Term
| Influence of Primary sequence |
|
Definition
| primary structure influences the 3D arrangement strongly |
|
|
Term
|
Definition
1. Noncovalent interactions act as strong stabilizing forces for protein structure.
2. H-bonds can occur b/w a.a. and with a.a and water
3. The most important noncovalent interactions for 2nd and 3rd structure are H-bonding, hydrophobic interactions, and ionic bonds |
|
|
Term
| Structure of Peptide bond |
|
Definition
1. The peptide unit is planar and the peptide bond is rigid and has resonance structure characteristics
2. The alpha-carbon-carboxyl and the amino nitrogen-alpha-carbon have free rotation
3. Domains can be defined as structure w/ between 50 & 500 a.a that have a structural and biological role
4. Domains with similar a.a. sequences will have very similar structure |
|
|
Term
|
Definition
1. stabilized by H-bonds b/w the H on the amino nitrogen and the O on the carboxyl carbon
2. H-bonds parallel to the helix axis
3. 3.6 residues per turn
4. VERY FLEXIBLE
5. NO R groups form H-bonds in the helix and R group interaction limit the type of a.a that can be part of an alpha-helix
Ex.
(3) Lysines or Glutamates in a row will disrupt the a-helix, as will a Proline, which forces a turn
6. The helix can wind in either direction, but the L-amino acids are more likley to wind in the right-handed from |
|
|
Term
|
Definition
1. Conformation is FULLY EXTENDED
2. H-bonds can be inTRA-chain or intER-chain
3. B-sheets are 2 or more regions of the polypeptide
4. B-sheets can be in 2 orientations= parallel or anti-parallel (more common)
5. A.A. constraints are SEVERE & LIMITED |
|
|
Term
|
Definition
Bends (reverse truns or B-bends) are used to reverse the direction of the 2e structure, *B-sheets
Usually composed of four A.A. will contain Glycine(due to its flexibility) & Proline b/c it crease a nature turn
Loops & bends show NO PERIODICITY
Loops are usually b/w 6 & 16 AA long & can change directions |
|
|
Term
|
Definition
Bends (reverse truns or B-bends) are used to reverse the direction of the 2e structure, *B-sheets
Usually composed of four A.A. will contain Glycine(due to its flexibility) & Proline b/c it crease a nature turn
Loops & bends show NO PERIODICITY |
|
|
Term
|
Definition
Loops & bends show NO PERIODICITY
Loops are usually b/w 6 & 16 AA long & can change directions |
|
|
Term
| Protein Architectural Function |
|
Definition
.. The functional activity of a protein under cellular conditions depends on
its folding into a distinct, 3D structure called the native conformation. |
|
|
Term
| General Principle of Protein Design |
|
Definition
-the amino acid sequence (1° structure) strongly influences a protein’s 3D
structure & function
-noncovalent interactions contribute to structural stability of a protein |
|
|
Term
| Elements of (2e) Secondary Structure |
|
Definition
-localized regions of a protein that fold into regular repeating structures such as the a-helix, ß-sheet, bends & loops
Bends (Reverse Turns) |
|
|
Term
| Protein (3e) Tetriary Structure |
|
Definition
-describes the position of all atoms in a polypeptide including side chains
-a protein with a unique 1° structure will fold spontaneously into its distinct, biologically active 3° structure (molecular chaperones may assist) |
|
|
Term
| Protein (4e) Quaternary Structure |
|
Definition
-4° structure defines the arrangement of subunits in a multisubunit protein
The association of separate folded monomeric protein subunits into
oliogomeric protein is the 4° structure (subunit organization) |
|
|
Term
| Protein Structure & Biological Function |
|
Definition
-hemoglobin transports O2 through bloodstream; binding of O2 at heme Fe2+
induces conformational changes within that subunit & in its adjacent
subunits (allosteric interactions & positive cooperativity) |
|
|
Term
| Importance in the structural stability of proteins |
|
Definition
-Extended polypeptide chain folds into “native” biologically active 3D
shape (conformation)
-Folded structure depends on noncovalent interactions, solvent
interactions, pH, ionic strength & sequence of amino acids in the protein |
|
|
Term
| Four Structural Characteristics of the Peptide Bond |
|
Definition
1) Trans Geometry
2) Partial Double Bond Character
3) Coplanar (Amide Plane)
4) Polar |
|
|
Term
|
Definition
1) rapid 2° structure formation/hydrophobic collapse (<5 µs)
2) continued growth of 2° structure, protein motifs combine to form protein
domains (5 – 1000 ms)
3) packing into a single compact structure, formation of disulfide bonds (>1 s) |
|
|
Term
|
Definition
Although many small proteins fold spontaneously after synthesis at the
ribosome, some are assisted in the protein folding process by molecular
chaperones |
|
|
Term
|
Definition
-Denaturation of a protein is the loss of 2° & 3° structure AND the loss of biological function. Sometimes is reversible.
EXAMPLE:
-When a protein denatures, are
the covalent peptides bonds (1° structure)
broken? |
|
|
Term
The relationship between the
structure of a protein & its biological function, specifically hemoglobin |
|
Definition
Myoglobin & hemoglobin serve as a paradigm for understanding 1º, 2º, 3º
& 4º structure in proteins
.. Myoglobin (Mb) |
|
|
Term
|
Definition
.. Myoglobin has a hyperbolic O2 binding curve (follows traditional
Michaelis-Menten enzyme kintics) |
|
|
Term
|
Definition
.. Hemoglobin has a sigmoidal O2 binding curve (exhibits positive
cooperativity & allosteric control among subunits) |
|
|
Term
| Conformational Change in Hemoglobin Upon O2 Binding |
|
Definition
.. Deoxy Hb & Oxy Hb have significant structural differences at the heme
active site & in subunit interactions |
|
|
Term
| O2 Binding Affinity of Hemoglobin Affected by pH & BPG |
|
Definition
.. The Bohr effect is the decrease in O2 binding affinity as the pH decreases
.. 2,3-Bisphosphoglycerate (BPG) also decreases O2 binding affinity |
|
|
Term
|
Definition
Proteins from all living organisms are biopolymers of 20 a-amino acids.
To understand the properties, functions & structures of proteins it is
imperative to understand the general & individual properties of the
building blocks of proteins – amino acids. |
|
|
Term
|
Definition
-amino acids are linked by covalent peptide bonds to form polypeptides
.. Amino acids polymerize to form long chains called peptides through
formation of covalent peptide bonds |
|
|
Term
|
Definition
| -proteins are classified according to their diverse biological roles |
|
|
Term
| Structural Properties of Proteins |
|
Definition
-proteins are classified according to size, composition & solubility
-the four levels of protein structure are primary (amino acid sequence),
secondary (local structure), tertiary (overall compact structure) &
quaternary (subunit organization) structure |
|
|
Term
| Protein Structure and Function |
|
Definition
-proteomics,
-isolating & purifying proteins,
-primary structure determination,
-DNA sequencing & amino acid sequence homology |
|
|
Term
| Optical Activity & Stereochemistry of Amino Acids |
|
Definition
The Chirality of Life: Most active biomolecules are chiral (only one
enantiomer is biologically active)
.. L-Amino Acids are predominantly used as building blocks for proteins |
|
|
Term
|
Definition
| are proteins that catalyze (i.e. accelerate) chemical reactions. |
|
|
Term
|
Definition
| study of life at the molecular level |
|
|
Term
| Early History (The Roots of Biochemistry) |
|
Definition
| Fredrich Wohler's chemical synthesis of urea |
|
|
Term
| The progress of science that lead to the emergence of biochemistry as a scientific discipline |
|
Definition
Medicine
-diagnose & monitor disease
-design drugs
-protein diseases
Agriculture
-new herbicides and pesticides
-transgenic crops
Industry
-synthesis
-detoxification |
|
|
Term
|
Definition
Conformational
-structure and 3D arrangments
Metabolism
-energy production & utilization
Informational
-language for communication inside & b/w cells |
|
|
Term
| Central Dogma of Biochemistry |
|
Definition
| DNA--->RNA----> Protein-----> Cellular Processes |
|
|
Term
| Elements found in "bulk" form & essential for life |
|
Definition
|
|
Term
| Elements in "trace" quantities in most organisms |
|
Definition
C,Mn,Fe,I
Calcium, Manganese, Iron and iodine |
|
|
Term
| Elements are "present" in some organisms |
|
Definition
| (As) Arsenic, (Br) Bromine, (Mo)Molybdenum, and (V) Vanadium |
|
|
Term
|
Definition
| Living cell contains thousands of organic & inorganic chemicals many of them large molecules |
|
|
Term
| Three Primary areas of Biochemistry |
|
Definition
1. Structure & function
2. Informational
3. Bioenergetics |
|
|
Term
|
Definition
| Any biological process that could not be understood in chemical terms |
|
|
Term
|
Definition
| studies at the interface of chemistry & biology |
|
|
Term
|
Definition
| building blocks of proteins |
|
|
Term
|
Definition
-involved as nutrients in energy metabolism
-play role in cell structure and molecular recognition |
|
|
Term
|
Definition
| diverse collection of organic compounds that display low water solubility |
|
|
Term
|
Definition
-broad assortment of orgnaic compounds,
-ensure proper growth & development by functioning in major biochemical processes |
|
|
Term
|
Definition
substituted porphyrin ring coordinated with a metal ion
Heme
-ring w/ iron is found in oxygen transport proteins myoglobin & hemoglobin
-respiratory proteins (cytochrome c, and in enzymes catalase)
Chlorophyll
-magnesium-porphyrin complex
-abundant in green plants & algae
-functions as a receptor of light energy |
|
|
Term
| Natural polymeric macromolecules found in biological cells |
|
Definition
| nucleic acids, proteins & polysaccharides |
|
|
Term
|
Definition
| reaction process that connects monomer units |
|
|
Term
|
Definition
the reverse process
-(hydrolysis) if water is used |
|
|
Term
| The product formed by condensation or polymerization of thousands of glucose monomers |
|
Definition
| starch or cellulose depending on the type of chemical linkage b/w the glucose units |
|
|
Term
|
Definition
| monomeric units comprising these polysaccharides are chemically identical |
|
|
Term
|
Definition
| 20 aa monomeric building blocks resulting protein |
|
|
Term
|
Definition
| "nucleic acids" are heteropolymers of ______ monomeric unit |
|
|
Term
|
Definition
chemical storage form of genetic information
-semi-conservative
-high-fidelity
-bi-directional
-5'-3'
-sugar-phosphate backbone
-minor and major groove
-A,T,G,C
-3.4nm |
|
|
Term
|
Definition
-transfer of genetic information
-biological catalysis, heteropolymer
AMP
GMP
CMP
UMP |
|
|
Term
|
Definition
-synthesis (anabolism)
-breakdown (catabolism)
of all biomolecules including macromolecules |
|
|
Term
| Adenosine Triphosphate (ATP) |
|
Definition
| Catabolism (exergonic) and anabolism (endergonic) are linked through the transfer of energy in the molecular form |
|
|
Term
|
Definition
Nucleus
-NO definite nucleus; DNA present but not separate from rest of cell
Cell Membrane
-Present
Mitochondria
-NONE; enzymes for oxidation rxns located on plasma membrane
ER
-NONE
Ribosomes
-Present
Chloroplasts
-NONE; photosynthesis localized in chromatophores |
|
|
Term
|
Definition
Nucleus
-PRESENT
Cell Membrane
-PRESENT
Mitochondria
-PRESENT
ER
-PRESENT
Ribosomes
-PRESENT
Chloroplasts
-PRESENT in green plants |
|
|
Term
|
Definition
|
|
Term
| Cell as the fundamental unit of life |
|
Definition
Eukaryotes, organism including plants & animals whose cells have a distinct membrane-enclosed nucleus
Prokaryotes simple unicellular organisms |
|
|
Term
| All living matter contains |
|
Definition
CHONPS
-essential elements that make up the bulk of mass of any living organism
-all biological molecules (aa, proteins, glucose, polysaccharides, lipids, nucleotides, DNA, RNA, etc.) are constructed from these elements |
|
|
Term
| Biological Macromolecules |
|
Definition
| major classes are proteins, polysaccharides (carbohydrates), nucleic acids (DNA, RNA); (lipids are a major class of biomolecules, but NOT polymeric) |
|
|
Term
| Organelles, Cells & Organisms |
|
Definition
-self-assembly of macromolecules into higher levels of order-->-->--> cell
-cell structure & organelles for prokaryotes & eukaryotes |
|
|
Term
| Storage & Transfer of Biological Information |
|
Definition
-DNA, RNA, protein & some carbohydrates are informatino rich (sequence)
-DNA replication, transcription & translation (protein synthesis) |
|
|
Term
|
Definition
(ancient bacteria)
archaebacteria
-able to thrive in an environment of high acidity, high salt, high temp and absence of oxygen
Ex.
Can be found in the "hot springs" of Yellowstone National Park or in volcanic areas on land & sea |
|
|
Term
| Storage & Transfer of Biological information |
|
Definition
-Energy metabolism
-Synthesis & breakdown of biomolecules
-storage & transport of biomolecules
-muscle contraction
-cellular communication (signal transduction) |
|
|
Term
|
Definition
| selectively permeable for entry & exit of nutrients & waste |
|
|
Term
|
Definition
| storage of genetic information; site of DNA replication & transcription to RNA |
|
|
Term
|
Definition
| surfaces on which ribosomes bind for protein synthesis |
|
|
Term
|
Definition
| secretion of cell waste products; site of protein processing |
|
|
Term
|
Definition
| site of energy metabolism & synthesis of high-energy ATP |
|
|
Term
|
Definition
| metabolism of materials ingested by endocytosis |
|
|
Term
| Peroxisomes (animal) or glyoxysomes (plant) |
|
Definition
| oxidative metabolism of nutrients using O2 to generate H2O2 |
|
|
Term
|
Definition
| sites of photoshynthesis;convert light energy into chemical energy (ATP) |
|
|
Term
|
Definition
| provides shape to cell; region where many metabolic rxns occur |
|
|
Term
| How to obtain cellular components using centrifugation |
|
Definition
using the centrifuge
-subjecting a biological sample to an extreme gravatational force, by spinning the sample at high speed,
-causes sedimentation of sample components at a rate that depends on their physical characteristics |
|
|
Term
| Describe the relationship b/w obesity & the hormone leptin |
|
Definition
Obese mice decrease their food intake, show increased activity, and lose weight when injected with leptin
Leptin
-a fat tissue derived, protein hormone
For humans, they show a decreased sensitivity to leptin or become "leptin resistant", a condition that may result from malfunctioning receptors or from a limited number of them |
|
|
Term
|
Definition
| discontinuous, consisting of coding regions called "Exons" and non-coding regions called "Introns" |
|
|
Term
| Water, the biological solvent |
|
Definition
Weak noncovalent interactions important to biological processes
Polar compounds
Ionic compounds
Nonpolar compounds- does NOT dissolve well in water
1. Van der Waal forces
2. Ionic Bonds
3. H-Bonds
4. Hydrophobic interactions |
|
|
Term
| Hydrogen Bonding & Solubility |
|
Definition
-H-bonds are EVERYWHERE!
-H-bonding is responsible for water's unusual physical properties
-molecules are classified as
hydrophilic
hyrophobic
amphiphilic |
|
|
Term
| Cellular Reactions of Water |
|
Definition
-self-ionization of water (Kw): H2O + H2O H3O+ + OH–
-many biomolecules are weak acids & bases: pH and pKa
-the Henderson-Hasselbalch equation can be used to calculate the following
variables: pH, pKa, [HA] & [A–] |
|
|
Term
|
Definition
-buffers are composed of a weak acid & its conjugate base (or weak base &
its conjugate acid)
-buffers resist change in pH when H+ or OH– are added
-major buffer system of blood is carbonic acid-bicarbonate (H2CO3/HCO3–) |
|
|
Term
| Why is a water a good solvent? |
|
Definition
-104.5
-universal solvent
-polar
-bent |
|
|
Term
| Ionization reaction of water |
|
Definition
H2O(l) + H2O(l) H3O+(aq) + OH–(aq)
H20-----> H+ +OH-
Calculate a quantity for:
[H+] and [OH-]
then to estimate the extent of self-dissociation
A value for [H20] can be estimated by dividing the weight of water in one L (1000g) by the molecular weight of water (18).
This will yield [H20] = 55.5 M
Example: |
|
|
Term
|
Definition
|
|
Term
| Characteristics of noncovalent interactions |
|
Definition
1. noncovalent interactions are WEAK
2. REVERVSIBLE
3. Binding b/w molecules is SPECIFIC |
|
|
Term
|
Definition
| membrane proteins that form channels through which water molecules are transported IN and OUT of cells |
|
|
Term
|
Definition
| the ability for molecules to recognize and interact (bind) specifically with other molecules |
|
|
Term
|
Definition
|
|
Term
| Van der Waals Interactions |
|
Definition
Between molecules with temporary dipoles induced by fluctuating electrons.
Occurs b/w any two atoms in "close" proximity
Example: |
|
|
Term
|
Definition
the tendency of nonpolar groups and molecules to stick together or cluster in aqueous solutions
Example: |
|
|
Term
|
Definition
attractive interactions that occur b/w oppositely charged atoms or groups
Example: |
|
|
Term
|
Definition
| self-assembly of the acid molecules into aggregates |
|
|
Term
|
Definition
equilibrium constant for the reaction
brackets for each chemical entity indicate concentration units in moles/L
(M) |
|
|
Term
| Calculate the H+ ion concentration in a fluid if given the pH, and visa versa |
|
Definition
pH- the negative logarithm of the [H+]
pH= -log[H+]
Example: |
|
|
Term
|
Definition
| substance that RELEASES a proton (H+) |
|
|
Term
|
Definition
| substance that ACCEPTS a proton (H+) |
|
|
Term
| An acid HA dissociates in aqueous solution accordingly |
|
Definition
| HA=======H+ (Acid) + A- (Base) |
|
|
Term
| Henderson-Hasselbalch Equation |
|
Definition
pH=pKa + log [conjugate base, A-]
-----------------------
[weak acid, HA]
From the H-H Equation:
1) When [A–] = [HA]; pH = pKa
2) When pH < pKa; species is protonated
3) When pH > pKa; species is deprotonated |
|
|
Term
|
Definition
| weak biochemical acid, and sodium hydroxide, a strong base |
|
|
Term
|
Definition
biochemical importance have (2) or more acidic protons
For example:
phosphoric acid has (3) dissociable protons & therefore, three pKa values |
|
|
Term
| Selecting and preparing buffers |
|
Definition
Criteria
-suitable pKa
-no interference with the reaction or detection of the assay
-suitable ionic strength
-suitable solubility
-no biological activity |
|
|
Term
|
Definition
1) Add predetermined amounts of the HA form & the A– form
2) Start with HA form & add NaOH until pH is correct
3) Start with A– form & add HCl until pH is correct |
|
|
Term
|
Definition
-nonlinear
-polar molecule
serves at least (3) functions in the cell
1. effective "solvent"
2. "reactant" molecule
3. "temperature" buffer
As a solvent, water is able to dissolve biomolecules that are ionic & polar |
|
|
Term
| Most Important RXN of water |
|
Definition
-reversible ionization to generate the hydronium ion (H3O+ or the proton, H+)
&
-hydroxide ion (OH-)
-the extent of ionization is quantified by the pH scale (pH= -log[H+]). |
|
|
Term
|
Definition
is defined by its pKa, the negative log of its dissociation constant
-the pKa for an acid is equivalent to the pH at which there is an equal concentration of an acid & its conjugate base |
|
|
Term
| Blood and other cellular fluids are maintained at a constant pH |
|
Definition
| by natural buffer systems inlcuding the carbonic acid-bicarbonate conjugate pair and the hydrogenphosphate-dihydrogenphosphate conjugate pair |
|
|
Term
| Describe the species of a buffer at the inflection point? |
|
Definition
|
|
Term
|
Definition
pHi= pK1 + pK2
--------------
2 |
|
|
Term
| Zwitterions German (inner salts) |
|
Definition
| having a positive & negative charge on the same molecule |
|
|
Term
| How amino acids can be used in the cell besides as part of a protein (reactivity) |
|
Definition
modified aa structures found in proteins
4-hyrdroxyproline and 5-hydroxylysine are found in collagen, a structural protein in animal tendons
phosphoserine & phosphotyrosine change the reactivity of regulatory proteins |
|
|
Term
| Condensation reaction used to make a dipeptide bond |
|
Definition
| (loss of a water molecule)brings together the carboxyl group of one amino acid with the amino group of the other to yield a dipeptide |
|
|
Term
|
Definition
| Each AA when incorporated into the polypeptide |
|
|
Term
|
Definition
| a covalent bond between the a-amino group of one amino acid and the a-carboxyl group of another amino acid; also an amide bond |
|
|
Term
|
Definition
| products with 10 to 100 amino acids |
|
|
Term
|
Definition
| products with more than 100 amino acids |
|
|
Term
| Explain the term C-terminus |
|
Definition
| amino acid with side chain R' (carboxyl terminus) |
|
|
Term
| Explain the term N-terminus |
|
Definition
| amino acid with side chain R (amino terminus) |
|
|
Term
|
Definition
| enzyme in carbohydrate metabolism that catalyzes phosphate group transfer from ATP to fructose-6-phosphate |
|
|
Term
|
Definition
| digestive enzyme (vertebrates) that catalyzes protein hydrolysis |
|
|
