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Biology 1A - Final Exam
Cards based on study guide (Chapters 1-18)
508
Biology
Undergraduate 1
04/28/2012

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Term
Chapter 1
Definition
Chapter 1
Term
7 Characteristics of all life
Definition
1. Cells and organization
2. Energy use and metabolism
3. Response to environmental changes
4. Regulation and homeostasis
5. Growth and development
6. Reproduction
7. Biological evolution
Term
Cells and Organization (characteristics life 1)
Definition
Organisms maintain an internal order.
The simplest unit of organization is a cell.
Term
Energy use and metabolism (characteristics life 2)
Definition
Maintenance of cellular organization requires energy input.
Energy is used in chemical reactions collectively know as metabolism.
Term
Response to environmental changes (characteristics life 3)
Definition
Organisms react to environmental changes to promote their survival.
Term
Regulation and Homeostasis (characteristics life 4)
Definition
Organisms regulate their cells and bodies, maintaining relatively stable internal conditions, a process called homeostasis.
Term
Growth and development (characteristics life 5)
Definition
Growth produces more or marger cells, whereas development produces an organism with defined characteristics.
Term
Reproduction (characteristics life 6)
Definition
To sustain life over many generations, organisms must reproduce. Due to the transmission of genetic material, offspring tend to have trait like their parents.
Term
Biological evolution (characteristics life 7)
Definition
Populations of organisms change over the chorus of many generations. Evolution results in traits that promote survival and reproductive success.
Term
Organism
Definition
Maintain an internal order that is separate from environment
Term
Cell Theory (3 items)
Definition
1. All organisms are made of cells.
2. Cells are the smallest unit of life.
3. Cells come from pre-existing cells via cell division.
Term
Hierarchal organization of life (10 items)
(also refer to page 4, where each level is described in detail)
Definition
1. Atoms
2. Molecules and macromolecules
3. Cells
4. Tissues
5. Organs
6. Organism
7. Population
8. Community
9. Ecosystem
10. Biosphere
Term
3 Domains of life
Definition
Bacteria, Archaea, Eukaryotes
Term
Domains of life - Prokaryotes
Definition
Bacteria & Archaea
Cell structure is relatively simple.
Have no cell nucleus.
Term
Domains of life - Eukaryotes
Definition
Have larger cells with internal compartments that serve various functions.
Have a cell nucleus.
Term
Eukaryotes (4 subcategories)
Definition
Protista (protists)
Plantae (plants)
Fungi
Animalia (animals)
Term
Taxonomy
Definition
Involves multiple levels in which species are placed in progressively small and smaller groups.
Term
Evolution
Definition
A phenomenon that populations of organisms change over the chorus of many generations. As a result, some organisms become more successful at survival and reproduction.
Term
Science (as defined in Biology)
Definition
The observation, identification, experimentation and theoretical explanation for natural phenomena.
Term
The scientific method
Definition
A series of steps to test a hypothesis. Often involves control vs experimental groups.
Term
Hypothesis
Definition
A proposed explanation for a natural phenomenon. A useful hypothesis makes predictions and is falsifiable.
Term
Theory
Definition
A broad explanation of some aspect of the natural world that is substantiated by a large body of evidence.
Term
Hypothesis testing (step 1/5)
Definition
Observations are made regarding natural phenomena.
Term
Hypothesis testing (step 2/5)
Definition
The observations lead to a hypothesis that tries to explain the phenomena. A useful hypothesis is one that is testable because it makes specific predictions.
Term
Hypothesis testing (step 3/5)
Definition
Experimentation is conducted to determine if the predictions are correct.
Term
Hypothesis testing (step 4/5)
Definition
The data from the experiment is analyzed.
Term
Hypothesis testing (step 5/5)
Definition
The hypothesis is considered to be consistant with the data or is rejected.
Term
End of chapter 1
Definition
Beginning of chapter 2
Term
Atoms
Definition
Smallest functional unit of matter.
Forms all chemical substances.
Every specific type of atom is a chemical element.
Term
Protons
Definition
1 of 3 subatomic particles.
Number of protons distinguishes one element from another.
Positive, found in nucleus, same number as electrons.
Mass relative to electron - 1,836
Term
Neutrons
Definition
1 of 3 subatomic particles.
Neutral, found in nucleus, number can vary.
Mass relative to electron - 1,839
Term
Electrons
Definition
1 of 3 subatomic particles.
Negative, found in orbitals, same number as protons.
Term
Valence Electrons
Definition
Electrons in the outer shell that are available to combine with other atoms.
Term
Atomic Number
Definition
Equal to the number of Protons in the atom.
Term
Periodic Table
Definition
Rows correspond to the number of electron shells.
Columns, from left to right indicate the numbers of electrons in the outer shell.
Elements within a column have similar bonding proporties.
Term
Atomic Mass
Definition
Number of protons plus number of neutrons.
Term
Dalton
Definition
Unit of measurement for atomic mass.
Carbon has an atomic mass of 12 Daltons.
Term
Mole
Definition
1 Mole of any element contains the same number of atoms -
6.022 x 10^23.
AKA Avagadro's number
Term
Isotopes
Definition
Multiple forms of an element that differ in the number of neutrons.
Atomic masses are averages of the weights of different isotopes of an element.
Term
Molecule
Definition
2 or more atoms bonded together.
Term
Molecular Formula
Definition
Contains chemical symbols of elements found in a molecule.
Subscript indicates how many of each atom are present.
Term
Compound
Definition
A molecule composed of two or more elements.
Term
Covalent Bonds
Definition
Atoms share a pair of electrons.
Occurs between atoms whose outer shells are not full.
Strong chemical bond, electrons behave as if belonging to both atoms.
Term
Octet Rule
Definition
Atoms are most stable when outer shell is full.
For many atoms that number is 8 electrons.
Hydrogen fills it's outer shell with 2 electrons.
Term
Polar Covalent Bonds
Definition
Atoms don't always share electrons equally.
Electronegativity, the more electronegative an atom, the more it pulls shared electron toward it's self.
Term
Hydrogen Bonds
Definition
Hydrogen atom from one polar molecule attracted to an electronegative atom.
Individually weak, but strong in numbers.
Holds strands of DNA together.
Term
Ion
Definition
An atom of molecule that has gained or lost one or more electrons.
Has a net electric charge.
Cation - net positive charge
Anion - net negative charge
Term
Ionic Bonds
Definition
When a Cation binds to an Anion.
Term
Molecule Shapes
Definition
Determined by the Bonds.
The 3D shape of a molecule influences the behavior of molecules in the body.
Term
Chemical Reactions
Definition
Occurs when one or more substances change into another substance.
All require energy source.
Require enzymes.
Occur in liquid environment.
Term
Enzymes
Definition
Catalysts for chemical reactions in living organisms.
Term
Solutions
Definition
Solvent - liquid.
Solutes - substances dissolved in solvent.
Term
Aqueous Solution
Definition
Water is the solvent.
Ions and molecules that contain polar covalent bonds will dissolve in water.
Term
Hydrophilic
Definition
"water-loving"
Readily dissolve in water.
Ionic and polar covalent molecules.
Term
Hydrophobic
Definition
"water-fearing"
Nonpolar molecules.
Do not dissolve in water.
Example - cholesterol
Term
Amphipathic Molecule
Definition
Have both polar and nonpolar regions.
May dissolve in water to form micelles.
Term
Micelles
Definition
Polar region at the surface.
Nonpolar ends orient toward the interior of the micelle.
Term
Concentration
Definition
1 gram per Liter = 1 g/L
Term
Water in living organisms
Definition
Participates in chemical reactions (hydrolysis/dehydration).
Provides force or support.
Removes toxic waste components.
Evaporative cooling.
Cohesion and adhesion.
Surface tention.
Term
Acids and Bases in pure water
Definition
Acids are molecules that release hydrogen ions when they are dissolved into pure water. This increases the H+ Bases lower the H+ concentration of a solution. -Some release OH-, some bind H+
Term
Acid Solution
Definition
pH 6 or below
Term
Alkaline (Basic) Solution
Definition
pH 8 or above
Term
A solution's pH level can effect...
Definition
The shapes and functions of molecules.
The rates of many chemical reactions.
The ability of two molecules to bind to each other.
The ability of ions or molecules to dissolve.
Term
Buffer
Definition
Help to keep a constant pH level.
Most organisms tolerate little change in pH.
Animals have buffers in their blood.
Term
4 essential elements that compose the majority of living matter.
Definition
Oxygen, Carbon, Hydrogen, Nitrogen
Term
The pH scale
Definition
Review in book (p39)
Term
End of chapter 2
Definition
Beginning of chapter 3
Term
Organic Chemistry
Definition
Organic Molecules contain Carbon.
Abundant in all living organisms.
Term
Macromolecules
Definition
Large, complex organic molecules.
Term
Carbon
Definition
4 electrons in outer shell (can contain 4 more).
Can have up to 4 bonds (usually single or double).
Can have polar or nonpolar bonds.
Term
Isomers
Definition
Two structures with an identical molecular formula but different structures and characteristics. Structural isomers contain the same atoms but in different bonding relationships.
Term
Cis-trans isomers
Definition
change in positioning around double bond.
Term
Enantiomers
Definition
mirror image of another molecule.
Term
Condensation/Dehydration Reaction
Definition
"removal" of water.
Links monomers to form polymers.
Term
Hydrolysis
Definition
"addition" of water.
Polymers broken down into monomers.
Term
4 major organic molecules and macromolecules
Definition
Carbohydrates, Lipids, Proteins, Nucleic acids
Term
Carbohydrates
Definition
Carbon, hydrogen, oxygen
Term
Lipids
Definition
Composed predominantly of hydrogen and carbon.
Defining feature - nonpolar thus very insoluble in water.
Term
Nucleic Acids
Definition
Responsible for te storage, expression and transmission of genetic information.
Two classes (DNA & RNA)
Term
Proteins
Definition
Carbon, hydrogen, oxygen, nitrogen and traces of others including sulfur.
Amino acids are the monomers
-Common structure with variable R-group.
-20 amino acids.
-Side-chain determines structure and function.
Term
Monosaccharides
Definition
Simplest sugars, Most common with 5 or 6 Carbons.
Term
Glucose isomers
Definition
Glucose and galactose.
Stereoisomers - identical arrangement of bonds, but different arrangement of atoms.
Term
Disaccharides
Definition
Carbohydrates composed of two monosaccharides.
Joined by dehydration or condensation (glycosidic bond).
Broken by hydrolysis.
Examples - sucrose, maltose, lactose
Term
Polysaccharides
Definition
Many monosaccharides linked together to for long polymers.
Examples - Energy storage- starch, glycogen.
Term
Fats
Definition
AKA triglycerides or triacylglycerols.
Formed by bonding glycerol to three fatty acids.
Term
Fatty Acids (saturated)
Definition
All carbons are linked by single covalent bonds.
Tend to be solid at room temp.
Term
Fatty Acids (unsaturated)
Definition
Contain one or more double bonds.
Tend to be liquid at room temp (oils).
Term
Phospholipids
Definition
Amphipathic molecule
-Phosphate region - polar, hydrophilic.
-Fatty acid chains - nonpolar, hydrophobic, tail.
-Form bilayer important in formation of cell membranes.
Term
Steroids
Definition
Four interconnected rings of carbon atoms.
Usually not water soluble.
Small different in chemical struct can mean the difference between testosterone and estrogen.
Term
Protein Bonding
Definition
Joined by dehydration of condensation reaction.
-Peptide bond.
-Forms polypeptides
-Proteins are made up of 1 or more polypeptides.
Broken apart by hydrolysis.
Term
Protein Structure
Definition
Primary - Amino acid sequence (determined by DNA)
Secondary - Folding into compact structure
-Alpha - helix
-Beta - pleated sheet
Tertiary - further folding into 3D shape.
Quaternary - 2 or more polypeptides.
Term
Multimeric Proteins
Definition
Proteins with multiple parts.
Term
5 Factors promoting protein folding and stability
Definition
1.Hydrogen bonds - many weak add to overall strong
2.Ionic bonds and polar reactions - different side chain charges may bond together.
3.Hydrophobic effects.
4.Van der Waal's forces - Weak attractions between atoms.
5.Disulfide bridges - Covalent bonds between 2 Cysteine side chains.
Term
Functional domains within Protein structures
Definition
Modules in proteins have distinct structure and functions.
Term
DNA
Definition
Deoxyribonucleic acid.
Stores genetic information coded in the sequence of their monomer building blocks.
Term
RNA
Definition
Ribonucleic acid.
Involved in decoding genetic information into instructions for linking together a specific sequence of amin acids to form a polypeptide chain.
Term
Monomer
Definition
An organic molecule that can be used to form larger molecules (polymers) consisting of many repeating units of the monomer.
Term
Polymer
Definition
A large molecule formed by linking many smaller molecules (monomers) together.
Term
Explain the importance of shape in macromolecules and give an example of the consequences of shape changes in molecules
Definition
Book
Term
Summarize the interactions involved in protein shape and explain why temperature and pH affect protein shape
Definition
Book
Term
End of chapter 3
Definition
Beginning of chapter 4
Term
Cell Theory
Definition
All living organisms are made up of one or more cells.
Cells are the smallest unit of life.
New cells only come from pre-existing cells via cell division.
Term
Magnification (microscope)
Definition
Ratio between the size of an image produced by a microscope and it's actual size.
Term
Resolution (microscope)
Definition
Ability to observe two adjacent objects as distinct from one another.
Term
Contrast (microscope)
Definition
How different one structure looks from another.
Enhance with dies.
Term
2 groups of microscopes
(based on source of illumination)
Definition
Light microscope - 0.2 um
Electron microscope - 2nm
Term
Electron microscope types
Definition
Transmission (TEM)
Beam of electrons passes through sample (some deflected)
Scanning (SEM)
Sample coated with heavy metal (beam makes 3d image)
Term
2 categories of life
Definition
Prokaryotes & Eukaryotes
Term
Prokaryotic Cells
Definition
Simple structure.
Lack membrane enclosed nucleus.
Term
2 Categories of Prokaryotic Cells
Definition
Bacteria - abundant, most not harmful.
Archaea - less common, often found in extreme environments.
Term
Compartmentalization
Definition
Found only in Eukaryotes.
Allows different biochemical processes to occur in different regions of the cell.
Term
Plant vs Animal cells
Definition
Plant cells do not possess - Lysosomes, Centrioles.
Animal cells do not possess - Cell wall, Central Vacuole, Chloroplasts.
Term
Genome
Definition
Genetic material within an organism - DNA
Term
Proteome
Definition
All types and relative amount of proteins found in a cell at any given moment under specific conditions.
Term
Differential gene regulation
Definition
Specific proteins found in one cell type may not be produced in another cells type.
Same proteins may be produced but different relative concentrations.
Term
Alternative Splicing
Definition
mRMA from a single gene may form different forms of a polypeptide (each with slightly different amino acid sequences)
Term
Protein alteration
Definition
After synthesis, cells may slightly alter protein structure.
Term
Cytosol
Definition
Region of a eukaryotic cell that is outside the cell organelles but inside the plasma membrane.
20-50% of cell volume.
Site of many chemical reactions.
Location of the Cytoskeleton.
Central coordinating region for many metabolic activities.
Term
Metabolism
Definition
Sum of all chemical reactions.
Term
Catabolism
Definition
Breakdown of a molecule into smaller components.
Energy utilization.
Synthesis of molecule building blocks.
Term
Anabolism
Definition
Synthesis oc cellular molecules and macromolecules.
e.g. Synthesis of polysaccharides from sugars.
e.g. Protein synthesis from amino acids.
Term
Translation
Definition
Process of polypeptide synthesis.
Information written in gene ultimately translated into the sequence of amino acids in a polypeptide.
Term
Ribosomes
Definition
Site of polypeptide synthesis (translation).
Transfer RNA (tRNA) - brings amino acids.
Messenger RMA (mRNA) - information to make a polypeptide.
Term
Cytoskeleton
Definition
Provides cell shape, organization and movement.
Network of three different type of protein filaments.
Term
Microtubules (cytoskeleton)
Definition
Made of Tubulin.
Dynamic instability
In non-dividing animal cells microtubules formed from the Centriole (microtubule organizing center).
In plant and many protists centrioles are absent - microtubules created at many cites throughout cell.
Term
Dynamic Instability (Microtubules) (cytoskeleton)
Definition
Oscillation between growing and shortening phases.
Important in various cell growth phases.
e.g. Shortening of chromosomes during cell division.
Term
Intermediate Filaments (cytoskeleton)
Definition
10 nm in size
Form twisted rope-like structure.
Tention bearing filaments - help maintain cell shape
Made of several proteins
Desmins - muscle cells
Keratins - skin, intestines, kidney, hair, nails
Lamins - inner nuclear membrane
Term
Actin Filaments
Definition
AKA Microfilaments
Long, thin fibers - around 7nm in diameter.
Polar. Composed from Actin monomers.
Concentrated around the plasma membrane - provide strength, shape and movement to cell.
Term
Motor Proteins
Definition
Use ATP as a source of energy to promote movement.
Three kinds of movement -
-carrying cargo, attaching and causing filament to move, attaching and causing filament to bend.
Term
ATP
Definition
Adenosine Triphosphate.
Hydrolyzed into ADP (Adenosine Diphosphate) and Phosphate ion.
Term
Flagella & Cilia
Definition
Microtubules & motor proteins facilitate movement pf cellular appendages.
Flagella - long, present in singles or pairs.
Cilia - short, often cover all of part of a cell surface
Both have 2+9 internal structure
Term
Endomembrane System
Definition
Network of membranes enclosing the nucleus, endoplasmic reticulum, golgi apparatus , lysosomes and vacuoles.
Also includes plasma membrane.
May be directly connected or pass materials via vesicles.
Term
Nuclear envelope
Definition
Double membrane structure enclosing nucleus.
Outer membrane is continuous with E.R. membrane.
Nuclear pores provide passageways for molecules.
Term
Nucleus
Definition
Protection, Organization, Replication and Expression of genetic material.
Term
Chromosomes
Definition
Composed or DNA and proteins = chromatin.
Proteins help make DNA fit inside the nucleus.
Term
Nuclear Matrix
Definition
Filamentous network.
Organizes chromosomes - each chromosome occupies a distinct (nonoverlapping) region.
Term
Endoplasmic Reticulum (E.R.)
Definition
Network of membranes that form flattened, fluid filled tubules of cisternae.
can form over 1/2 of membranes in some cells.
E.R. membrane encloses a single compartment call the E.R. lumen.
Term
Rough E.R.
Definition
Studded with Ribosomes - bumpy appearance.
Involved in protein synthesis and sorting.
Glycosylation.
Term
Glycosylation
Definition
Attachment of carbohydrates to proteins.
Term
Smooth E.R.
Definition
Lacks ribosomes - smooth appearance.
Large surface area for key enzyms and metabolism.
Detoxification, Carb metabolism, calcium balance, synthesis and modification of lipids.
Term
Golgi Apparatus
Definition
Stack of flattened, membrane-bound compartments.
Vesicles transport materials between stacks.
Three overlapping functions.
-Secretion - packages material into secretory vesicles.
-Processing - Glycosylation of proteins and lipids
-Protein sorting
Term
Lysosomes
Definition
Found in animal cells.
Contain acid hydrolyses that preform hydrolysis.
Requires acidic condition (interion pH 4.8)
Autophagy - recycling
Term
Central Vacuoles (plants)
Definition
Surrounded by tonoplast.
Storage - water enzymes proteins, inorganic ions.
Support plants.
Term
Contractile Vacuoles (protists)
Definition
Water continually enters cell.
Vacuole increases in size. Sudden contraction expels water to outside of cell.
Term
Phagocytic Vacuoles
Definition
Protists and white blood cells for degradation.
Contain enzymes that:
break down food.
Engulf bacterial cells - immune system.
Term
Peroxisomes - found in eukaryotic cells
Definition
Single membrane fluid-filled lumen.
Catalyses reactions the break down molecules by removing hydrogen or adding oxygen.
Large amounts found in liver of animals.
Byproduct in hydrogen peroxide which is then broken down into water and oxygen.
Term
Plasma Membrane
Definition
Proteins in plasma membrane perform important functions affecting activities inside of cell.
Term
Plasma Membrans Functions (membrane transport)
Definition
Essential nutrients or ions into cell.
Substances exported from cell.
Selectively permeable.
Term
Plasma Membrane Functions (Cell signaling)
Definition
Sense environment changes.
Coordinating with other cells.
Signaling molecules bind to receptors (signal transduction pathway)
Term
Plasma Membrane Functions (Cell adhesion)
Definition
Protein to Protein interactions.
Allows formation of tissues and organs.
Formation of multicellular organisms.
Allows cells to recognize each other.
Term
Semiautonomous organelles
Definition
Can grow and divide to reproduce themselves.
Depend on other parts of the cell of their internal components.
Mitochondria and Chloroplasts.
Term
Mitochondria
Definition
Primary role is to make ATP (powerhouse of cells)
Sugars, fats, amino acids broken down (release energy making ATP)
Some cells (muscles) may have a few thousand mitochondria.
Divide by binary fission.
Term
Chloroplasts - a kind of plastid (found in all plant and alge)
Definition
Photosynthesis - Capture light energy to synthesize organic molecules such as glucose.
Outer and inner membrane with an inter membrane space and a thylakoid membrane.
Term
Thylakoid membrane
Definition
Thylakoids can stack on each other fo form grana.
Stroma is inside the inner membrane, but outside the thylakoids.
Term
Chromoplasts
Definition
Synthesize and store color pigments.
Term
Amyloplasts
Definition
Synthesize and store starch.
Term
Eukaryotic Protein sorting
Definition
Sorting signals:
short trenches of amino acids direct proteins to correct destinations.
Term
Cotranslational Protein Sorting
Definition
Proteins are built partly before and partly after being sorted.
Term
Posttranslational Protein Sorting
Definition
Protein is built and then sorted to it's destination.
Term
4 features shared by all cells
Definition
DNA, Cytoplasm, Cell membrane, Ribosomes
Term
Theory of Endosymbiosis
Definition
A theory that mitochondria and chloroplasts originated from bacteria that took up residence within a primordial eukaryotic cell.
Term
End of chapter 4
Definition
Beginning parts of animal cells
Term
Centrosome
Definition
Site where microtubules grow and centrioles are found.
Term
Cytoskeleton
Definition
Protein filaments that provide shape and aide in movement.
Term
Cytosol
Definition
Site of many metabolic pathways.
Term
Nucleus
Definition
Area where most of the genetic material is organized and expressed.
Term
Nuclear Pore
Definition
Passageway for molecules into and out of the nucleus.
Term
Rough E.R.
Definition
Site of protein sorting and secretion.
Term
Smooth E.R.
Definition
Site of detoxification and lipid synthesis.
Term
Mitochondrion
Definition
Site of ATP synthesis.
Term
Peroxisome
Definition
Site where hydrogen peroxide and other harmful molecules are broken down.
Term
Golgi Apparatus
Definition
Site of modification, sorting sorting and secretion of lipids and proteins.
Term
Plasma Membrane
Definition
Membrane that controls movement of substances into and out of the cell; site of cell signaling.
Term
Chromatin
Definition
A complex of protein and DNA.
Term
Ribosome
Definition
Site of polypeptide synthesis.
Term
Lysosome
Definition
Site where macromolecules are degraded.
Term
Nucleolus
Definition
Site for ribosome subunit assembly.
Term
Nuclear Envelope
Definition
Double membrane the encloses the nucleus.
Term
End parts of animal cell
Definition
Beginning parts of plant cells
Term
Central Vacuole
Definition
Site that provides storage; regulation of cell volume.
Term
Chloroplast
Definition
Site of Photosynthesis.
Term
Cell Wall
Definition
Structure that provides cell support.
Term
Cytoskeleton
Definition
Protein filaments that provide shape and aide in movement.
Term
Cytosol
Definition
Site of many metabolic pathways.
Term
Nucleus
Definition
Area where most of the genetic material is organized and expressed.
Term
Nuclear Pore
Definition
Passageway for molecules into and out of the nucleus.
Term
Rough E.R.
Definition
Site of protein sorting and secretion.
Term
Smooth E.R.
Definition
Site of detoxification and lipid synthesis.
Term
Mitochondrion
Definition
Site of ATP synthesis.
Term
Peroxisome
Definition
Site where hydrogen peroxide and other harmful molecules are broken down.
Term
Golgi Apparatus
Definition
Site of modification, sorting sorting and secretion of lipids and proteins.
Term
Plasma Membrane
Definition
Membrane that controls movement of substances into and out of the cell; site of cell signaling.
Term
Chromatin
Definition
A complex of protein and DNA.
Term
Ribosome
Definition
Site of polypeptide synthesis.
Term
Nucleolus
Definition
Site for ribosome subunit assembly.
Term
Nuclear Envelope
Definition
Double membrane the encloses the nucleus.
Term
End parts of plant cells
Definition
Beginning of chapter 5
Term
Amphipathic nature of phospholipids
Definition
Have a hydrophobic (nonpolar) region and Hydrophilic (polar) fatty acyl tails. The talis face each other and form the interior of the membrane.
Term
Membrane is semi-fluid because...
Definition
The lipids and proteins embedded in the layer can move freely relative to one another. (fluid-mosaic model)
Term
Hypertonic solution
Definition
Any solution that causes a cell to shrink due to osmosis of water leaving the cell
Term
Hypotonic solution
Definition
Any solution the causes a cell to swell when placed in it.
Term
Isotonic solution
Definition
Conditions in which the solute concentrations are on both sides of the plasma membrane are equal. (cell does not shrink of swell)
Term
Passive transport
Definition
The transport of a substance across a membrane from a region of high concentration to a region of lower concentration.
Term
Active transport
Definition
Moves a substance from an area of low concentration to high concentration of against the chemical gradient with the aide of a transport protein.
Term
Facilitated diffusion
Definition
A transport protein provides a passageway for the substance to cross the membrane.
Term
Diffusion
Definition
When a substance moves across a membrane from an area of high concentration to an area of lower concentration.
Term
Osmosis
Definition
The movement of water across membranes to balance solute concentrations. Water diffuses from a solution that it hypotonic to hypertonic.
Term
End of chapter 5
Definition
Beginning of chapter 6
Term
Catabolic pathway
Definition
Result in the breakdown of molecules into smaller components. (exergonic)
Term
Anabolic pathway
Definition
Involves the synthesis of larger molecules from small. (endergonic)
Term
Exergonic reaction
Definition
Chemical reactions that release free energy and occur spontaneously.
Term
Endergonic reaction
Definition
Chemical reactions that require an addition of free anergy and do not proceed spontaneously.
(ADP+P -> ATP)
Term
ATP hydrolysis in driving other reactions
Definition
Coupling ATP hydrolysis with other reactions can change a reaction that would have been endergonic to one that is exergonic.
Term
Enzymes as catalysts
Definition
Enzymes lower the activation energy needed for the substrates to reach a transition state.
(APT + glucose -> Glucose-phosphate + ADP)
Term
Enzyme shape changes in enzyme-catalyzed reactions
Definition
Enzymes may donate amino acids to catalyze reactions, but the amino acids are returned to the enzyme after the reaction is complete.
Term
Cause of substrate specificity in enzymes
Definition
Conformational changes in the enzyme-substrate complex cause the substrate to bind tightly with the enzyme called an induced fit. Only after this can the reaction take place.
Term
Affects on enzymes - temperature
Definition
High temperatures may inhibit an enzyme's ability to function properly. Very high temperatures my cause it to become denatured and not at all functional.
Term
Affects on enzymes - pH
Definition
Enzymes may not functional as well if the pH is altered from that which they normally function in.
Term
Affects on enzymes - inhibitors (competitive)
Definition
Molecules that bind to the active site on an enzyme and inhibit the ability of the substrate to bind.
Term
Affects on enzymes - inhibitors (noncompetitive)
Definition
Binds to noncovelently an enzyme at a location outside the active site (allosteric site) and inhibits the enzyme's function.
Term
NAD+
Definition
Can be used to make NAHD which can be used to produce ATP
Term
End of chapter 6
Definition
Beginning of chapter 7
Term
Respiration - Glycolysis yields what?
Definition
2 pyruvate
2 ATP (substrate-level phosphorylation)
3 NADH
(occurs in cytosol)
Term
Respiration - Pyruvate breakdown yields what?
Definition
2 acetyl group (2 carbons each)
2 CO2
2 NADH (redox with NAD+)
(occurs in mitochondrial matrix)
Term
Respiration - Citric acid cycle yields what?
Definition
4 CO2
2 ATP
6 NADH
2 FADH2
(occurs in mitochondrial matrix)
Term
Respiration - Oxidative Phosphorylation
Definition
Redox reactions remove electrons from NADH and FADH2 to produce an H+ electrochemical gradient. Chemiosmosis uses H+ gradient to synthesize ATP from ADP & Pi (30-34 ATP)
(occurs along the wall of the mitochondrial matrix)
Term
What receives electrons in anaerobic respiration?
Definition
Nitrate
Term
Define fermentation
Definition
Organic molecules are broken down without any net oxidation.
Term
What are two examples of fermentation?
Definition
Lactate production (muscle cells)
Ethanol production (yeast)
Term
End of chapter 7
Definition
Beginning of chapter 8
Term
Define a heterotroph
Definition
An organism that cannot produce their own organic molecules and thus must obtain organ food from other organisms.
Term
Define an autotroph
Definition
An organism that has metabolic pathways that use energy from either inorganic molecules of light (photoautotrophs) to make organic molecules.
Term
Photosynthesis
Definition
Read processes in book (page 157)
Term
What colors of light are most effective for photosynthesis?
Definition
Blue (450 nm)
Term
What colors of light are least effective for photosynthesis?
Definition
Green -> yellow (500-600 nm)
Term
End of chapter 8
Definition
Beginning of chapter 9
Term
Adaptation
Definition
A response by a living cell to a change in it’s environment.
Term
Autocrine signaling
Definition
In autocrine signaling, a cell secretes signaling molecules that binds to receptors on it’s own surface. This may affect neighboring cells of the same type.
Term
Auxin
Definition
a signaling molecule transmitted from cell and inhibited by light. (Darwin and plants)
Term
Apoptosis
Definition
-Genetically predetermined cell death. (occurs in eukaryotes)
-Cell shrinks due to destruction of nucleus and cytoskeleton.
-Plasma membrane forms blebs.
-Different pathways have been discovered that lead to Apoptosis.
Term
Caffeine
Definition
inhibits phosphodiesterase (causes heart to beat faster)
Term
Contact-dependent signaling
Definition
Some molecules are bound to the surface of cells and provide a signal to other cells that make contact with the surface of that cell. The cell has a membrane-bound signaling molecule that receptors on the surface of other cells can recognize.
Term
Cyclic AMP
Definition
may be synthesized by adenylyl cyclase via ATP. (example of 2nd messenger) (p.186)
Term
Direct intercellular signaling
Definition
In multicellular organisms, cells adjacent to each other may have contacts (cell junctions) that enable them to pass ions, signaling molecules from cytosol to cytosol.
Term
Endocrine signaling
Definition
Signaling that covers long distances using hormones. Hormones secreted into the bloodstream can affect virtually all cells.
Term
Epinephrine
Definition
Fight-or-flight hormone. Acts differently on different cells:
-Promotes breakdown of glycogen in skeletal muscle cells
-Relaxes airways in lungs
Term
First (primary) messengers
Definition
The small molecules or ions that bind surface receptors on the plasma membrane of a cell. (p. 186)
Term
G-Protein function
Definition
They activate adenylyl cyclase and they activate phospholipase C
Term
Growth factors
Definition
cause a rapid increase in the expression of many genes in mammals. (involved in cancer)
Term
Kinase
Definition
An enzyme that transfers a phosphate group to another molecule
Term
Ligand
Definition
signaling molecule that binds noncovelently with high specificity to receptor causing a conformational change. (creates a ligand-receptor complex). Receptors do not change the ligand like enzymes and substrates. (p.177)
Term
Paracrine Signaling
Definition
A specific cell secretes a signaling molecule that does not affect the cell secreting the signal but instead influences the behavior of target cells in close proximity. Typically short duration. Example - Synaptic signaling - Neurotransmitters.
Term
Phosphatase
Definition
An enzyme that removes a phosphate group from another molecule
Term
Receptor tyrosine kinases
Definition
category of enzyme-linked receptor. Recognize various type of signaling molecules (animals only)
Term
Second messengers
Definition
small molecules or ions that relay signals inside the cell. (speed and size & amplification)
Term
Signals
Definition
agents that influence the properties of cells. Affects the conformation of a receptor, leading to a response in the cell. (ex. Glucose acts as a signal to yeast to increase transporters and enzymes.)
Term
Enzyme-inked receptors...
Definition
function by phosphorylation of a protein from ATP in their intracellular domain. (p.182)
Term
Occurs during the signal transduction phase in G protein activation...
Definition
Promotion of cellular responses due to dissociation of activated (Alpha) subunit and (Beta/Gamma) subunit. (p. 182-183)
Term
The receptor for the steroid hormone estrogen is found...
Definition
in the nucleus. (p.183)
Term
Cell-to-cell communication:
Direct intercellular communication
Definition
cell junctions between cell are able to pass signaling molecules from cell to cell
Term
Cell-to-cell communication:
Contact-dependent signaling
Definition
Signaling molecules on the surface of cells make contact with adjacent receptors on other cells
Term
Cell-to-cell communication: Autocrine signaling
Definition
A cell secretes signaling molecules that bind to receptors on it’s own surface but make also affect adjacent cells
Term
Cell-to-cell communication:
Paracrine signaling
Definition
A cell secretes signaling molecules that are aimed at adjacent target cells. (ex. Neurotransmitters / synaptic signaling.)
Term
Cell-to-cell communication: Hormones
Definition
Hormones travel long distances and affect many cells. Can last a longer period of time than other forms of signaling. (steroid hormone receptors are intracellular)
Term
Signal Response - Receptor activation (1)
Definition
A signaling molecule attaches to a receptor and causes a conformational change. (usually an activation of enzymes).
Term
Signal Response - Signal transduction (2)
Definition
The initial signal is changed to another signal inside the cell. Signal Transduction Pathway - the series of changes proteins go through as a result of the signal.
Term
Signal response - Cellular response (3)
Definition

-can cause different responses in the cell by affecting different components:

i. Enzymes - Altered metabolism or other cell functions.

ii. Structural proteins - Altered cell shape and/or movement.

iii. Transcription factor - Altered gene expression, which changes the types and the amounts of proteins in the cell.

Term
Cell surface receptors - Enzyme-linked receptors
Definition
Has extracellular domain (allows for signal binding) and intercellular domain (has a catalytic function). Many function as protein-kinases: enzymes that transfer a phosphate group from an ATP to a specific amino acid in a protein.
Term
Cell surface receptors - G-Protein-Coupled Receptors (GPCRs)
Definition
Typically contain 7 trans-membrane segments and interact with G Proteins. Called G Protein because can bind with GTP or GDT. Creates GTP from GDT and P.
Term
Cell surface receptors - Ligand-Gated Ion Channels
Definition
Ligand allows receptor to open and allows the flow of ions through the membrane.
Term
Active Caspase
Definition
-Functions as a protease (an enzyme that digests other proteins)
Term
Protein-kinases are...
Definition
enzymes that transfer a phosphate group from an ATP to a specific amino acid in a protein.
Term
A protease is...
Definition
an enzyme that digests other proteins.
Term
End of chapter 9
Definition
Beginning of chapter 10
Term
The function of the extracellular matrix (ECM) in animals is...
Definition
-to provide strength
-to provide structural support
-to organize cells and other body parts
-cell signaling
Term
The protein found in the ECM of animals that provides strength and resistance to tearing when stretched is...
Definition
collagen
Term
The polysaccharide that forms the hard outer covering of many invertebrates is...
Definition
chitin
Term
The extension sequence found in procollagen polypeptides does what?
Definition
-causes procollagen to form a triple helix.
-prevents procollagen forming large collagen fibers.
Term
The dilated state of plasmodesmata allows the passage of...
Definition
-water
-ions
-small molecules
-macromolecules and viruses
Term
Gap junctions of animal cells differ from the plasmodesmata of plant cells in that...
Definition
gap junctions are formed by specialized proteins that form channels through the membranes of adjacent cells but plasmodesmata cannot allow the same type of exchange.
Term
What is involved in the process of tissue and organ formation in multicellular organisms? (6 processes)
Definition
-cell division
-cell growth
-cell differentiation
-cell connection formations
-cell migration
-apoptosis
Term
The tissue type common to animals that functions in the conduction of electrical signals is...
Definition
nervous
Term
A type of tissue that is rich in ECM or has cells with a thick cell wall would be...
Definition
-ground tissue in plants
-connective tissue in animals
Term
Dermal tissue of plants is similar to _______ tissue of animals.
Definition
-epithelial
-they both provide a covering for the organism
Term
The epithelial tissue of animals and the dermal tissue of plants have special characteristics that...
Definition
limit the movement of material between cell layers
Term
The ______ tissue of plants and the ________ tissue on animals provide structural support of the organism.
Definition
ground, connective
Term
The extracellular matrix is...
Definition
a network of material that forms a complex meshwork outside of animal cells.
-Plant cells are surrounded by cell walls.
Term
________ and ________ are the major constituants of animal's ECM.
Definition
Proteins, polysaccarides
Term
In the ECM proteins and polysaccarides provide... (4 things)
Definition
-strength
-structural support
-organization
-cell signaling
Term
Adhesive proteins such as ________ and _______ help adhere cells to the ECM.
Definition
fibronectin, laminin
Term
In the EMC, __________ fibers provide tensile strength and _______ fibers allow regions of the body to stretch.
Definition
collagen, elastic
Term
Glycosaminoglycans (GAGs) are...
Definition
polysaccarides of repeating disaccharide units that give a gel-like character to the ECM.
Term
In plants, the primary cell wall is composed largely of...
Definition
cellulose
Term
The three common types of cell junctions in animals are...
Definition
anchoring, tight, gap
Term
The two common types of cell junctions in plants are...
Definition
middle lamella, plasmodesmata
Term
The four types of anchoring junctions are...
Definition
-adherens junctions
-desmosomes
-hemidesmosomes
-focal adhesions
Term
The two types of cell adhesion molecules (CAMs) are...
Definition
Cadherins - link cells to one another
Integrins - link cells to the ECM
Term
Tight junctions between cells, composed of _________ and ________ prevent the leakage of material across a layer of cells.
Definition
occludin, claudin
Term
The cells walls of adjacent plant cells are cemented together via ____________.
Definition
middle lamella
Term
Tissue:
Definition
A group of cells that have a similar structure and function.
Term
Organ:
Definition
composed of two or more tissues and carries out a particular function or functions.
Term
What six processes produce tissues and organs?
Definition
cell division, cell growth, differentiation, migration, apoptosis, the formation of cell connections
Term
The four general kinds of tissue found in animals are...
Definition
epithelial, connective, nervous, muscle
Term
The three general kinds of tissues found in plants are...
Definition
dermal, ground, vascular
Term
________ and ________ form layers of cells that are highly connected. These layers can be one cell thick or several cells thick. They serve as protective coverings.
Definition
Epithelial, dermal
Term
Glycosaminogylcans (GAGs) are...
Definition
polysaccarides of repeating disaccaride units. (give ECM gel-like character)
Term
Proteoglycans consists of...
Definition
a core protein, surrounded by GAGs
Term
End of chapter 10
Definition
Beginning of chapter 11
Term
DNA allows for physical traits to be passed from generation to generation. Must be able to: (4 things)
Definition
1. Carry genetic information - must contain all the necessary information to replicate the organism.
2. Undergo replication - be copied with high degree of accuracy.
3. Undergo transmission - must be transferable from parent to offspring.
4. Allow for genetic variation - variation within and between species must be possible.
Term
DNA Purines
Definition
A,G
Term
DNA Pyrimidines
Definition
C,T
Term
RNA Purines
Definition
A,G
Term
RNA Pyrimidines
Definition
C,U
Term
One unit of DNA contains _____ base pairs.
Definition
ten
Term
Opposing DNA strands run:
-Parallel?
-Antiparallel?
Definition
Antiparallel
Term
Meselson and Stahl used density studies to prove DNA replication is...
Definition
semiconservative
Term
Avery, McCarthy and MacLeod did what four things?
Definition
-Biochemically isolated macromolecules from Griffiths S-Strain bacteria.
-Based their work on Griffiths.
-Concluded DNA is genetic material.
-Added DNA and RNA digesting enzymes to samples to keep trace elements from altering results.
Term
Franklin used x-ray crystallography to...
Definition
figure the double helix shape of DNA.
Term
Erwin Chargoff discovered what?
Definition
Analyzed amounts of bases and discovered amounts related. (A=T/U and G=C)
Term
Frederick Griffith and bacteria
Definition
-Streptococcus pneumoniae
-Strains that secrete capsules look smooth (S) and can cause fatal infections in mice.
-Strains that look rough ® do not secrete capsules, infections are not fatal.
-Mice injected with heat-killed type S survive.
-Mice injected with live R and heat-killed S die.
-Blood contains living type S (transformation).
Term
Hershey and Chase - T2 virus infecting E. Coli
Definition
-DNA found inside capsid
-Shearing force of blender will separate the phage coat from the bacteria.
-35S will label proteins only, 32P will label DNA only.
-Results support DNA jets injected and in the genetic material.
Term
Humans have ______ or more DNA polymerases
Definition
twelve
Term
DNA structure level 1:
Definition
Nucleotides: the building blocks of DNA (& RNA).
Term
DNA structure level 2:
Definition
A strand of DNA - nucleotides linked covalently.
Term
DNA structure level 3:
Definition
Two strands forma double helix (linked via hydrogen bonds).
Term
DNA structure level 4:
Definition
DNA associates with different proteins to form chromosomes.
Term
DNA structure level 5:
Definition
Genome: a complete complement of an organism’s genetic material.
Term
DNA Replication: Bacteria
Definition
Circular DNA, one point of replication.
Term
DNA Replication: Eukaryotes
Definition
Multiple origins or replication.
Term
DNA leading strand synthesis is ________, lagging strand synthesis is _______.
Definition
continuous, discontinuous
Term
DNA Replication 1 - DNA helicase...
Definition
binds to one strand of DNA at the replication fork and travels in the 5’ to 3’ direction using ATP to separate the strands.
Term
DNA Replication 2 - DNA Topoisomerase...
Definition
in responsible for relieving the supercoiling caused by the unwinding of the double helix by DNA helicase.
(enzyme)
Term
DNA Replication 3 - Single-strand binding proteins...
Definition
coat each strand to keep them from binding back together.
Term
DNA Replication 4 - DNA Primase...
Definition
synthesizes short RNA primers. (start points for synthesis)
Term
DNA Replication 5 - DNA polymerase III...
Definition
travels in a 5’ to 3’ direction on the template strand as it synthesizes the adjacent strand in a 3’ to 5’ direction. (Deoxynucleoside Triphosphates, two phosphates bonds are broken and energy is used to create the covalent bonds)
-Cannot begin DNA synthesis without primers (made of RNA) from DNA primase. (primers get removed and replaced by DNA polymerase I)
-Can work only in 5’ to 3’ direction (because of phosphates)
Term
DNA Replication 6 - DNA Ligase...
Definition
joins adjacent DNA fragments. (including Okazaki Fragments)
Term
DNA Replication 7 - Telomerase
Definition
prevents chromosome shortening by attaching many copies of a DNA repeat sequence (telomeres) to the ends of chromosomes.
Term
Telomeres are what?
Definition
-Series of short nucleotide sequences repeated at the ends of eukaryotic chromosomes.
-Protects the end of the chromosomes
-Prevents fusion with other chromosomes.
Term
A chromosomes is...
Definition
-A discrete unit of genetic material.
-Human somatic cells have 46 chromosomes.
Term
Chromatin is...
Definition
-A DNA-Protein complex.
-What chromosomes are made of.
Term
1st level of DNA compaction:
Definition
-DNA wraps around 8 histone proteins to form nucleosome.
-Histones have a net positive charge.
-146 to 147 nucleotides.
-Shortens length of DNA 7 fold.
Term
2nd level of DNA compaction:
Definition
-30nm fiber.
-Current model suggests asymmetric, 3D zigzag of nucleotides.
-Shortens another 7 fold.
Term
3rd level of DNA compaction:
Definition
-Radial loop domains.
-Loops can be 25,000 to 200,000 nucleotides in length.
Term
Heterochromatin (level of chromosome compaction)
Definition
Highly compacted due to radial loop domains.
Term
Euchromatin (level of chromosome compaction)
Definition
Less compact - radial loop domains are not compact.
Term
End of chapter 11
Definition
Beginning of chapter 12
Term
Archibald Garrod
Definition
-1908 - Proposed relationship between genes and the production of enzymes. - Studied patients with metabolic defects.
- Hypothesized disease due to missing enzyme. - Knew it had a recessive pattern of inheritance (need defect from both parents) -Patients missing gene that encodes for Phenylalaine Hydroxylase - “inborn error of metabolism” - Structure and function of genetic material was unknown at the time of his work.
Term
Alkapeonuria
Definition
Patient’s body accumulates abnormal levels of homogentisic acid (alkapton).
-Causes damage to cartilage
-Damage to heart valves
Term
Beadle and Tatum
Definition
-became aware of Garrod’s work in early 1940s
-Studied Neurospora crassa (common bread mold)
-Only carbon source (sugar), inorganic salts and biotin needed for growth.
-Enzyme synthesizes molecules it needs
-Mutant strains unable to grow unless supplemented
-Their hypothesis - A single mutation would result in the requirement for a single type of vitamin or supplement.
-Stimulated research into other substances including arginine
-Isolated several mutants requiring arginine for growth
-Wild-type can grow without the added supplements
-Types 1,2,3 require addition of a supplement
-Beadle and Tatum concluded that single gene controls the synthesis of a single enzyme.
Term
One gene = one enzyme hypothesis
Definition
-Beadle and Tatum concluded that single gene controls the synthesis of a single enzyme.
-Hypothesis has been modified
-Enzymes are only a single category of cellular proteins, genes also code for other proteins.
-Some proteins composed of one or more polypeptides
-More accurate to say one gene encodes one polypeptide
-Hemoglobin composed of 4 polypeptides, each required for proper function
-NEW - One gene = one polypeptide
Term
Central Dogma of Biology
Definition
-Proposed by Francis Crick in 1958
Transcription > Translation
(DNA > RNA > Protein)
Term
Transcription (part of central dogma)
Definition
-Produces an RNA copy or transcript of a gene
-Structural genes produce messenger RNA (mRNA) that specifies the amino acid sequence of a polypeptide.
Term
Translation (part of central dogma)
Definition
Process of synthesizing a specific polypeptide on (at) a ribosome.
Term
1st stage of transcription
Definition
Initiation - recognition step
-In Bacteria (only), sigma factor causes RNA polymerase to recognize prometer region
-Stage is complete when DNA strands separate near promoter to form an open complex.
Term
2nd stage of transcription
Definition
Elongation - RNA polymerase synthesizes RNA
-Template or coding strand used for RNA synthesis (opposing strand not used)
-Synthesized 5’ to 3’ (template read 3’ to 5’)
-Uracil substituted for Thymine
Term
3rd stage of transcription
Definition
Termination - RNA polymerase reaches termination sequence
- Causes RNA polymerase and RNA to disassociate from DNA
Term
RNA processing (Bacteria vs. Eukaryotic)
Definition
-Bacterial mRNA proceeds directly to translation
-Eukaryotic pre-mRNA must be processed into mature mRNA
Term
RNA procession - eukaryotes (only)
Definition
-Introns - transcribed but not translated (found in many eukaryotic genes)
-Discovered in the 1970s
-Considered ‘junk’ DNA
-Exons - coding sequence bound into mature mRNA
Term
RNA transcription - Splicing - eukaryotes (only)
Definition
removes introns and connects exons.
Term
Spliceosome
Definition
-Removes introns precisely
-Complex molecule
-Composed of snRNPs (small nuclear RNA)
Term
Alternative splicing
Definition
if a strand is spliced in a different way may produce a different product
-rRNA and tRNA are self-splicing (includes ribosome molecules)
Term
RNA adenine tail
Definition
-3' end
-Consists of 100-200 nucleotides
-Increases stability and lifespan in cytosol
-Not encoded in genome
Term
RNA cap
Definition
-5' -Modified guanosine -Needed for proper exit from nucleus and binding to ribosome
Term
Translation
Definition
-Coded mRNA is used to create polypeptide by ribosomes
-Cells use a lot of energy for this (E.Coli =90%)
-Requires mRNA, tRNA and ribosomes
Term
Codons
Definition
groups of three base pairs in mRNA
-Most codons specify a specific amino acid (also start and stop codons)
-Degenerate - more than one code can specify the same amino acid
Term
Start codon
Definition
-codon: AUG
-5' - binds with ribosomal binding site.
Term
Stop codons
Definition
UAA, UAG, UGA
Term
tRNA
Definition
-Different tRNA molecules encoded by different -Common features of all tRNA
-Cloverleaf shape
-Anticodon
-Acceptor system for binding to specific amino acid
Term
Each tRNA is unique
Definition
-Has Anticodon - 3 RNA nucleotide that recognizes mRNA specifically
-Proper Amino acid attaches to opposing binding site
Term
Aminoacyl-tRNA synthetase
Definition
Catalyzes attachment of amino acids to tRNA
-One for each of the 20 amino acids
-Ability to recognize and attach has been called ‘second genetic code’
Term
Charged tRNA
Definition
tRNA with amino acid attached
Term
Ribosomes
Definition
-Prokaryotes have one kind of ribosome
-Eukaryotes have distinct ribosomes in different cellular compartments
-Found most abundantly in cytosol
-Also in mitochondria and chloroplasts (similar to bacterial ribosomes)
Term
Antibiotics
Definition
-Specifically target and shut down ribosomes in bacteria only
Term
rRNA
Definition
Determines ribosome shape
Term
Ribosomal Structure - A site
Definition
aminoacyl site (1st site/where tRNA enters)
Term
Ribosomal Structure - P site
Definition
peptidyl site (where amino acids are joined together)
Term
Ribosomal Structure - E site
Definition
exit site (tRNA is released)
Term
Stages of Translation - 1. Initiation
Definition
-mRNA, tRNA and ribosomal units form a complex
I. Requires ribosomal initiation factors
II. Requires energy input from GTP via hydrolysis
Term
Stages of Translation - 2. Elongation (1st of 3)
Definition
I. Aminoacly tRNA brings a new amino acid to the a Site. i. Binding occurs due to codon/anticodon reaction. ii. Elongation factors hydrolyze GTP to provide energy to bind tRNA to A site. iii. Peptidyl tRNA is in the P site. iv. Aminoacyl tRNA is in the A site.
Term
Stages of Translation - 2. Elongation (2nd of 3)
Definition
II. A peptide bond is formed between the amino acid at the A site and the growing peptide chain.
i. The polypeptide is removed from the tRNA in the P site and transferred to the amino acid at the A site - peptidyl transfer reaction.
ii. rRNA catalyzes peptide bond formation - ribosome is a ribozyme.
Term
Stages of Translation - 2. Elongation (3rd of 3)
Definition
III. Movement of the ribosome toward the 3’ end of the mRNA by (length of one codon). i. Shifts tRNA to E and P sites. ii. Next codon in now at the A site. iii. Used (uncharged tRNA) exits from E site.
Term
Stages of Translation - 3. Termination
Definition
-Ribosome reaches a stop codon. Polypeptide is released and units disassemble.
I. Stop codon arrives at A site.
II. Release factor binds to stop codon at the A site.
III. Bond between polypeptide and tRNA hydrolyze to release polypeptide.
IV. Ribosomal subunits and release factors disassociate.
Term
End of chapter 12
Definition
Beginning of chapter 14
Term
Mutation
Definition
-A heritable change in the genetic material
-Essential to the continuity of life (source of variation for natural selection)
-New mutations more likely to be harmful than beneficial (may cause death and not be passed on)
-DNA repair system reverse DNA damage (attempt to fix mutation before it becomes permanent)
Term
Point mutation
Definition
-Affects only a single base pair
1. change base sequence (substitution)
2. add or remove nucleotide(s)
Term
Silent mutation
Definition
-Does not alter the amino acid sequence (even with substitution the same amino acid is coded for)
Term
Missense Mutation
Definition
-Changes a single amino acid in a polypeptide
-May not alter function if new amino acid is similar to original (Galamate to Asparate)
Term
Sickle-cell disease
Definition
-The result of a single amino acid substitution
-(BETA)-globin gene
-Change in amino acid sequence causes blood cells to become sickle shaped(Glu to Val)
Term
Nonsense mutation
Definition
-Change from a normal codon to a stop or a termination codon (UAA, UGA, UAG)
-Produces truncated polypeptide (results in reduced or no function)
Term
Frameshift Mutation
Definition
-Addition of deletion of nucleotides that are not multiples of 3
-protein function likely to be completely inhibited
-Results in completely different amino acid sequence downstream
Term
Gamete
Definition
A cell that fuses with another cell during fertilization.
Term
Germ-line mutation
Definition

-Mutation in a gamete

-Because all other cells rise from these cells, a mutation this early on will cause all other cells to be affected.

Term
Somatic mutation
Definition
Can occur at any time and often lead to 'patches' of affected cells. (referred to as mosaic)
Term
Spontaneous mutations
Definition
Spontaneous mutations result from abnormalities in biological processes -Rates vary from species to species and from gene to gene
Term
Expected rate of mutation?
Definition
1 mutation for every 1 million genes
Term
Induced mutations are brought on by environmental agents
Definition
-Mutation rate higher than spontaneous mutation
-Mutagens are chemical or physical agents (can alter DNA in various ways)
-Disrupt pairing by:
-Modifying nucleotide structure
-Nitrous acid deaminates bases so that modified bases to not pair with proper nucleotide
-Using base analogue similar to particular bases
-Akylating bases
-Interfering with replication - inserts between bases and distorts helix
Term
Ionizing radiation
Definition
-Has high energy and can penetrate deeply into biological materials to create free radicals
-X-rays and gamma rays
-Cause base deletions or breaks in one or both DNA strands
Term
UV rays can cause formation of...
Definition
-A thymine dimer causing gaps or incorporation of
incorrect bases (two adjacent thymine bases become covalently bonded)
Term
Ames test
Definition
A test to determine the mutagenic activity of chemicals by observing whether they cause mutations in sample bacteria.
Term
DNA repair (3 types)
Definition
-All organisms must have the ability to repair changes that occur in DNA to minimize mutation
-Requires: DNA damage to be detected and Repair or DNA damage
1. Direct Repair
2. Altered DNA strand removed and replaced
3. Nucleotide Excision Repair (NER)
Term
Types of DNA repair - 1. Direct Repair
Definition
Enzyme removes modification
Term
Types of DNA repair - 2. Altered DNA strand removed and new segment synthesized
Definition
-more common than direct repair
- “Methyl-directed mismatch repair”
-base-pair mismatch
-DNA strand is removed
-replaced from complementary strand
Term
Types of DNA repair - 3. Nucleotide Excision Repair (NER)
Can repair what 4 things?
Definition
-Most common DNA repair -Can repair: -UV damage -chemically modified bases -missing bases -Crosslinks such as thymine dimers
Term
Types of DNA repair - 3. Nucleotide Excision Repair (NER)
Definition
-Region encompassing several nucleotides in the damage strand is removed from DNA
-Intact, undamaged strand is used as a template for re-synthesis of a normal complimentary strand
-Found in all Eukaryotes and Prokaryotes
-Four Key proteins: UvrA, UvrB, UvrC, UvrD
-involved in ultraviolet repair
Term
NER and human genetic disease
Definition
-NER system was discovered in humans by the analysis of genetic diseases that affect DNA repair
-Xeroderma pipmentosum (XP)
-Cockayne’s syndrome (CS)
-PIBIDS
-Photosensitivity is a common characteristic in all three syndromes because of an inability to repair UV-induced lesions
Term
Cancer
Definition
-Disease of multicellular organisms that is characterized by uncontrolled cell devision.
-1.5 million americans diagnosed each year
-In about 10% of cancers, a higher predisposition to develop the disease is an inherent trait
-Most cancers (90%) do no involve genetic changes that are passed down from parent to child
-Most cancers are caused by mutagens
-A few viruses are known to cause cancer (Rous sarcoma virus (RSV))
Term
Carcinogens
Definition
-About 80% of all human cancers are related to exposure to carcinogens
-Agents that increase the likelihood of developing cancer
-Most carcinogens, such as UV light and certain chemicals in cigarette smoke, are mutagens that promote genetic changes in somatic cells.
-DNA alterations can lead to effects on gene expression that ultimately affect cell division and thereby lead to cancer.
Term
Tumor
Definition
-Tumor may begin a benign or pre-cancerous (do not invade or spread)
-Malignant stage
-Lost normal cell growth regulation
-Invasive - can invade healthy tissues
-Metastatic - can migrate to other parts of the body
-Left untreated, will cause death of the organism
Term
Oncogenes
Definition
-Cell division regulated by hormones called grown factors
-Bind to cell surface and initiate cascade leading to cell division which includes activating specific genes
-Mutations in genes producing cell growth signaling proteins can change them into oncogenes producing abnormally high level of activity in some proteins
-An oncogene may promote cancer by keeping the cell division signaling pathway in a permanent ‘on’ position
-In some cancers the amount of gene product is abnormally high
-In others, the gene produces a functionally hyperactive protein
Term
Ras - intracellular signaling protein (relate to oncogenes)
Definition

-GTPase that hydrolyzes GTP to GDP -When GTP is bound, Ras promotes cell division

-Oncogenic mutations may decrease ability of Ras to hydrolyze GTP or exchange GDP for GTP factor (both keep signaling pathway on).

Term
Proto-oncogene (also see table 14.7)
Definition
-Normal gene that, if mutated, can become an oncogene
-4 common genetic changes
Term
Proto-oncogene 1 - Missense Mutation
Definition
-Chemical mutations have been shown to cause missense mutations leading to cancer
Term
Proto-oncogene 2 - Gene Amplifications
Definition
-Abnormal increase in copy number results in too much of the encoded protein
-Many human cancers are associated with the amplification of some proto-oncogenes
Term
Proto-oncogene 3 - Chromosomal translations
Definition
-Two different chromosomes break, and the ends of the chromosomes fuse incorrectly
-Very specific types of chromosomal translocations have been identified in certain tumors
-Chimeric genes are composed of two genes fragments fused together
Term
Proto-oncogene 4 - Retroviral Insertions
Definition
-Viral DNA may insert into a host chromosome in such a way that a viral promoter and response elements are next to a proto-oncogene. (may result in the over-expression of the proto-oncogene, thereby promoting cancer)
-Alternatively, a virus may cause cancer if it carries an oncogene in the viral genome
Term
Tumor-supressor gene functions (2)
Definition
1. Proteins that maintain the integrity of the genome by monitoring and/or repairing alterations in the genome. (Checkpoint proteins check the integrity of the genome and prevent a cell from progressing past a certain point in the cell cycle).
2. Proteins that are negative regulators or inhibitors of cell division. (Function is necessary to properly halt cell division otherwise cell division in abnormally accelerated).
Term
Checkpoint proteins
Definition
Proteins called cyclins and cyclin-dependent protein kinases (sdks) are responsible for advancing a cell through the four phases of the cell cycle.
Term
Protein Checkpoint - p53
Definition
Responsible for monitoring the integrity of the genome and preventing it's progression throught the cell cycle if abnormalities are detected.
Term
Cancer is a series of changes (3)
Definition
-Cancer usually requires multiple genetic changes to the same cell
-Begin with a benign genetic alteration that over time, with additional mutations lead to malignancy
-Malignancy can continue to accumulate genetic changes that make it even more difficult to treat
Term
Lung Cancer
Definition
-Diagnosed in approximately 170,000 men and women each year in the US
-1.2 million cases diagnosed worldwide
-Nearly 90% of these cases are caused by smoking and are preventable
-Unlike other cancers for which early diagnosis is possible, lung cancer is usually detected only after it has become advanced and is difficult, if impossible to cure.
-The five-years survival rate of a lung cancer patient is 15%
Term
Leukemia can be caused by...
Definition
gene amplification of a proto-oncogene
Term
End of chapter 14
Definition
Beginning of chapter 15
Term
Karyotype reveals...
Definition
number, size and form of chromosomes in actively dividing cells
Term
Mitosis
Definition
Cell divides into two cells identical to mother cell
Term
Interphase (1) - Mitosis
Definition
-Phase of the cell cycle during which the chromosomes are de-condensed and found in the nucleus
-When G1, S, G2 phases happen
Term
G1 (interphase)
Definition
-Cell accumulates molecular changes that cause progression through the cell cycle
-Passes restriction point where cell is committed to enter S phase
-If cell is not ‘in shape’ to divide, division stops at this step
Term
S (interphase)
Definition
-Chromosomes replicate
-After replication, 2 copies stay joined to each other and are called sister chromatids
-Human cells now temporarily have 92 chromatids
Term
G2 (interphase) - Mitosis
Definition
-Cell synthesizes proteins needed during mitosis and meiosis
Term
Prophase (2) - Mitosis
Definition
-Chromosomes have already replicated to produce 12 chromatids, joined as six sister pairs
-Nuclear membrane dissociates into small vesicles
-Chromatids condense into highly compacted structures (readily visible by light microscopy)
Term
Prometaphase (3) - Mitosis
Definition
-Nuclear envelope completely fragments
-Mitotic spindle is fully formed during this phase
-Centrioles move apart and demarcate the two poles
-Spindle fibers interact with sister chromatids
-Two kinetochores on each pair of sister chromatids are attached to kinetochore microtubules from opposite sides
Term
Metaphase (4) - Mitosis
Definition
-Pairs of sister chromatids are aligned along a plane halfway between the poles called the metaphase plate (organized into a single row)
-When alignment is complete, the cell is in metaphase
Term
Anaphase (5) - Mitosis
Definition
-Connections between the pairs of sister chromatids are broken
-Each chromatid , now an individual chromosome, is linked to only one of the two poles by one or more kinetochore microtubules
-Kinetochore microtubules shorten, pulling chromosomes toward the pole to which attached
-Two poles more farther apart as overlapping polar microtubules lengthen (push on each other)
Term
Telophase (6) - Mitosis
Definition
-Chromosomes have reached their respective poles and decondense
-Nuclear membranes now re-form to produce two separate nuclei
Term
Cytokinesis
Definition

-In most cases mitosis is quickly followed by cytokinesis

-Two nuclei are segregated into separate daughter cells

-Process of cytokinesis is quite different in animals and plants

-Animals - cleavage furrow constricts like a drawstring to separate cells

-Plants - cell plate forms a cell wall between the two daughter cells (made of vesciles from golgi apparatus)

Term
Mitotic spindle
Definition
-responsible for organizing and sorting the chromosomes during mitosis
-Astral - position spindle in cell
-Polar - Separate to poles
-Kinetochore - attached to kinetochore bound to centromeres of each chromosome
Term
Meiosis
Definition
-Sexual reproduction requires a fertilization event in which two haploid gametes unite to create a diploid cell called a zygote.
-A process by which haploid cells are produced from a diploid cell. (cells going through meiosis must go through G1, S and G2 before beginning)
Term
Bivalent/Tetrad
Definition
Homologous pairs of chromatids associate together and Cross Over (swap pieces of genetic material).
Term
Chiasma
Definition
After crossing over, chromosomes stay attached at crossing over site called a chiasma
Term
Crossing Over
Definition
Physical exchange between chromosome pieces of the bivalent complex. (increases genetic variation).
Process is carefully controlled by cells.
Term
Prophase 1 - Meiosis 1
Definition
Replicated chromosomes condense and bivalents form as the nuclear membrane breaks down.
Term
Prometaphase 1 - Meiosis 1
Definition
Spindle apparatus complete and the chromatids are attached to kinetochore microtubules.
Term
Metaphase 1 - Meiosis 1
Definition
Bivalents are organized along metaphase plate.
Term
Anaphase 1 - Meiosis 1
Definition
-Connections between bivalents break, but not the connections that hold sister chromatids together.
-Each joined pair of chromatids migrates to the pole.
Term
Telophase 1 and cytokinesis - Meiosis 1
Definition
Sister chromatids have reached their respective poles and decondense. Nuclear membranes form.
Term
Meiosis 2
Definition
-No S phase between Meiosis 1 & 2.
-Sorting events are similar to mitosis, but concludes with haploid cells because there was no S-phase after meiosis 1.
Term
# of chromosomes - Humans
Definition
46
Term
# of chromosomes - Dogs
Definition
78
Term
# of chromosomes - Fruit Fly
Definition
8
Term
# of chromosomes - Tomato
Definition
24
Term
Giemsa Stain does what?
Definition
Stains chromosomes for G banding identification
Term
Location of a Metacentric centromere is where?
Definition
middle
Term
Location of a Submetracentric centromere is where?
Definition
slightly off center
Term
Location of a Acrocentric centromere is where?
Definition
near end (not at end)
Term
Location of a Telocentric centromere is where?
Definition
at end
Term
Chromosomal mutation - Duplication
Definition
Selection occurs 2 or more times in a row.
Term
Chromosomal mutation - Inversion
Definition
Change in direction along a single chromosome
Term
Chromosomal mutation - Translocation
Definition
-One segment becomes attached to another chromosome.
-Simple or reciprocal.
Term
Diploids have...
Definition
2n chromosomes
Term
Triploids have...
Definition
3n chromosomes
Term
Tetraploids have...
Definition
4n chromosomes
Term
Aneuploidy (chromosomes)
Definition
-Alteration of particular chromosomes.
-Total number not an exact multiple of a set.
-(if happens in eukaryotes is detrimental)
-(5-10% of all human eggs result in and embryo with abnormal chromosome number)
Term
Trisomic (chromosomes)
Definition
-Normal 2 copies of a chromosome plus a 3rd.
-2n+1
Term
Monosomic
Definition
-Missing one of the normal copies of a chromosomes
-2n-1
Term
Nondisjunction (chromosomes)
Definition
-Chromosomes do not sort properly during cell division.
-During meiosis, can produce gametes with too many chromosomes of too few.
Term
End of chapter 15
Definition
Beginning fo chapter 16
Term
Gregor Mendel
Definition
Tested around 29,000 Peas
Term
Advantages to testing peas
Definition
-Many testable characteristics and traits.
-Normally self-fertilizing
-Easy to true-breed
-Large flowers make for easy crossing
Term
Mendel observed (traits)
Definition
-Flower color
-Flower position
-Seed color
-Seed shape
-Pod shape
-Pod color
-Height
Term
Monohybrids
Definition
-Generation differ on one trait
Term
Important ideas in simple inheritance (1/3)
Definition
Dominant and Recessive traits
Term
Important ideas in simple inheritance (2/3)
Definition
Genes and Alleles
Term
Important ideas in simple inheritance (3/3)
Definition
Segregation of Alleles
-Approx 3:1 ratio
Term
Mendel's Law of segregation
Definition
2 copies of a gene segregate from each other during transmission from parent to offspring
Term
Law of independent assortment
Definition
Alleles of different genes assort independently of each other during gamete formation
Term
Genotype
Definition
Genetic composition of individual
Term
Phenotype
Definition
Characteristics that are a result of gene expression
Term
Two-factor cross possible patterns (2)
Definition
-2 genes linked so that variants found together in parents are always inherited as a unit.
-2 genes and independent and randomly distributed
Term
Dihybrid offspring
Definition
Offspring are hybrids with respect to both traits
Term
Chromosome Theory of inheritance (1/5)
Definition
Chromosomes contain DNA, which is the genetic material. Genes are found in chromosomes.
Term
Chromosome Theory of inheritance (2/5)
Definition
Chromosomes are replicated and passed from parent to offspring. They are also passed from cell to cell during the development of a multicellular organism.
Term
Chromosome Theory of inheritance (3/5)
Definition
the nucleus of a diploid contains two sets of chromosomes, which are found in homologous pairs. The maternal and paternal sets of homologous chromosomes are functionally equivalent; each set carries a full complement of genes.
Term
Chromosome Theory of inheritance (4/5)
Definition
At meiosis, one member of each chromosomes pair segregates into each daughter nucleus.
Term
Chromosome Theory of inheritance (5/5)
Definition
Gametes are haploid cells that combine to form a diploid cell. Each gamete contains one set of chromosomes.
Term
Locus
Definition
The physical location of a gene on a chromosome
Term
Pedigree analysis
Definition
Inherited trait in analyzed over the course of a few generation in one family.
Term
Pedigree analysis - Cystic Fibrosis
Definition
-3% of American of European descent carry recessive allele.
-Homozygous individuals exhibit symptoms:
-Abnormal transport of chloride and sodium ions across membranes
-Viscous secretions in lungs, pancreas
Term
Sex chromosomes
Definition
X-Y system, XX=male, XY=female
X-O system, X or XO=male, XX=female
Z-W system, ZZ=male, ZW=female
Term
Some species such as ____ and ____ have sex controlled my environmental conditions.
Definition
reptiles, fish
Term
Hemophilia A (sex-linked)
Definition
-Caused by recessive X-linked gene
-"Royal Disease"
-Endcodes defective clotting protein
Term
Morgan's experiments showed a correlation between a genetic trait and the inheritance of a sex chromosome in Drosophila
Definition
-X-linked gene the first to be located on a specific chromosome.
-Found a true-breeding line with white-eyed males rather than red eyes.
-Results suggested a connection between alleles for eye color and sex.
-Lower than expected number of white-eyed flies explained by a decreased survival rate
-1933, Morgan first geneticist to receive Nobel Prize
Term
Mendelian Inheritance
Definition
-Inheritance pattern of genes that segregate and assort independently.
-Simple Mendelian inheritance - one trait is completely dominant over the other.
-X-linked inheritance - pairs of dominant and recessive alleles found on the X chromosome
Term
Pleiotropy
Definition
When one gene influences multiple phenotypic trates
Term
Incomplete dominance
Definition
-Heterozygote has intermediate phenotype
-Neither allele is dominant
-Phenylketonuria (PKU) - Heterozygotes appear phenotypically normal but heterozygotes have double the normal phenylalanine levels
Term
Multiple alleles
Definition
-3 or more variants in a population
-Phenotype depends on which two phenotypes are inherited
-ABO blood types in humans
Term
Role of environment
Definition
-Norm or reaction - effects of environmental variation on a phenotype (phenotypic plasticity)
-Genetically identical plant grow different height at different temperatures
People with PKU can develop normally if given a diet free of phenylaline (if not can develop retardation)
Term
Random sampling error
Definition
-Deviation between observed and expected outcome.
-Larger amples have less error.
-Small families can expect deviation from expectant
Term
Product rule
Definition
-Probability that two or more independent events will occur is equal to the product of their individual probabilities.
Term
Sum rule
Definition
Probability that one of two or more mutually exclusive outcomes will occur is the sum of the probabilities of the posible outcomes.
Term
End of chapter 16
Definition
Beginning of chapter 17
Term
Epistasis
Definition
The type of gene interaction in which the alleles of one gene mask the effects of a dominant allele of another gene.
Term
Discrete traits
Definition
Phenotypes do not overlap.
Term
Quantitative traits
Definition
Phenotypes overlap. (in humans - height, weight, skin color)
Term
Polygenic
Definition
Meaning several traits contribute to the outcome.
Term
Non-recombinants
Definition
Look like P generation.
Term
Recombinants
Definition
Look different than P generation.
Term
Linkage
Definition
When two genes are close together on the same chromosome and tend to be transmitted as a unit. (a linkage group)
Term
Continuous Variation
Definition
Variations do not fall into categories directly. (height)
Term
End of chapter 17
Definition
Beginning of chapter 18
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