Biochemistry: Fundamentals of Acids, Bases, Water, Amino Acids, and Proteins

Comprehensive practice flashcards covering the biochemical foundations of acids and bases, biological buffer systems, water chemistry and hydrogen bonding, amino acid structure, stereochemistry, peptide synthesis, and the four hierarchical levels of protein structure.

What is the definition of biochemistry?

The study of the chemical processes within and relating to living organisms, investigating the structure, function, and interactions of biological molecules.

What are the three core aspects of biomolecules investigated in biochemistry?

Structure (essential for understanding function), Function (diverse roles from providing energy to mediating signaling), and Interactions (through metabolism, signaling, and regulation).

How is cellular metabolism defined?

The sum of all chemical reactions that occur within a cell or organism, including energy production, nutrient breakdown, and biosynthesis.

What does cellular signaling involve?

Communication between cells through a complex network of pathways involving the production, transmission, and reception of chemical signals.

Through what mechanisms do cells regulate their biological processes?

Mechanisms including gene expression, protein modification, and feedback loops to ensure processes are coordinated and efficient.

How does the focus of a biochemist differ from that of an organic chemist?

Organic chemists focus primarily on reactions that take place in the laboratory, whereas biochemists seek to understand how chemical reactions occur inside living cells.

What was the significance of Eduard Buchner's discovery in 1897?

He demonstrated that cell-free extracts of yeast cells could catalyze the fermentation of glucose to alcohol and carbon dioxide, proving that biological catalysts (enzymes) do not require living cells to function.

What key discovery was made by Oswald Avery, Colin MacLeod, and Maclyn McCarty in 1944?

They showed that DNA extracted from a pathogenic strain of Streptococcus pneumoniae permanently transformed a nonpathogenic strain into a pathogenic one, providing the first conclusive evidence that DNA is the genetic material.

Which four chemical elements constitute over $98\,\%$ of all biological matter?

Oxygen ($65\,\%$), Carbon ($18\,\%$), Hydrogen ($10\,\%$), and Nitrogen ($3\,\%$).

What do the six abundant elements denoted by the acronym CHNOPS represent in living organisms?

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur, which collectively represent $97\,\%$ of the weight of most organisms.

Which five essential mineral ions are required in relatively large amounts by living cells?

Calcium ($\text{Ca}^{2+}$), Potassium ($\text{K}^+$), Sodium ($\text{Na}^+$), Chlorine ($\text{Cl}^-$), and Magnesium ($\text{Mg}^{2+}$).

How are trace elements defined, and what are common examples found in cells?

Elements required in small amounts that make up less than $0.01\,\%$ of body mass, such as Copper ($\text{Cu}$), Iodine ($\text{I}$), and Iron ($\text{Fe}$).

How do micromolecules differ from macromolecules in terms of molecular weight, solubility, and structure?

Micromolecules are small, have low molecular weight, high solubility, and simple conformation (e.g., water, minerals, sugars, amino acids); macromolecules are large polymers with high molecular weight, lower solubility, and complex conformation (e.g., proteins, nucleic acids, polysaccharides).

What structural varieties can carbon atoms form due to their bonding capabilities?

Carbon can form single, double, and triple covalent bonds with other atoms, producing linear chains, branched chains, and cyclic structures.

What is the most significant difference between reactions in an organic chemistry lab and cellular biochemical reactions?

Cellular biochemical reactions are catalyzed by enzymes and proceed at exceptionally high rates under physiological conditions.

Which chemical linkages are characteristically found in fatty acids and lipids?

Ester and ether linkages.

What type of chemical linkage connects individual nucleotides in nucleic acids?

Phosphate ester (phosphodiester) linkages.

What type of chemical linkage is present in proteins?

Amide (peptide) linkages.

What are four major applied sectors of biochemistry listed in the lectures?

Medicine (drug development, disease diagnosis, gene therapy), Agriculture (crop improvement, pest control), Industry (biofuels, bioremediation), and Food technology (food development and quality improvement).

In the provided diagram of a prokaryotic cell, what are the identity and functions of structures 1, 2, 4, and 7?

1 is the Nucleoid (region containing prokaryotic DNA), 2 is the Plasmid (extrachromosomal circular DNA encoding specific genes), 4 is the Ribosome (70S site of protein synthesis), and 7 is the Cell Wall (rigid protective layer made of peptidoglycan).

What proportion of total cell mass is typically composed of water?

Water accounts for $60\,\%$ to $90\,\%$ of total cell mass, typically constituting about $70\,\%$ of cell mass in mammalian cells.

How is water distributed between the inside and outside of human body cells?

Approximately $\frac{2}{3}$ of the body's water is located inside the cells (intracellular fluid), while $\frac{1}{3}$ is outside the cells (extracellular fluid).

How do hydrolysis and dehydration synthesis differ regarding the role of water?

Hydrolysis breaks down macromolecules into smaller subunits by consuming/adding a water molecule; dehydration synthesis joins subunits together into larger polymers by removing/releasing a water molecule.

Approximately what proportion of known enzymatic reactions involve water as a reactant or product?

Approximately one-third to one-half ($\frac{1}{3}$ to $\frac{1}{2}$) of all known enzymatic reactions.

What intermolecular interaction allows ionic compounds to readily dissolve in water?

Ion-dipole interactions between the charged ions and the partial charges of the polar water dipoles.

Why do non-ionic polar compounds dissolve readily in water?

They dissolve because of dipole-dipole interactions and hydrogen bonding with water molecules.

What structural reorganization occurs when nonpolar compounds are introduced into an aqueous environment?

Water molecules reorganize to form an ordered, clathrate-like cage around the hydrophobic solute, which decreases entropy and causes nonpolar molecules to aggregate together to minimize contact with water.

What structures do single-chain and double-chain amphiphilic molecules form in water?

Single-chain amphiphiles typically form spherical micelles or surface monolayers; double-chain amphiphiles form lipid bilayers and vesicular liposomes.

How does water dictate the three-dimensional helical structure of double-stranded DNA?

The hydrophilic sugar-phosphate backbones face outward to interact with the aqueous environment, whereas the hydrophobic nitrogenous base pairs are buried inside, where exclusion of water strengthens base-stacking and hydrogen bonding.

What is the bond angle and geometric shape of a water molecule?

The $\text{H}-\text{O}-\text{H}$ bond angle is $104.5^\circ$, giving the molecule a bent or V-shape.

Why does a water molecule possess a permanent dipole moment?

Oxygen has a significantly higher electronegativity than hydrogen, creating polar covalent bonds; the bent $104.5^\circ$ geometry prevents these bond dipoles from canceling out.

What is a hydrogen bond in biological systems?

An electrostatic attraction between a hydrogen atom covalently bonded to a strongly electronegative donor atom (typically $\text{O}$ or $\text{N}$) and a lone pair of non-covalent electrons on an electronegative acceptor atom.

Which two electronegative atoms primarily serve as hydrogen bond donors and acceptors in biological molecules?

Oxygen ($\text{O}$) and Nitrogen ($\text{N}$).

How much heat energy is released when hydrogen-bonded water molecules form under standard conditions?

Approximately $20\,kJ\,mol^{-1}$ of heat energy is released (meaning $+20\,kJ\,mol^{-1}$ is required to disrupt the bond).

How does the bond energy of a hydrogen bond compare to covalent O-H and C-H bonds?

A hydrogen bond requires about $20\,kJ\,mol^{-1}$ to break, whereas breaking a covalent $\text{O}-\text{H}$ bond requires $460\,kJ\,mol^{-1}$ and a covalent $\text{C}-\text{H}$ bond requires $410\,kJ\,mol^{-1}$.

How many hydrogen bonds can each water molecule form in the solid state (ice)?

Four aligned $\text{O}-\text{H}\cdots\text{O}$ hydrogen bonds with four neighboring water molecules, forming a rigid tetrahedral crystal lattice.

What molecular arrangement is represented in this figure showing the solid phase of water?

A central water molecule coordinated to four neighboring water molecules via four $\text{O}-\text{H}\cdots\text{O}$ hydrogen bonds arranged in a tetrahedral geometry.

How many hydrogen bonds does a liquid water molecule typically form at any given instant, and what is its average lifetime?

An average of $2$ to $3$ hydrogen bonds at any given moment, with an average lifetime of only $10\,\text{picoseconds}$ ($10^{-11}\,s$).

Based on this comparative diagram, why does ice float on liquid water?

Upon freezing, water molecules form a stable, open hexagonal crystal lattice holding the molecules further apart than in liquid water, resulting in a lower density for ice.

How does the high specific heat of water benefit living cells?

Because breaking extensive hydrogen bonds requires a large input of heat, water minimizes temperature fluctuations within cells and tissues, supporting thermal homeostasis.

According to this structural diagram, what geometric orientation yields the strongest hydrogen bond?

A linear arrangement where the donor atom, the hydrogen atom, and the acceptor atom lie along a straight line ($180^\circ$ apart); non-linear (bent) hydrogen bonds are significantly weaker.

According to this diagram, what thermodynamic factor provides the push toward forming an enzyme-substrate complex?

The displacement and release of ordered water molecules from the enzyme and substrate into bulk water increases system entropy, providing a favorable thermodynamic driving force.

What types of interactions occur between water and carbohydrates versus water and proteins?

Carbohydrates interact via hydrogen bonding with their hydroxyl ($-\text{OH}$) groups; proteins interact via hydrogen bonding with peptide backbone groups ($\text{C}=\text{O}$ and $\text{N}-\text{H}$) and polar side chains, as well as ionic and hydrophobic interactions.

What is the optimal pH range for most biochemical processes in biological systems?

Between pH $6$ and pH $8$.

What clinical conditions result when human blood pH deviates significantly from normal?

Metabolic acidosis (blood pH dropping below normal) or metabolic alkalosis (blood pH rising above normal), both of which impair cellular functions and enzyme activity.

What is the normal physiological pH range of human arterial blood?

$7.35$ to $7.45$, with an average around $7.40$ (or $7.45$).

Based on this physiological scale, what pH values define clinical acidosis and alkalosis?

Acidosis occurs at a blood pH below $7.35$ (down to $7.0$); normal pH is between $7.35$ and $7.45$; alkalosis occurs at a blood pH above $7.45$ (up to $7.8$).

What is a chemical buffer, and what components typically comprise it?

A solution that resists changes in hydrogen ion concentration ($\text{pH}$) upon the addition of small amounts of acid or base; it typically consists of a weak acid and its conjugate base.

How does the addition of an acid or base affect pure water versus a buffered solution?

In pure water, the pH changes drastically; in a buffer solution, the pH is maintained and changes very little.

How are strong acids/bases distinguished from weak acids/bases in aqueous solutions?

Strong acids and bases (e.g., $\text{HCl}$, $\text{H}_2\text{SO}_4$, $\text{NaOH}$, $\text{KOH}$) ionize completely in water, whereas weak acids and bases (e.g., $\text{H}_3\text{PO}_4$, $\text{H}_2\text{CO}_3$, $\text{CH}_3\text{COOH}$) only partially ionize.

What is the mathematical expression for the acid dissociation constant ($K_a$) of a weak acid $\text{HA}$?

$K_a = \frac{[\text{H}^+][\text{A}^-]}{[\text{HA}]}$, or $K_a = \frac{[\text{H}^+][\text{deprotonated}]}{[\text{protonated}]}$.

How is $\text{p}K_a$ defined, and how does its numerical value correlate with acid strength?

$\text{p}K_a = -\log_{10}(K_a)$; the smaller the $\text{p}K_a$ value, the stronger the weak acid.

State the Henderson-Hasselbalch equation.

$\text{pH} = \text{p}K_a + \log\left(\frac{[\text{A}^-]}{[\text{HA}]}\right)$, or $\text{pH} = \text{p}K_a + \log\left(\frac{[\text{deprotonated}]}{[\text{protonated}]}\right)$.

What is the relationship between pH and pKa when the concentrations of conjugate base and weak acid are equal?

$\text{pH} = \text{p}K_a$, because $\log(1) = 0$.

According to the Henderson-Hasselbalch relationship, what is the net protonation state when $\text{pH} < \text{p}K_a$ versus $\text{pH} > \text{p}K_a$?

When $\text{pH} < \text{p}K_a$, the substance is predominantly protonated ("H+ on"); when $\text{pH} > \text{p}K_a$, the substance is predominantly deprotonated ("H+ off").

What is the pH of a solution containing $0.1\,\text{M}$ acetic acid and $0.2\,\text{M}$ sodium acetate, given that the $\text{p}K_a$ of acetic acid is $4.76$?

$\text{pH} = 4.76 + \log\left(\frac{0.2}{0.1}\right) = 4.76 + 0.301 = 5.06$.

In an acid-base titration curve, what is the inflection point?

The point at which exactly $50\,\%$ of the acid has been neutralized by added base, where $[\text{acid}] = [\text{conjugate base}]$ and $\text{pH} = \text{p}K_a$.

In an acid-base titration, what is the equivalence point (or endpoint)?

The point at which enough base (or acid) has been added to exactly neutralize $100\,\%$ of the acid (or base).

What is buffer capacity, and what determines its magnitude?

The ability of a solution to resist changes in pH upon the addition of acid or base; the greater the absolute concentrations of the weak acid and its conjugate base, the greater the buffer capacity.

What is the effective buffering range of a weak acid buffer relative to its pKa?

Within approximately one pH unit below to one pH unit above its $\text{p}K_a$ ($\text{p}K_a \pm 1$).

Based on this titration curve for the dihydrogen phosphate system, what are the pKa and effective buffering range?

The $\text{p}K_a$ is $7.2$ (at the inflection point where $[\text{H}_2\text{PO}_4^-] = [\text{HPO}_4^{2-}]$), and the effective buffer region spans from$\text{p}K_a - 1$($6.2$) to$\text{p}K_a + 1$($8.2$$).

This titration curve of phosphoric acid ($\text{H}_3\text{PO}_4$) shows three midpoints; what are their corresponding pKa values and equivalents of base?

First midpoint at $0.5$ equivalents ($\text{p}K_{a1} = 2.2$), second midpoint at $1.5$ equivalents ($\text{p}K_{a2} = 7.2$), and third midpoint at $2.5$ equivalents ($\text{p}K_{a3} = 12.7$).

What are the three main physiological buffer systems that stabilize pH in the human body?

The bicarbonate buffer system, the phosphate buffer system, and hemoglobin (protein buffering).

What is the principal inorganic buffer system operating inside living cells?

The dihydrogen phosphate buffer system ($\text{H}_2\text{PO}_4^- / \text{HPO}_4^{2-}$), which has a $\text{p}K_a$ of $7.2$.

What are the major inorganic phosphate species present at physiological pH (~7.4)?

Dihydrogen phosphate ($\text{H}_2\text{PO}_4^-$) and monohydrogen phosphate ($\text{HPO}_4^{2-}$).

How does the carbonic acid-bicarbonate buffer system regulate blood pH?

Through the reversible equilibrium: $\text{CO}_2 + \text{H}_2\text{O} \rightleftharpoons \text{H}_2\text{CO}_3 \rightleftharpoons \text{H}^+ + \text{HCO}_3^-$. When blood pH drops, $\text{HCO}_3^-$ consumes $\text{H}^+$; when blood pH rises, $\text{H}_2\text{CO}_3$ dissociates to release $\text{H}^+$.

How do hyperventilation and hypoventilation affect blood pH?

Hyperventilation expels excessive $\text{CO}_2$, shifting equilibrium left and decreasing $[\text{H}^+]$, which increases blood pH (respiratory alkalosis); hypoventilation retains $\text{CO}_2$, increasing $[\text{H}^+]$ and decreasing blood pH (respiratory acidosis).

What are the key clinical applications of understanding pH buffers and acid-base balance?

Regulating blood pH, diagnosing metabolic and respiratory acid-base disorders, drug formulation, and managing patient homeostasis in critical care.

What two chemical functional groups are present in all amino acids?

An amino group ($-\text{NH}_2$) and a carboxylic acid group ($-\text{COOH}$).

What defines an alpha-amino acid?

An amino acid in which the amino group is attached to the alpha-carbon (the carbon directly adjacent to the carboxyl group).

What is the zwitterionic structure of a standard amino acid at pH 7?

The amino group is protonated as a positively charged ammonium ion ($-\text{NH}_3^+$) and the carboxyl group is unprotonated as a negatively charged carboxylate ion ($-\text{COO}^-$), resulting in a net neutral dipole.

How many standard amino acids are utilized in the ribosomal synthesis of proteins?

20 standard amino acids.

Into what three primary categories are standard amino acids classified based on their R-groups?

Non-polar (hydrophobic) amino acids, Polar uncharged amino acids, and Polar charged amino acids (acidic and basic).

Which amino acid has a single hydrogen atom as its side chain, making it the smallest and only achiral standard amino acid?

Glycine (Gly, G).

Which three amino acids are collectively called the branched-chain amino acids (BCAAs)?

Valine (Val, V), Leucine (Leu, L), and Isoleucine (Ile, I).

Which amino acid possesses a cyclic pyrrolidine ring where its side chain is bonded back to the alpha-amino nitrogen?

Proline (Pro, P).

Which two standard amino acids contain sulfur in their side chains?

Methionine (Met, M), which has a thioether, and Cysteine (Cys, C), which has a sulfhydryl/thiol group.

Why does methionine hold a special role in protein synthesis?

It is encoded by the initiation codon (AUG) and serves as the first amino acid incorporated into a growing polypeptide chain during translation.

Which standard amino acids have uncharged polar side chains containing hydroxyl (-OH) groups?

Serine (Ser, S), Threonine (Thr, T), and Tyrosine (Tyr, Y).

Which amino acids contain amide groups in their side chains?

Asparagine (Asn, N) and Glutamine (Gln, Q).

What unique covalent reaction can cysteine undergo in the presence of mild oxidizing agents?

Two cysteine molecules can oxidize at their sulfhydryl ($-SH$) groups to form a covalent disulfide bond ($-S-S-$), yielding the dimer cystine.

Which three amino acids contain basic nitrogenous side chains that can carry a positive charge at physiological pH?

Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H).

Which two amino acids contain dicarboxylic acidic side chains carrying a negative charge at pH 7?

Aspartate / Aspartic acid (Asp, D) and Glutamate / Glutamic acid (Glu, E).

Name the three non-standard amino acids that are directly incorporated into proteins during translation.

N-formylmethionine (initiator in bacteria), Selenocysteine (contains selenium instead of sulfur), and Pyrrolysine (found in some methanogenic archaea).

Which stereochemical configuration (D or L) of amino acids predominates in natural proteins?

L-amino acids (described by the Fischer convention relative to L-glyceraldehyde).

Give examples of non-standard amino acids generated by post-translational modification of residues within proteins.

4-hydroxyproline, 5-hydroxylysine, phosphoserine, and phosphotyrosine.

What is the definition of the isoelectric point (pI) of an amino acid?

The specific pH at which the molecule carries no net electric charge (net charge = 0); calculated as $\text{pI} = \frac{1}{2}(\text{p}K_i + \text{p}K_j)$.

Which standard amino acids have three ionizable acid-base groups?

Lysine, Arginine, Histidine, Glutamic acid, Aspartic acid (as well as Cysteine and Tyrosine).

By what chemical reaction do two amino acids condense to form a dipeptide?

A condensation/dehydration reaction where the alpha-carboxyl group of one amino acid reacts with the alpha-amino group of another, eliminating a water molecule to form an amide (peptide) bond.

What resonance feature gives the peptide bond its rigidity and planar geometry?

Delocalization of the lone pair on the amide nitrogen onto the carbonyl oxygen produces a partial double bond ($\sim 40\,\%$) between carbon and nitrogen, preventing free rotation around the $\text{C}-\text{N}$ bond.

Why is the trans configuration of a peptide bond favored over the cis configuration, and by how much energy?

The trans configuration minimizes steric hindrance between adjacent R-groups and is favored over the cis conformation by approximately $8\,kJ\,mol^{-1}$.

What is the exceptional behavior of proline regarding cis-trans peptide bond isomerism?

About $10\,\%$ of proline residues in proteins adopt a cis peptide bond conformation due to the unique cyclic geometry of its pyrrolidine side chain.

What is the chemical identity and common commercial use of the dipeptide shown in this figure?

L-Aspartyl-L-phenylalanine methyl ester, commercially known as Aspartame (NutraSweet), used as an artificial sweetener.

Identify the tripeptide shown in this structure and describe its biological function.

Glutathione ($\gamma\text{-Glutamate}-\text{Cysteine}-\text{Glycine}$), a cellular antioxidant that protects cells from damage by reactive oxygen species (ROS) and free radicals.

What are Leucine enkephalin and Methionine enkephalin, and what are their amino acid sequences?

Naturally occurring pentapeptide pain relievers: Leucine enkephalin is $\text{Tyr}-\text{Gly}-\text{Gly}-\text{Phe}-\text{Leu}$ and Methionine enkephalin is $\text{Tyr}-\text{Gly}-\text{Gly}-\text{Phe}-\text{Met}$.

What are Oxytocin and Vasopressin, and what structural feature stabilizes their cyclic shapes?

Cyclic peptide hormones containing nine amino acid residues, stabilized into a ring structure by an intramolecular disulfide bond between two cysteine residues.

What defines the primary structure of a protein?

The linear sequence of amino acids in a polypeptide chain, covalently linked by peptide bonds.

What is the conventional direction used to describe a polypeptide chain?

From the N-terminus (amino-terminal residue) to the C-terminus (carboxyl-terminal residue).

What defines the secondary structure of a protein, and what bonds stabilize it?

Localized regular folding patterns of the polypeptide backbone (such as alpha-helices and beta-pleated sheets), stabilized by hydrogen bonds between peptide backbone atoms.

What are the structural dimensions and characteristics of the alpha-helix shown in this figure?

A right-handed spiral coil with $3.6$ amino acid residues per turn and a pitch (vertical rise per turn) of $5.4\,\text{Å}$ ($0.54\,nm$), with side chains extending outward.