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Biochemistry Exam #1
Chapters 1-4
123
Chemistry
Undergraduate 4
09/10/2007

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Term
Influence of Primary sequence
Definition
  • primary structure influences the 3D arrangement strongly
  • Term
    Noncovalent Interaction
    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
    The Alpha Helix
    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
    The Beta Sheet
    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
    Bends & Loops
    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
    Bends
    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
    Loops
    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
    Protein Folding
    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
    Molecular Chaperons
    Definition
    Although many small proteins fold spontaneously after synthesis at the
    ribosome, some are assisted in the protein folding process by molecular
    chaperones
    Term
    Protein Unfolding
    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
    Myoglobin
    Definition
    .. Myoglobin has a hyperbolic O2 binding curve (follows traditional
    Michaelis-Menten enzyme kintics)
    Term
    Hemoglobin
    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
    Proteins
    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
    Polypeptides & Proteins
    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
    Protein Function
    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
    Enzymes
    Definition
    are proteins that catalyze (i.e. accelerate) chemical reactions.
    Term
    Biochemistry
    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
    Three Areas of Study
    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
    C,H,O,N,P,S
    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
    Macromolecules
    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
    Vitalism
    Definition
    Any biological process that could not be understood in chemical terms
    Term
    Molecular biology
    Definition
    studies at the interface of chemistry & biology
    Term
    Amino acids
    Definition
    building blocks of proteins
    Term
    Carbohydrates
    Definition
    -involved as nutrients in energy metabolism
    -play role in cell structure and molecular recognition
    Term
    Lipids
    Definition
    diverse collection of organic compounds that display low water solubility
    Term
    Vitamins
    Definition
    -broad assortment of orgnaic compounds,
    -ensure proper growth & development by functioning in major biochemical processes
    Term
    Heme & Chlorophyll
    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
    Condensation
    Definition
    reaction process that connects monomer units
    Term
    Cleavage or hydrolysis
    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
    Homopolymers
    Definition
    monomeric units comprising these polysaccharides are chemically identical
    Term
    Heteropolymers
    Definition
    20 aa monomeric building blocks resulting protein
    Term
    Nucleotides
    Definition
    "nucleic acids" are heteropolymers of ______ monomeric unit
    Term
    DNA
    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
    RNA
    Definition
    -transfer of genetic information
    -biological catalysis, heteropolymer
    AMP
    GMP
    CMP
    UMP
    Term
    Metabolism
    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
    Prokaryotes
    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
    Eukaryotes
    Definition
    Nucleus
    -PRESENT

    Cell Membrane
    -PRESENT

    Mitochondria
    -PRESENT

    ER
    -PRESENT

    Ribosomes
    -PRESENT

    Chloroplasts
    -PRESENT in green plants
    Term
    Structure of a virus
    Definition
    Draw here....
    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
    Arcaebacteria or archaea
    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
    Cell membrane
    Definition
    selectively permeable for entry & exit of nutrients & waste
    Term
    Nucleus
    Definition
    storage of genetic information; site of DNA replication & transcription to RNA
    Term
    ER with Ribosomes
    Definition
    surfaces on which ribosomes bind for protein synthesis
    Term
    Golgi apparatus
    Definition
    secretion of cell waste products; site of protein processing
    Term
    Mitochondria
    Definition
    site of energy metabolism & synthesis of high-energy ATP
    Term
    Lysosomes (animal)
    Definition
    metabolism of materials ingested by endocytosis
    Term
    Peroxisomes (animal) or glyoxysomes (plant)
    Definition
    oxidative metabolism of nutrients using O2 to generate H2O2
    Term
    Chloroplasts (plant)
    Definition
    sites of photoshynthesis;convert light energy into chemical energy (ATP)
    Term
    Cytoplasm
    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
    Eukaryotic Genes
    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
    Buffer systems
    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
    pH and pK
    Definition
    HA H+ +A-
    Term
    Characteristics of noncovalent interactions
    Definition
    1. noncovalent interactions are WEAK
    2. REVERVSIBLE
    3. Binding b/w molecules is SPECIFIC
    Term
    Aquaporins
    Definition
    membrane proteins that form channels through which water molecules are transported IN and OUT of cells
    Term
    Molecular Recognition
    Definition
    the ability for molecules to recognize and interact (bind) specifically with other molecules
    Term
    Hydrogen bonds
    Definition
    Example
    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
    Hydrophobic Interactions
    Definition
    the tendency of nonpolar groups and molecules to stick together or cluster in aqueous solutions

    Example:
    Term
    Ionic Bonds
    Definition
    attractive interactions that occur b/w oppositely charged atoms or groups

    Example:
    Term
    Micelles
    Definition
    self-assembly of the acid molecules into aggregates
    Term
    Keq
    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
    Acid
    Definition
    substance that RELEASES a proton (H+)
    Term
    Base
    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
    Monoprotic
    Definition
    weak biochemical acid, and sodium hydroxide, a strong base
    Term
    Polyprotic acid
    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
    Ways to prepare buffers
    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
    Summary of Water
    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
    Strenth of Acid
    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
    Example:
    Term
    How to calculate pHi
    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
    Residue
    Definition
    Each AA when incorporated into the polypeptide
    Term
    Peptide
    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
    Polypeptide
    Definition
    products with 10 to 100 amino acids
    Term
    Proteins
    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
    Phosphofructokinase
    Definition
    enzyme in carbohydrate metabolism that catalyzes phosphate group transfer from ATP to fructose-6-phosphate
    Term
    Trypsin
    Definition
    digestive enzyme (vertebrates) that catalyzes protein hydrolysis
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