Cell Biology 1st exam-def.

• Every cell in the body has the same DNA
• Different cells express different subset

Plasma Membrane

yeast

• Ribosomes
• protein synthesis

• no ribosomes
• lipid synthesis
• Ca2+ storage

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

DNA->RNA->Proteins

• Phospholipid bilayer with embedded proteins
• Selective passage of molecules into and out of cell

• Nuclear envelope surrounding nucleoplasm, chromatin, and nucleolus
• Storage of genetic information

• Located within nucleus
• Concentrated area of chromatin, RNA, and proteins
• Site for ribosome synthesis

• Protein and RNA in two subunits
• Protein synthesis

• Membranous saccules and canals
• Synthesis and/or modification of proteins and other substances, and transport by vesicle formation

• Having no ribosomes
• Various; lipid synthesis in some cells

• Stack of membranous saccules
• Processing, packaging, and distribution of molecules

• membranous sacs
• Storage and transport of substances

• Membranous vesicle containing digestive enzymes
• Intracellular digestion

• Inner membrane(with cristae) within outer membrane
• Cellular respiration

• Microtubules, actin filaments, and intermediate filaments
• Shape of cell and movement of its parts

• pattern of microtubules
• Movement of cell

• 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

(height x width) x sides x number of boxes

Height x width x length x number of boxes

surface area / volume

Brightfield Stained

Brightfield unstained

Confocal

Deconvolution

Differential Interference Contrast

Electron Microscopy

Fluorescence

Phase contrast

Super-resolution

Robert Hook 1665

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

• Adenosine 5-triphosphate
• 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

• Deoxyribonucleic Acid
• 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+)

• Ribonucleic Acid
• 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.

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

• Adenosine diphosphate
• Adenosine triphosphate

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

For a reversible chemical rxn, the ratio of substrate to product when the rates of the forward and reverse rxns are equal

Energy that can be harnessed to do work, such as driving a chemical rxn

• 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

A molecule on which an enzyme acts

The number of substrate molecules an enzyme can convert into product per second

polymerication

Thermal Dynamic

Glycosidic Linkage

Proteins

• Nucleic Acid
• DNA
• RNA

• Carbohydrates
• saccharides

• Lipids
• glycerol
• steroids
• cholesterol

Ester Linkage

Phosphate bond

• Micelle
• Bilayer

Ampaphatic

• monosaturated fatty acid
• Cholesterol signalers

4 fused rings

Phosphodiester Linkage

Because it has 3 negative energies, readily wants to repel them

Adenine

cytosine

guanine

thymine

• Thymine
• Cytosine

• Adenine
• Guanine

• Alanine
• Leucine
• Isoleucine
• Proline
• Cysteine
• Methionine
• Phenylalanine
• Tryptophan
• Glycine
• Valine

• Asparagine
• Serine
• Threonine
• Tyrosine
• Glutamine

• Histidine
• Lysine
• Arginine

• Aspartic Acid
• Glutamic Acid

Peptide bond

• * proteins
• * Peptide bonds
• * Bacterial cell walls
• * Antibiotics
• * Signal molecule in brain

• Peptide Bond
• Polar Covalent
• Condensation

N-C-COOH

Proteins

• DNA
• RNA
• ATP

• Phosphodiester Linkage
• Covalent
• Hydrogen bonding

• Nucleic Acid
• DNA
• RNA

• Glycosidic Linkage
• Covalent
• Hydrogen Bonding

• (CH(2)O)n
• N=3,4,5,6
• Isomers
• Ring formations

• Carbohydrates
• Disaccharides
• Oligosaccharides
• POlysaccharides

• Production & storage of energy
• Plant cell walls
• insect exoskeletons
• slime & mucus
• Plasma Membrane

• Fats
• membrane lipids
• phospholipids
• triacylglycerols
• Steroids
• Cholesterol

• primary building block of all membranes
• energy source

• Ester Linkage
• Amphipathic

Composed of Carbohydrates: cellulose or chitin

Involved in hydrogen peroxide synthesis and degradation

site of photosynthesis

non-green pigments

Stores starch

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

• DNA
• RNA

• the components of nucleic acids, three subunits
• 1. Sugar
• 2. Phosphate
• 3. Nitrogenous base

over 30,000

• Anabolic
• creates order
• requires energy

• Catabolic
• breaks down,

release energy

an enzyme that oxidizes a substrate by a reduction rxn that transfers one or more hydrides (H-) to an electron acceptor

ATP

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

Metabolism: totality of an organisms chem rxns

Metabolic Pathway: begins w/a specific molecule and ends w/a product

• -movement
• -thermal energy
• -light energy

the capacity to cause change

energy that matter possesses because of its location or structure

• -Chemical energy
• -Positional energy

• 1. Thermodynamics
• 2. Isolated system
• 3. Open system 
• 4. Organisms are open systems
• 5. These laws apply to the universe as a whole

1. 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

• 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

• ecosystem
• light
• heat

• structures
• materials

• Matter
• Energy

second law of thermodynamics

The transfer of partial transfer of an electron from one atom to another

• Sunlight->Heat
• H20->O2
• CO2->glucose

• Glucose->CO2 & heat
• O2->H2O
• ADP->ATP

Cellular work and heat

• Oxidized: CH4 -> CO2
• Reduced: 2O2 ->2 H2O

• CO2
• H2O

with a net release of free energy and is spontaneous

absorbs free energy from its surroundings and is nonspontaneous

in direction that causes a loss in free energy which increases in net disorder

a measure of a system's total energy available to do work, w/o reference to the surroundings

no

yes

When the net change of G is negative, the rxns are spontaneous

• Na+ is the positive ion that gets oxidized
• Cl- is the negative ion that gets reduced

• closed system
• equilibrium
• no work

• not in equilibrium
• open

• metabolism
• equilibrium

• catabolic
• free energy

• exergonic
• endergonic

• -chemical
• -transport
• -mechanical

energy coupling

ATP

the negative charges don't like being so close

Hydrolysis

when the terminal phosphate bond is broken

chemical change to a state of lower free energy

no energy

• 1. NAD+ -> NADH
• 2. NADP+ -> NADPH
• 3. FAD -> FADH2

• Enzymes
• Lowering

Catalyst

Enzyme

activation energy

Activation Energy

cofactors

coenzyme

vitamins

Competitive inhibitors

Noncompetitive inhibitors

toxin, poisons, pesticides and antibiotics

Nucleic acids

gene

Genes

nucleotides

DNA

mRNA

• store & transmit hereditary information
• regulate gene expression

Phosphate group & Nitrogenous base

• Selective acceleration of chem rxns
• EX: digestive enzymes catalyze the hydrolysis of bonds in food molecules

• Protection against disease
• ex: antibodies inactivate and help destroy viruses and bacteria

• Storage of amino acids
• ex: Plants of storage proteins in their seeds

• Transport of substances
• ex: hemoglobin, iron protein->oxygen from lungs to body

• Coordination of an organism's activities
• ex: insulin, causes other tissues to up take glucose which regulates blood sugar concentration

• Response of cell to chemical stimuli
• Ex: built into membrane of nerve cell detect signaling molecules released by other nerve cells

• Movement
• ex: actin and myosin proteins are responsible for the contraction of muscles

• Support
• Keratin, collagen, elastin and silk fibers

Glycosidic LInkage

Ester LInkage

phosphodiester

Peptide Linkage

• amino acid
• fatty acid
• nucleic acid
• monosaccharides

OH and H of two amino acids and connect the C and N together

• Hydrogen bonds
• Electrostatic attractions
• Van der Waals
• Hydrophobic interaction

conformation

renaturation

chaperone protein

Amino acid sequence

Folds that form in certain segments of the polypeptide chain

full, three-dimensional conformation of the entire polypeptide chain

More than one polypeptide chain

intrinsically disordered sequences

Globular Proteins

fibrous proteins

collagen

ligand

binding site

hydrolase

nuclease

protease

Ligase

Isomerase

Polymerase

Kinase

Phosphatase

oxido-reductase

ATPase