biochem test 1 Word Scramble

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Question	Answer
chemistry that deals with the chemical compounds and processes occurring in organisms; and the chemical characteristics and reactions of a particular living organism or biological substance.	biochemistry
biochem is the chemistry of what?	living matter
basic principles of biochemistry can be applied towards all living organisms. T or F	true
Glycolysis, an almost________ central pathway of glucose metabolism.	universal; greek - glykys = "sweet" and lysis = "splitting"
glycolysis - The chemistry of the glycolytic reaction sequence has been completely_________ in the course of evolution (common thermodynamic principles and the types of regulatory mechanisms).	conserved
biochemistry is _______ in our daily life	indispensible (absolutely necessary) - ex: eating lunch
what 4 things does biochemistry impact?	human biology and medicine, agriculture, industrial applications, and the environment (and more)
5 important characteristics of living matter?	LECTURE 1 ANSWER
living matter - High degree of________ at molecular and organismal levels.	complexity
living matter must be able to Extract, transform, and utilize______ from their environment for maintenance, regeneration, and function.	energy
energy _______ and _______ keep organisms alive	transduction; transformation
living systems extract energy from what two main sources?	1) from sunlight - plants, green bacteria, cyanobacteria 2) from nutrients/fuels- animals and most bactiera
living matter must be able to ________ between self and non self and ______ and _______ to change in the surrounding; immune system recognizes a bacteria, virus, etc. and mounts an immune response	distinguish; sense; respond
living matter - regulated interactions between individual components that are ______ and ________ ex: cell signaling map and brain signaling for movment	dynamic; coordinated
living matter - fairly _______ self replication (DNA) while allowing enough _____ for evolution. biological reproduction with near-perfect fidelity	precise; change
3 distinct domains of life? prokaryotes or eukaryotes?	prokaryotes: bacteria and archaea eukaryotes: eukarya
structural heirarchy of living matter?	elements --> monomers --> polymers --> supramolecular structures --> organelles --> cells --> tissues --> organisms
simple organic compounds	monomers
macromolecules	polymers
most abundant essential elements (structural components)	C, H, O, N, P, S
less abundant essential elements (homeostasis)	Na+, K+, Ca2+, Cl-
trace amounts of these essential elements (metabolism, enzymatic cofactors)	Mg++, Zn++, Fe++, Mn++, Cu++
what simple organic compound? components: nitrogenous base, five carbon sugars, phosphate	nucleic acids
what simple organic compound? long chains of hydrophobic, insoluble	lipids
what simple organic compound? parent sugar is glucose	carbohydrates
macromolecules - biological molecules typically have multiple _______ _______	functional groups
GO OVER COMMON FUNCTIONAL GROUP FLASH CARDS HOE
interactions between biomolecules are _______	specific.
1. Macromolecules have______ binding domains. 2. Only certain molecules can bind – ______ and ______. 3. Binding of chiral biomolecules is________.	specific; lock and key; stereospecific
Biological Molecules’ Function Depends on ______ ______ Structure	Three-Dimensional
biological molecules function depends on 3D structure - what were the 4 3D structures we talked about?	1) geometric isomers (cis vs trans) 2) stereoisomers (four, 2 asymmetric carbon) 3) enantiomers (mirror images, 2 pairs) 4) diastereomers (all non-mirror image pairs)
major macromolecules? (4)	proteins, nucleic acids, polysaccharides, lipids
what is structural hierarchy: molecules --> cells?	monomeric units (nucleotides, amino acids, sugars) --> marcomolecules (DNA, protein, cellulose) --> supramolecular complexes (chromatin, plasma membrane, cell wall) --> cell/organelles
• All living organisms are made of______. • Cells are NOT all the same. • The simplest living organisms are_______-celled. • Larger organisms consist of many cells that are different in _____, _____, and _______	cells;single; origin, morphology, and function.
what do eukaryotes have that prokaryotes don't?	eukaryotes have nucleus, nuclear membrane, and membrane bound organelles and because of compartmentalization, they have spatial separation of energy yielding and energy consuming reactions
PROKARYOTE VS EUKARYOTE LECTURE 1
life is a coordinted series of _______ reactions	chemical
2 parts of metabolism?	catabolism and anabolism
part of metabolism that is oxidative, destructive, and releases energy ; goes from a complex thing (stored nutrients) to a small molecule; energy released as ATP or NADPH	catabolism
part of metabolism that is reductive, constructive, and stores energy; goes from simple molecules to complex molecule; low energy --> high energy molecules and requires in put of ATP and reduced electron carrire	anabolism
catabolic reaction pathways are _______ and anabolic reaction pathways are __________	exergonic; endergonic
anabolic pathways proceed ________ with catabolic pathways in a dynamic steady state	simultaneously
example of catabolism?	oxidation of glucose (C6H12O6 + 6O2 --> 6CO2 AND 6H20
catabolism is oxidative and degradative; it generates _______ and reduces ________	ATP; coenzymes ; lecture 2 page 1 catabolism
release of energy	exergonic
why is ATP the chemical currency of energy?	phosphoanhydride bonds are high energy --> broken, energy released
. For any physical or chemical change, the total amount of energy in the universe remains constant; 2. Energy may change form or it may be transported from one region to another, but it can not be created or destroyed.	thermodynamics - principle of the conservation of energy
Cells are efficient_______ of energy (convert energy from one form to another) , capable of interconverting _____, ________, _______, and _______ energy with great efficiency.	transducers; chemical, electromagnetic, mechanical, and osmotic
; Living cannot create energy; Living cannot destroy energy (“used up”).; Living organism may_______ energy from one form to another (e.g., energy stored in chemical bonds into kinetic energy of heat and motion).	; convert
organisms perform energy ______ to accomplish work and stay alive	transduction - lecture 2
Anabolic pathways________ cellular components from simple precursor molecules; _______ chemical energy (ATP and NADH or NADPH); they are ______ when compared to oxidative catabolic pathways	synthesize; Consume; reductive
“New formation of sugar” that converts pyruvate and related three- and four-carbon compounds to glucose.	gluconeogenesis
in gluconeogenesis, Essentially same reactions in all tissues and all species. The_______ context and the________ of gluconeogenesis differ between species and tissues.	metabolic; regulation
important gluconeogenesis precursors in animals?	lactate --> pyruvate, glucogenic amino acids, and glycerol
process that requires energy	endergonic
The universe always tends towards increasing disorder: in all natural processes, the entropy of the universe increases.	second law of thermodynamics
(the amount of energy capable of doing work during a reaction at constant temperature and pressure).	gibbs free energy
the heat content of the reaction system).	enthalpy (H)
a quantitative expression for the randomness or disorder in a system).	entropy (S)
a ______∆G is a favorable reaction - ___∆S and ____∆H	negative (exergonic) +∆S - increasing disorder; products more disordered than reaactants -∆H - release heat
relationship between ∆G, ∆H, and ∆S in biological systems for constant temp and pressure	∆G = ∆H - T∆S
_______ΔG: endergonic reaction that gains free energy. _______ ΔG: exergonic reaction that releases energy.	Positive; Negative
ü Endergonic ü ΔG > 0 ü Reactants are stable ü Reaction is not spontaneous	unfavorable - ex: synthesis
ü Exergonic ü ΔG < 0 ü Products are stable ü Reaction is spontaneous	favorable - ex: breakdown
Chemical________ of exergonic and endergonic reactions allows otherwise unfavorable reactions. • The “high-energy” molecule (______) reacts directly with the metabolite that needs “activation.”	coupling; ATP ∆G3 = ∆G1 + ∆G2
A thermodynamically unfavorable (endergonic) reaction can be driven in the forward direction by coupling it to a thermodynamically favorable (exergonic) reaction through a_______ ________	common intermediate; LECTURE 2 EQUATION!!
kinetics - intermediate between substrate and product;unstable; and distinct conformation.	transition state - lecture 2 page 5
kinetics - energy required to reach the transition state.	activation energy
the higher the activation energy, the _______ the reaction rate	slower
At the equilibrium concentrations of substrates and products, the forward rate_____ the reverse rate and there is no further______ in the system.	equals; change
When a reaction is not at equilibrium, the driving force that moves the reaction towards equilibrium is expressed quantitatively as the free energy change for the reaction, _____.	ΔG
Keq =?	EQUATION ON LECTURE 2 PAGE 5
For chemical reactions, ΔG'o is dependent on the ______	K'eq. - KNOW THIS EQUATION LECTURE 2 PAGE 6
with a larger Keq, that means the concentrations of products are increased, and standard free energy change (∆G) is more negative, which means its more ________	favorable ; large Keq = favorable ∆G
when Keq is greater than 1, ∆G is negative, and starting with all components at 1M, the reaction proceeds _______	forward
when Keq = 1, ∆G is zero, and starting with all components at 1 M the reaction is ___________	at equlibirum
when Keq <1, ∆G is positive and starting with all components at 1 M then the reaction proceeds _________	in reverse
v Standard free energy change (ΔG'o): • Standard conditions- initial concentration of each component is 1.0 M, 25°C, pH 7, and 101.3 kPa. • Characteristic and unchanging________ for a given reaction.	constant
Living cells are different from test tubes!_______ free energy change (ΔG) (not standard) determines the spontaneity of a reaction. ∆G (actual) = ∆G (standard) + RT lnKeq	Actual
how to speed up reactions, that would work in test tube but not suitable for living organisms	-Higher temperatures (may destabilize macromolecules) -Higher concentrations of reactants (need more valuable starting material)
how to speed up reactions, that would work in living organisms?	-Lower activation barrier by catalysis (i.e., enzymes) - Change the reaction by coupling to a fast one
Enzymes Lower the _____ ______ to Increase the Reaction Rate	Activation Energy
LECTURE 2 NOTES - CHANGE REACTION BY COUPLING WITH A FAST ONE NOTES !
who did this experiment? Abiotic formation of organic compounds under primitive atmospheric conditions; “Primordial Soup” Simple Organic Compounds (Biomolecules)	miller and urey
evolutionary benchmarks - Modern Humans ________y ears ago First land vertebrates _______ years ago	160,000 ; 350,000,000
Life evolved in______. Biochemical reactions often occur in______ setting. ______ is Crucial for the structure and function of biomolecules and most abundant substance in living organisms - why it is so important for life	water; aqueous; water
water is a good solvent for _____ and _____ substances (amino acids, peptides, carbohydrates - hydroxyls, nucleic acids, etc)	charged; polar
water is a poor solvent for ________ substances (nonpolar gases, N2, O2, lipids, others)	NONPOLAR
required for degradation for high energy chemicals (oxidation), so because our blood is aqueous, water is poor solvent for oxygen so need proteins to carr it	oxygen
molecule that has both polar and nonpolar grups	amphipathic
what has a higher solubility in water? oxygen or CO2? why?	CO2 - oxygen has poor solubility in water. O2 is very nonpolar, and so is CO2 but CO2 has some partial negative on the oxygens
________of the oxygen atom induces a net dipole moment (2 electric dipoles per water molecule, one along each of the H−O bonds).	Electronegativity
water molecule's shape is a distorted _______	tetrahedron - 2 pairs bond to H and 2 lone pairs
Each water is able to form H-bonds with as many as___ other water molecules. • H-bond distance is____ times the distance between the covalent O and H bond. energy to break H-bond vs energy to break the covalent O-H bond: __: __	4; 2; energy to break H-bond vs energy to break the covalent O-H bond: 1:20
In ice, each water molecule can form hydrogen bonds with four neighboring water molecules. A crystal lattice structure makes ice less_____ than liquid water, and thus ice floats on liquid water.	dense
Melting of ice and evaporation of water occur_______ at room temperature. ΔG = ΔH − TΔS; melting and evaporation at room temp have +∆H --> release heat and ∆S - increase entropy	spontaneously - ∆G is negative
4 noncovalent bonds?	hydrogen, ionic, van der waals, hydrophobic
for hydrogen bonding you have to have an _______, and a _________. water can serve as both of these	acceptors and donors; hydrogen acceptors differ as long as its partial negative/ has LP, but donor has to have a hydrogen that has a partial positive
a hydrogen bond in a biomolecule is stronger when it is ________ rather than when it is ________	direction and strength; straight - stronger, bent - weaker
ionic interactions are Electrostatic interactions between permanently_______ species • Electrostatic interactions between the_____ and a permanent______	charged; ion; dipole
ion-dipole interactions - Water is dipole that interacts electrostatically with charged solutes by orienting H toward______ and O toward______.	anions; cations; water and NaCl
Van der Waals interactions are: • Weak interatomic attractions (reversible, easily broken) • Universal: occur between two _______ atoms that come next to each other	uncharged
which noncovalent forces are important to determine steric complementarity • stabilize biological macromolecules (stacking in DNA) • facilitate the binding of polarizable ligands	van der waals
2 components of van der waals?	attractive and repulsive force
van der waals force that (London dispersion) that dominates at longer distances (typically 0.4-0.7 nm).	attractive
van der waals (Steric repulsion) that dominates at short distance.	repulsive
compounds that have hydrophilic group and hydrophobic group	amphipathic
hydrophobic interactions - lipid in water, water will try to form cage and they are highly ordered --> entropy decreased. so the lipid ______ and hydrophobic groups condense and releases trapped water and allows entropy to increase bc random h20 released	aggregates
• amphipathic • nonpolar group in the middle • polar group facing out, interacting with water • energy wise – more favorable ; minimize ordered shell of water molecules; increase entropy of water	micelles
_____Interactions are Crucial to Macromolecular Structure and Function	Weak - summary lecture 3
Certain properties of solution such as boiling point, melting point, and osmolarity that do not depend strongly on the chemical nature of the dissolved substance.	colligative properties
Properties such as viscosity, surface tension, taste, and color, etc. that depend strongly on the chemical nature of the solute.	non-colligative properties
Cytoplasm of cells are highly_______ solutions and have high_______ pressure.	concentrated; osmotic
the measure of solute concentration	osmolarity
_______ - No net movement of water. ü _______solution- Water moves out and cell shrinks. ü ______solution - Water moves in and cell burst.	Isotonic; Hypertonic; Hypotonic
it is very rare that 2 water molecules connected by a hydrogen bond disassociate into hydronium ion (H3O+) and hydroxyl ion; most water remains _______ in the pure water form	uncharged
what is wrong with this commonly seen formula? H2O --> H+ + OH-	free protons do not exist in solution; proton H+ is written in place of H3O+
ionization of water - ______ ______:rapid net movement of a proton, because the covalent and H- bonds are interchangeable. very rapid	proton hopping ; lecture 5 page 1
proton hopping applies to the hydroxyl ion in water, except in the ________ direction	opposite
constant that is a Fixed value that is characteristic for each specific reaction. concentration of products over reactants ; determined by electrical conductivity measurements	equilibrium constants - Keq
equilibrium constant for water?	1.8 x 10^-16 M
Kw, ion product of water is equal to what?	Keq x [H2O] or [H+]x[OH-]
at pH=7, the concentration of[H+] and [OH] are what? Kw = [H+][OH-]= 1 x 10^-14 M^2	equal to each other... so [H+]=[OH-] soooo [H+][OH-] = [H+]^2 SOOOO SQUARE ROOT OF THAT GIVES 1 X 10^-7 =[H+]
a mathematical term that means the negative log of.	p
pH = what mathematically?	-log [H+]
pH + pOH = ?	14
alkaline conditions 􏱬 [H+] lower 􏱪 [OH-] higher... pH is what?	pH > 7
neutral condition water, [H+] = [OH-]	pH = 7
acidic conditions 􏱪 [H+] greater; 􏱬 [OH-] smaller	pH <7
GO OVER LOGS AGAIN
strong acids and bases completely dissociate in water and there is no equlibrium T or F	true
Strong Acid + Strong Base = ??? HCl + NaOH	Water + Salt
acids that only dissociate to a limited degree in water	weak acids
for weak acids, the extent of dissociation is ___-dependent	pH
for weak acids: ow pH, high [H+] push the reaction to the______ very little of the weak acid will be dissociated into ions.	left; HA (equilibrium arrows) (H+) + (A-) increase H+, shift towards the left
for weak acids, high pH, low [H+] push the reaction to the_____ most of the weak acid will be dissociated into ions.	right; HA (equilibrium arrows) (H+) + (A-)
acid dissociation constant	Ka = [H+][A-]/[HA]
LOOK AT HENDERSON-HASSELBACH
weak acids - When the pH = pKa, ____ _____ of the weak acid will be dissociated into ions.	one half
when [A-] =[HA], then pH=?	pH = pKa; pH = pKa + log([A-]/[HA]) = pKa + 0 = pKa
LECTURE 5 PAGE 6 TITRATION
when pKa = pH, the weak acid is ______ dissasociated	50%
based on pKa values out of these 3 weak acids, which is strongest and which is weakest? titration curve: [CH3COOH] = [CH3COO-] pH = pKa = 4.76 [H2PO4–] = [HPO42–] pH = pKa = 6.86 [NH4+] = [NH3] pH = pKa = 9.25	Acetic acid is the strongest acid (pKa = 4.76). - lowest pKa Dihydrogen phosphate is in the middle (pKa = 6.86). Ammonium ion is the weakest acid (pKa = 9.25).
the smaller the pKa, the ________ the acidity	stronger
what is the conjugate acid base pair? which is proton donor which is proton acceptor? CH3COOH (equilibrium arrows) 􏱩 H+ + CH3COO-	acetic acid and acetate are conjugate acid/base pair; acetic acid is proton donor and acetate is proton acceptor
acid that gives up only one proton - CH3COOH(equilibrium arrows) 􏱩 H+ + CH3COO-	monoprotic
acid that gives up two protons;H2CO3 --> 􏱩 H+ + HCO3- pKa = 3.77 HCO3- 􏱩--> H+ + CO32- pKa = 10.2	diprotic acid
acid that gives up three protons (H3PO4)	phosphoric acid
for diprotic and triprotic, which is the stronger weaker acid?	the first proton removal is always the strongest weak acid
Almost every biological process is_____- dependent. 􏱩􏱩 A small change in pH produces a______ change in the rate of the process.	pH; large
􏱩 Cells and organisms maintain a specific and constant______ pH (usually pH 7.0) to keep biomolecules in their optimal ionic states. 􏱩􏱩 Biological______ – mixtures of weak acids and their conjugate bases are employed to achieve pH________.	cytosolic; buffers; constancy
aqueous systems that resist changes in pH when small amounts of acid (H+) or base (OH-) are added.	buffers
Buffer is composed of a______ acid (proton donor) and its ______ _____(proton acceptor). Each conjugate acid-base pair has a characteristic pH zone to function as an effective buffer.	weak; conjugate base
a flat zone on the titration curve – addition of given amounts of acid (H+) or base (OH-) has less effect on pH that outside the zone. EX: acetic acid, pH=pKa @4.76, this region is between 3.76 and 5.76 for acetic acid/acetate	buffering region
2 important physiological buffers?	phosphate and bicarbonate
important physiological buffer that acts in cytoplasm of cells - In mammals, extracellular fluids and most cytoplasmic compartments have a pH in the range of 6.9 to 7.4.	phosphate buffer system - pH 5.9 to 7.9 H2PO4 --> H+ + HPO4 -
which important physiological buffer? good for blood plasma buffer; effective buffer near pH 7.4, the pH depends on concentrations of CO2 gas, dissolved CO2 converted into H2CO3 and HCO3-	bicarbonate buffer; H2CO3 􏱩 --> H+ + HCO3- carbonic acid (H2CO3) is from dissovled CO2 and water
when the CO2 bicarbonate buffer system is disrupted, pH<7.35 and you get what condition?	acidosis - pathological condition or exercise
the most abundant biological macromolecules, found in all cells and all parts of cells.	proteins
Proteins are the main agents of biological functions, mediating virtually every process in a cell. • Proteins are_______ in both structure and function.	diverse
building blocks of proteins	amino acids
Proteins (from bacteria to human beings) are constructed from a common set of____ amino acids.	20;
Cells produce structurally and functionally diverse proteins by covalently linking the same 20 amino acids in different ________ and ________	combinations and sequences.
general structure of alpha amino acids - a carboxyl group and an amino group bond to the same alpha carbon - applies to 19 of the AAs but not ________ why?	proline is cyclic
2 conventions to identify carbons:	organic nomenclature and biochemical designation
identifying carbons in proteins 12 conventions: _______nomenclature: start from the carboxyl end. • _______ designation: start from the α-carbon and go down the R-group.	Organic; Biochemical
the alpha carbon is ________ in 19 common amino acids, but not glycerine; which means there are two possible stereosiomers that are nonsuperimposable mirror images or what?	chiral ; enantiomers
for most amino acids, if the amino group is on the left and R group below, it is "___" conformation but if amino group is on the right and R group below it is "____" conformation	L, D
L and D only refer to the absolute configuration of the four substituents around the chiral α-carbon in amino acids. Virtually all amino acid residues in proteins are____ stereoisomers.	L
Cells use enzymes with_________ active sites to select L amino acids!	asymmetric
Depending on the R substituents, the 20 common amino acids can be placed into______ groups. R groups vary in structure, size, charge, and solubility in water	five
AMINO ACID FLASHCARDS!
Amino acids that are Not incorporated by ribosomes.Post-translational modifications of proteins. • Important biological functions. For example, reversible phosphorylation that is important in signaling.	uncommon amino acids
lecture 6 biochem page 6 post translational modification
in a reducing agent, a disulfide bond would be _______ in cystine to form 2 cysteine amino acids with sulflhydryl bonds	broken
ionization of amino acids - At acidic pH, the______ group is protonated and the amino acid is in the cationic form.	carboxyl
ionization of amino acids - At neutral pH, the carboxyl group is______ but the amino group is______. The net charge is zero; such ions are called______.	deprotonated; protonated; Zwitterions
ionization of amino acids At alkaline pH, the amino group is______ : NH2 and the amino acid is in the anionic form.	neutral
amino acid net charge is zero	zwitterions - lectrue 6 page 6
titration of amino acid notes and lecture lecture 6 page 7 notes and highlighted notes
α-carboxyl group is much_____ acidic than in carboxylic acids • α-amino group is slightly_____ basic than in amines	more; less -- because of unique structure of amino acid it is not pure acid or pure base pKa of acetic acid = 4.8 but for carboxyl group is 2.34 pKa of methylamine is 10.6 and for alpha amino acid is 9.6
Zwitterions_______ at pH values between the pKa values of the amino and carboxyl groups.	predominate
For amino acids without ionizable side chains, the Isoelectric Point (equivalence point, pI) is = ???	pI = Pk1 + pK2/ 2 the average of pK's
At the isoelectric point, AA: o net charge is_____ o ______ soluble in water o does not_____ in electric field	zero; least; migrate
Ionizable side chains can be________. • Titration curves are more complex. • pKa values are discernable if two pKa values are more than two pH units apart.	titrated
how do you calculate pI with more than 2 ionizable things in side chains?	1) identify zwitterion (net charge = 0) 2) identify pKa that defines ACID strength 3) identify pKa value that defines base strength 4) average those 2 pKa values - lecture 6 page 8
at pH = 7 Aspartate and Glutamate are______ charged • Lysine and Arginine are________ charged • ________ may be positively charged or uncharged	negatively; positively; Histidine MAKE SURE LECTURE 6 PAGE 8 MEMORIZE CHART IS IN THERE
biochem lecture 6 notebook notes
Peptides are chains of amino acids covalently joined through a substituted amide linkage, termed a _____ ______	peptide bond.
peptide bonds are formed from a __________ reaction	condensation - loses water; OH on COOH and H oh NH2
the peptide bond: is less_______ (more stable) ² exhibits_______ moment in the trans configuration (favored) ² is______ and nearly________ (this one has to do with structure)	reactive; dipole; rigid; planar
The peptide bond has some________ bond character, because of the resonance or partial pairing between the carbonyl oxygen and the amide nitrogen.	double; chem 471 09_06 lecture page 1
in a peptide, which bonds can rotate?	the alpha carbon-C bond can rotate and the alpha carbon and nitrogen can torate, but the carbon nitrogen bond is RIGID and cannot rotate
in peptides, numbering starts from the _______ terminal (left) to the _______ terminal (right)	N-terminal to C-terminal
CHAPTER 3 PROBLEM 11	answer in notes biochem lecture 6 and on laptop highlight
No generalization can be made to relate the size of peptides and proteins to their functions. True or False?	true ; Naturally occurring peptides range from 2 amino acid residues to many thousands. bioactive small peptides - hormones, pheromones, neuropeptides, toxins
terminology for few amino acids in a peptide	oligopeptides
terminology for many amino acids in a peptide	polypeptide
generally, polypeptides have a molecular weight less than ???? and proteins have a molecular weight greater than ???? the average weight of an amino acid is ????	10,000; GENERALLY - EACH AMINO ACID THE AVERAGE WEIGHT IS 110 G
proteins are made of polypeptides, but polypeptides are NOT made of protein. T or F	true
proteins may contain: a single polypeptide; two or more polypeptides held by both _______ and _________ interactions	noncovalent; covalent
• Proteins may contain: – _______ (metal ions or organic molecules). – ________ (organic compounds, e.g. NAD+) – ________ groups (covalently attached cofactors, e.g. heme) – Other modifications.	Cofactors; Coenzymes; Prosthetic
proteins that contain permanently associated chemical groups, in addition to amino acids.	conjugated proteins
________group is the non-amino acid part of a conjugated protein.	Prosthetic; 09/06 lecture page 5 table 3-4
Protein function depends on its _____ _______sequence. classical methods sequence one amino acid at a time	amino acid sequence = identity).
The amino acid sequences of millions of proteins have been determined indirectly by_______ sequencing. • Automation and_______ spectrometry provide faster alternative methods to determine amino acid sequences.	DNA; mass
before sequencing a protein, what must be done first?	purify the target protein and reducing the level of complexity by cleaving it into smaller peptides by proteases or chemicals and then sequence each peptide
in protein methods, for proteolysis, Some proteases cleave proteins into smaller polypeptides, by catalyzing the hydrolytic cleavage of the peptide bond adjacent to particular _____ _______residues.	amino acid
for protein methods, in order to break up proteins into smaller pepties to sequence, how do you break a disulfide bond in say insulin?	oxidizing and reducing agents
what protein method? Identify one amino acid residue from the N-terminal at a time; repeat; sequence up to 40 sequential residues. attach chemical group to N-termianl end, cleave, then identify AA one at a time	chemical sequencing - edman degradation
what molecules are to be analyzed in mass spectroscopy?	analytes
analytes are ü ionized in a vacuum ü introduced into an electric or magnetic field ü measures mass to charge ratio (m/z)	mass spectroscopy
how does mass spectroscopy sequence proteins/peptides?	each AA has a specific mass to charge ratio (m/z) and then you assemble the peptide sequence based on m/z values
when membrane has this lipid, it allows the membrane to curve which allows machinery for ETC in mitochondria; required for mitochondrial structure and function	cardiolipin
when laying out a research plan, you want to monitor the _________ for all throughout the isolation process. (ex: change pH --> protein can change conformation)	bioactivity
in research plan: lyse cells /cell structure breaks apart = __________ separate organelles from cell debris/ separate soluble proteins from insoluble proteins = __________	homogenation; centrifugation
in research example with CLS, to separate CLS protein from other components is done by _________, analyzing the CLS protein is done by _______, and resolving the structure of the CLS protein is done by ________	chromatography; electrophoresis; sequencing
protein methods: Two components (to be performed repeatedly): o Determine the protein concentration for monitoring yield. o Assay for CLS activity do this for each step during separation proceudre	bioassay-guided isolation - "quality control" that just makes sure sample is active before initiating isolation effort
separates substances based on density	centrifugation
on low speed for centrifugation of homogenized tissue, there are what 2 main densities/	supernatant - organelles and pellet that contains whole cells, nuclei, cytoskeleton,e tc.
on high speed for centrifugation of homogenized tissue, there are what 2 main densities/	supernatant - smaller subcellular structures pellet - mitochondria, lysosomes, peroxisomes
how do you use centrifugation to separate organelles? aka separate mitochondria, lysosomes, peroxisomes etc after regular centrifugation?	sucrose density centfigugation -- prepare series of sucrose solutions and different layers of sucrose with different densities then poke hole and collect fraction
how do you acquire soluble proteins in protein methods? lecture 09/08 page 3	centrifugation to separate soluble proteins from isnoluble; place them in a hypotonic solution and water gushes in cell and lyses it; only thing left is insoluble proteins and membrane components, and soluble proteins in solution
chromotagraphy is used in protein _________	separation
3 phases of chromotagraphy	stationary, mobile, effluent
solid porous matrix inside the column. what chromotagraphy phase?	stationary
the solution pumped into the column. what chromotagraphy phase?	mobile
the solution that comes out of the column, collected as fractions. what chromatagraphy phase?	effluent
Three Chromatographical Methods for Protein Purification:	ion exchange, size exclusion, affinity
2 types of ion exchange chromatography	anion exchange and cation exchange
ion exchange chromatography - AnionExchange 1. Matrix (____) charged. 2. Proteins (____) bind. 3. Elution: High salt,________ conditions.	+ (positively) ; negative; acidic - bc column is positive, protein are negative, want to pull protein from positive matrix, the acidic solution gives more protons and helps protein fall off the matrix
cation ion exchange chromatagraphy - Matrix (_____) charged. 2. Proteins (______) bind. 3. Elution: High salt,_________ conditions.	negative; positive; basic - negatively charged basic eludes and pulls positive proteins from negative matrix
with cation ion exchanges in chromatography, proteins with a more ________ charge will move faster and elute earlier	negative
ch 3 problem 17	in notebook biochem lecture 7
in size exclusion chromatography, 1. Larger molecules elute_______ . 2. Smaller molecules elute _______.	first; last ; smaller can get stuck in matrix and larger cannot
chromatography where separation by binding specificties between ligand and a protein	affinity chromatography
how does affinity chromatography work?	immobilized ligand is linked to the matrix. protein of interest binds to the ligand. unwanted proteins washed through the column protein of interest is eluted with ligand solution
with affinity chromatography, how do you remove ligand from protein of interest once it is out of the column?	dialysis
in electrophoresis, Gel matrix_______ the mobility of proteins according to their size and shape. and Running buffer_________ electricity.	hinders; conducts
in electrophoresis, what electrode to they migrate to?	from negative to positive
After electrophoresis: the proteins can be visualized by staining the gel (i.e., Coomassie blue).Each band corresponds to a ________. small migrate faster compared to larger proteins	protein
what does SDS page do to a protein?	proteins can have different charges, so it is a negative detergent that makes all proteins negative so it eliminates charge. it also eliminates shapes of proteins by denaturing it into a long strand. so all that it does is spearate by WEIGHT
how do you find relative migration? on a gel	distance traveled on gel/total gel length
PROTEIN METHODS - ESTIMATE MW BY SDS PAGE LOOK AT lecture 09/08
what are the 2 dimensions in 2D electrophoresis?	first - isolectric focusing on pI point and charge second: SDS-PAGE - molecular/weight and size
2D electrophoresis resolves hundreds of distinct proteins and provdies a snapshot of relative protein abundance ; adds in another dimension to separate proteins apart	ok
Isoelectric focusing (2D electrophoresis) Separate native proteins according to their______ _________ 2. Ampholytes establish a stable pH gradient on a gel strip. 3. In an electric field, proteins migrate to pH = pI (protein net charge is____).	isoelectric points.; zero
Protein molecules adopt a specific 3-dimensional conformation (called the _____ _______). this conformation is mainly held together by favorable_________ interactions.	native fold; noncovalent
Proper folding of a protein requires________, because of the decrease in conformational entropy.	energy
protein structure: AA sequence that determines function	primary
protein structure: Local folding: α-helix, β-sheet, random coil	secondary
protein structure: “Global” folding of a single polypeptide chain	tertiary
proteins tructure: Subunit arrangement: assembly of folded proteins into multi-subunit macromolecules– dimer, trimer, tetramer, etc.	quaternary
if a protein is a single polypeptide, can it form a quaternary structure?	no - bc it doesn't have multiple subunits
peptide bond________ links amino acids in a protein molecule.	covalently
Secondary structure: a local three-dimensional folding of the polypeptide chain. • Defined by patterns of________ bonds between the backbone amide groups. and between 2 different peptide BONDS, not same peptide bond	hydrogen
secondary protein structure: Chain is coiled like a spring, Held together by H- bonds between nearby residues; R groups protrude outwards ; very compact, peptide bonds align roughly parallel with helical axis	alpha helix
alpha helix is a Very________ structure: • Inner diameter: 4 – 5 Å, too small for anything to fit ‘inside’ • Outer diameter (with side chains): 10 – 12 Å, fits into dsDNA major grove	compact
Peptide bond has a strong dipole moment. "Carbonyl O negative "Amide N positive • The___ _____ secondary protein structure has a large macroscopic dipole moment. carboxylic end is negative and amino terminus is positive	α helix ; dipole between N+ and O-...
_________Affects α-Helix Stability	Sequence
Strong alpha helix formers: ______, ___________ amino acid residues (e.g., Ala and Leu)	small hydrophobic
alpha Helix breakers: _____ (cyclic R-group, can’t rotate). _____ (tiny R-group (H) supports other conformations)	Pro; Gly
why can't proline rotate well?	because between peptide and R group, the R can usually rotate, but proline can't because it is cyclic and attached to the amino group
beta strand: Extended peptide chains naturally make a pleated geometry. • α-Carbons are the_______. • R-groups________ (up, down, up, down....) • Planar peptide bonds are in the_______.	apices; alternate; pleat
what secondary structure for protein? -Peptide chains align side-by-side. -Interstrand H-bond-Parallel and Antiparallel	beta SHEET
same direction of beta sheet vs opposite direction beta sheet	parallel and antiparallel
Connecting elements that link segments of α helix and/or β sheet.	beta turn
_______ or _______ residues are commonly found in beta turns	Proline or glycine
type I beta turn:	• Proline in 2nd position. • Proline: conformationally restricted with fixed φ angle, keeps turn rigid.
type 2 beta turn:	Glycine in 3rd position • Glycine: small and flexible, allows for tight corners.
type 1 beta turns occurs _____ times more frequently than type 2	2
for type 1 and 2 beta turns, why can't glycine or proline be in 1 or 2 AA position?	becaust there is a H-bond between carbonyl oxygen in AA1 and amino group hydrogen in AA 2
Peptide bond configuration: • Nearly all peptide bonds not involving proline are in the_______ configuration (>99.95%).	trans
Peptide conformation is defined by dihedral angles (or torsion angles). Dihedral angles: o Φ (phi): what angle? ψ (psi): ?	phi - angle between nitrogen and alpha carbon psi - angle between alpha carbon and carbon
with ramachandran plot, it shows the distribution of phi and psi dihedral angles that are found in a protein. certain secondary structures can only exist with certa phi and psi values
in ramachandran plot for secondary structrues Unfavorable ones (i.e., steric crowding, white) • Favorable ones (i.e. H- bonding interactions, blue)	ok
structural asymmetry causes differences in the absorption of left- handed versus right- handed circularly polarized light. canbe used to assess secondary structure and to monitor protein folding.	circular dichroism (CD) analysis for secondary structure
Three-dimensional arrangement of all atoms in a protein. v Three-dimensional condensing of all secondary structural elements.	tertiary structure
2 major classes of tertiary structure:________ proteins: long strands or sheets_________ proteins": spherical or global shape	Fibrous; Globular
Repeat a single type of secondary structure. • High percentage of hydrophobic amino acids. • Insoluble in water. • Important sructural proteins.	tertiary structrure: fibrous proteins
Contain several types of secondary structure. • Important enzymes and regulatory proteins. o allows them to interact with other biomolecules n can be water soluble and lipid soluble (plasma membrane)	tertiary structure: globular proteins
The arrangement of two or more polypeptide chains (subunits) in 3-D complexes.	quaternary structure
2 main methods to determine higher-order protein structures	x-ray crystallography and NMR spectroscopy
1) Crystallize the protein 2)Blast with X-ray 3)Collect diffraction data 4) Construct a 3D arrangement of atoms	x-ray crystallography
pros and cons of x ray crystallography?	pros - no size limits, high resolution cons - proteins must be able to crystallize, structure may stay the same
1)Dissolve the protein 2) Collect NMR data 3) Assign NMR signals 4) Calculate the structure	NMR spectroscopy
pros and cons of NMR spec?	Pros: No need to crystallize the protein; motional dynamics of whole molecule. Cons: only suitable for small proteins
chapter 4 problem 7	IN NOTES LECTURE 9 BIOCHEM
for beta turns, _______ is preferred as the turn because it is easier to turn as cis rather than trans	proline
when an amino acid is More________ in hydropathy, more likely it interacts with water well	negative
term for protein balance	proteostasis; like homeostasis but for proteins
misfolded proteins _______	aggregate
proteostasis pathways?	synthesis --> folding --> unfolding --> misfolded, aggregates --> remodling --> degradation
Most proteins must maintain conformational flexibility in order to function. v The native structure is__________ most favorable, but also only marginally stable.	thermodynamically
Protein folding is a fast process. Sometimes protein folding happens spontaneously. More often it occurs with the assistance of specialized enzymes and complexes called________ .	chaperones
proteins that Interact with partially folded or misfolded polypeptides and facilitate correct folding.	chaperone proteisn
chaperone proteins are present in organisms franging from bacteria to humans. they require energy in the form of _______ to function because thermodynamic prefers randomness, and going from misfolded to a more organized correct fold requires energy	ATP
2 major families of chaperone proteins: 1) ________ - prevent misfolding 2) _________ facilitate folding	Hsp70 and Chaperonins
loss of a protein's 3D structure	denaturation
when a protein loses its 3D structure it doesnt carry out the biological function T or F	true
denaturation: Unfolding is________ (loss of 3D-structure in one part destabilizes other parts). Most proteins can be denatured by heat. • ______ ________ (Tm): midpoint of the range of denaturing temperatures. 50% of protein is unfolded here	cooperative; Melting temperature
how could circular dichroism be used to monitor signals of protein denaturation?	CD • Has the alpha helix, beta conformation, and random coil • Change structure (no longer alpha, beta, or something) change in Beta conformation is different (or whatever your secondary structure is)
5 denaturants	heat, extremes of pH, miscible organic solvents, solutes, detergents
-Heat disrupts____-bonds. - Extremes of pH disrupt______ interactions and ______-bonds. Miscible organic solvents (i.e. alcohol or acetone) disrupt________ interactions.	- hydrogen; ionic (alter pH, alter charge); hydrogen; hydrophobic
_______(i.e., urea) disrupt hydrophobic interactions and H-bonds. § _______ disrupt hydrophobic interactions.	Solutes; Detergents
chapter 4 probelm #4 in lecture 9 computer notes
when you remove a denaturing agent, the protein spontaneously refolds into the _______ conformation and regains function	native
organelle that is major consumer of cellular oxygen	mitochondria
o to go through ETC,_______ is the final electron acceptor o ATP mainly produced through ETC and mitochondria and oxygen helps create_______ gradient	oxygen; proton
o Proton gradient is like a________ ♣ When it goes form intermembrane space to membrane ATP synthase turns and connects ADP and phosphate	turbine - lecture 9/13 page 4
WHY WE NEED OXYGEN, MITOCHONDRIA, ETC, FOR COMPLEX___ IN ETC – COMPLEX USES OXYGEN HAS ELECTRON ACCEPTOR, NEED PROTON GRADIENT TO PRODUCE ATP Enzyme for complex is cytochrome c oxidase - forms water	FOUR
• Oxygen is critical but has________ water solubility and most chemical rxns occur in aqueous environment	poor
oxygen supply issues:	poor water solubility - can't ge carried to tissues in sufficient quantitiy and ineffective diffusion over long distance in larger multicellular animals
what oxygen binding proteins? A) transports oxygen; tetramer B) stores oxygen; monomer	A) hemoglobin B) myoglobin
protein family involved in oxygen binding proteins are ______	globins
globin that is a monomer, protect neurons from hypoxia and ischemia	neuroglobin
globin who is a monomer and function is unknown	cytoglobin
hemoglobin and myoglobin are the most-studied/best-understood proteins. they are first ones with 3D structures determined. they are ______ proteins, so their tertiary structure contains several types of secondary structure; important enzymes/regulatory	globular
hemoglobin and myoglobin - examples ofr how other proteins work: a. ________ interactions with other molecules. b. ______ – conformational changes essential for function. c. ________ binding – specific and reversible.	Dynamic; Flexible; Ligand
Hemoglobin and myoglobin are________ proteins (conjugated proteins with the bound prosthetic group heme).	heme
protoporphyrin IX with a bound iron (Fe2+).	heme
Heme:________ oxygen binding. key function	reversible
true or false: None of the amino acid side chains can bind oxygen.	true
Transition metals such as____ and ______r have a strong tendency to bind oxygen. Free iron is highly reactive& generates ____ _____ ______(ROS) that damage macromolecules.	iron and coppe; reactive oxygen species
Heme: binds and transports oxygen without excessive amount of______.	ROS - reactive oxygen species (damage macromolecules)
‘Free’ heme molecule leaves the Fe2+ with two _____ ______ bonds that can react with oxygen. • Once the Fe2+ is oxidized to Fe3+, heme can no longer bind oxygen.	‘open’ coordination
Proteins sequester heme molecules deep inside the structure to prevent Fe2+________.	oxidation
protein that Stores O2 in muscles for metabolism.	myoglobin
myoglobin structure is Eight __--______segments connected by β–turns. there is______ heme per molecule	α-helical ; One
_______ is a ligand for myoglobin. • Myoglobin binds oxygen at the specific binding site. • Same applies to hemoglobin, except that the binding is more complex.	O2
a molecule that binds (typically a small molecule).	ligand
a region in the protein where the ligand binds.	binding site
Ligand binds to the protein via ____-_______ forces – transient and reversible interactions.	non-covalent
________expression describes the reversible binding of a ligand (L) to a protein (P):	Equilibrium; P + L ⇌ PL
chapter 5 problem 1
association and disassociation constant for ligand and protein	Ka = [PL]/[P][L] Kd = 1/Ka
fraction of ligand- binding sites on the protein that are occupied by ligand. ____ = [PL]/([PL] +[P])	θ(theta)
Kd = _____when θ= 0.5; θ depends on the free [ligand] and Kd;	[L] ; θ = [L]/[L]+Kd
The fraction of bound sites θ depends on: 1) the____ ______ concentration, and 2) ________	free ligand; Kd - disassociation constant
if one protein has a higher association constant for a ligand, (Ka) , than another protein, what does that mean?	the one with the higher association constant has a higher affinity for the ligand
for ligand analysis, the smaller the disassociation constant, the ________ the affinity	higher
practice problems lecture 09/15 from galina's notes page 4 and page 6 with myoglobin	ok
is this strong or week binding strength? Kd<10 nM	strong
is this weak or strong binding strength? Kd> 10 μM	weak
________motions (“breathing”) produce transient cavities in myoglobin for oxygen to move in and out. • The distal His (His E7 or His64) facilitates O2 binding by forming a hydrogen bond.	Molecular
in equation for binding of O2 to myoglobin - The _____ _______of oxygen (pO2) is used in place of [O2], because [O2] is proportional to pO2.	p artial pressure
theta for fraction of ligand binding sites that are occupied by ligand for O2 to myoglobin is what	θ = pO2/pO2+Kd
Mb is relatively insensitive to change in O2 concentration/ pressure. if pO2 in tissues is about 4 kPa and the pO2 in lungs is about 13 kPa, can myoglobin be a good O2 transporter?	its good for O2 storage but not O2 transport because its theta is still about 1 fro 4 kPa and will not release the oxygen
Effective O2 Transport Requires ____-Dependent Affinity	pO2
_______(cooperative) binding curve- more sensitive to small differences in O2	Sigmoid
there can be _____ oxygens per hemoglobin	4
hemoglobin is a tetramer of two subunits (α2β2). α and β______ form a dimer.Tetramer is a dimer of αβ dimers.	protomers;
Hemoglobin in________ (red blood cells) binds and carries nearly all the O2 in the whole blood. these cells transport O2	erythrocytes
Formed from hemocytoblasts (precursor stem cells) Incomplete, vestigial cells without intracellular organelles. life spand 120 days and main fucntion is to carry hemoglobin	erythrocytes
myoglobin is a monomers, so can it have quaternary structure?	no
each subunit of hemoglobin is_______ to myoglobin in 3D structure; alpha helix with beta turn and heme in the middle that binds oxygen	similar
there is a low identical sequence between alpha and beta subunits in hemoglobin, and there is no D-helix in alpha subunit, but in the Heme binding pocket: ___ and _____ helices in both subunits.	E and F
what are the subunit interactions in hemoglobin for the 4 subunits (alpha 1, alpha 2, beta 1, beta 2 = tetramer)	hydrophobic, hydrogen bonds, and ionic interactions
2 major conformations for hemoglobin	tense state and relaxed state
predominant conformation of deoxyhemoglobin.	tense state
hemoglobin conformation that has a higher affinity for O2 than the T state. central cavity is collapsed and binds oxygen	relaxed state
• T state conformation • Large central cavity • Low affinity for O2 what state of hemoglobin?	apo state
• R state conformation • Collapsed central cavity • High affinity for O2 what state of hemoglobin?	saturated state
_____ binding triggers the tense state to relaxed state transition lecture 09/18 slide 2 figure	oxygen
hemoglobin: 1st O2 moleculebinds weakly to a subunit in the____- affinity T state. undergoes a transition from T state to the_____- affinity R state. More O2 molecules bound to the R state, making hemoglobin an ______ protein	low; high; allosteric
o Upon binding of first oxygen and the rest of the hemoglobin affinity of oxygen is_______	increased
cooperative ligand binding - hill equation in lecture 11 notebooks
(slope of Hill plot, degree of interaction): nH	Hill coefficient
Hill coefficient values and ligand binding co- operativity: nH = 1: ______ nH>1:_______ nH<1: _______	none - binding of first ligand has no effect on binding of the rest of ligands; positive - first ligand binding has low affinity, but once first is bound, affinity increases ; negative - binding of first causes low affinity for others to bind
in an allosteric protein (like hemoglobin), A protein with_______ binding sites. • Binding sites/subunits______ with each other. Associated with ligand binding-induced _______ change.	multiple; interact; conformational
first binding event increases affinity at remaining sites.	positive cooperatity - nH > 1
first binding event reduces affinity at remaining sites.	negative cooperativity - nH< 1
Positive co-operativity can be recognized by_______ binding curves.	sigmoidal
Tissues generate CO2 from cellular respiration. Carbonic anhydrase catalyzes: CO2 + H2O--> H+ + HCO3−. INCREASE IN H+, LOWER PH, MORE ACIDIC, ______ O2 BINDING BY HEMOGLOBIN	DECREASES
Hb also carries 15-20% of the CO2 to the lungs and kidneys to be excreted. CO2 binds to the amino terminal in the form of a carbamate, stabilizes the T state, and promotes O2______.	dissociation
the effect of pH and [CO2]/pCO2 on the binding and release of O2 by Hb. high oxygen, Hb binds O2 and releases H+. low oxygen (tissue), hemoglobin binds H+ and releases O2	bohr effect
o When pH is_____, the hemoglobin has lower affinity for oxygen releases oxygen o pH is_____, binds more oxygen	lower; higher
when pH jumps from 7.4 to 7.2 what is the impact on affinity of hemoglobin for oxygen?	pH is lower, theta is lower, hemoglobin has a decreased affinity for oxygen
chapter 5 problems 3a and 3B in lecture 11 notes
intermediate in glycolysis, Polyanion, high in erythrocytes. LECTURE 09/18 PAGE 5	2,3-BPG
2,3-BPG _____ hemoglobin affinity for O2; binds to hemoglobin (one per tetramer) and stabilizes the tense state. it ensures tissue oxygen delivery at high altitide	reduces
chapter 5 problem 3a,3b,3c lecture 11
CO fits in the same binding site as O2. • CO binds Hb 250 times better than O2. • CO is highly toxic. It blocks the function of myoglobin, hemoglobin, and others.	CO poisioning
carbon monoxide increases affinity for oxygen, but binds it so tight it doesn't release. true or false	true
• Life-threatening. • Individuals homozygous for the sickle-cell allele of the gene encoding Hb β subunit. • Normal Hb (Hb A) remains soluble upon deoxygenation. Mutated deoxygenated Hb (Hb S) forms insoluble fiber.	sickle cell anemia
sickle cell - Genetic disease: homozygous for Glu6 to Val6 mutation in Hb β chain. • Mutation creates a______ patch on the surface of deoxyhemoglobin S. bc globular, no longer charged AA on outsiide makes it curve inward	hydrophobic

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