help destroy viruses and bacteria
Storage proteins func & ex
Storage of amino acids
ex: Plants of storage proteins in their seeds
Transport proteins func & ex:
Transport of substances
ex: hemoglobin, iron protein->oxygen from lungs to body
Hormonal Protein func & ex
Coordination of an organism's activities
ex: insulin, causes other tissues to up take glucose which regulates blood sugar concentration
Receptor Proteins func & ex
Response of cell to chemical stimuli
Ex: built into membrane of nerve cell detect signaling molecules released by other nerve cells
Contractile and motor proteins func & ex
ex: actin and myosin proteins are responsible for the contraction of muscles
Structural proteins func & ex:
Keratin, collagen, elastin and silk fibers
What do you call a polysaccharide(carbohydrates) linkage?
What do you call a lipid linkage?
What do call a nucleic acid linkage?
What do you call a amino acid linkage?
4 basic monomers
How do you form a peptide bond?
OH and H of two amino acids and connect the C and N together
The four bonds involved in the folding and maintence of proteins:
Van der Waals
The final folded structure of a protein is called:
When a protein refolds spontaneously to its original conformation after its been denatured
Molecule that steers proteins along productive folding pathways, helping them to fold correctly and preventing them from forming aggregates inside the cell
The primary structure of a protein:
Amino acid sequence
Secondary Structure of a protein:
Folds that form in certain segments of the polypeptide chain
Tertiary Structure of the protein:
full, three-dimensional conformation of the entire polypeptide chain
Quarternary Structure of a protein:
More than one polypeptide chain
regions of polypeptide chain lacking any definite structure
intrinsically disordered sequences
Shape name in which the polypeptide chain folds up into a compact shape like a ball with an irregular surface
Shape name for protein that have a relatively simple, elongated three-dimensional structure
Most abundant fibrous protein
A substance that is bound by a protein
Region of a protein that associates with a ligand
Enzymes that catalyze a hydrolytic cleavage rxn
Enzyme class that breaks down nucleic acids by hydrolyzing bonds btwn nucleotides
Enzyme class that breaks down proteins by hydrolyzing peptide bonds btwn amino acids
Enzyme class that joins two molecules together
Enzyme class that catalyzes the rearrangement of bonds within a single molecule
Enzyme class that catalyzes polymerization reactions such as the synthesis of DNA and RNA
Enzyme class that catalyzes the addition of phosphate groups to molecules
Enzyme class that catalyzes the hydrolytic removal of a phosphate group from a molecule
Enzyme class tha catalyze rxns in which one molecule is oxidized white the other is reduced