tasnimjaisee's version from 2017-10-21 07:25

Lecture 1

Question Answer
What is Biochemistry? Biochemistry is... (4)Molecular level - chemistry→biology - organism reactions & principles - molecular logic of life
Distinguishing Features of Living Organisms (6)microscopic - energy - Compartments - Alteration response - Self-replication & Assembly - Evolution
Living state in terms of five foundationsChemical - Cellular - Energy - Genetic - Evolutionary
Three elements ___, ___ and ___ account for 98% of most organismsC, O, H
Carbon is the ___ most common element in living organismsThird
What is the “next-best” candidate as a chemical foundation for lifeSilicon
What is the “next-best” candidate as a chemical foundation for life, and why (2) ?Silicon: 4 covalent bonds - Abundant in crust
Why are we based in carbon rather than silicon? C-C bonds are more...stronger - combustible - soluble combustion products
The ___ ___ of the ___ ___ within a biomolecule will determine the structure, function and properties of the biomoleculeCollective properties - Functional groups
Conformation (2)Flexible - Changed without breaking bonds
Configuration (2)Fixed spatial arrangement of atoms - Can't change without breaking bonds
Configuration is conferred by either types (2)Double bonds - Chiral centers
Double bonds: Around which there is no freedom of ___Rotation
Chiral centers, around which substituent groups are arranged in a ___ ___specific positioning
Cis (2)“on this side” - groups on the same side of the double bond
Trans (2)“across" - groups on opposite sides of the double bond
Chiral centers (2)4 different substituents attached - yielding 2 stereoisomers differing in configuration
A molecule with “n” chiral carbons will have ___ stereoisomers2n
Chircal Molecule: Rotated molecule ___ be superimposed on mirror image (Cannot/Can)Cannot
Achircal Molecule: Rotated molecule ___ be superimposed on mirror image (Cannot/Can)Can
Stereoisomers (2)Non-superimposable - Chiral center configurations
Types of StereoisomersEnantiomers - Diastereomers
EnantiomersMirror images
Racemic mixture (2)Enataniomers equimolar solution - No optical rotation
Enantiomers rotate the plane of polarized light in ___ but ___ ___equal - opposite directions
Advantages of Polymers (3)Simplicity - Recycling - Sequence diversity
In vitroIn glass - behaviour of molecules outside context of cell
In vivoIn the living - behaviour of molecules within context of cell
First Law of ThermodynamicsTotal amount of energy in the universe remains constant; though form may change
Second Law of ThermodynamicsTendency in nature is toward disorder; entropy increasing
EndergonicΔG > 0
ExergonicΔG < 0
How can cells drive thermodynamically unfavorable reactions?Coupling endergonic reactions to exergonic reactions
Perpetuation of biology requires that genetic information be (3)Stable - Accurate - Reproduced with minimal errors
Nucleotide sequence within genes dictates the sequence of ___ ___AA
AA sequence within genes dictates the structure of ___Protein
Protein structure within genes dictates the ___ ___ of proteinbiological activity

Lecture 2

Question Answer
The most abundant molecule in living organismsWater
Water has both ___ and ___ roles in biological systemsActive - Passive
Water's passive roleBiomolecules (proteins, membranes, nucleic acids) are formed in response to water interactions
Water's active roleParticipant in biochemical reactions
O has partial (___) charge and each H has partial (___) charge-, +
The dipole of water will dictate it’s ability to... (2)Electrostatic interactions with charged molecules - Form Hbonds
Hydrogen bondsElectrostatic interaction between hydrogen linked (donor) with free electron pair (acceptor)
Most common hydrogen bond donors and acceptorsO and N
Oxygen and nitrogen each have the ability to serve as either ___ ___ donors or acceptorsHydrogen Bond
Are hydrogen bonds are covalent or non-covalent?Non-covalent
Hydrogen bonds are approximately ___ the length of a covalent bonddouble
The large number of hydrogen bonds in water contributes to the high _______ and _______ of waterHeat of vaporization - Specific heat capacity
Heat of VaporizationHeat requires to vaporize liquid at boiling temp
Specific Heat CapacityHeat required to raise temperature of a substance 1 degree
Water has a higher ___ point, ___ point, and _______ than most other common solventsMelting - Boiling - Heat of vaporization
IsothermicNeed to regulate and maintain their temperatures
In ice, each water molecule participates in ___ ___ ___ with other water molecules4 HBonds
Ice has a ___ density than liquid water (lower/higher)Lower
Why is water is an extremely effective hydrogen-bonder (2)Accept & donate hydrogen bonds - Small size
Water molecules can interact, and dissolve, charged solutes through formation of..layers of hydration
Is CO2 polar or nonpolar?Non-Polar
Is O2 polar or nonpolar?Non-Polar
Hydrophobic interactionsHold non-polar regions of molecule together
Non-covalent forces influence (3)Stabilization - Interactions - Enzyme binding reactants
Non-covalent interaction of importance to biomolecules includeHBonds - Ionics - Hydrophobics - Van der Waals
These non-covalent interactions enable functions relating toFlexibility - Transients
Biomolecules have functional groups with hydrogen bonding capacity bond with (3)Water - Intramolecular - Intermolecular
Hydrogen bonds are critical for the ____ of biomolecular interactions but not for the ____ of biomolecular structuresSpecificity - Formation
Magnitude of contribution of ionic interactions to biomolecular structures is greatly reduced by..Shielding by water molecules
Strength of electrostatic interactions depends on (2)Distance separation - Intervening medium
Interaction between permanent and induced dipoles (Range, Magnitude)Short range - Low magnitude interactions
Van der Waals Forces are abundant in the core of protein due to close packing of..hydrophobic side chains
Hydrophobic EffectAssociation of a non-polar molecule or group with other non-polar molecules
In hydrophobic effect. how do non-polar side chains exist?Cluster in interior of protein; away from water
In hydrophobic effect, which side do the polar and charged side chains remain in?outer surface facing water
Thermodynamics of the Hydrophobic Effect: introduction of the non-polar molecule has caused a ___ in the entropy of waterdecrease
Thermodynamics of the Hydrophobic Effect: The association of non-polar molecules with each other ___ some of the ordered water molecules, resulting in an ___ in the entropyreleases - increase
Thermodynamics of the Hydrophobic Effect: Nonpolar molecules are driven together not because their association ___ ___ water molecules.releases ordered
Kwion product of water
[H+] > 10^-7 MpH under 7 acid
[H+] < 10^-7 MpH over 7 basic

Lecture 3

Question Answer
Except for ___, all amino acids have a chiral carbon and are therefore ___Glycine - Stereoisomers
Typically only the ___ stereoisomers are found in proteinsL
All amino acids haveCarboxyl group - Amino group - Alpha carbon - R group
Carboxyl groupCOO-
Amino groupH3N+
Chiral centerAlpha carbon is bonded to four different groups
Does glycine have a chiral center?No
Biologically proteins are made almost exclusively from ___ amino acidsL
Where do hydropobic chains of non-polar amino acids bury?Core of protein
PhosphorylationRegulate protein function
Disulfide bonds form through..Oxidation of sulfhydryl groups of 2 cysteine residues
Side chain functional groupsLys-primary amino - Arg-guanidino group - His-imidazole
A fraction of cellular histidines will be ___ and the rest will carry a net charge of ___ because of it's imidazole has a pKa near ___+1 / 0 / pH
ZwitterionDipolar ion of AAs
Every amino acid has at least two groups that accept and donate protons (___); the carboxyl group (pKa ___) and the amino group (pKa ___)diprotic - 2 - 10
TriproticIonizable groups in their side chains
pIisoelectric point
Isoelectric point of an amino acidpH = zero molecule net charge
Ionizable groups in the amino acids (3)Carboxyl group - Amino group - Side chains of the triprotic amino acids
pKapH range at which that group changes its protonation state
pH below the pKa, the ___ form predominates protonated (HA)
pH above the pKa, the ___ form predominates unprotonated (A-)
At pH 7.4 carboxylic and amino groups will be in which forms?COO- and NH3+
Titration of GlycinepI = ½ (pKa1 + pKa2)
Titration of HistidinepI = ½ (pKaR + pKa2)
Titration of GlutamatepI = ½ (pKaR + pKa1)
2 amino acids can be covalently linked through which type of bond?Peptide
How do peptide bonds form?Condensation reactions between carboxyl of 1 AA and amino group of another acid
Amino acid ___ compose peptide chainsresidues
Formation of peptide bonds eliminates the ionizable ___ and ___ of the free amino acidsα-carboxyl AND α - amino groups
Retro-inverso (RI) peptidesNatural peptides isomers which sequence in reversed and D- amino acids are employed
RI isomers of biological peptides are often ___ to D isomersuperior


Question Answer
Which AAs can be considered positively charged (3)?Histidine - Lysine - Arginine
Which AAs can be considered negatively charged? (2)Aspartate - Glutamate


Question Answer
Which AAs can serve as a proton acceptor/donor in many enzymatic reactions? (1)Histidine
Which AAs can carry a net charge of -1 at physiological pH? (2)Aspartate - Glutamate
Which AAs can be considered negatively charged? (2)Aspartate - Glutamate
Which AAs can have carboxyl groups in their side chains (2)Aspartate - Glutamate
Which AAs can be responsible for umami (1)Glutamate
Which AAs can be used as a flavor enhancer (1)Glutamate --> MSG
Which AAs can be considered positively charged (3)?Histidine - Lysine - Arginine
Which AAs can always carry a +1 net charge at physiological pH (2)?Lysine - Arginine
Which AAs can be a precursor of serotonin? (1)Tryptophan
Which AAs can be considered as hydroxyl group (3)?Tyrosine - Serine - Threonine
Which AAs can be considered as Polar, Uncharged (5)? GCASTGlutamine - Cysteine - Asparagine - Serine - Threonine
Which AAs can undergo kinase-mediated phosphorylation (2)?Serine - Threonine
Which AAs can form a covalent linkage called a disulfide bond2 Cystines
Which AAs can be found at turns of polypeptides? (1)Proline
Which AAs can be usually in combinations with glycine? (1)Proline
Which AAs can have a sulfur group within its side chain? (2)Methionine - Cystine
Which AAs can be considered aromatics (4)?Histidine - Phenylalanine - Tyrosine - Tryptophan
Which AAs can be considered non-polars (7)?Glycine - Alanine - Proline - Valine - Leucine - Isoleucine - Methionine
Which AAs can undergo post-translation modification through phosphorylation? (3)Tyrosine - Serine - Threonine

Lecture 4

Question Answer
smallest proteininsulin (15)
largest proteintitin
Most important forces stabilizing the specific structures of a given protein are...non-covalent
Native proteins are ___ stablemarginally
StabilityDifference in the free energies of the folded/unfolded states
Folded proteins occupy a ___-energy state that makes the native structure most stable.Low
Protein folding a ___ process (rapid/slow)rapid
Protein folding and unfolding is a ___ processcooperative
Primary Structurelinear sequence of amino acids
Secondary Structurelocalized interactions within a polypeptide
Tertiary Structurefinal folding patter of a single polypeptide
Quaternary Structurefolding pattern with multiple polypeptides
What does primary structure tell of the 3d structure?Nothing
Primary Structure can be determined by..investigation of the protein or corresponding gene
Secondary Structure important typesa-Helicies and b-Sheets
Secondary structure regularities in local conformation is maintained by Hydrogen bonds between (2) amide hydrogen and carbonyl oxygen
To represent a viable form of secondary structure the folding pattern must... (2)Optimize the hydrogen bonding potential and polypeptide chain conformation
Oxygen of the carbonyl group and the hydrogen of the amide nitrogen are ____ to each othertrans
Rotation around C-N bond is restricted due to the partial double-bond nature of the peptide bond, which is?No freedom of rotation
Most residues within biological peptides and proteins tend to be in the ____ configurationtrans
Each α-carbon is held within the _______ through single bonds, about which there is complete ______main-chain - freedom of rotation
phi and psi can range from –180 to 180
Which handed helix is A-HelixRight-Handed
Each C=O (residue ___) forms a hydrogen bond with the amide hydrogen of residue ___n and n+4