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BIOSC 0150: EXAM 1
Cell & Organization |
Example: each cell can only perform the job associated with its specific function such as heart cells, brain cells etc.
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Energy use and metabolism |
To maintain their internal order, energy is needed by organisms. Energy is utilized in chemical reactions.
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Regulation and homeostasis |
internal regulation of our body to maintain a stable environment
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Growth and development |
all living things get larger and more complex throughout the organism's life
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Reproduction |
everything an organism does contributes to one goal: replication itself
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Biological evolution |
the change over time of living organisms and their populations continue to evolve
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Information of an organism |
hereditary info encoded in units called genes; response to environmental changes responds to stimuli
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Theory |
an explanation for a very general class of phenomena or observations for which there is a wide body of supporting evidence
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Cell Theory |
All organisms are made of membrane-bound cells (pattern). All cells come from preexisting cells (process).
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Microscope |
Robert Hooke 30x of cork cell; Anton Leewenhoek 300x 1660s
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Hypothesis |
a testable statement that explains a set of observations
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Spontaneous Generation Hypothesis |
(1880s) cells arise spontaneously from non-living material under the right conditions
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Virchow's All-Cells-From-Cells Hypothesis |
cells are produced only when preexisting cells grow and divide
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Prediction |
a measurable or observable result that must be correct if a hypothesis is valid
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Charles Darwin and Alfred Russell Wallace prediction |
all distinct, identifiable types of organisms are connected by common ancestry
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4 Macromolecular Chemical Building Blocks of Life |
Proteins, Nucleic Acids, Carbohydrates, Lipids
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Valence |
number of unpaired electrons
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Covalent Bonds |
a strong attraction where two atoms share one or more pairs of electrons
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How atoms form molecules |
making strong covalent bonds that have specific lengths and geometry
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Hydrogen number of covalent bonds |
1 |
Oxygen number of covalent bonds |
2 |
Sulfur number of covalent bonds |
2 |
Nitrogen number of covalent bonds |
3 |
Carbon number of covalent bonds |
4 |
Phosphorus number of covalent bonds |
up to 5
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Electronegativity |
a measure of the ability of an atom to attract electrons toward itself from an atom to which it is bonded
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Polar Covalent Bonds |
electrons are not shared equally (asymmetric)
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Nonpolar Covalent Bonds |
The sharing of electrons in a covalent bond can be equal
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Polar |
Molecules with partially charged atoms
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Molecular Formulas |
indicate only the number and types of atoms in a molecule
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Structural Formulas |
indicate which atoms in a molecule are bonded together
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Ball-and-Stick Models |
provide information on the 3-D shape of molecules and the relative size of atoms involved
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Space-Filling Models |
more accurately depict the spatial relationships between atoms
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Ionic bonds |
electrons are completely transferred from one atom to another; the closer the two ions are to each other, the stronger the attraction (non directional)
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Ion |
atom or molecule that carries a full charge
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Cation |
loss of electron
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Anion |
gain of electron
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Electronegativities of 4 most abundant elements in organisms |
0>N>C (about equal to) H
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Hydrogen Bonds |
weak interactions formed between two molecules (or different parts of the same molecule)
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Hydrophobic |
substances that do not interact with water
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Solvent |
agent for dissolving substances and getting them into solution
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Solutes |
when the substance are dissolved in a solvent like water
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Hydrophobic substances |
no H bond donors or acceptors
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Hydrophobic interactions |
interactions with water are minimal or nonexistent so they are forced to interact with each others
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Hydrophilic |
substances that interact with water
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Hydrophilic= Polar |
fully or partially charged; can form ionic or H bonds
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Hydrophobic= Nonpolar |
uncharged, cannot form ionic or H bonds
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Van Der Waals Interactions |
favorable interactions between hydrophobic surfaces (stabilize hydrophobic surfaces)
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Van Der Waals Interactions |
two electrically neutral molecules; transient fluctuations in electrons create electric dipoles; dipoles synchronize, molecules thus attract each other
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Cohesion |
attraction between like molecules; tendency of certain molecules to cling together due to attractive forces
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Adhesion |
attraction between unlike molecules; tendency of certain dissimilar molecules to cling together due to attraction
ex: liquid and solid
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A meniscus forms as a result of two forces: |
1) Water molecules at the perimeter of the surface adhere to the glass, resulting in an upward forces
2) Water molecules at the surface hydrogen-bond with water molecules next to them and below them, resulting in a net lateral and downward pull that resists the upward pull of adhesion
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Surface Tension |
When water molecules are at the surface, there are no water molecules above them for hydrogen bonding, they exhibit stronger attractive forces between their nearest neighboring molecules; cohesive force that causes molecules at the surface of a liquid to stick together and resist deformation of the liquid's surface
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Specific heat |
amount of energy required to raise the temperature of 1 gram of substance by 1 degree Celcius
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Heat of Evaporation |
the energy required to change 1 g of water from a liquid to a gas
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The chemical reaction that takes place between water molecules is called a "dissociation" reaction. |
H20 <--> H+ + OH-
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Hydrogen ion |
H+
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Hydroxide ion |
OH-
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Acids |
molecules or ions that acquire protons during chemical reactions
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Bases |
molecules or ions that lower the hydronium ion concentration of water
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Adding an acid to a solution... |
increases the concentration of protons
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Adding a base to a solution... |
lowers the concentration of protons
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pH |
way in which to express the concentration of protons in a solution
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Buffers |
compounds that minimize changes in pH
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Homeostasis |
constant conditions
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Organic Molecules |
molecules that contain carbon bonded to other elements, such as hydrogen
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Carbon atoms... |
provide the structural framework for virtually all the important compounds associated with life, with the exception of water
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Functional Groups |
the critically important H-, N-, O-, P-, and S- containing groups found in organic compounds that determine the type of reactions the molecule will participate in; can participate in chemical reactions
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Amino and Carboxyl functional groups |
Amino groups function as bases, Carboxyl groups function as acids; both of these groups function participate in hydrogen bonding and are important functional groups in amino acids, where it can form a covalent bond with each other to link amino acids
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Carbonyl Groups |
the site of reactions that link these molecules into larger, more complex organic compounds; acts as ACID; important functional group in amino acids where it can form covalent; found in aldehydes and ketones
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Hydroxyl Groups |
act as weak acids; molecules containing hydroxyl groups will form hydrogen bonds and tend to be soluble in water
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Phosphate Groups |
carry two negative charges; phosphates that are bonded together store chemical energy that can be used in chemical reactions; when transferred from one organic compound to another, the change in charge can dramatically affect the structure of the recipient molecule
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Sulfhydryl Groups |
consist of a sulfur atom bonded to a hydrogen atom. They are important because sulfhydryl groups can link to one another via disulfide bonds
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When you encounter an organic compound that is new to you, its important to follow three steps: |
1) Examine the overall size and shape provided by the carbon framework
2) Identify the type of covalent bonds present based on the electronegativities of that atoms. Use this information to estimate the polarity of the molecule and the amount of potential energy stored in its chemical bonds
3) Locate any functional groups and note the properties these groups give to the molecule
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The unique properties of water stem from its structure |
small size; bent shape; highly polar covalent bonds; overall polarity; able to form hydrogen bonds
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The atoms is a given functional group... |
are bonded together in a precise configuration and impart specific chemical properties to the molecule
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Organic compounds commonly contain... |
>1 functional group (eg amino acid)
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Polymer |
any large molecule composed of small repeating units covalently bonded together
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monomer |
small repeating units
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Monomers polymerize through... |
condensation reactions
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Condensation Reaction |
(dehydration synthesis) a chemical reaction in which two molecules are joined covalently with the removal of an -OH from one molecule and an -H from the other molecule to form water (monomer in, water out)
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Hydrolysis |
a chemical reaction in which a molecule is split into smaller molecules by reacting with water (water in, monomer)
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Proteins are... |
the most abundant and versatile macromolecule in life
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Protein |
macromolecule consisting of one or more polypeptide chains composed of amino acids linked together
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alpha carbon |
central carbon atom
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each amino acid is composed of: |
alpha carbon, hydrogen atom, amino group, carboxyl group, side chain (R-group)
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Ionized Amino Acids |
Charges are important cause they 1) keep amino acids in solution (to promote interactions) 2) affect the amino acid's chemical reactivity
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Functional groups of the 20 R groups of amino acids affect reactivity |
Some R groups contain functional groups that can participate in chemical reactions (sulfhydryl, carboxyl, hydroxyl, or amino); other R groups that are devoid of functional groups rarely participate in chemical reactions (contribute to protein function through size and shape rather than reactivity)
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Side chain polarity affects solubility |
Hydrophobic nonpolar side chains cannot form hydrogen bonds with water. Hydrophilic polar or charged side chains can readily hydrogen bond with water
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Amino acids can be grouped into four general types based on their side chains |
1) nonpolar 2) uncharged polar 3) acidic 4) basic
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Nonpolar Amino Acids |
cannot form H or ionic bonds; are found in the hydrophobic core of folded proteins (due to hydrophobic effect, van der waals interactions)
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Special amino acids with nonpolar side chains |
Gylcine, Cysteine, Porline
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Glycine |
H instead of side chain; allows peptide chain make a sharp turn
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Cysteine |
can forma a covalent bond (disulfide) between two distant parts of the peptide chain
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Proline |
side chain makes a covalent bond to the amino group; makes kink in polypeptide chain
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Amino Acids with polar side chains |
O has partial negative charge (hydrogen bond acceptor). H has partial positive charge (hydrogen bond donor)
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Polar Amino Acids |
are often found on the surface of a protein, where they can hydrogen bond with water; can also hydrogen bond with each other
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Charged Amino Acids |
usually on outside of a protein; can also make ionic bonds with each other inside a protein
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Amino Acids polymerize through condensation reactions to form... |
peptide bonds
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Peptide bonds |
covalent bond formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of another; are unusually stable; have double bond characteristics; are planar (no free rotation around these bonds)
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Amino Acids linked by peptide bonds are... |
referred to a "residues" (to distinguish them from free monomers)
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Nomenclature: PEPTIDE vs. Protein |
Peptide (or Oligopeptide): polymer has <50 Amino Acids
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Nomenclature: Peptide vs. Protein |
Polypeptide: polymer has >50 amino acids
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Nomenclature: Peptide vs. PROTEIN |
Protein: any chain of amino acids, but usually refers to the folded (provide function for protein), functional form of the molecule
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R-Group orientation |
side chains face out, where they can interact with water and each other
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Directionality |
amino (N)-terminal and carboxy (C)- terminal ends. Amino acid sequence written N- to C- terminus
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Flexibility |
single bond on either side of each peptide bond can freely rotate
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Humans have ~30,000 types of proteins |
Each protein is typically a few hundred amino acids long, is made of a unique sequence of amino acids, has a unique 3D shape, has a unique function
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Primary Structure |
the unique sequence of amino acids residues in a protein; stabilized by PEPTIDE BONDS
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Order and Type of Residues in the 1st structure are important because... |
R- groups present affect chemical reactivity and solubility (thereby determining overall properties and function)
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Secondary Structure |
localized folding of a polypeptide chain into regular structures (ie α-helix and β-pleated sheet); stabilized by hydrogen bonding between atoms of the peptide backbone (DO NOT involve side chains); found within the almost all proteins, but which structure forms depends on 1st structure
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Hydrogen bonding between components of the peptide backbone results in secondary structure |
Hydrogen bonding between sections of the same backbone is only possible when a polypeptide bends in a way that puts C=O (partial negative) and N-H (partial positive) groups together
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α-helix |
2nd structure where the peptide backbone coils into a spiral; stabilized by hydrogen bonds; increase stability of the protein as a whole and help define its overall shape
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β-pleated sheet |
2nd structure where the peptide backbone folds into a sheetlike shape; stabilized by hydrogen bonds; increase stability of the protein as a whole and help define its overall shape; folding tends to be spontaneous (BUT because the chemical bonds, hydrophobic interactions, and van der waals forces that occur release enough energy to overcome the decrease in entropy)
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Tertiary Structure |
the overall 3D shape of a single polypeptide chain, resulting from multiple interactions among the amino acid side chains and the peptide backbone; stabilized by bonds and other interactions between R-groups, or between R-groups and the peptide-bonded backbones, depends on primary structure
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Five types of interactions involving side chains are important for tertiary structure |
1) Hydrogen bond: between polar side chain and carbonyl group on backbone
2) Hydrogen bond: between two polar side chains
3) Hydrophobic interactions and Van Der Waals interactions
4) Disulfide bond (covalent)
5) Ionic bond
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Quaternary structure |
the overall 3D shape formed from two or more polypeptide chains; shape is determined by the number, relative positions, and interactions of the subunits; subunits are held together by the same types of bonds and interactions as for 3rd structure; stabilized by bonds and other interactions between R-groups, or between R-groups and the peptide-bonded backbones, depends on primary structure
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Prefixes |
homo- subunits are identical
hetero- subunits are diverse
di- 2 subunits
tri- 3 subunits
tetra- 4 subunits
(ex: homodimer, heterotetramer)
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Protein structure is hierarchical |
4th structure is based on 3rd structure, which is based in part on 2nd structure. All three of the higher-level structures are based on 1st structure
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Amino Acid |
building blocks of proteins; 20 different amino acids; all amino acids share same core structure
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R-group |
or side chains, vary from single hydrogen atom to large structures containing carbon atoms linked into rings. the properties of amino acids vary because their R-groups vary
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Hydrophobic interactions in Tertiary structure |
in an aqueous solution, water molecules interact with the hydrophilic polar side chains of a polypeptide and force the the hydrophobic nonpolar side chains to coalesce into globular masses. When these nonpolar R groups come together, the surrounding water molecules form more hydrogen bonds with each other increasing the stability of their own interactions
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Normal folding is crucial for protein function |
in terms of energy, a folded protein is more stable than an unfolded protein; if you place a newly synthesized polypeptide in an aqueous solution, it will spontaneously fold into shape dictated by its 3rd structure
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Lowest energy conformation |
maximizes the four non-covalent interactions (ie ionic and hydrogen bonds, hydrophobic and van der waals interactions); avoids "steric" (clash) pronlems
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Chaperones |
proteins that facilitate the folding of other proteins into their correct 3D shape; recognize denatured proteins by binding to hydrophobic patches that would not normally be exposed in properly folded proteins (via hydrophobic interactions with hydrophobic hollow chamber)
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General Protein function |
catalysis
defense
movement
signaling
structure
transport
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Catalysis (protein) |
act as enzymes to catalyze chemical reactions
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Defense (protein) |
attack and destroy foreign particles
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Movement (protein) |
move cells themselves or large molecules inside the cell
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Signaling (protein) |
transduce signals to detect, transform, and transmit info
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Structure (protein) |
make up body components, and define cell shape
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Transport (protein) |
allow molecules to enter and exit cells
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Folding into functional forms can be regulated in the following ways: |
interaction of the protein with a particular ion or molecule; chemical modification of the protein
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The protein toolbox: techniques for isolating and visualizing proteins |
1) protein purification by column chromatography
2) SDS polyacrylamide gel electrophoresis
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Cell Lysate |
fluid containing the contents of lysed cells
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Column chromatography |
a method used to purify individual molecules from a more complex mixture (separating proteins)
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3 different types of column chromatography |
anion exchange chromatography and cation exchange chromatography; gel filtration (size exclusion) chromatography; affinity chromatography
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SDS polyacrylamide get electrophoresis analysis separates proteins on the basis of... |
charge, size and shape
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Gel electrophoresis |
a technique for separating macromolecules on the basis of their size and electrical charge, both of which affect the rate of movement through an electrical field in a gel made of a polymer (agarose, polyacrylamide)
-creates a negatively charged elliptical shell around unfolded proteins that mask the net charge on a polypeptide chain (hydrophobic)
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Molecules that are alike form bands on a gel |
1) Well- start with a mixture of molecules in a well
2) as electrophoresis starts, molecules begin to separate by size and charge
3) as electrophoresis continues, separation increases. Molecules with the same size and charge "run" at the same rate
4) if each molecule is visualized, the result is a set of bands
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Nucleic Acids |
polymers specialized for the storage, transmission, and use of genetic information
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Deoxyribonucleic Acid |
encodes heredity info and passes it from generation to generation
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Ribonucleic Acid |
intermediate that allows for the info encoded in DNA to specify the amino acid
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