Chapter 2: the chemical basis of life

chaperonin

-cylindrical protein complexes that contain chambers in which newly synthesized polypeptides can fold without interruption from other macromolecules in cell

disulfide bridge...

-help stabilize the intricate shapes of proteins, particularly those present outside of cells where they are subjected to added physical and chemical stress

cation

lost electrons, gains positive charge

4 protein levels of structure

primary secondary tertiary quanternary

molecular chaperones

-"helper proteins" that selectively bind to short stretches of hydrophobic amino acids that tend to be exposed in non-native proteins but buried in proteins having native conformation

Water

-Able to dissolve more types of substances than any other solvent. -Reactant or product in many cellular reactions (condensation/hydrolysis). -Can form hydrogen-bonds to itself and with other biological molecules. -Helps maintaining the structure and function of macromolecules.

Identity of a Protein is Determined by..

-Amino Acid Sequence and 3-D Shape *Properly folded: Functional *Unfolded: Not functional

Quaternary Structure

-Can be described by the composition of the subunits *Two identical subunits: 1. Homodimer *Four non-identical subunits 1. Heterotetramer -Adult human hemoglobin contains two copies of α-globin and two copies of β-globin:allosteric properties

covalent bond continued

-Can be single, double, or triple covalent bonds. -Can be polar or unpolar. -More electronegative nucleus = greater attractive force on electrons.

Cysteine Residues Can form Covalent Bonds

-Can improve stability of the protein (intramolecular) -Can impact 3-dimensional shape of the protein -Can link different proteins (intermolecular) -Fun fact: Breaking and reforming used to 'perm' hair -PTMs can modify 3D-structure, activity, interactions, localization

Peptide bond

-Carboxyl group reacts with amino group -One molecule of water is released: Condensation Reaction -A covalent bond is formed: Peptide Bond -Catalyzed by the ribosome in energy consuming process (ATP) -Bond is relatively unreactive under physiological conditions

functions of proteins include

-Catalyze covalent bond breakage or formation (enzymes) -Regulation (hormones) -Response to signals (receptors) -Transport (hemoglobin, ferritin) -Movement (motor proteins) -Mechanical support (collagen)

Consequences of Side Chain Properties

-Character of side chain important for structure and function -Soluble proteins: *Polar residues at surface *Non-Polar tightly packed in core -Hydrophobic interactions drive protein folding

PyruvateDehydrogenase: Multiprotein Complex

-Consists of 60 polypeptide chains constituting three different enzymes -Product of one enzyme can be channeled directly to the next enzyme -Entry enzyme complex to channel carbon into mitochondrial energy production

Ionic Bonds

-Do not depend on shared electrons. -NaCl crystal is held together by electrostatic attraction. -Attraction between charged atoms. -May be broken by polar solvents such as water -Govern many important interactions between biological molecules.

Side Chains with Unique Properties

-Glycine: small R group. Makes backbone flexible ('hinge') -Cysteine: reactive -SH group can form -S-S- bridges (often grouped with polar amino acids) -Proline: forms bulky ring disrupting ordered secondary structure -Glycine and proline are often grouped with the nonpolar amino acids -glycine side chain consist only of hydrogen atom and can fit into either a hydrophilic or hydrophobic environment. Often resides at sites where 2 polypeptides come into close content -cysteine has polar, uncharged character, it has the unique property of forming a covalent bond with another cysteine to form a disulfide link -proline side chain has hydrophobic character, though it has the unique property of creating kinks in polypeptide chains and disrupting ordered secondary structure

Hydrogen (H) Bonds

-H bears partial positive charge when bonded to electronegative atom. -H can interact with second electronegative atom. -H-bonds are easily broken. -Strength is additive (e.g. DNA stability). -Govern important interactions between biological molecules. -weak attraction interaction between a hydrogen atom covalently bonded to an electronegative atom and a second electronegative atom -easily broken

Nonpolar Amino Acids

-Hydrophobic -Buried inside of proteins -Lack oxygen and nitrogen -Associate via hydrophobic interactions ('hide' from water - weak force) -Associate via Van der Waals forces (proton of one atom attracts another molecule's electron - weaker effect) -unable to form electrostatic bonds or interact with water -Alanine, Valine, Leucine, Isoleucine, Methionine, Phelylaline, tryptophan

Additional Secondary Structures

-Include hinges, turns, loops, and finger‐like extensions -Often the most flexible portions of greatest biological activity -Interactions of antibody with antigen mediated by series of flexible loops

functional groups

-Many biological molecules contain chains of C-atoms, with certain hydrogen atoms are replaced by functional groups. -Functional groups can behave as a unit (7 major groups). -Some organic molecules can form macromolecules using functional groups. -particular grouping of atoms that often behave as a unit and give organic molecules their physical properties, chemical reactivity, and solubility in aqueous solution -several groups can ionize and become positively or negatively charged

Tertiary Structure

-May be exclusively stabilized by noncovalent interactions of side chains: *ionic bonds *hydrogen bonds *Van der Waals forces -Disulfide bridges may be involved -Determined by X-ray crystallography -describes conformation of entire polysaccharide -stablaized by array of noncovalent bonds between the diverse side chains of the protein -disordered segments tend to have a predictable amino acid composition, being enriched in charged and polar residues and deficient in hydrophobic residues -determines the interactions and enzymatic activity of a protein, similarity indicates two proteins may have similar function

Polar Uncharged Amino Acids

-More soluble in water than unpolar amino acids (amid or hydroxyl groups) -Can form hydrogen bonds, associate with water -Act as proton donor or acceptor when forming hydrogen bonds -Often quite reactive (hydroxyl group can be phosphorylated) -asparagine (Asn or N), glutamine (Gln or Q), tyrosine (Tyr or Y), serine (Ser or S), and thereonine (Thr and T)

Other Interactions

-Nonpolar molecules are hydrophobic. -Hydrophobic interaction: forced into aggregates to reduce exposure to water. -Van der Waals forces: transitory dipoles with a weak attractive force in a nonpolar molecule - at optimal distance (~3.2 A). -Complementary shapes facilitate interactions of biological molecules.

A Protein Contains Different Motifs and Domains

-Overall structure can be composed of α-helix, β-sheet and random coil -Domains: parts that contain different secondary structures -Sum of domains and linkers: tertiary structure

The 20 amino acids found in proteins can be classified into 4 groups based on the behavior of the side chain

-Polar charged (5) -Basic (3) -Uncharged polar (5) -Nonpolar (7) -Acidic (2) -Unique (3)

Sulfhydryl

-SH

The Basics

-Sequence of amino acids reads N-terminus to C-terminus. -N-terminus is encoded by the 5'-end and C-terminus is encoded by the 3'-end of mRNA -Polymers made of amino acid monomers: peptide bonds -Side chains have different chemical properties and can be organized into 4 different groups

covalent bond

-Sharing of electrons -pairs of electrons are shared between pairs of atoms -atom is more stable when its outer most electron shell is filled -# of bonds an atom can form depends on # of electrons needed to fill outer shell. -formation of bond is accompanied by release of energy, will be absorbed at a later time if bond is broken -lots of energy to break C-H, C-C, or C-O bond

Posttranslational Modifications (PTM)

-Side chains in existing proteins can be modified. -Ser, Thr, and Tyr can be phosphorylated -Lysine can be acetylated -PTMs can modify 3D-structure, activity, interactions, localization -alterations to the side chains of 20 basic amino acids after their incorporation to peptide chain -allows a single polypeptide to exist as a number of distinct biological molecules -phosphoserine, phosphothreonine, phosphotyrosine (OPO3^-)

The Case of Myoglobin

-Storage site for oxygen in muscle tissue -Over 75% of the protein is α-helix -No disulfide bridges -Globular protein with fixed 3D structure -Some proteins lack defined structures: Intrinsically Disordered

Higher Levels of Organization of α-Helices

-Two α-helical proteins can form a coil-coil structure -Coiled-coil: 2-7 alpha-helices are coiled together like the strands of a rope -The helices are attached to each other by the interaction of hydrophobic side chains

C-terminus

-a free alpha carboxyl group

homodimer

-a protein complex composed of two identical subunits

van der Waals force

-a weak attractive force due to transient asymmetries of charge within adjacent atoms or molecules -single one is very weak and sensitive to distance that separates the two atoms

PH

-acidity of a solution is measured by concentration of hydrogen ions -an increase of one pH unit corresponds to a ten fold decrease in H+ concentration (or a 10 fold increase in OH- concentration)

peptide bond

-amino acids are joined by this. Results from linkage of the carboxyl group of one amino acid to amino group of neighbor, with loss of water molecule

base

-any molecule capable of accepting a proton -acid always contains one or more positive charge than its conjugate base

ionic bond

-attraction between fully charged components -strength of ionic bonds in a cell is generally weak due to the presence of water, but deep within core of a proteins, where water is often excluded, bonds can be much stronger

side chain (R group)

-bonded to the alpha carbon is highly variable and it is this variability that gives proteins their diverse structures and activities

structure of amino acids

-chemical capabilities of a protein can be understood by examining the chemical properties of it's constituent amino acids -all amino acids have carboxyl and amino group which are separated from each other by a single carbon atom, alpha carbon -with the acception of glycine, the alpha carbon of amino acids bonds to 4 different groups so that the amino acids can exist in either a O or an L form

possible reactions involving a proton include:

-combination with a water molecule to form hydronium ion (H3O+) *H+ + H2O --> H3O+ -combination with a hydroxyl ion (OH-) to form molecule of water *H+ + OH- --> H2O -combination with an amino group (-N2) in a protein to form a charged amine H+ + -NH2--> -NH3^+

globular proteins

-compact shape

buffers

-compounds that react with free hydrogen or hydroxyl ions, resisting change in pH -contain weak acid together with its conjugate base -fluid in cells is regulated by phosphate buffer system -Buffers resist changes in pH (cytoplasm: ~7.2).

Secondary Structure: β-sheet

-consist of several segments of a polypeptide lying side by side -folded or pleated conformation -resist pulling forces -N-H groups in the backbone of one region establish hydrogen bonds with the C=O groups in the backbone of the adjacent region. Common structure -The β-sheet is composed of laterally connected strands that form a twisted, pleated sheet -The interactions occur between regions of the strand

polar molecules

-contain one or more electronegative atoms, usually O, N, and or S

N-terminus

-contains amino acid with free alpha amino group

Primary structure:

-linear sequence of amino acids -20 ^n (n is the number of amino acids in chain) will tell you how many polypeptides can be formed -First order of complexity: linear sequence of aa -Changes may be tolerated depending on effect on 3D-shape or critical functional residues ('active site') -Most amino acids play structural role for correct folding

Polar Charged: Basic Amino Acids

-lysine (Lys or K), arginine (Arg or R), histidine (His or H) -Polar -Very hydrophilic -Positively charged at pH values below their pKa values -Histidine: partially charged at pH 7.0 - most common aa in active/binding sites -May form salt bridges (ionic bonds) in core of proteins -bc of its ability to gain or lose a proton in physiology pH ranges, histidine is important aa in the active site of many proteins

subunits

-may be linked by covalent disulfide bonds but most often they are held together by non covalent bonds as occur typically b/n hydrophobic "patches" on complementary surfaces of neighboring polypeptides

acid

-molecule that is capable of releasing (donating) a hydrogen ion

macromolecules

-molecules that form the structure and carry out the activities of cells are huge, highly org -complex task with great precision -macromolecules are constructed from monomers by a process of polymerization

nonpolar molecule

-molecules that lack electronegative atoms and strongly polarized bonds

the role of molecular chaperons

-not all proteins are able to assume their final tertiary structure by self assembly bc proteins undergoing folding have to be prevented from interacting nonselectively with other molecules in the crowded compartments of the cell

alpha helix

-one possible structure of polypeptides, in which the backbone of the carbon forms a spiral conformation -stabilized by hydrogen bonds -The α-helix is formed when a polypeptide chain turns around itself to form a rigid cylinder. Very common structure -The α-helix is a right-handed spiral conformation and completes a full turn every 3.6 amino acids -For every 4th amino acid, the C=O and N-H on the peptide backbone form a hydrogen bond

prosthetic group

-portion of the protein that is not composed of amino acids, is joined to polypeptide chain after its assembly on ribosome -most globular proteins contain both alpha helixes and beta sheets

conformational changes

-predictable (nonrandom) movements within a protein that are triggered by a specific molecule binding -almost every activity a protein takes part in is accompanied by a conformational change within a molecule

heterodimer

-protein complex composed of 2 nonidentical subunits

specificity

-proteins have shapes and surfaces that allow them to interact selectively with other molecules

metabolic pathway

-series of chemical reactions

secondary conformation

-stable conformations in stretches of the proteins, e.g. α-helix, β-sheet, or random coil. -Also found in: Trans-membrane proteins, typically have amino acids of non-polar side chains -Shielding: A. The backbone is hydrophilic B. Hydrophobic side chains will shield backbone C. Protein can be embedded in the hydrophobic lipid bilayer -describes conformation of portions of polypeptide chain

hydrophobic interaction

-tendancy of nonpolar molecules to aggregate so as to minimize as to minimize their collective interaction with surrounding polar water molecules -not classified as true bonds because they don't result from attraction but rather from energetic drive to exclude water away from hydrophobic surfaces

electronegative atom

-the atom with a greater attractive force; atom can capture the major share of electrons in covalent bond

denaturation

-unfolding or reorganization of a protein -the linear sequence of amino acids contained all of the information required for the formation of polypeptides 3D conformation -tertiary structure that a polypeptide chain assumes after folding is the accessible structure with the lowest energy, which makes it the most thermodynamically stable structure formed by a chain

protein domains

-unlike myoglobin, most eukaryotic proteins are composed of two or more spatially distinct modules, or domains, that fold independent of one another -protein domains are identified with a specific function

Correct Folding is Achieved by the Accumulated Effects of Several Types of Forces

1. Electrostatic attractions between side chains. 2. Hydrogen bonds (backbones and/or side chains). 3. Van der Waal forces and hydrophobicity 4. Stepwise process of secondary structure formation and compaction *proteins initially explore a wide range of different conformations when they first begin to fold but eventually funnel down into an increasingly restricted set of possible configurations

GroEL and GroES

1. GroEL (group 1 chaperonin in bacteria) acts in conjunction with GroES (cochaperonin). 2. Binding of GroES and ATP hydrolysis induces conformational change in GroEL 3. The GroEL-GroES complex assist other proteins to achieve its native state. 4. The assisted folding process requires energy inform of ATP hydrolysis. 5. Hydrophobic interactions between the unfolded protein and GroEL combine with ATP-fueled conformational changes drive the folding process.

Protein Folding

1. Not all proteins can assume their final tertiary structure by self‐assembly. 2. Helper proteins induce proper folding: chaperones 3. Heat Shock Proteins (HSPs) belong to an important family of chaperones. 4. Chaperonins are another subgroup of chaperones (GroEL, TRiC/CCT).

life supporting properties of water

1. water is highly asymmetric molecule with the O atom at one end and the two H atoms at opposite ends 2. each of the two covalent bonds in molecule is highly polarized 3. all 3 atoms in a water molecule are adept at forming hydrogen bonds -each water molecule can form up to 4 hydrogen bonds -when water is heated, most of the thermal energy is consumed in disrupting hydrogen bonds rather than molecular motion

arginine pKa

12.5

double bond

2 pairs of electrons are shared

triple bond

3 pairs of electrons are shared

Bicarbonate and carbonic acid system

A buffer mechanism that is the largest system in the extracellular fluid. Carbonic acid and bicarbonate (base) are the key players in this system. -buffers blood HCO3- + H+ ↔ H2CO3

salt bridge

A tube that allows the slow transfer of ions and maintains the neutrality of the electrolyte solutions.

Protein Condensation Reaction

Amino acid + amino acid forms polypeptide chain/protein + H₂O (produces water).

hydrolysis

Breaking down complex molecules by the chemical addition of water

carboxyl

COOH

Molecules of miscellaneous function

Include vitamins, hormones, ATP, and metabolic waste products -includes substances as vitamins, which function as adjuncts to proteins; certain steroid or amino acid hormones; ATP; cyclic AMP; and metabolic waste

Ion product constant:

Kw = [H+][OH-] = 10^-14

amino

NH2

methyl

Nonpolar -CH3

hydroxyl

OH-

pKa of Aspartic Acid

Pka= 3.7

pKa of glutamic acid

Pka=4.3

Polar Charged: Acidic Amino Acids

aspartic acid (Asp, or D), glutamate (Glu, or E) -polar -Very hydrophilic -Negatively charged at physiological pH (cytoplasm ~ 7.2) -May form salt bridges (ionic bonds) in core of proteins -Salt bridges are relatively strong interactions

conformation

The particular three-dimentional shape of a protein molecule -refers to 3-D arrangements of the atoms of a molecule that is to their spatial organization

Ka: Acid Dissociation Constant

[H+][A-]/[HA] -pKa = -log10Ka -The lower the pKa value, the stronger the acid. -If pH = pKa than 50% protonated. -pka is the pH value at which a chemical species will accept or donate a proton

carbonyl group

a chemical group consisting of a carbon atom linked by a double bond to an oxygen atom

amphoteric

a substance that can act as both an acid and a base -ex: water H3O+ <--> H+ + H2O <--> OH- + H+

The β-sheet can be

a)anti-parallel b) parallel -Depends on the N to C orientation of the strands -Both types of β-sheets produce a rigid, pleated structure and form the core of many proteins

free radical

atoms or molecules that have orbitals containing a single unpaired electron tend to be highly unstable -can be formed when covalent bond is broken such that each portion keeps 1/2 of shared electrons or when a atom or molecule accepts single electron transferred during oxidation reduction reaction -extremely reactive -ex: superoxide and hydroxyl radicals

Glu and Lys

almost always fully charged

polypeptide chain

amino acids becomes joined to two other amino acids forming this

ionization

any process that results in the formation of an ion -some atoms are so strongly electronegative that they capture electrons from other atoms during a chemical reaction

Histidine

can loose or gain proton - important in enzyme active sites.

metabolic intermediates

compounds formed in metabolic pathways -compounds formed along the pathways leading to an end product may have no function

Biochemicals

compounds produced by living organisms -carbon containing backbones may be linear, branched, cyclic -more carbons are added, skeletons of organic molecules increase in length and structures become more complex

list functional groups

hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl

protocell

earliest cell made up of just nucleic acids surrounded by a membrane

ester bonds

form b/n carboxylic acids and alcohols

amide bonds

form between carboxylic acids and amines

anion

gain electrons, negative charge

strands of DNA are held together by

non covalent hydrogen bonds

Proteins Fold into a Conformation...

of Lowest Energy

polarized

one of the atoms has a partial negative charge and other has a partial positive charge

Acidity is measure using the pH scale:

pH = -log [H+]

pk

pH at which 50% of side chains are ionized and 50% are unionized

lysine pKa

pKa= 10.5

histidine pKa

pKa=6

Unpolar covalent bonds:

pair of electrons is equally shared between two atoms.

Polar covalent bonds:

pair of electrons is unequally shared.

hydrophilic

polar molecules such as sugar and amino acids, interact with water

fibrous proteins

proteins shaped like long fibers -have an elongated shape

hydrophobic

water fearing, nonpolar molecules are insoluble in water bc they lack the charged regions that would attract them to the poles of water molecules -when nonpolar compounds are mixed with water, the nonpolar molecules are forced into aggregates which minimizes exposure to the polar surrounding