Term
| organisms are remarkably ___ at the molecular level, this is frequently referred to as the ___ |
|
Definition
| uniform; unity of biochemistry |
|
|
Term
| there are __ naturally occurring elements that have been identified, but __, ___, ___ make up 98% of atoms in an organism |
|
Definition
| 90; hydrogen; oxygen; carbon |
|
|
Term
biological fuels react with oxygen to produce __ and __
- this is called __ |
|
Definition
carbon dioxide and water
- combustion |
|
|
Term
| carbon is more effective than silicon because c-c bonds are __ and carbon is __ and can exist as a __ |
|
Definition
| stronger; soluble in water; gas |
|
|
Term
| biomolecules can be divided into what 4 classes |
|
Definition
| nucleic acids; lipids; proteins; and carbohydrates |
|
|
Term
proteins
- are constructed from 20 building blocks called ___
- are linked by __ to form long unbranched polymers
-- these polymers fold into precise __ that facilitate a vast array of biochemical structures |
|
Definition
- amino acids
- peptide bonds
- 3d structures |
|
|
Term
proteins
- serves as ___ and as __ for ___
- proteins also play __ roles, allow __, and provide __ against the environment |
|
Definition
-signal molecules; receptors; signal molecules
- structural; mobility; defenses |
|
|
Term
proteins
- perhaps the most prominent role of proteins is that of __, agents that enhance the rate of a chemical reaction without being permanently affected themselves
- protein __ are called __ |
|
Definition
- catalysts
- catalysts; enzymes |
|
|
Term
nucleic acids
- the primary function of nucleic acids is to ___
- they contain instructions for ___
- nucleic acids are constructed from only four building blocks called __
-- each above is made up of a __, either a __ or __, attached to a __ structure called a base and at least one ___ |
|
Definition
- store and transfer info
- all cellular functions
- nucleotides
- five carbon sugar; deoxyribose; ribose; heterocyclic ring; phosphoryl group |
|
|
Term
DNA
- differs from one another only in the __
- four nucleotides are ___
- the info content of dna is the sequence of ___ linked together by ___
- exist in all higher organisms as __ |
|
Definition
- ring structure of the base
- adenosine, cytosine, guanine, and thymine
- nucleotides; phosphodiester bonds
- double stranded |
|
|
Term
RNA
- is a ___ form of nucleic acid
- some regions of dna are copied as a special class of RNA called ___
-- unlike DNA, __ is frequently ___ after use
- RNA is similar to DNA in components except that __ is replaced by __, and the __ component of the ribonucleotides contain __ |
|
Definition
- single stranded
- messenger RNA
- mRNA; broken down
- thymine; uracil; sugar; hydroxyl group |
|
|
Term
lipids
- they are much __ than proteins or nucleic acids.
- lipids are not __ made of __, as are proteins or nucleic acids
- a key component of many lipids is a __ and a __ |
|
Definition
- smaller
- polymers; repeating units
- hydrophilic head; hydrophobic tail |
|
|
Term
lipids
- the dual nature of lipids allows is to form __ and __
-lipids are also an important storage form of __
- the hydrophobic head of lipids can undergo __ to provide __
- lipids are crucial __ as well |
|
Definition
- barriers; membranes
- energy
- combustion; large amounts of cellular energy
- signal molecules |
|
|
Term
carbohydrates
- an important __ source for most life
- the most common carbohydrate fuel is the __
-- glucose is stored in animals as __
-- in plants, it is stored as __ |
|
Definition
- fuel
- simple sugar glucose
-- glycogen
-- starch |
|
|
Term
carbohydrates
- chains of carbs play important roles in helping cells to __
- many of the components of the cell exterior are decorated with various carbohydrates that can be ___ |
|
Definition
- recognize one another
- recognized by other cells and serve as sites of cell to cell interactions |
|
|
Term
the central dogma states that info flows from __ to __ and then to __
DNA to DNA:
DNA to RNA:
RNA to protein: |
|
Definition
DNA; RNA; protein
replication
transcription
translation |
|
|
Term
dna constitutes the heritable info, the __
- this info is packaged into discrete units called __
- a group of enzymes called __ collectively catalyze the DNA replication process |
|
Definition
genome
- genes
- dna polymerase |
|
|
Term
transcription
- catalyzed by ___
- it is this __ that defines the function of a cell or tissue
- translation renders this genetic info into a ___ |
|
Definition
- RNA polymerase
- selective expression
- functional form |
|
|
Term
structure and properties of water
- water possesses two ___, ___ between oxygen and hydrogen
- unequal sharing of electron pair (differences in __) result in a __ |
|
Definition
- polar; covalent
- (electronegativity); dipole moment |
|
|
Term
intermolecular interactions of water
- water forms intermolecular __
-- above is __ of a covalent oxygen-hydrogen bond
-- above is __ as a covalent oxygen-hydrogen bond |
|
Definition
- hydrogen bonds
-- 5% the strength
-- twice as long |
|
|
Term
consequences of hydrogen bonding
- high __ and __
- __ decreases on freezing
- high __ and __ point
- high __ which minimizes temp fluctuations
- high __, which is a protective value in cooling mechanism with little volume loss |
|
Definition
- viscosity; surface tension
- density
- melting; boiling
- specific heat
- heat of vaporization |
|
|
Term
| three types of non-covalent interactions |
|
Definition
| hydrogen bonding; electrostatic interactions; van der waals interactions |
|
|
Term
hydrogen bonding (__)
- many possible pairing of a __ bearing a __ with another __ bearing an electron pair
- generally strongest with three atoms in hydrogen bond are __ and __ |
|
Definition
(2 to 20kj/mole)
- heteroatom (non-carbon atom); hydrogen; heteroatom
- coplanar; coaxial |
|
|
Term
electrostatic interaction (__)
- weakened substantially for charged, __ on the __ surface because of competing interactions with __
- important for charged polar groups in the __ of a __ (where water is largely __)
- important for charged polar groups on the __ between two __ ( where water is also largely __)
-- ie ___ |
|
Definition
(40 to 200 kj/mole)
- polar groups; exterior; water
- interior; protein; (excluded)
- surfaces; interacting proteins; (excluded)
-- salt bridges |
|
|
Term
van der Waals interactions (__)
- __ atomic interactions
- short range __ |
|
Definition
(0.4 to 4 kj/mole)
- transient
- dipole driven interactions |
|
|
Term
water dissolves some but not all compounds
- __ compounds dissolve readily and the dissociated ions are surrounded by water molecules
- __ compounds do not dissolve in water
- __ compounds have both hydrophobic and hydrophilic features |
|
Definition
- hydrophilic
- hydrophobic
- amphipathic |
|
|
Term
amphipathic molecules
- some lipids have a __ and __ |
|
Definition
| -hydrophilic polar head; hydrophobic nonpolar tail |
|
|
Term
__: associate of non-polar molecules with other non-polar molecules in aqueous solution
- results from combo of __ with increased __
- free energy equation |
|
Definition
hydrophobic effect
- van der waals; entropy
- G (free energy) = H (enthalpy) - TS(entropy) |
|
|
Term
|
Definition
|
|
Term
water undergoes __ to form the __ and __
- equation:
- Keq = |
|
Definition
self-ionization; hydronium ion H3O+; hydroxide ion HO-
- H20 + H20 > H3O+ + HO-
- [H+][HO-]/[H2O] |
|
|
Term
| since ver few molecules of water ___, the concentration remains constant , and the equilibrium constant simplifies as follows: |
|
Definition
| ionize; [H+][HO-] = 1 x 10^-14 |
|
|
Term
| pH can be defined from the concentration of H+ as __ or ___ |
|
Definition
|
|
Term
for bronsted lowry; acids are __ and bases are __
- this is the principel terminology used in the course |
|
Definition
| proton donors; proton acceptors |
|
|
Term
| lewis acids are __ and lewis bases are __ |
|
Definition
| electron pair acceptors; electron pair donors |
|
|
Term
strong versus weak acids
- strong acids exhibit __ in aqueous solution
- weak acids exhibit __ in aqueous solution |
|
Definition
- complete dissociation
- incomplete dissociation |
|
|
Term
weak acids exhibit __ dissociation
- equilibtium between the __ and its __ is given by __
-- formulas: |
|
Definition
incomplete dissociation
- weak acid; conjugate base; Ka or pKa
- Ka = [H+][A-]/[HA]; pKA = log (1/Ka) |
|
|
Term
| the pKa is the __ in a titration curve |
|
Definition
|
|
Term
buffers are mixtures of a __ and its __ that resist change in pH when either __ or __ is added
- buffers having a particular pH range are constructed from __ having a __ from desired pH |
|
Definition
weak acid; conjugate base; strong acid; strong base
- weak acids; pKa value +/- 1 pKa |
|
|
Term
buffers
- __ maintains a relatively constant pH
- what are the three mechanisms that work to maintain normal pH using several buffer systems: |
|
Definition
- blood plasma
- hemoglobin; phosphate (H2PO4- and HPO4-2); carbonic acid/bicarbonate (H2CO3 and HCO3-) |
|
|
Term
buffers
- the pH of blood is controlled by the ratio of __ to __ in the air spaces of the lungs
- when the pH of blood decreases due to excess acid, more __ is generated, __ increases in the lungs, and __ is exhaled, thereby ___ |
|
Definition
- bicarbonate; CO2
- carbonic acid; pCO2; CO2; restoring equilibrium |
|
|
Term
Amino Acid Structure
- there are __ common amino acids that have different side chains that impart different __ and __ character |
|
Definition
| 20; hydrophobic; hydrophilic |
|
|
Term
aliphatic amino acids
- hydropathy values generally ___
- the aliphatic amino acids include: |
|
Definition
- positive (hydrophobic)
- glycine, alanine, valine, leucine, isoleucine |
|
|
Term
Hydropathy
- hydropathy is a measure of how __ a molecule is
-- the more positive the hydropathic value is ___
- for amino acids, the __ is responsible for differences in hydropathy |
|
Definition
- hydrophobic/hydrophilic
-- the more hydrophobic it is
- side chain |
|
|
Term
Hydropathy
- Free energy change
-- + = ___
-- - = ___ |
|
Definition
-- unfavorable (hydrophobic)
-- favorable (hydrophilic) |
|
|
Term
| the aromatic amino acids include: |
|
Definition
| phenylalanine; tryptophan; tyrosine |
|
|
Term
|
Definition
| an amine; proton; carboxylic acid; and side chain |
|
|
Term
hydrophilic amino acids contain hydropathy values that are ___
- hydrophilic amino acids include: |
|
Definition
negative (hydrophilic)
- serine; threonine; asparagine; glutamine |
|
|
Term
acidic amino acids
- hydropathy values are ___
- the acidic amino acids include: |
|
Definition
- negative (hydrophilic)
- aspartate; glutamate |
|
|
Term
| the central carbon in an amino acid is the __ |
|
Definition
|
|
Term
structure and hydropathy
- arrangement of amino acids in proteins is directly related to ___
- hydrophilic amino acids often appear on the ___ of __ and __
- hydrophobic amino acids often appear in __ and in the ___ |
|
Definition
- function
- exterior surfaces; membrane bound proteins; globular proteins
- membrane spanning domains; interior core of globular proteins |
|
|
Term
ionic states
- amino acids possess functional groups that can function as __ or __
- __ properties of enzymes (type of protein) critically depend on the presence of the __ in particular __ in a catalytic site |
|
Definition
- weak acids; bases
- catalytic; functional groups; ionic states |
|
|
Term
| amino acids are __ at physiological pH |
|
Definition
|
|
Term
__ is the pH at which the amino acid will not migrate in an electric field
- calculated by: |
|
Definition
isoelectric point
- pK1 - pK2 |
|
|
Term
amino acid structure
- there are __ common amino acid structures that have different side chains and impart different __ and __ character |
|
Definition
| twenty; hydrophobic; hydrophilic |
|
|
Term
| aliphatic amino acids have hydropathy values that are generally ___ |
|
Definition
|
|
Term
hydropathy
- hydropathy is a measure of how __ a molecule is
- for amino acids, the __ is responsible for differences in hydropathy
- positive free energy change is ___
- negative free energy change is __ |
|
Definition
- hydrophobic/hydrophilic
- side chain
- unfavorable (hydrophobic)
- favorable (hydrophilic) |
|
|
Term
| hydrophilic amino acids generally have hydropathy values that are ___ |
|
Definition
|
|
Term
proteins are ___
- __ bond linkage between the __ group of one amino acid and the __ group of a second |
|
Definition
polymers
- peptide; ammonium; carboxylate |
|
|
Term
Configuration
- different spacial arragenments that ___
- no variation in __, ___ |
|
Definition
- do not normally interconvert
- structure with T, solvent |
|
|
Term
conformation
- different spacial arrangements that ___
- structure may ___ |
|
Definition
- may interconvert fairly readily
- vary with T, solvent |
|
|
Term
|
Definition
|
|
Term
trans and cis peptides
- the cis conformation possesses ___, and the trans conformation is ___ |
|
Definition
| - unfavorable steric interaction; favored for most amino acids |
|
|
Term
peptide bond
- the chiral center (alpha carbon) has a ___
- bonds involving the alpha carbon have ___
-- __ limit the range values of __ and __ |
|
Definition
-fixed configuration
- many possible conformations, phi and psi
- steric interactions; phi; psi |
|
|
Term
| it is important to understand the concept that proteins are __ of __ |
|
Definition
| linear polymers; amino acids |
|
|
Term
secondary structure
- definition: regularities in __ maintained by ___
-- in three cases, secondary structure arises when a number of consecutive amino acids have similar ___
- secondary structure includes __, __, __, __ |
|
Definition
- local conformations; networks of hydrogen bonds
-- phi and psi values
- alpha helix, beta strand or beta sheet, loop and turn, random coil |
|
|
Term
alpha helix
- __ with __ amino acids per turn |
|
Definition
| - right handed (chiral); 3.6 |
|
|
Term
alpha helix
- ___ occurs on the ___ of the __ amino acid and the __ of the __ on the __ amino acid |
|
Definition
| - hydrogen bonding; carbonyl oxygen; nth; hydrogen; amide; n+4th |
|
|
Term
amino acids in alpha helices
- __ of alpha helix occurs for specific amino acids
-- __ destabilizes alpha helix because absence of __ results in greater __
-- __ produces a kink in alpha helix because __ occupies space that __ would otherwise occupy |
|
Definition
- destabilization
-- G; side chain; freedom of rotation
-- P; cyclic structure; neighboring amino acid |
|
|
Term
helical wheel
- view along helical axis displays the outward, radial projection of ___
- organizations of __ and __ side chains along different faces correlate with function |
|
Definition
- side chains
- polar; non-polar |
|
|
Term
you should understand that alpha helices in proteins:
- possess a narrow band of acceptable __ and __ values
- destabilized by __ and __
- are __ with __ per turn and stabilized by __ between __ to __ amino acids
- have side chains that project ___ |
|
Definition
- phi; psi
- G, P
- right handed (chiral); 3.6 amino acids; hydrogen bonding; nth; n+4th
- outward from alpha helix |
|
|
Term
ramachandran plot
- steric interactions limit the range of values for __ and __ |
|
Definition
|
|
Term
beta sheets can run __ or __
- they also have ___ and a __ |
|
Definition
parallel; antiparallel
- alternating side chains: right-handed twist |
|
|
Term
Beta sheets
- stabilized by ___
- __ or __
- side chains project __ and __
- a beta sheet with multiple strands has ___
-- __ arises out of the fact that the amino acids that comprise proteins are constructed from ___ |
|
Definition
- long range cross-sheet hydrogen bonds
- parallel; anti-parallel
- alternately above; below the chain
- a slight right handed twist
-- twists; L-amino acids |
|
|
Term
Loops
- regions of proteins that cause __, appear on surface of __, and possess ___
- typically possess ___ amino acid residues |
|
Definition
- directional charges; proteins; hydrophilic amino acids
- more than five |
|
|
Term
turn or beta turns
- a subclass of loops with __ amino acids connecting ___
- often contain the amino acids __ or __ |
|
Definition
- five or fewer; two secondary structural features (ie two alpha helices)
- P; G |
|
|
Term
a special case: proline
- the __ is still less stable than the __, but the __ conformation is not as __ for proline as for other amino acids |
|
Definition
| - cis conformation; trans; cis; disfavored |
|
|
Term
a special case: glycine
- with no __, glycine can adopt many more conformations of __ and __ |
|
Definition
|
|
Term
random coil
- is a portion of a __ that does not adopt a __, but is __
-- often sites that control __ or __, undergo __, __, and are modified in __ |
|
Definition
- protein; single conformation; flexible
- regulation; signaling; covalent modification; bind drugs; alternative splicing |
|
|
Term
you should understand that
- a beta sheet possesses a __ or __ arrangements with __ between strands
- __ project __ or __ the sheet plane
- there are __ to sheets
- loops and turns produce __ and possess certain types of ___
- __ provide important flexibility |
|
Definition
- parallel; antiparallel; hydrogen bonding
- side chains; above; below
- slight right handed twists
- directional change; amino acids
- random coils |
|
|
Term
tertiary structure
- folding of __ into a closely packed ___
- tertiary structure provides a stable __ platform to ___ and ___, primarily different __ atoms and ___ |
|
Definition
- polypeptide; 3-D structure
- 3-D; spatially organize; orient functionality; amino acid; functional groups |
|
|
Term
tertiary structure
- largely stabilized by __, especially the ___
- features within the tertiary structure include:
1. __: combo of secondary structures
2. __: independently folded unit
3. __: overall protein architecture - one or more domains |
|
Definition
- non-covalent interactions; hydrophobic effect
1. motifs
2. domains
3. folds |
|
|
Term
Two common ways to represent tertiary structure
1. __ shows only the __ which is useful in showing __ and in comparing structures
2. ___ that gives an outline of the ___ surface |
|
Definition
1. ribbon model; backbone; secondary structures
2. solvent accessible surface model; van der Waal's |
|
|
Term
Motifs
- common combinations of __ such as ___, __, and ___ |
|
Definition
| - secondary structural features; alpha helices; beta sheets; turns/loops |
|
|
Term
coiled-coil motif
- isolated __ are unstable in solution but stable in ___ structures because of the interactions between them |
|
Definition
| - alpha helices; coiled-coil |
|
|
Term
coiled coil motif
- coiled coils have a ___
- nonpolar residues at position __ and __
- electrostatic interaction between residues __ and __ |
|
Definition
- heptad repeat "abcdefg"
- a/a' ; d/d'
- e/e' ; g/g' |
|
|
Term
domains and fold
- domains are __, __ units within proteins
-- size of a domain varies over a considerable range but generally from __ to __ amino acid residues
- fold: overall ___ composed of __
-- different domains are connected by __ and bound by ___ between ___ |
|
Definition
- independently folded, compact
-- 60; 300
- protein tertiary structure; one or more domains
-- loops; weak interactions; side chains |
|
|
Term
domains are classified according to presence of ___
- all alpha: __ and __
- all beta: ___ and ___ that link the __
- mixed alpha/beta: contain __ such as __
- alpha + beta domains: consist of local clusters of __ and __ in __, __ regions of the polypeptide chain |
|
Definition
secondary structures
- alpha helices and loops
- beta sheets; non-repetitive structures; beta strands
- supersecondary structures; alpha beta alpha motif
- alpha helices; beta sheet; separate; contiguous |
|
|
Term
you should understand
- ___ elements combine to form __
- ___ are organized in __
- __ are ___
- a folded protein possesses one or more ___
- __ structure allows specific spatial organization of amino acids
- similar topology can emerge from ___ |
|
Definition
- secondary structure; motifs
- motifs; domains
- domains; independently folding units
- domains
- tertiary
- different protein sequences |
|
|
Term
levinthal's paradox
- 100 residue protein would take __ to fold
- proteins generally take __ to fold |
|
Definition
- 10^87 sec
- less than a second |
|
|
Term
| __ is arguably among the most important processes in biology |
|
Definition
|
|
Term
misfolded proteins and aggregates
- causes many disease, particularly neurodegeneration
1. __: beta amyloid peptide aggregates of plaques
2. __: lewy body mainly aggregated alpha synuclein
3. __: aggregation of huntington protein |
|
Definition
1. alzheimer's
2. parkinson's
3. huntington's |
|
|
Term
reversible protein folding
- native shape: unique __, precisely __, __, __
- denatured state: random __, highly __, subject to __, __ |
|
Definition
- shape; ordered; stable; functional
- shape; mobile; degradation; inactive |
|
|
Term
protein folding funnels
- protein folding is not due to ___
- protein folding is __ |
|
Definition
- random sampling of conformations
- cooperative |
|
|
Term
what drives protein folding
- ___: protein collapses rapidly around __ with the release of bound, __
-__: neighboring residues in sequence form some element of the native __ that acts as a nucleus for ___
- __, charge to charge
- many protein fold ___ |
|
Definition
- hydrophobic collapse model (entropy driven); hydrophobic side-chains; water molecules
- nucleation model (hydrogen bonding); secondary structure; cooperative folding
- van der waals
- spontaneously |
|
|
Term
what drives protein folding
- ___: protein collapses rapidly around __ with the release of bound, __
-__: neighboring residues in sequence form some element of the native __ that acts as a nucleus for ___
- __, charge to charge
- many protein fold ___ |
|
Definition
- hydrophobic collapse model (entropy driven); hydrophobic side-chains; water molecules
- nucleation model (hydrogen bonding); secondary structure; cooperative folding
- van der waals
- spontaneously |
|
|
Term
assisted folding of proteins
- __ or __ that inhibit or reverse formation of improperly folded proteins
- __ that shuffles disulfides in a protein until a stable native disulfide is formed
- ___ that catalyzes the interconversion of the cis and trans conformations of proline residue |
|
Definition
- molecular chaperones; heat shock proteins
- protein-disulfide isomerase
- peptidyl prolyl cis-trans isomerase |
|
|
Term
protein-disulfide isomerases (PDI)
- PDI's ___ disulfides in a protein
- they can function __ until a ___ is formed
- critical for correct ___ |
|
Definition
- isomerize (shuffle)
- repeatedly; stable native disulfide
- extracellular protein folding |
|
|
Term
summary
- protein folding is a __, __ process
- protein folding is largely driven by __
-- blueprint for __ is encoded in the __
-- in silico protein folding is still __
- not all proteins fold ___
-- __, __, __ |
|
Definition
- rapid; cooperative
- primary structure
-- tertiary structure; primary sequence
-- primitave
- spontaneous
-- chaperones, PDI, proline cis/trans isomerases |
|
|
Term
quarternary structure
- proteins with multiple subunits (individual amino acid chains) are called __ or __ proteins
- subunits are held together by __ and/or ___
-- defined __
-- does not include __ or __ |
|
Definition
- multimeric; organic
- non-covalent forces; disulfide bonds
-- stoichiometry
-- clusters; aggregates |
|
|
Term
quarternary structure
- oligomeric proteins are often more stable than ___
- __ for the binding of ligands may be formed at the interface of several subunits
- __ may change quarternary (and tertiary) structure allows for cooperativity |
|
Definition
- dissociated subunits
- active sites
- ligand binding |
|
|
Term
Example: cro dimer
- dimeric quaternary structure is necessary for ___ |
|
Definition
|
|
Term
antibody schematic
- held together by __ and ___
- antibody tertiary structure elements include __ |
|
Definition
- non-covalent forces; inter-molecular disulfides
- beta sandwich motif |
|
|
Term
antibody: antigen binding
- very ___; very ___; and highly __ |
|
Definition
| - binding; specific; diverse |
|
|
Term
|
Definition
|
|
Term
__ is a measure of the accuracy of the data and the size of the atoms that can be detected.
- stated in __, smaller numbers correspond to ___ |
|
Definition
resolution, R
- angstroms; higher resolutions |
|
|
Term
| greater resolution means to greater __ and __ |
|
Definition
|
|
Term
To characterize a proteins function biochemically, we need to __ the protein
- __ of proteins by inherent physio-chemical properties such as __, __, __, __... |
|
Definition
purify
- purification; localization, solubility, size, charge |
|
|
Term
The __ is the pH as which there is no net charge on the protein taking into account side chains, N-terminus, and C-terminus
- acidic groups tend to have a __ while basic groups tend to have a ___ |
|
Definition
pI value
- low pI; high pI |
|
|
Term
__ allows separation by mass
- __ binds for every ___ > proteins migrate based on size |
|
Definition
SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis)
- one SDS; two amino acids |
|
|
Term
SDS-PAGE electrophoresis
- SDS bound proteins migrate on the basis of ___
- assignment of mass to unknown protein done by ___ |
|
Definition
-mass
- comparison with known standards |
|
|
Term
| above the pKa is where there is a ___ |
|
Definition
| neutrally charged species |
|
|
