BCH 100: Biochemistry and the Role of Water

These flashcards cover key concepts and definitions related to biochemistry, specifically focusing on the properties and roles of water in biochemical processes.

Biochemistry

The study of chemical processes related to living organisms.

Universal Solvent

Water's ability to dissolve and interact with a wide variety of substances.

Polarity

The property of a molecule having a positive charge on one side and a negative charge on the other, as seen in water.

Hydrogen Bond

An electrostatic interaction between the partial negative charge of an oxygen atom and the partially positively charged hydrogen of another water molecule.

Hydrogen bonds readily form between an electronegative atom (the hydrogen acceptor) and a hydrogen atom covalently bonded to another electronegative atom (the hydrogen donor)

• In the donor, the hydrogen must be attached to a very electronegative atom – e.g. N, O, or F

Directionality: strongest when the acceptor atom is in line with the covelant bond betweent he donor atom and H

Hydrophilic

Describes compounds that dissolve easily in water; generally charged or polar compounds.

Hydrophobic

Nonpolar molecules that do not dissolve in water; also described as water-fearing.

Amphipathic

Molecules that contain regions that are both polar (or charged) and nonpolar.

Hydrophobic Effect

The tendency of nonpolar regions to cluster together in water, maximizing interactions among polar regions and with the solvent

Bond Energy

The average amount of energy required to break a bond.

• Formation: When a bond forms, energy is released.

• Breakage: When a bond breaks, energy is absorbed

Cohesion

The attraction between molecules of the same substance, such as water molecules sticking to each other.

Adhesion

The attraction between molecules of different substances, allowing water to stick to other surfaces.

Hydrolysis

A cleavage process accompanied by the addition of water.

Condensation

A reaction where the elements of water are eliminated as a product.

Micelle

A thermodynamically stable structure of amphipathic compounds in water.

Noncovalent Interactions

Interactions among biomolecules that are much weaker than covalent bonds, including hydrogen bonds and van der Waals interactions.

Weak Interactions

Interactions that are continually forming and breaking, but when accumulated, can significantly stabilize structures like DNA and proteins.

Ex:
Hydorgen Bonds

Ionic Interactions

Hydrophobic interations

van der Waals interactions

Importance of Water

Universal Solvent:

– dissolve and interact with a wide variety of substances

• Chemical Reactions:

– It participates in many biochemical reactions

• Temperature Regulation:

– high specific heat capacity* helps maintain a stable temperature in organisms

*requires lot of energy to change the temperature

• Transportation:

– primary component of blood and other bodily fluids

– facilitates transport of nutrients, hormones, and waste products

• Structural:

– It contributes to the 3D structure of proteins and nucleic acids

• Catalysis:

– Water often acts as a reactant or a product in enzymatic reactions

Properties of Water

Water is a polar molecule

– Polar covalent bonds

• Unequal sharing of electrons b/w O and H

• Creates a charge across the bond (dipole)

– Hydrogen bonding !!!

– Universal solvent

• high specific heat

  • melting and boiling point;

    excellent solvent - dissolves

    polar and charged

    (hydrophilic) molecules

Water Can Be Essential to Protein Function

H2O molecules are often found to be bound so tightly to biomolecules that they are part of the crystal structure

• For many proteins, associated water can have a specific function:

✓ example – cytochrome f – five H2O molecules provide path for protons to move through the membrase

Brønsted-Lowry definition

Acids are proton donors and bases are proton acceptors

Lewis definition

Acids are electron pair acceptors and bases are electron pair donors

Conjugates

Species that differ by only one hydrogen

Strong vs Weak Acids

Compounds have different tendency to ionize

• Strong acids and bases dissociate completely in solution

• Weak acids and bases only partially dissociate.

Henderson-Hasselbalch Equation

pH = pKa so [Base] = [Acid]

pH < pKa so [Base] < [Acid]

pH > pKa so [Base] > [Acid]

Titration Curve

A. Initial Point:

• Mainly HA, with some conjugate base (A-) depending on the acid dissociation

B. ½ equivalence point:

• [HA] = [A-]

• pH = pKa ← HH Equation

C. Equivalence point

• all conjugate base A-

• pH>pKa

Buffers

• prevent extreme changes in pH upon addition of a small amount of base or acid.

• Weak acid or base, and its conjugate, can have buffering property

• The buffering region is surrounding the pKa approx. +/- 1 pH, where relatively big changes in OH- addition do lead to mild changes in the pH

Buffer Capacity

The ability of a buffer to resist changes in pH.

Proportional to the [weak acid] and [conjugate base] (or vice versa)

• The greater the concentration - [HA] and [A-], the greater the buffer

capacity (the more effective the buffer!)

• i.e. 100 mM Tris-HCl buffer has a greater capacity than a 50 mM Tris-

HCl buffer

• The best buffering capacity is when pH = pKa

Buffers in Biological Systems

The phosphate buffer system acts in the cytoplasm of

all cells:

H2PO4− ⇌ H+ + HPO42−

The pH of blood is buffered by the conjugate acid-base

pair of carbonic acid and bicarbonate (H2CO3/HCO3–).

called the bicarbonate buffer system

• hypoventilation increases blood CO2 (retention) and lowers blood pH

• hyperventilation raises blood pH the body has that can sense pH and, through the brain stem, can quickly adjust breathing to maintain pH –response within mins

• acidosis = pH of blood plasma below the normal value of 7.4 common in people with severe, uncontrolled diabetes.

• alkalosis = pH of blood plasma above the normal value of 7.4

Structure of α-Amino Acids

α-Amino Acids

• Amino group (-NH3+)

• Carboxylic acid group (-COO-)

• α-carbon is called the carbon attached to a key functional group, commonly carbonyl in o-chem; here the amino group is attached to the α-C, so α-amino acids

zwitterionic form

at physiological pH (~7), the amine is protonated (NH3+) and the carboxyl group is deprotonated (COO-)

D- configuration

bottom OH is on right side

L-configuration

bottom OH is on left side

Chirality of Amino Acids

Amino acids are naturally L-configuration

Chirality of Carbohydrates

Carbohydrates are naturally D- configuration

Amino Acids Can Act as Acids or Bases

the alpha- amino group and the alpha-carboxyl group can be proton donor/acceptors => act as Lowry acids/bases

7 of the 20 amino acids have readily ionizable side chains. They are able to form ionic bonds, and to donate or accept protons (called acid–base catalysis) to facilitate reactions.

Proteins are made of

amino acids

Proteins are synthesized as linear polymers of amino acids in the ribosome

• The sequence of the amino acids in the protein chain is determined by the sequence of the corresponding gene (DNA); protein sequences involves mRNA intermediate

DNA -> RNA -> protein

polypeptide chains

linear polymers of amino acids in the ribosome

What determines the folding of proteins

multiple factors, importantly, weak interactions

– hydrogen bonds, hydrophobic effect, etc.

Primary Protein Structure

Polypeptide chain

Secondary Protein Structure

• alpha-helix

• beta-(pleated) sheet

Secondary (2°) structure refers to local areas of repeating 3D structure

• Held together with hydrogen bonds in the backbone between the amide nitrogens (N-H) and the carbonyl (C=O) carbons

Tertiary Protein Structure

The final folded version of 1 chain

tertiary (3°) structure refers to the spatial arrangement of the secondary structural elements in the polypeptide chain

important interactions:

• Noncovalent, weak interactions

• Hydrogen bonding

• α-carbonyls and α-amides

• Rs that can hydrogen bond (which?)

• Hydrophobic – nonpolar side chains

• Electrostatic – attraction or repulsion of charged Rs

• prosthetic groups (such as heme or metal

ions) – additional compounds embedded

into the proteins

• disulfide bridges – covalent bonds between Cysteines

Quaternary Protein Structure

Assembly of several chains (each is called subunit)

Quaternary (4°) structure refers to the spatial arrangement of multiple polypeptide chains to form multi-subunit complexes; Not all proteins have quaternary structure!

• primarily held together by non-covalent bonds, S-S bonds can participate

globular proteins = folded into a spherical or globular shape

fibrous proteins = arranged in long strands or sheets

Peptide bonds

• chains of amino acids joined by amide bonds

• These bonds are called PEPTIDE BONDS

• Peptide bonds connect the α-carboxyl group of one amino acid to the α-amino

group of the next amino acid.

• Peptide bonds are covalent bonds formed through condensation and broken

through hydrolysis; this reaction is catalyzed in the ribosome by the rRNA

Rotation around Bonds in a Polypeptide Backbone

Because the bond between the carbonyl carbon and the (the peptide bond) has a partial double bond character (resonance), the atom positions in the amide plane are basically fixed

The alpha-Helix is a Common Protein Secondary Structure

simplest arrangement, maximum number of H- bonds

– R groups protrude out from the

backbone

– each helical turn = 3.6 residues,∼5.4 Å

– H bonds are nearly parallel to the helix axis

– C=O to N-H four residues away

– often with distinct hydrophilic and hydrophobic faces

– Entire helix has a dipole

– Most are

Held together with hydrogen bonds in the backbone between the amide nitrogens (N-H) and the carbonyl (C=O) carbons

alpha-helix disruption

Several things can disrupt α-helices

• Proline: rigid cyclic structure ⟶ “helix breaker”

• Prevents rotation

• α-amino group not available for

hydrogen bonding

• Strong electrostatic repulsion between R groups with the same charges, i.e., Lys and Arg (+) or Asp and Glu (-)

• Steric hinderance of bulky R groups, Like Ile, Thr

Overall:

• charge, size, and shape of R chains candestabilize

• formation of ion pairs and hydrophobic effect can stabilize

Beta Pleated Sheets

Formed between adjacent parts of a polypeptide chain

• These are very extended compared to the compact helix

• side chains alternate sides of the sheet

• stabilized by interchain H bonds (C=O and N-H)

– Perpendicular to the direction of the sheet.

Beta Sheet can be ___ or ___

Antiparallel or Parallel

• antiparallel = opposite orientation

– more common

– N→C, C →N, N →C

• parallel = same orientation

– All N→C

Super-secondary Structures

Also called Motifs: combo of secondary structures

Common examples:

• Leucine Zipper:

• 2 α-helices that bind to DNA

• Has Leucine every 7 residues

• Helix-Turn-Helix:

• 2 α-helices separated by a turn

Insulin: example of processing and cross-chain bridges

• Insulin is a complex peptide hormone held together by disulfide bonds.

  • It is synthesized in the ER as precursor protein with disulfide bonds

  • Then the middle portion is cleaved, and two remaining chains – A and B –

  remain linked thanks to some of these bonds

Domains

domain = part of a polypeptide chain that is independently stable or could undergo movements as a single entity

• domains may appear as distinct or be difficult to discern

• small proteins usually have only one domain

• Larger proteins often contain two or more distinct “domains” of compact folded structure

• A domain frequently possesses some defined function (e.g., D N A recognition, oligomerization, cofactor binding, etc.)

Intrinsically disordered regions

• part of the polypeptide chain that does not fold into a secondary structure

• Provide flexibility; can act as flexible scaffolds; target for modifications, etc.

Determining Protein Structures

Structural biology = study of the 3D structures of biomolecules (proteins, nucleic acids, lipids,

carbohydrates) to understand function; uses biochemical, biophysical, and computational

methods

• X-ray crystallography: X-rays diffract from a protein crystal; Diffraction patterns are mathematically

reconstructed into a 3D structure. It provides high-resolution atomic detail. Limitations: requires crystallization;

not the same environment as in the cell; less suitable for flexible or disordered proteins; no information about

the movements; data quality depends on crystal order

• NMR spectroscopy: Provides insight into protein dynamics and flexibility; Limitation: best for small

proteins

• Modern advances:

– Cryo-EM enables structure determination without crystallization

– Computational prediction (e.g., AlphaFold) complements experimental methods

Protein Denaturation

• Loss of the structure (2°, 3°, 4°, or a combo) that gives a protein its biological activity; the loss of structure leads to loss of function

• Denaturation (unfolding) can happen due to:

• Heat

• Large changes in pH

- alters charges on side chains, -COO- to -COOH or –NH3+ to –NH2

• Detergents (soaps!) disrupt hydrophobic interactions

• Urea or guanidine decrease hydrophobic effect

• Reducing agents such as β-mercaptoethanol reduces

disulfide bonds in proteins

Is denaturation reversible?

In principle, denaturing does NOT affect primary structure

• Anfinsen hypothesis (in the 1950s) – the entire information required for a protein to fold into its correct three- dimensional structure is encoded solely within its primary amino acid sequence

Intrinsically disordered proteins (IDPs)

do not have a defined structure under physiological conditions until they interact with other molecules.

• Metamorphic proteins exist in an ensemble of structures of approximately equal energies that are in equilibrium.

Protein Misfolding and Aggregation Are Associated with

Some Neurological Diseases

Prion diseases

Some infectious neurological diseases are caused by infectious proteins called prions. Prions exist in two states

• one α-helix-rich (PrPC)

• β-sheet-rich (PrPSC)

• PrPSC forms aggregates that disrupt cell

function.

• Template-Driven Misfolding – the “SC” form

binds and converts the native form into SC

• Human PrP protein – mutations can cause

  different inherited prion diseases e.g.

  Creutzfeldt-Jakob Disease (CJD)

Fibrous Proteins are Specialized for a Structural Function

• overall linear shape: do not fold back on themselves

  • give strength and/or flexibility to structures

  • simple repeating element of secondary structure

  • H2O insoluble due to high concentrations of hydrophobic residues

The Structure of α-Keratin in Hair

α-keratin helix is a right-handed α helix

• two strands of α-keratin, oriented in parallel, wrap about each other to form a supertwisted coiled coil

– supertwisted helical path is left-handed

The Structure of Collagen

Each polypeptide chain = left-handed helix, not an α-

helix

• Single helix: procollagen

• Single helix not formed by H-bonds, but Pro steric repulsion

• 3 procollagens ⟶ 1 tropocollagen

• Three strands held together by H bonding

• Every 3rd amino acid is Gly

• Repeating sequences are X-Pro-Gly and X-Hyp-Gly

• X = any amino acid

• Hyp = hydroxyproline <- modified Proline (a PTM); helps

H boinding

Collagen Deficiencies

Osteogenesis imperfecta

• brittle bone disease

• Genetic – caused by mutation, where Gly→ another amino acid.

• Scurvy

• Occurs when vitamin C is deficient; (GULO gene, which codes for the enzyme needed to make vitamin C, was lost in primate ancestors around 60-70 MYA)

• Vit C is required for the synthesis of Hyp, which is important for collagen stability

• The unstable collagen causes a range of symptoms

• The Scourge of the Seas: “In 1499, Vasco da Gama lost 116 of his crew of 170; In 1520, Magellan lost 208 out of 230; ... all mainly to scurvy” (from Wikipedia) Researcher estimated over 2 million sailors died of scurvy over the centuries…

Globular Proteins

• Proteins that are folded to a spherical (Glob) shape

  • Shape based on direction and 2° structure folding

  • Usually have many α-helices and β-sheets

  but can also have just α-helices or β-sheets only, depending on the protein

Porins

Found in outer mitochondrial membrane (eukaryotes)

• Outer membrane (prokaryotes)

• β-barrel (no α-helices)

• Antiparallel β-sheet with 16-18 strands in a cylinder

Exterior has hydrophobic residues

• Interact with lipid core of membrane

• Interior has hydrophilic residues

• Water, ions, and small molecules can pass