Intro To BC - Exam 1

Metabolism

the sum total of all reactions of an organism

Macromolecules & H2O Affinity

Hydrophilic/Polar - proteins, carbohydrates, nucleic acids

Hydrophobic/Nonpolar - fatty acids (technically is not a polymer like the others)

Metabolic Pathways that yield complex molecules from simple precursors are:

anabolic (input of energy)

Dipole Moment

any molecule that has a net separation of charges (ex: CHCl3)

In a bacterial cell, DNA is in the

nucleoid

In eukaryotes, the nucleus is enclosed by a double membrane called

the nuclear envelope

In place of a nucleus a prokaryotic cell has a

nucleoid

Hydrogen Bond Donors

partially charged hydrogens (due to H being bonded to a highly electronegative atom - F, O, or N)

examples: NH3+, H2O, Alcohols, HF, Amines

Hydrogen Bond Acceptors

electronegative atom with lone pairs to attract the partially positive charge on the donor hydrogen (F, O, N, CL, S, P, or even a pi bond in alkenes or aromatic rings)

examples: water oxygen, ether oxygen, or carbonyl oxygen found in ketones, amides, and aldehydes

Weak Interactions in Order of Most to Least Energy needed to Disrupt

charge-charge (ionic), covalent, H bond, van der Waals

Types of van der Waals Interactions

charged-dipole: partially charged molecule (dipole) (polar molecules have dipoles) interacts with fully charged molecule (cation/anion)

dipole-dipole: 2 dipoles face opposite partial charges to each other

charge-induced dipole: molecule that was originally neutral becomes a dipole due to close proximity of an anion/cation

dipole-induced dipole: strong enough dipole can take a neutral molecule and create a dipole in it

dispersion forces: weak partial charge distribution interactions within two molecules in close proximity

Which of the following factors is responsible for the fact that water is liquid at room temperature

H-bonds holds water molecules close together

Hydronium Ion

H3O+

Hydroxide Ion

OH-

Which properties of water promote relatively constant climate of earth

high heat of fusion

high heat of vaporization

high heat capacity

Why does the hydrolysis of ATP to ADP have a middle road, negative delta G value

if the value was too negative, the overall metabolism of ATP would be too difficult

What molecules is this?

ATP

What can lead to the determination of delta G?

delta E of a rxn

ratio of products to reactants of a reaction

entropy & enthalpy of a rxn

delta G naught of a rxn

In biological systems, most energy generating redox rxns involve hydride ion transfer or hydrogen atom transfer using which of the following? (electron carriers)

NADH & FADH2

In order to determine the standard voltage of a rxn

the standard cell must be written as they occur in the rxn and the voltages are added

In a redox rxn, an electron acceptor is

converted to an electron donor with the gain of one or more electrons

oxidizing agent

gets reduced

Amino Acids with Hydrophobic Side Chains

aliphatic AAs: glycine, alanine, valine, leucine, proline, isoleucine

aromatic AAs: phenylalanine, tyrosine, tryptophan

Amino Acids with Hydrophilic Side Chains

Polar Uncharged: amide, glutamine, asparagine, threonine, cysteine, serine

Acidic: aspartic acid & glutamic acid

Basic: lysine, histidine, arginine

Local folding of a protein occurs at what defined level of protein folding

Secondary

Types of Bonds within an Amino Acid (omega Ω, psi Ψ, phi Φ)

Omega Ω: peptide bond (between carboxylic acid C & amine N) - no free rotation because they are partial double bonds - planar geometry

Psi Ψ: bond between alpha-carbon and carbonyl carbon

Phi Φ: bond between alpha-carbon and amide nitrogen

The following amino acid would stabilize the 3˚ protein folding through which interaction?

hydrogen bond

Salt bridges in proteins are an exmaple of what type of attraction?

ionic interactions

Examples of post translational modification of proteins

phosphorylation, acetylation, proteolytic cleavage, glyocsylation, hydroxylation, carboxylation

The three-dimensional structure of a protein is determined mainly by

the sequence of AAS in the protein

When looking at a double reciprocal graph of data from an uncompetitive enzyme compared to data from a competitive enzyme, which properties will show up differently on the graph

Km & Vmax

NOT concentrations or time

Km represents the..

formation of ES

4 Main Macromolecules (monomer, polymer, linkage, polarity)

Polar (polymer - monomer - linkage)

• protein - amino acid - peptide bond

• carbohydrate (polysaccharide) - monosaccharide - glycosidic (ether)

• nucleic acid - nucleotide - phosphodiester

Nonpolar

• Lipids are NOT polymeric because they do not link together, but rather group together (usually to hide from water)

• fatty acids are the “monomers”

• linked via ester bonds

Most Abundant Chemical Elements in Living Systems

CHON

Most biomolecules can be considered to be derivatives of

hydrocarbons

Amphipathic Molecules

have both a hydrophilic & hydrophobic portion

example: CH3CH2CH2COOH

The plasma membrane…

provides support

present in both eukaryotes and prokaryotes

control the flow of substances in and out of the cell

Prokaryotes are more efficient because they are:

polycistronic: single messenger RNA (mRNA) that contains coding instructions to make different proteins

Which of the following compounds is capable of hydrogen bonding with like molecules?

CH3NH2 & HOCH2CH2OH

both of these molecules have partially positive H!

Noncovalent Interactions

H bonds, ionic interactions, van der waals, hydrophobic interactions (aggregation of hydrophobic molecules in a polar solvent to hide from water)

noncovalent interactions do not include sharing electrons

Examples of Weak Acids

anything that is NOT a strong acid (HCl, HBr, HI, HNO3, HClO4, H2SO4, HClO3)

example: HCO3-

acids typically have an H in them to donate

In any redox reaction, an electron donor is

the reducing agent

gets oxidized

Strongest Reducing Agents a Standard Reduction Potential that is

more negative

reducing agent gets oxidized, meaning a lower reduction potential

higher reduction potential means it is more likely to get reduced

A constant source of ___ is required for maintenance of a cell’s ordered state

energy

Enzymes are biological catalysts that enhance the rate of reaction by

decreasing the activation energy

Cellular Components arranged in order of increasing size

amino acid < protein < ribosome < mitochondrion

What is not true about the nucleus

found in both eukaryotes and prokaryotes

Which of the following is present in only prokaryotes:

nucleus

endoplasmic reticulum

plasma membrane

nucleolus

none of the above

nucleus, ER, & nucleolus are in eukaryotes

prok have a nucleoid region

plasma membrane is in both prok & euk

the delta G naught of a rxn can

be used to calculate whether a rxn is thermodynamically favorable under defined non-standard conditions

The enzyme fumarase catalyzes the reversible hydration of fumaric acid to l-malate, but it will not catalyze the hydration of maleric acid, the cis isomer of fumeric acid. this is an example of

stereospecificity

the function of a lyase enzyme

to facilitate a rxn of one substrate to form two products without the use of water

What bond (pink) / macromolecule is this? (label parts of molecule)

phosphodiester bond

nucleic acid

ether ring = ribose

ring with letters = base

What is this macromolecule (broad term)? What bond is forming & what comes out of this bond?

carbohydrate

glycosidic bond (ether —> R-O-R)

h2o released (1 O, 2 H’s from the reacting OH groups)

What macromolecule? What bond is forming? Favorable?

protein

peptide bond (amide bond)

condensation reaction between −COO- group (carboxyl) and −NH3+ (amino) group with water elimination (dehydration rxn facilitated by ribosome)

not thermodynamically favorable (∆G >0)

What are the two molecules being added to form the product (name this too)? Bond being formed?

lipids are usually chains of hydrocarbons! (hydrophobic)

4-membered hydrocarbon ring = steroid

bond = ester linkage (RCOOR)

Compare & Contrast Prok & Euk

prok

• no internal division

• DNA is in nucleoid region

• binary fission for cell division

euk

• internal division

• DNA is in nucleus

• mitosis/meiosis

both

• ribosomes

• cell walls

• plasma membrane - support, regulates what enters cell & what leaves

Water’s Unique Properties

2 H-bond donor sites (2 Hydrogens) & 2 H-bond acceptor sites (LPs on oxygen)

permanent dipole

high heat capacity

surface tension

amphipathic

Buffer

resists pH change following the addition of acid or base within about + 1 pH unit of the pKa (50-50 point) of a solution

weak acid/conjugate base pair = buffer

Henderson-Hasselbach Equation

pH = pKa + log ([A-]/[HA])

pH & pKa Relationships

• pH < pK_a - [HA] > [A^-] (favoring acid form)

• pH = pK_a - [HA] = [A^-] (50% protonated & 50% deprotonated)

• pH > pK_a - [HA] < [A^-] (favoring conjugate base form)

K_^a

acid dissociation constant

indicates strength of acid (higher = stronger)

 [H⁺][A^-] / [HA]

Isoelectric Point

pH at which the average charge on the molecule is zero

pI = (pKa1 + pKa2)/2 (average of the two pKa values surrounding the isoelectric species

Methods of Separating Biomolecules

gel electrophoresis: separates DNA by size (smallest go farther on gel)

• DNA moves toward positive anode because DNA is negative

• agarose gel or acrylamide gel

isolectric focusing

• Tube with different sections (Each with different pH) - molecules loaded in - charge to molecules will bring molecule toward anode until it hits the pI since charge in now 0 & molecule will not be attracted/repelled by anode/cathode

Thermodynamic Systems

Closed: can exchange energy (heat/work) but not matter with the surroundings

Open: can exchange matter & energy with surroundings

Isolated: can exchange neither matter nor energy with surroundings

living systems generally operate at a constant T & pressure

First Law of Thermodynamics

energy is conserved

closed system - E exchanged in formed of work/heat

enthalpy is the heat exchanged between system & surroundings at constant pressure (typical condition of living systems)

Heat of a Rxn

at constant pressure, the heat of the reaction is equal to change in enthalpy (ΔH)

in reversible rxns, the magnitude of ΔH doesnt change, only sign flips

Exothermic Reactions: Δ𝐻 < 0, meaning the system releases heat to the surroundings

Endothermic Reactions: Δ𝐻 > 0, meaning the system absorbs heat from the surroundings

Reversible/Irreversible Rxns

• Reversible Process: near a state of equilibrium

  • Process @ equilibrium: 

    • Lowest energy state of the system

    • Forward & reverse rates of process are equal

  • Example: ice melting at 0^oC

• Irreversible Process: set up far from an equilibrium state, and then proceed towards that state 

  • Example: burning paper

2nd Law of Thermodynamics

Entropy of an isolated system will tend to increase to a maximum value

Entropy (S): the measurement of degree of randomness or disorder of a system

2nd Law of Thermodynamics Equation (open system)

ΔG = ΔH - TΔS

ΔG Definition & Meaning of Values

portion of total energy change that is available to do useful work at constant T & P

ΔG > 0 → thermodynamically unfavorable (reverse process = favorable); endergonic process; free energy is required to do work

ΔG = 0 → zero free energy; rxn is reversible - system @ equilibrium

ΔG < 0 → thermodynamically favorable (reverse process = unfavorable), spontaneous; free energy is available to do work; exergonic process; free energy is available to do work

Effect of T on ΔG

Equilibrium Equations (ΔG = …. , K = ….., Q = ……., R = ….., Standard Temp=?

ΔG = ΔG˚ + RTlnk (WHEN RXN IS AT EQUILIBRIUM)

• because ΔG = 0 @ equilibrium:

  • ΔG˚ = -RTlnk

  • k = e^(-ΔG˚/RT)

ΔG = ΔG˚ + RTlnQ (WHEN RXN IS NOT AT EQUILIBRIUM)

K (uses concentrations @ equilibrium) or Q (uses concentrations not @ equilibrium) = ([C]^c[D]^d) / ([A]^a[B]^b) for rxn: aA + bB —> cC + dD

R = 8.314 J/molK

T = 298k (standard! K = 273 + celsius)

Equilibrium Constant & Corresponding Delta G Naught Values Meaning

K_^eq > 1 → [product] Favored → ΔG˚ < 0

K_^eq = 1 → [product] = [reactant] → ΔG˚= 0

K_^eq < 1 → [reactant] Favored → ΔG˚ > 0

Equilibrium vs Homeostasis

Concentrations of reactants & products are constant in both

Energy is required to maintain homeostasis

• maintains Q far from K such that ΔG does not equal 0

Q < K → ΔG < 0 → fwd rxn is favored (products)

Q = K → ΔG = 0 → equilibrium, neither direction is favored

Q > K → ΔG > 0 → reverse rxn is favored (reactants)

Coupling Favorable & Unfavorable Rxns

Living systems couple favorable (ΔG˚’ < 0) & unfavorable (ΔG˚’ > 0) processes to drive the unfavorable process forward

(FAVORABLE = EXERGONIC ⇒ DELTA G NAUGHT IS NEGATIVE)

Standard Conditions for Biochemical Gibb’s Energy ∆G°′

Activity of H+ is at 1 and pH 7 ( [H+] = 10^-7M )

Activity of H2O is defined by convention to be 1

Molecules Involved in Energy Change

ATP, ADP, AMP

Molecule?

Adenosine Monophosphate AMP

Molecule?

Adenosine Diphosphate ADP

Redox Reaction Terminology

OIL RIG

• Oxidation Is Loss of electrons (or loss of hydrogen, or gain of oxygen)

  • the one that gets oxidated is the reducing agent/reductant

• Reduction Is Gain of electrons (or gain of hydrogen, or loss of oxygen)

  • the one that gets reduced is the oxidizing agent/oxidant

Biochemical Standard Reduction Potential (E˚’)

the greater the reduction potential, the greater the tendency for a given electron carrier to become reduced

stronger oxidizing agents have higher values of H

standard reduction potential is measured at pH = 7

ΔG˚ in Redox Rxns

ΔG˚’ = -nFΔE˚’ = -nF [ΔE˚’_{(e- acceptor) ^-} ΔE˚’_{(e- donor)}

F= Faraday’s constant = 96.5J/molV

Identify all 20 AAs by Single Letter Code, Full Name, and Structure (label structure with carboxylic acid group, amino group, alpha carbon, R group, phi/psi/omega bonds)

Alpha Amino Acid Stereochemistry

All Alpha Amino Acids, except Glycine, contain an asymmetric alpha carbon → chiral

D (large group to the right) & L (large group to the left) structures = enantiomers

Biological Amino Acids are always L

Sugars are always D

Geometry of Peptide Bond & Favored Form

peptide bond is nearly planar, and the trans form is favored over cis, partial double bond character for C—N bond

Oligopeptide vs Polypeptide

Oligopeptides (NOT PROTEIN, TOO SHORT) are peptide chains consisting of only a few residues, while polypeptides (PROTEIN) contain greater than 15-20 residues

Peptides can be cleaved at specific sites by

proteolytic enzymes: chymotrypsin, trypsin, pepsinogen

chemical agents: CNBr

Peptide Termini

one amino terminus (N-terminus) and one carboxyl terminus (C-terminus), always write the N-terminal residue to the left and the C-terminal residue to the right

Polyampholyte

Peptides are polyampholytes: can have many charges

as pH increases, overall charge on peptide becomes more negative

as pH decreases, overall charge on peptide becomes more positive

pKa of Side Chain

pKa of a side chain is influenced by its environment 

• Unperturbed, the pKa of glutamic acid is 4.2

• In proximity to a negative charge, the pKa of a glutamic acid is raised

• In proximity to a positive charge, the pKa of a glutamic acid is lowered

Genetic Code

3 bases = 1 amino acid

Start codon: AUG

Stop codon: UAA, UGA, UAG

2˚ Structures & Bonds Involved

local folding

alpha helix, beta plated sheet, 3₁₀ helix

H bonds

1˚ Structures & Bonds Involved

Amino Acid Sequence

peptide bonds

3˚ Structures & Bonds Involved

ultimate 3D shape

• Disulfide bonds (prevalent in cysteine - have a terminal sulfur)

• Hydrogen bond (betwen polar R groups)

• Nonpolar/hydrophobic R group interactions (nonpolar R groups typically want to hide from water)

• Ionic bonds (some R groups are charged and will interact)

4˚ Structures & Bonds Involved

more than one 3˚ structure

• Disulfide bonds (prevalent in cysteine - have a terminal sulfur)

• Hydrogen bond (betwen polar R groups)

• Nonpolar/hydrophobic R group interactions (nonpolar R groups typically want to hide from water)

• Ionic bonds (some R groups are charged and will interact)

Ramachandran Plot: What is it & what are the significant ranges

Shows sterically allowed psi Ψ & phi Φ angles

bond angles are very defined when trying to form secondary structures

L & R handed alpha helix have equal & opposite degree rotation

Fibrous Protein Structures

fibrous proteins are elongated molecules with well-defined 2˚ structures

• Keratin - hair, fingernails, feathers, scales, or intermediate filaments (intracellular)

  • coiled-coil structure

• Fibroin - silk cocoons

  • stacked beta sheet

• Collagen - abundant connective tissue protein; matrix material in bone on which mineral components precipitate

  • triple-strand left-handed helix

Globular Protein Domains

globular proteins fold into defined proteins

domains are regions that fold independently and frequently possess some defined function

Anfinsen’s Experiment

proved that info needed for structure & function of protein is contained in primary structure of amino acid (AA sequence)

process:

used ribonuclease from cown

1. anfinsen used Urea & Beta-mercaptoethanol (BME) to denature the molecule instead of heat

   1. BME reduces sulfur (causes disulfide bond to become H bond)

2. took denatured protein and put it through two diff processed

   1. first, he oxidized it, which caused protein to form disulfide bonds, then he removed urea - wrong cysteines were bonded = incorrect structure

   2. second, he took the denatured protein and removed urea first then slowly oxidized it allowing protein to choose favorable folds = original structure is back!

3 Thermodynamic Factors Influence the Folding & Stability of Proteins

1. Favorable intermolecular enthalpic interactions

   1. Charge-charge interactions (ionic bonds; salt bridges) 

      1. Ionic bonds = salt bridges between charge entities 

      2. These charged entities can be between two R groups or something that gets in between two oppositely charged R groups, forming a salt bridge (electrostatic bridge that gets groups close enough to have interactions that matter)

   2. Intermolecular hydrogen bonds

   3. Van der waals interactions; proteins are densely packed

2. Unfavorable loss of conformational entropy

   1. Unfolded state has many conformations (high entropy)

   2. Folded state has only a few closely related conformations (low entropy)

3. Favorable gain of solvent entropy from burying hydrophobic groups (“hydrophobic effect”)

   1. Hydrophobic side chains cluster in the interior, they release ordered solvent molecules from clathrate structures

Protein Folding Landscape

as the unfolded protein begins to fold, even just once, it narrows down the possibilities of the native state (more folds = less possibilities - funnel!)

“Rugged landscape of funnel” → sometimes proteins can thermodynamically unfold, but if it's too far into folding, it is less likely to do this (energetically too hard to change the fold - ends up breaking back down to amino acids to be remade into another protein)

chaperones prevent making the wrong folds!