Biochem Exam Ch:1-3

Chapter 1: The foundations of Biochemistry

What are biomolecules?

-a molecule that is produced by a living organism
-compounds of carbon with a variety of functional groups (stereospecific)

What is the definition of biochemistry?

describes in molecular terms the structures, mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie lie in all its diverse forms

what are two things that biochemistry does?

1. Asks how the remarkable properties of living organisms arise from thousands of different biomolecules
2. Shows how the collections of inanimate molecules that constitute living organisms interact to maintain and perpetuate life governed solely by the same physical and chemical laws that govern the nonliving universe

What are 5 features that define a living organism?

1. Cells are the fundamental unit of life
2. Cells use a relatively small set of carbon-based metabolites to create polymeric machines, supramolecular structures, and information repositories
3. Living organisms exist in a dynamic steady state (homeostasis)
4. Cells have the capacity for precise self-replication and self-assembly using chemical information stored in the genome
5. Living organisms change over time by gradual evolution

What limits the dimensions of a cell?

LOWER LIMIT:
-the minimum number of each type of biomolecule required by the cell
UPPER LIMIT:
-the rate of transport of nutrients into the cell and waste products out

What are three fundamental properties that all cells share?

1. They are bound by a plasma membrane
2. Have a cytosol containing metabolites, coenzymes, inorganic ions, and enzymes
3. Have a set of genes contained within a nucleoid (bacteria or archaea) or a nucleus (eukaryotes)

What are the four most abundant elements in living organisms?

CHON (they are the lightest elements; lightest elements form the strongest bonds)

the chemical personality of a compound is determined by...

determined by the chemistry of its functional groups and their disposition in three-dimensional space

What are the four classes of macromolecules?

1. Proteins
2. Nucleic acids
3. Polysaccharides
4. Lipids

4 Classes of Macromolecules:
1. Proteins-

-long polymers of amino acids, constitute the largest mass fraction (besides water) of a cell
-the most versatile of all biomolecules
-sum of all proteins is proteome

4 Classes of Macromolecules:
2. Nucleic acids-

-DNA + RNA are polymers of nucleotides.
-they store and transmit genetic information
-some RNA molecules have structural and catabolic roles
-entire sequence of a cell's DNA is called the genome

4 Classes of Macromolecules:
3. Polysaccharides-

-polymers of simple sugars such as glucose
Three major functions:
1. Energy-rich fuel stores
2. Rigid structural components of cell walls
3. Extracellular recognition elements that bind proteins on other cells

4 Classes of Macromolecules:
4. Lipids-

-water-insoluble hydrocarbon derivatives
-not classified as a macromolecule, but they can associate noncovalently into very large structures
-lipid molecules are much smaller
-sum of all lipids is lipidome

Three functions of lipids

1. structural components of membranes
2. energy-rich fuel stores
3. pigments and intracellular signals

What are stereoisomers?

molecules with the same chemical bonds and same chemical formula but different configuration (the fixed spacial arrangement of atoms)

configuration is conferred by the presence of either:

1. Double bonds (little to no freedom in rotation)
2. Chiral centers (around which substituent groups are arranged in a specific orientation)

What are geometric isomers?

-also known as cis-trans isomers
-they differ in arrangement of their substituent groups with respect to the non-rotating double bond
-"cis"= same side
-trans"= across

What are chiral centers?

-a carbon atom with four different substituents; asymmetric carbon (either R or S)
-a molecule with only one chiral center can have two stereoisomers
-when 2 or more (n) chiral carbons are present, there can be 2^n stereoisomers

What are enantiomers?

-stereoisomers that are non-superposable mirror images of each other (left and right hand)
-have different optical activity (the capacity of a substance to rotate the plane-polarized light)

What are diastereomers?

-pairs of stereoisomers that are not mirror images of each other
-cis-trans isomers are examples of diastereomers

What are achiral carbons?

-when a tetrahedral carbon has only three dissimilar groups, only one configuration is possible and the molecule is symmetric (or achiral)
-can be superposed on its mirror image
-compounds without chiral centers do not rotate the plane of plane-polarized light

what is a racemic mixture?

an equimolar solution of the two enantiomers; shows no optical rotation

List the priority of common substituents in the RS nomenclature system:

1. -OCH3
2. -OH
3. -NH2
4. -COOH
5. -CHO
6. -CH2OH
7. -CH3
8. -H

What are the three steps to the nomenclature of chiral centers?

1. The chiral atoms is viewed with the lowest priority group pointing away from the viewer
2. If the priority of the 3 groups decreases in clockwise order, the configuration is (R)
-right or running with the clock
3. If the priority decreases counterclockwise then the configuration is (S)
-sinister or left

What is conformation?

-the spacial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space (due to freedom of rotation about single bond)
-when one or more of the hydrogen atoms on each carbon is replaced by a functional group that is either very large or electrically charged, freedom of rotation around C-C bond is hindered

what are the two things that are of the utmost importance when it comes to interactions between biomolecules are:

1. Configuration
2. Conformation

What is an open system?

-is a system that has external interactions. Such interactions can take the form of information, energy, or material transfers into or out of the system boundary
-exchanges both energy and matter with its surroundings

what is a closed system?

-a natural physical system that does not allow transfer of matter in or out of the system
-exchanges energy but not matter with its surroundings

what is an isolated system?

-a system so far removed from other systems that it does not interact with them. Also can be a thermodynamic system enclosed by rigid immovable walls through which neither mass nor energy can pass
-exchanges neither mass nor energy with its surroundings

a living organism is what type of system?

-it is an open system; it exchanges both matter and energy with its surroundings
-living organisms exist in a dynamic steady state

what is the first law of thermodynamics?

-the principle of the conservation of energy; in any physical or chemical exchange, the total amount of energy in the universe remains constant, although the form of the energy may change
-PE-->KE or vice versa
-PE= chemical bonds; KE=heat and motion

What is enthalpy?

-the heat content of a system (delta H)

what is the change of enthalpy?

-reflects the kinds and numbers of chemical bonds and non-covalent interactions broken and formed
-exothemic reactions have a negative delta H (release of energy)
-endothermic reactions have a positive delta H (absorbs energy)

what is the difference between exothermic and exergonic reactions?

-exothermic reactions deals with enthalpy change in any chemical process that is measured in terms of heat in a closed system (only delta H)
-exergonic reactions deal with free energy change of any chemical reaction called Gibbs free energy (relates to delta G)

What is the second law of thermodynamics?

-the tendency in nature is toward even-greater disorder in the universe
-randomness in the universe is constantly increasing

second law of thermodynamics:
1. Closed system
2. Open system

1. Chemical reactions proceed spontaneously until equilibrium is reached
2. The second law of thermodynamics is universal and valid without exceptions. In all space and time scales useful energy is dissipated in heat and entropy is generated

what is entropy?

-refers to the randomness or disorder of the components of a chemical system
-life requires continual maintenance of order in the face of nature's tendency to increase randomness

describe the entropy of living organisms.

-living organisms are highly ordered, nonrandom structures, immensely rich in information and thus entropy-poor

what is the change of entropy?

-delta S
-any change in randomness of the system
-has a positive value when randomness increases
-delta S=+, randomness increases
-delta S=-, randomness decreases

what is Gibbs free energy?

-the G in any closed system can be defined by 3 quantities:
1. Enthalpy (H)
2. Entropy (S)
3. Temperature in kelvin
formula: G= (H)-T(S)

what is the change in Gibbs free energy?

-the amount of free energy released (-delta G) or absorbed (+delta G) in a reaction of constant temperature and pressure
formula: delta G= (delta H)-T(delta S)

Energy-coupling links reaction in biology:

-in biological processes, the cell function is dependent on molecules, such as proteins and nucleic acids, for which the free energy of formation is positive
-to carry out these thermodynamically unfavorable, energy-requiring (endergonic) reactions, the cells couple them to reactions that liberate free energy (exergonic reactions)
-so the overall process is exergonic: the sum of the free-energy changes is negative
-in living organisms, an exergonic reaction can be coupled to an endergonic reaction to drive otherwise unfavorable reactions

what is an exergonic reaction?

-delta G= negative
- Keq >1
-in reactions that occur spontaneously, the products have less free energy than the reactants and thus the reaction releases free energy, which is then available to do work
-decline in free energy from reactants to products is negative

what is an endergonic reaction?

-delta G= positive
- Keq

what is equilibrium constant?

-the tendency of a chemical reaction to go to completion
- Keq is dimensionless
-a large value of Keq means the reaction tends to proceed until the reactants are almost completely converted into the products
formula: Keq= [products]^n/[reactants]^n

what is the standard free-energy change?

-the free-energy change for a reaction occurring under a set of standard conditions:
1. temperature (298 k)
2. pressure, 1 atm (101.3 kPa)
3. and all the solutes at 1M concentration
formula at equilibrium: (^G0)= -RT(Keq)

Describe the Keq in delta G0.

-when Keq>>1, delta G0 is large and negative
-when Keq<

what is catabolism?

-the phase of intermediary metabolism concerned with the energy-yielding degradation of nutrient molecules, typically oxidative process
-the energy released from catabolic reactions drives the synthesis of ATP
-results in the production of NADPH
-ALWAYS EXERGONIC

what is anabolism?

-the phase of intermediary metabolism concerned with the energy-requiring biosynthesis of cell components from smaller precursors, typically reductive process
-ALWAYS ENDERGONIC

what is internal energy?

-relates to the first law of thermodynamics
-the energy in a system arising from the relative positions and interactions of its parts
-in an isolated system, the internal energy is constant
-the total amount of kinetic and potential energy possessed by the molecules of a body and their ultimate parts owing to their relative positions and their motions

what is the change in internal energy?

-delta E
-the sum of the heat transferred and the work done
formula: (^E)= q + w

What conditions reduce the internal energy of system?

1. q= negative (heat loss)
2. w= negative (work done by system)

What conditions increase the internal energy of system?

1. q= positive (heat gained)
2. w= positive (work done on system)

when the change of internal energy of system is negative, what does this mean?

the final energy is lower than the initial energy
-energy out of the system

when the change of internal energy of system is positive, what does this mean?

the initial energy is lower than the final energy or the final energy
-energy into the system

oxidation reduction reactions

-a reaction in which electrons are transferred from a donor to an acceptor molecule; also called a redox reaction
-one reactant is oxidized (loses electrons) as another is reduced (gains electrons)

Chapter 2: Water, the solvent of life

the theme of this chapter can be broken down into three interrelated principles. What are they?

1. The unique structure of each macromolecule determines its function
2. Non-covalent interactions play a critical role in the structure and thus the function of macromolecules
3. The monomeric subunits in polymeric macromolecules occur in specific sequences, representing a form of information on which the ordered living state depends

covalent vs. non-covalent interactions in macromolecules:

-covalent bonds, at the monomeric and macromolecular level, place constraints on the shapes assumed by large biomolecules
-it is the numerous non-covalent interactions that dictate the stable, native conformations of large molecules while permitting the flexibility necessary for their biological function

non-covalent interactions are essential for what three reasons?

1. The catalytic power of enzymes
2. The arrangement and properties of lipids in membranes
3. The critical interaction of complementary base pairs in nucleic aicds

Weak interactions in aqueous systems:
polar biomolecules

polar biomolecules dissolve readily in water because they can replace water-water interactions with energetically favorable water-solute interactions

Weak interactions in aqueous systems:
non-polar biomolecules

non-polar biomolecules are poorly soluble in water because they interfere with water-water interactions but are unable to form water-solute interactions
-in aqueous solutions, nonpolar molecules tend to cluster together

what happens when an amphipathic compound is mixed with water?

-the hydrophobic effect
-the nonpolar regions of the molecules cluster together to present the smallest hydrophobic area to the aqueous solvent
-the polar regions are arranged to maximize their interaction with each other and with the solvent (micelles)
-by clustering together, non-polar regions of the molecules achieve the greatest thermodynamic stability by minimizing the number of ordered water molecules required to surround hydrophobic portions of the solute molecules, increasing the entropy of the system

what is the hydrophobic effect?

-the aggregation of non-polar molecules in aqueous solution, excluding water molecules; caused largely by an entropic effect related to the hydrogen-bonding structure of the surrounding water

Describe what happens in the hydrophobic effect of protein folding.

-upon folding, a protein buries its non-polar amino acids into a core, which causes the ordered water molecules to become more disordered and return to the bulk solvent
-entropy-driven process meaning that T(^S) is larger than (^H)
-delta H would be positive (because some hydrogen bonds are broken due to the formation of the hydrophobic region)
-delta G is negative because protein folding is favorable

What happens to the entropy in the hydrophobic effect of protein folding.

1. delta S of non-polar substance: negative (decreases in disorder)
2. delta S of water molecules: positive (increases in disorder)
3. Net delta S of hydrophobic effect: positive (overall increase in disorder)

what is the thermodynamic driving force behind the hydrophobic effect?

the resulting increase in the water molecules' entropy

what sign is delta H when bonds are broken?

delta H is positive (energy, or heat, is required to break a bond)

what sign is delta H when bonds are formed?

delta H is negative (bond formation is favored so release of heat)

what are the four non-covalent interactions? (strongest to weakest)

1. Ionic interactions (charge-charge)
2. Hydrogen bonding (dipole-dipole)
3. Hydrophobic bonds/effect (entropy-driven process)
4. Van der Waals interactions (induced dipole)

What are van der waals interactions?

-weak inter-molecular forces between molecules as a result of each inducing polarization in the other
-also known as london dispersion forces
-as the two nuclei draw closer together, their electron clouds begin to repel each other. At the point where the net attraction is maximal, the nuclei are said to be van der waals contact

why are numerous weak interactions bestow much greater molecular stability than would be expected intuitively from a simple summation of small binding energies?

-Because the interactions fluctuate randomly, such simultaneous disruptions are very unlikely.
-To dissociate two biomolecules (such as an enzyme and its bound substrate) that are associated non-covalently through multiple weak interactions, all these interactions must be disrupted at the same time (making disruption very unlikely)

what is the ion product of water?

-the product of the concentration of H+ and OH- in pure water
-Kw= [H+][OH-]= 1x10^-14 at 25 degrees celsius
-Kw= [H+][OH-]= [H+]^2= [OH-]^2
-[H+]= sqrt(Kw)= sqrt(1x10^-14)

the pH scale designates the H+ and OH- concentrations: how to solve for pH

pH= log(1/[H+])= -log[H+]

what is the bronsted-lowry definition of an acid? bases?

-acids are proton donors (the stronger the acid, the greater its tendency to lose its proton)
-bases are proton acceptors

what is a conjugate acid-base pair?

-a proton donor and its corresponding de-protonated species
-for example, acetic acid (donor) and acetate (acceptor)

what is an acid dissociation constant?

-designated Ka
-the dissociation constant (Ka) of an acid, describing its dissociation into its conjugate base and a proton
-stronger acids (phosphoric and carbonic acid) have larger ionization constants
-weaker acids (monohydrogen phosphate) have smaller ionization constants

what is the pKa?

pKa= log(1/Ka)= -log(Ka)
-the stronger the acid, the lower its pKa
-the lager the pKa, the weaker the acid
-can be determined experimentally; it is the pH at the midpoint of the titration curve

what is a titration curve?

-a plot of pH versus the equivalents of base added during titration of an acid
-reveals the pKa of a weak acid
-at 0.5 [OH-] added, the number of protonated and deprotonated species is equal meaning that the pH=pKa
- 0-0.499: protonated
- 0.56-1.0: de-protonated

at the midpoint of the titration curve....

-the concentration of the proton donor and the proton acceptor are equal
-pH is numerically equal to the pKa
-buffering region can be determined +1/-1 from where pH=pKa

describe the buffering against pH changes in biological systems.

-the enzymes that catalyze cellular reactions, and many of the molecules on which they act, contain ionizable groups with characteristic pKa values
-constancy of pH is achieved primarily by biological buffers: mixtures of weak acids and their conjugate bases
-the intracellular and extracellular fluids of multicellular organisms have a characteristic and nearly constant pH

what are buffers?

-aqueous systems that tend to resist changes in pH when small amounts of acid or base are added
-consists of a conjugate acid-base pair in which the ratio of proton acceptor and proton donor is near unity

how do buffers work?

-buffering results from two reversible reaction equilibria occurring in a solution of nearly equal concentrations of proton donor and its conjugate proton acceptor
-whenever H+ or OH- is added to a buffer, the result is a small change in the ratio of the relative concentrations of the weak acid and its anion (-) and thus a small change in pH
-the decrease in concentration of one component of the system is balanced exactly by an increase in the other
-the sum of the buffer components does not change; only their ratio changes

which equation relates to pH, pKa, and buffer concentration?

-henderson-hasselbalch equation
-The shape of the titration curve of any weak acid is described by the Henderson-Hasselbalch equation, which is important for understanding buffer action and acid-base balance in the blood and tissues of vertebrates

What is the Henderson-Hasselbalch equation?

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

how is blood plasma buffered?

-blood plasma is buffered in part by the bicarbonate system, consisting of carbonic acid (H2CO3) as a proton donor and bicarbonate (HCO3-) as a proton acceptor
-the pH of a biocarbonate buffer system depends on the concentration of H2CO3 and the HCO3-, the proton donor and acceptor components
-the bicarbonate buffer system is an effective physiological buffer near 7.4, because the H2CO3 of blood plasma is in equilibrium with a large reserve capacity of CO2(g) in the air space of the lungs

what is the effect of CO2 in blood pH?

-carbon dioxide (CO2) influences pH of blood by reacting with water to form carbonic acid (H2CO3), which can dissociate to form a hydrogen ion (H+) and a hydrogen carbonate ion (HCO3-).
-increasing the concentration of CO2 in the blood therefore results in more H+ ions and a lower pH (dissociation of H2CO3 into H+ and HCO3-)

what is the effect of hyperventilation on the blood pH?

-when a person hyperventilates they exhale more carbon dioxide than normal (decrease in CO2 levels in the body)
-as a result, the carbon dioxide concentration in the blood is reduced and the bicarbonate/carbonic acid equilibrium shifts to the left
-the drop in (H+) concentration causes an increase in pH

what is the optimum pH in the human body?

many of the enzymes that function in the blood have evolved to have maximal activity between pH 7.35 and 7.45, the normal pH range of human blood plasma

what feature of sodium bicarbonate contributes most to its effectiveness as a biological buffer?

carbonic acid (H2CO3), which can be formed from CO2 and water, can dissociate into H+ and HCO3- in order to provide H+ and lower blood pH (more acidic)

Chapter 3: Amino acids, peptides, and proteins

the material is organized around what three principles?

1. In every living organism, proteins are constructed from a common set of 20 amino acids
2. In proteins, amino acids are joined in characteristic linear sequences through a common amide linkage, the peptide bond
3. For study, individual proteins can be separated from the thousands of other proteins present in a cell, based on differences in their chemical and functional properties arising from their distinct amino acid sequences

What are the common structural features of amino acids?

1. All 20 amino acids are alpha-amino acids (a chiral center)
2. They have a carbonyl group and amino group bonded to the same carbon atom (alpha)
3. They differ from each other in their side chains (R-groups)

describe the implications of a chiral center in amino acids.

-amino acids have two possible stereoisomers
-since they are nonsuperposable mirror images of each other, the two forms represent a class of stereoisomers called enantiomers
-are also optically active

what type of stereoisomers are amino acid residues in proteins?

-the amino acid residues in proteins are L stereoisomers (the -OH is on the left-hand side)
-cells are able to specifically synthesize the L isomers of amino acids because the active sites of enzymes are asymmetric, causing the reactions they catalyze to be stereospecific

Which amino acids have nonpolar, aliphatic R groups?

1. Glycine (Gly, G)
2. Alanine (Ala, A)
3. Proline (Pro, P)
4. Valine (Val, V)
5. Leucine (Leu, L)
6. Isoleucine (Ile, I)
7. Methionine (Met, M)

Which amino acids have aromatic R groups?

PrettyTinyTigers
1. Phenylalanine (Phe, F)
2. Tyrosine (Tyr, Y)
3. Tryptophan (Trp, W)

Which amino acids have polar, uncharge R groups?

TAGSC
1. Serine (Ser, S)
2. Threonine (Thr, T)
3. Cysteine (Cys, C)
4. Asparagine (Asn, N)
5. Glutamine (Gln, Q)

Which amino acids have positively charged R groups?

LaughAllHours
1. Lysine (Lys, K)
2. Histidine (His, H)
3. Arginine (Arg, R)