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BMZ Exam #1
First BMZ test
197
Biology
Undergraduate 4
02/11/2009

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Term
Inorganic Chemistry
Definition
The nature of atoms and molecules with the exception of those that contain rings or chains of carbon
Term
Organic chemistry
Definition
Carbon containing molecules
Term
Atoms
Definition

The smallest functional units of matter that form all chemical substances and that cannot be further broken down into any other substances by ordinary chemical or physical means

Term
Each specific type of atoms (N, H, O, ...) occurs as...
Definition
A chemical element
Term
What are the subatomic particles found within atoms?
Definition
Protons, neutrons, and electrons.
Term
The protons and neutrons are in the ________ of the atom, also known as the ___________.
Definition
Center of the atom, atomic neuclus.
Term
The electrons are found...
Definition
In regions at various distances from the neucleus.
Term
Which subatomic particles are identical? Which vary?
Definition
Protons and electrons are identical, neutrons vary
Term
Protons have a ______ charge, electrons have a ________ charge, neutrons have a ______ charge.
Definition

Protons = positive

Electrons = negative

Neutrons = neutral

Term
Orbitals
Definition
The regions the electrons travel in surrounding the nucleus.
Term
Atomic number
Definition
The number of protons in an atom
Term
Isotopes
Definition
When elements can exist in multiple forms (differ in the number of neutrons they contain)
Term
Radioisotopes
Definition
Isotopes found in nature that are inherently unstable and do not exist for long periods of time, they lose energy by emitting subatomic particles and/or radiation
Term
Molecule
Definition
Two or more atoms bonded together
Term
Compound
Definition
A molecule composed of two or more different elements
Term
Covalent bonds
Definition

Atoms sharing a pair of electrons, can occur between two atoms whose outer shells are not full

Term
Atoms tend to be most stable when...
Definition
Their outer shells are full of electrons.
Term
Double bond
Definition

Occurs when atoms share two pairs of electrons rather than one pair

Term
Electronegativity
Definition
The measure of an atom's ability to attract electrons in a bond from another atom
Term
Polar covalent bonds
Definition
When two atoms with different electronegativites form a covalent bond, the shared electrons are more likely to be closer to the atom with higher electronegativity than the atom of lower electronegativity; the distribution of electrons around the atoms creates a polarity (difference in electric charge) across the molecules, ex: water
Term
Polar molecules
Definition
Molecules containing a significant number of polar bonds
Term
Nonpolar molecules
Definition
Molecules composed primarily of nonpolar bonds
Term
Hydrogen bond
Definition
When a hydrogen atom from one polar molecule becomes electrically attracted to an electronegative atom (such as an oxygen or nitrogen atom) in another polar molecule; these bonds are very weak, however, DNA is actually very strong because of the very large number of hydrogen bonds
Term
Ion
Definition
Atoms are electrically neutral because they contain an equal number of positive protons and negative electrons. If an atom or molecule gains or loses one or more electrons, it acquires a net electric charge and becomes an ion (when sodium loses an electron, it becomes a net positive atom with the same number of protons and one less electron)
Term
Cation
Definition
An ion that has net positive charge
Term
Anion
Definition
An ion that has a net negative charge
Term
Ionization
Definition
The process of ion formation which can occur in single atoms or atoms that are covalently linked in molecules
Term
Ionic bond
Definition
When a cation bonds to an anion
Term
Chemical reaction
Definition
Occurs when one or more substances are changed into other substances
Term
Solutes
Definition

Substances dissolved in a liquid

Term
Solvent
Definition
Liquid in which substances are dissolved
Term
Solution
Definition

Solutes dissolved in a solvent

Term
Aqueous solutions
Definition
Solutions made with water
Term

Hydrophillic

Definition
"Water loving", molecules that contain polar covalent bonds which dissolve in water
Term
Hydrophobic
Definition
"Water fearing", molecules composed predominantly of carbon and water are insoluable in water because these bonds (carbon-carbon, carbon-hydrogen) are nonpolar (these molecules do not have partial positive and negative charges and therefore are not attracted to water molecules)
Term
Hydrolysis
Definition
What water is used to break apart another molecule
Term
Dehydration
Definition
The removal of a water molecule and the formation of a covalent bond between two separate molecules
Term
Isomers
Definition
Term
Carbohydrates
Definition
Composed of carbon, oxygen, and hydrogen atoms in this formula: Cx(H2O)x; carbon containing compounds that are hydrated
Term
Sugars
Definition
Monosaccharides; pentoses (five carbons - ribose, deoxyribose); hexoses (six carbons - glucose)
Term
Disaccharides
Definition

Carbohydrates composed of two disaccharides (sucrose, glucose + fructose = table sugar), formed by a dehydratrion reaction

Term
Polysaccarides
Definition
Many monosaccarides linked together (starch, glycogen)
Term
Lipids
Definition
Store energy and form membranes and hormones, composed predominantly of hydrogen and carbon atoms, nonpolar (insoluable in water)
Term
Fats
Definition
A mixture of triglycerides
Term
Saturated fatty acid
Definition
When all the carbons in a fatty acid are linked by single covalent bonds
Term
Unsaturated fatty acids
Definition
Fatty acids that contain one or more carbon-carbon double bonds, one carbon-carbon double bond = monounsaturated fatty acid, two or more carbon-carbon double bonds = polyunsaturated fatty acid
Term
Amino acids
Definition
The building blocks of proteins (proteins are polymers of amino acids)
Term
Peptide bond
Definition
The covalent bond formed between a carboxyl and an amino group
Term
Polypeptide
Definition
When many amino acids are joined by peptide bonds
Term
Primary structure of a polypeptide
Definition
Its amino acid sequence from beginning to end
Term
Secondary Structure
Definition
A polypeptide that folds into a more complex structure, amino acids rotate around bonds, repeating pattenrs (alpha helix and beta sheets)
Term
Alpha helix
Definition
The polypeptide backbone forms a repeating helical structure that is stabilized by hydrogen bonds
Term
Beta sheet
Definition
regions of the polypeptide backbone come to lie parallel to each other
Term
Tertiary structure
Definition
As the secondary structure becomes established due to the particular primary structure, a polypeptide folds and refolds upon itself to assume a comlpex 3-D shape, the 3-D shape of a single polypeptide
Term
Quaternary structure
Definition
When proteins consist of more than one polypeptide chain
Term
Critical factors for protein folding and stability
Definition
  1. hydrogen bonds - creates a strong force that promotes protein folding and stability
  2. ionic bonds and polar interactions - some amino acid chains are positively charged, some negatively charged, positively charged side chains may bond to negatively charged side chains via ionic bonds, also, uncharged polar side chains may interact with ionic amino acids
  3. hydrophobic effect - some amino acid side chains are nonpolar, these amino acids tend to avoid water; as the protein folds the hydrophobic amino acids are likely to be found in the center of the protein to avoid contact with water
  4. van der waals forces - atoms within molecules have weak attractions for each other if they are optimal distance apart (van der waal radius), the weak attraction is the force
  5. disulfide bridges - disulfide bonds are covalent bonds that can occur within a single polypeptide or between different polypeptides
Term

The two classes of nucelic acids are...

Definition
deoxyribose nucleic acid (DNA) and ribose nucleic acid (RNA)
Term
DNA...
Definition
stores genetic information
Term
RNA...
Definition
decodes this information
Term
Nucelotide
Definition
The building blocks of DNA and RNA, 3 components of a neucleotide: a phosphate group, a 5-carbon sugar (ribose or deoxyribose), and a single or double ring of carbon and nitrogen atoms (known as a base)
Term
What is DNA made of?
Definition
the nucleotides in DNA contain the 5-carbon sugar deoxyribose, 4 different nucleotides are present in DNA corresponding to the 4 different bases that can be linked to deoxyribose: the purine bases (adenine and guanine have double fused rings of nitrogen and carbon atoms, the pyrimidine bases (cystosine and thymine have only a single ring; two strands of nucleotides coiled around each other to form a double helix (A-T pairing and C-G pairing)
Term
What is RNA made of?
Definition
Thymine is replaced by uracil, messenger RNA vs. transfer RNA: responsible for converting the information contained in DNA into the formation of a new polypeptide
Term
How is a strand of DNA or RNA formed?
Definition
By the covalent linkage of nucleotides in a linear manner
Term
How is a double helix formed?
Definition
Two strands of DNA can hydrogen-bond with each other to form a double helix, in a double helix two DNA strands are twisted together to form a structure that resembles a spiral staircase
Term
In living cells, DNA is...
Definition
associated with an array of different proteins to form chromosomes
Term
Genome
Definition
The complete complement of an organism's genetic material
Term
Compared to ribose, deoxyribose is missing...
Definition
a singular oxygen atom
Term
Cell theory
Definition
all living things are composed of one or more cells; cells are the smallest units of living organisms, new cells come only from pre-existing cells by cell division
Term
Prokaryotes
Definition

uni-cellular, no histone proteins in their DNA, no membrane-bound nucleus, generally have a cell wall to protect the plasma membrane and cytoplasm

Term
Two categories of prokaryotes
Definition
bacteria and archaea (both are relatively small microorganisms)
Term
Most bacteria are not _____ to humans, but some may cause ______
Definition
harmful, disease
Term
Plasma membrane
Definition
a double layer of phospholipids and embedded proteins, forms an important barrier between the cell and its external environment
Term

Cytoplasm

Definition
the region of the cell that is contained within the plasma membrane
Term
Nucleoid
Definition
Region of the cell where its genetic material (DNA) is located
Term
Ribosomes
Definition
Involved in polypeptide synthesis
Term
Cell wall
Definition
Supports and protects the the plasma membrane, porous so it does not prevent most nutrients in the environment from reaching the plasma membrane
Term
Glycocalyx
Definition

an outer viscous covering surrounding the bacterium, traps water and helps protect bacterium from dying out

Term
Capsule
Definition
Some bacteria that enter the body create a thick gelatenous glycolyx called a capsule that may help them from being destroyed by the animal's defense system
Term
Pili
Definition
allow prokaryotes to attach to surfaces and to each other
Term
Flagella
Definition
provides a way for prokaryotes to swim
Term
Eukaryotic cells
Definition
protists (paramecia, algae), fungi (yeast, mold), plants, and animals
Term
Where is the DNA located in eukaryotic cells?
Definition
The nucleus
Term
Organelle
Definition
a subcellular structure,membrane-bound compartment with its own unique structure and function (ex: nucleus)
Term
Eukaryotic cells exhibit compartmentalization, which means...
Definition
they have many organelles which separate the cells into different regions; allow a cell to carry out specialized chemical reactions in different places (ex: protein synthesis and potein breakdown occur in different compartments of the cell)
Term
Centrosome (animal cell)
Definition
site where microtubles grow and centrioles are found
Term
Rough ER (animal cell)
Definition
protein synthesis, sorting, and secretion
Term
Smooth ER (animal cell)
Definition
detoxification and lipid synthesis
Term
Mitochondrion (animal cell)
Definition

site of ATP synthesis

Term
Cytoskeleton (animal cell)
Definition
shape and movement
Term
Peroxisome (animal cell)
Definition
breakdown of hydrogen peroxide and other harmful molecules
Term
Golgi apparatus (animal cell)
Definition
modification, sorting, and secretion of lipids and proteins
Term
Cytosol (animal cell)
Definition
site of many methabolical pathways, polypeptide synthesis
Term
Plasma membrane (animal cell)
Definition
movement of substances into and out of the cell, cell signaling
Term
Lysosome (animal cell)
Definition
degradation of macromolecules
Term
Nuclear envelope (animal cell)
Definition
double membrane that encloses the nucleus
Term
Nuclear pore (animal cell)
Definition
passageway for molecules into and out of the nucleus
Term
Nucleus (animal cell)
Definition
organization and expression of the genetic material
Term
Nucleolus (animal cell)
Definition
site for ribosome assembly
Term
Central vacuole (plant cell)
Definition
storage, digestion, and regulation of cell volume
Term
Cytosol (plant cell)
Definition
site of many metabolic pathways, polypeptide synthesis
Term
Mitochondrion (plant cell)
Definition
site of ATP synthesis
Term
Cytoskeleton (plant cell)
Definition
shape and movement
Term
Peroxisome (plant cell)
Definition
breakdown of hydrogen peroxicide and other harmful molecules
Term
cell wall (plant cell)
Definition
cell support
Term
Rough ER (plant cell)
Definition
protein synthesis, sorting, and secretion
Term
Smooth ER (plant cell)
Definition
detoxification and lipid synthesis
Term
Nuclear pore (plant cell)
Definition
passageway for molecules into and out of the nucleus
Term
Nucleus (plant cell)
Definition
organization and expression of the genetic material
Term
Nuclear envelope (plant cell)
Definition
double membrane that encloses the nucleus
Term
Nucleolus (plant cell)
Definition
site for ribosome assembly
Term
Chromatin (plant cell)
Definition
a complex of protein and DNA
Term
Unlike animal cells, plant cells have ________, ________, and _______.
Definition
an outer cell wall, a large central vacuole, and chloroplasts which carry out photosynthesis
Term
The ______ and ______ of proteins are responsible for the _______ and _______ of cells.
Definition
functions and structures, functions and structures
Term
Proteome
Definition
all of the types and relative amounts of proteins that are made in a particular cell at a particular time under specific conditions, the proteome of a cell determines its structure and function
Term
Cytosol
Definition
the region of the eukaryotic cell that is outside the cell organelles but inside the plasma membrane, responsible for beaking down food molecules into smaller components which causes the release of energy which causes the creation of new cellular molecules and macromolecules; synthesizes celullar proteins
Term
Metabolism
Definition
the sum of the chemical reactions by which cells produce the materials and energy that are necessary to sustain life
Term
Catabolism
Definition
the breakdown of a molecule into smaller components
Term
Anabolism
Definition
the synthesis of cellular molecules and macromolecules
Term
Polypeptide
Definition
composed of a linear sequence of amino acids, unit of structure, one or more polypeptides assemble into a 3-D protein that performs a particular function
Term
Translation
Definition
synthesis of polypeptides, the information within the gene is ultimately translated into the sequence of amino acids in a polypeptide
Term

Cytoskeleton

Definition
a network of 3 different types of protein filaments: microtubules, intermediate filaments, actin filaments
Term
What are the roles of the cytoskeleton components?
Definition
cell shape, strength, cell organization, chromosome sorting and cell division, movement of cell "cargo", cell motility/movement
Term
Dynamic instability
Definition
a single microtubule can oscillate between growing and shortening phases, important in the sorting of chromosomes during cell division
Term
Centrosome
Definition
microtubule-organizing center
Term

Centrioles

Definition
within the centrosome, conspicuous pair of structures arranged perpendicular to each other
Term
Actin filaments
Definition
microfilaments, thinnest cytoskeletel filaments
Term
Motor proteins
Definition
a category of cellular proteins that use ATP as a source of energy to promote movement
Term
Microtubules and motor proteins fascillitate movement involving...
Definition
cell apendages called cilia and flagella
Term
_________ are longer than _______ and present singly or in pairs, they have the same __________.
Definition
Flagella, cilia, internal structure
Term
Axoneme
Definition
the arrangement containing microtubules, the motor protein dynein, and linking proteins
Term
Basal bodies
Definition
anchored to the cytoplasmic side of the plasma membrane, provide a site for microtubules to grow
Term
Cytoplasmic streaming
Definition
the cytoplasm circulates throughout the cell to distribute resources efficiently in large cells
Term
Nucleus (cell biology)
Definition
an organelle found in eukaryotic cells that contains most of the cell's genetic material
Term
Endomembrane system
Definition
Nuclear envelope (encloses nucleus), the endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles
Term
Other organelles of the endomembrane system pass materials to each other via ______
Definition
vesicles
Term
Nucelar pores are formed where...
Definition
the inner and outer membranes make contact with each other, they provide a passageway for movement of molecules and molecules into and out of the nucleus
Term

Chromatin

Definition
refers to the biochemical composition of chromosomes, which contain DNA and many types of proteins
Term

Nuclear matrix

Definition
a filamentous network of proteins that is found inside the nucleus and lines the inner nuclear membrane; serves to organize the chomosomes; two parts: nuclear lamina and an internal nuclear matrix
Term
Primary function of the nucleus:
Definition
the protection, organization, and expression of genetic material, also the assembly of ribosomes (occurs in the nucleolus, a prominent region in the nucleus of nondividing cells)
Term
Ribosomes
Definition
a structure composed of proteins and rRNA that provides the site where protein synthesis occurs
Term
Each _______ occupies its own distinct, nonoverlapping territory within the cell nucleus
Definition
chromsome
Term

Endoplasmic reticulum

Definition
a convoluted network of membranes that form flattened, fluid-filled tubules of cisternae
Term
Lumen
Definition
internal space of an organelle
Term
The ER membrane encloses a single compartment called the _________.
Definition
ER lumen
Term
Rough ER vs. Smooth ER
Definition
Rough ER is studded with ribosomes (purpose: when bound to the ER membrane, the ribosomes actively synthesize proteins through the ER membrane)
Term
Smooth ER
Definition
continuous of the rough ER, more smooth ER = more alchohol breakdown, plays a role in carbohydrate metabolism, plays a role in the accumulation of calcium ions (contains calcium pumps that transport Ca2+ into the ER lumen), critical in the sythesis and the modification of lipids
Term
Golgi apparatus
Definition
consists of a stack of flattened membranes, each flattened membrane encloses a single compartment, 3 functions: secretion, processing, protein sorting
Term
Golgi packages different types of materials into secretory vesticles, which are...
Definition
a membrane vesticle carrying different types of materials that later fuses with the cell's plasma membrane to release the contents extracellularly, that fuse with the plasma membrane and release the contents outside the plasma membrane
Term
Lyososmes
Definition
small organelles found in animal cells that are able to lyse macromolecules, they contain many acid hydrolases (hydrolitic enzymes that use a molecule of water to break a covalent bond - hydrolysis)
Term
Autophagy
Definition
the eating of one's self, cellular material (such as a worn-out organlle) becomes enclosed in a double membrane, this autophagosome then fuses with a lysosome and the material inside the autophagasome is digested, the small molecules that are released from this digestion are recycled back into the cytosol
Term

Vacuole

Definition
specialized compartments found in eukaryotic cells that function in storage, the regulation of cell volume, and degradation
Term
Tonoplost
Definition
membrane of central vacuole, stores a large amount of water, enzymes, and inorganic ions such as calcium and other materials including proteins and pigments; performs a space-filling function, puts pressure on the cell wall maintaining the structure of cells and the plant
Term
Many plasma membrane proteins are involved in __________.
Definition
membrane transport: transport essential nutrients or ions into the cell or export of substances - for this reason the plasma membrane is selectively permeable
Term
Cell signaling
Definition

another vital function of the plasma membrane, to survive cells must be able to sense changes in the environment, cells need to communicate with each other to coordinate their activities, once signaling molecules bind to a receptor this initiates the signal cascade that causes the cell to respond the the signal, in animal cells the plasma membrane is also involved in cell adhesion

Term
Semiautonomous
Definition
cells can grow and divide and reproduce themselves but they depend on other parts of the cell for internal components (mitochondria, chloroplasts, peroxisomes)
Term
What supplies cells with most of their ATP?
Definition
Mitochondria (convert chemical energy that is stored in covalent bonds in organic molecules into a form that can be readily used by cells)
Term
Photosynthesis
Definition
carried out by chloroplasts, capture light energy and use some of that energy to synthesize organic molecules such as glucose
Term
Peroxisomes
Definition
catalyze detoxifying reactions, peroxisomes contain an enzyme called catalase that breaks down hydrogen peroxide to make water and oxygen gas
Term
The plasma membrane separates the _________ of a cell from its __________
Definition
internal contents, external environment
Term

Lipids form the ________ of a membrane

______ are embeded in the membrane and loosely attached to the surface

__________ may be attached to lipids and proteins

Definition

basic matrix

proteins

carbohydrates

Term
Phospholipid bilayer
Definition
framework of the membrane
Term
Passive transport
Definition
the diffusion of a solute across a membrane in a process that is energetically favorable and does not require an input of energy, can occur by passive diffusion or fascillitated diffusion (involves the aid of transport proteins)
Term
Osmosis
Definition
the movement of water across membranes to balance solute concentrations
Term
When the solute concentrations on both sides of the membrane are  equal, the two solutions are said to be _______
Definition
isotonic
Term
When the solute concentration inside the cell is higher, it is said to be _______ relative to the outside of the cell, which is _________
Definition
hypertonic, hypotonic
Term
Transport proteins cause biological membranes to be ___________
Definition
selectively permeable
Term
Channels
Definition
transmembrane proteins that form an open passageway for the fascillitated diffusion of ions or molecules across the membrane
Term
Most channels are gated which means:
Definition
they can open to allow the diffusion of solutes and close to prohibit diffusion
Term
________ and _______ display diverse types of nutrition and response to oxygen
Definition
bacteria and archaea
Term
Autotrophs
Definition
self feeders, ex: cyanobacteria, two categories: photoautotophs and chemoautotrophs
Term

Photoautotrophs

Definition
are able to use light as a source of energy for synthesis of organic compounds from CO2 and H2O or H2S
Term
Chemoautotrophs
Definition
able to use energy obtained by chemical modifications of inorganic compounds to synthesize organic compounds
Term
Heterotrophs
Definition
"other feeders", organisms that requrire at least one organic compound and often more
Term
Photoheterotrophs
Definition
they are able to use light energy to generate ATP but they must take in organic compounds from their environment
Term
Chemoheterotrophs
Definition
must obtain organic molecules for both energy and as a carbon source
Term
Obligate aerobes
Definition
require oxygen
Term
Aerotolerant anaerobes
Definition
do not use O2, not poisoned by O2 either, they obtain their energy by anaerobic respiration which uses electron acceptors other than oxygen in electron transport processes
Term

Diazotrophs

Definition
dinitrogen consumers that conduct a specialized metabolic process called nitrogen fixation
Term
Nitrogen fixation
Definition
the removal of nitrogen from the gaseous phase is called fixation, during nitrogen fixation the enzyme nitrogenase converts atmospheric gas (N2) into ammonia (NH3), plants and eukaryotic algae can use ammonia to produce proteins and other essential nitrogen-containing molecules
Term
Heterocysts
Definition
they display many adaptation that reduce nitrogenase exposure to oxygen (thick walls, absence of oxygen-producing photosystems, increased respiration (consumes oxygen))
Term
______ and _______ play important roles in Earth's carbon cycle
Definition

bacteria and archaea

Term
Cyanobacteria
Definition
along with other autotrophic bacteria, is an important producer--the bacteria together with algae and plants synthesize the organic compounds used by other organisms for food
Term
Decomposers (sacrobes)
Definition
include heterotrophic microorganisms, these organisms break down dead organisms and organic matter, releasing minerals for uptake by living things
Term
Methanogens
Definition
convert CO2, methyl groups, or acetate to methane and release it from their cells
Term
Methanotrophs
Definition
consume methane
Term
Symbiosis
Definition
bacteria live in symbiotic associations with eukaryotic organisms, if symbiotic associations are benefical to both partners, the association is referred to as mutualism, if one partner benefits at the expense of the other it is referred to as parasitism and the partner that benefits is a parasite/pathogen
Term
Pathogens
Definition
the name of parasitic microbes that cause disease symptoms in their host
Term
How do pathogenic bacteria attack cells?
Definition

by binding to the target cell surfaces and injecting substances that help them utilize cell components. once within a host's cell, pathogenic bacteria use the cell's resources to reproduce and spread to nearby tissues

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