PCB3134 Module 2 Content

What is the term for specific arrangements of atoms that commonly act as a cohesive unit, influecning the physical properties, chemical reactivity, and solubility of organic molecules in aqueous solutions?

a. amphipathic groups

b. idiosyncratic groups

c. functional groups

d. aspirational groups

c. functional groups

Covalent Bonds

• pairs of elections shared between pairs of atoms

• bonds made up a molecule

• atom most stable when its outermost election shell is filled (8 electrons)

• formation accompanied by release of energy (reabsorbed when bond broken)

• strong covalent bonds: energy required to break much greater than TE

• weak covalent bonds: energy required to break is same/smaller than TE

Thermal energy (TE)

• .6 kcal/mol in a molecule

Energy required to cleave C-H, C-C, or C-O covalent bonds

80-100 kcal/mol (large)

Polar Molecules

• Molecules with asymmetric distribution of charge

• contain O, N, S

• ex. Water (H2O)

Nonpolar molecules

• molecules that lack electronegative atoms and strongly polarized bonds

• contain C, H

  • ex. Fats

Noncovalent bonds

• weaker linkages that govern interactions between molecules

• weak attractive forces between atoms with opposite charges/polarity

• 1-5 kcal/mol of TE

• ionic bonds

• hydrogen bonds

Acids

• release/donate protons

• released proton combines with another molecule

  • combine with hydroxyl ion (OH-) to form water

  • combine with amino grouo (NH2) in protein to form charged amine

  • combine with water to form hydronium ion (H3O+)

• after donating proton, becomes conjugate base of the acid

• ex. Acetic acid (CH3COOH)

Bases

• accept protons

• after accepting proton, it forms conjugate acid of the base

Amphoteric molecules

• can act as either acid or base

• ex. water, amino acids, proteins, many metal oxides and hydroxides

pH

• measures acidity of a solution

• pH = -log[H+]

Buffers

• resist changes in pH

• react with free hydrogen or hydroxyl ions

Biochemicals

• compounds produced by living organisms

• centered around chemistry of C

• chains of C can be linear, cyclic, or branched

Functional groups

• behave as a unit and give organic molecules their physical properties, chemical reactivity, and solubility in aqueous solution

Ester bond

bond between carboxylic acid and alcohol

Amide bond

bond between carboxylic acid and amine

Macromolecules

• highly organized molecules

• contain dozens to millions of carbon atoms

• divided into proteins, nucleic acids, polysaccharides, and lipids

• most are short-lived (except DNA)

Building blocks of macromolecules

• Sugars → polysaccharides

• Amino acids → proteins

• Nucleotides → nucleic acids

• Fatty acids → lipids

Metabolic Intermediates (Metabolites)

• compounds formed along metabolic pathways leading to an end product

• might have no function except as intermediate to final product

Molecules of miscellaneous function

• vitamins

• steroid or amino acid hormones

• ATP (energy)

• cyclic AMP (regulatory)

• urea (waste)

Carbon fixation

• process plants use to harvest carbon from the CO2 in air

• need carbon to make biochemicals needed for growth

Legume/Rhizobia symbiosis

• plant cells cannot fix nitrogen from the air

• some plants (legumes) have symbiotic relationship with rhizobia (bacteria) that fix nitrogen

• rhizobia grows in roots of legumes in root nodules

  • colonize plant cells in specialized membrane compartments, bacteroids

  • fix nitrogen into ammonia, which plants can use to synthesize amino acids

  • amino acids left in dead plant after harvesting degraded to nitrate, used by other plants as a nitrogen source

Crop rotation

• non-legminous plants planted after legumes harvested to use up the left over nitrogen

Chemical Fertilizers

• include phosphorus as chemical source for production of ATP, DNA, and RNA

• phosphorus exists in ground in rocks/minerals like hydroxyapatite

  • leeches out of rock and into groundwater for absorption by plants

• Phosphorus can become depleted after consumption by plants (not replaced by fixation)

• Phosphorus abundant in US, China, Morocco

  • other countries must import for crops

Carbohydrates

• aka glucans

• simple sugars (monosaccharides- 1 sugar) constructed of sugar building blocks

• function as stores of chemical energy and materials for biological construction

• general formula (CH2O)n

• Important ones in cell metabolism have 3-7 carbons (trioses, tetroses, petonses, hexoses, heptoses)

Carbohydrate Structure

• highly water soluble because of hydroxyl groups

• backbone of carbon atoms linked in linear array by single bonds

• Ketoses: bears carbonyl group in chain (ketone); Fructose

• Aldolases: one end carbonyl (aldehyde); Glucose

• C can bond w 4 other atoms

Steriosomers: Enantiomers

• Same chemical reactivities, but their structures are mirror images

• D-glyceraldehyde if hydroxul group of C2 projects to right

• L-glyceraldehyde if projects to left

Glycosidic bonds

• covalent bonds that join sugars together

• C1 of one sugar and hydroxul group of another sugar (C-O-C)

Disaccharides

• Molecules composed of 2 sugar units

• serve as readily available energy stores

• ex. sucrose (glucose+fructose), major component of plant sap, lactose (glucose-galactose), found in milk for newborn mammals

Oligosaccharides

• small chains of linked sugars

• covalently attached to lipids (form glycolipids) and proteins (form glycoproteins)

Polysaccharides

• identical sugar monomers joined by glycosidic bonds

Nutritional Polysaccharides

• ex. glycogen: animal product made of branched glucose polymers, chemical energy for most animals

• ex. starch, plant product made of both branched and unbranched glucose polymers, chemical energy for plants

Structural Polysaccharides

• cellulose

• chitin

• glycosaminoglycans (GAGs)

Cellulose

• unbranched glucose polymer

• plant cell wall

Chitin

• insects, spider, crustacean exoskeleton, fungi cell wall

• unbranched polymer of sugar N-acetylglucosamine (similar structure to glucose but w acetyl amino group instead of hydroxyl group bonded to C2 of ring)

Glycosaminoglycans (GAGs)

• rare

• different sugars (A-B-A-B)

• secreted by cells in lungs/tissues in response to tissue injury

• ex. Heparin: inhibits blood coagulation

Lipids

• non-polar

• most important: fats, steroids, phospholipids

• dissolve in organic solvents, not water

• hydrocarbon chain is hydrophobic

• carboxyl group (-COOH) bears negative charge at physiological pH, hydrophilic

• amphipathic (has both hydrophobic and hydrophilic regions)

Fatty acids

• long, unbranched hydrocarbon chains with single carboxyl group at one end

Fats: soaps

• hydrophobic end of each fatty acid can embed itself in grease (solubilize it)

• hydrophilic end can interact with water

  • greasy materials converted into complexes (micelles) that can be dispersed by water

Fats

• glycerol moiety linked by ester bonds to 3 fatty acids (triacylglyerol)differ in length (14-20 carbons) and presence of double bonds

Saturated fatty acids

• lack double bonds

• common component of animal fats and remains in solid state well above room temperature

• ex. Tristearate

Unsaturated fatty acids

• have double bonds

• ex. vegetable fats, liquid state (oils)

• highly volatile lipid (linseed oil)

Hydrogenation

• generated from unsaturated fats by chemically reducing the double bonds with hydrogen atoms

• cis double bonds into trans double bonds

  • partially hydrogenated or trans-fats

• ex. solid shortenings (margarine) generated from unsaturated vegetable oils

Steroids

• built around 4-ringed hydrocarbon skeleton

• ex. cholesterol: found in animal cell membrane and is precursor of steroid hormones (testosterone, progesterone, estrogen), not in plants

Phospholipids

• resembles fat but has only 2 fatty acid chains, not 3 (diacylglyerol)

• glycerol backbone whose hydroxyl groups are covalently bonded to 2 fatty acids and a phosphate group

• negatively charged phosphate is bonded to small, positively charged choline group

• used in cell membrane

Proteins

• macromolecules that carry out cell’s activities

• ex. antibodies, toxins, enzymes, hormones, receptors, etc

• form blood clots, absorb/refract light, transport substances

Enzymes

• proteins

• accelerate metabolic reactions

Structural proteins

• provide mechanical support

Regulatory proteins

• hormones, growth factors, gene activators

Signaling proteins

• membrane receptors and transporters

• determine what cell reacts to and what types of substances enter or leave the cell

Contractile filaments and molecular motors

• protein

• constitute machinery for biological movements

Amino acid structure

• monomers that make up proteins

• 20 amino acids

• all amino acids have a carboxyl and amino group, separated by a single C (alpha carbon) and a side chain (R group)

• R group is highly variable among the 20 amino acids, which gives proteins their diverse structures and activites

• linked by peptide bonds to form protein

Amino Acids side chain properties

• amino acids are classified by character. of their side chains

• 4 categories:

  • Polar/charged (Asp, Gly, Lys, His)

  • Polar/uncharged (Ser, Thy, Gln, Asn, Tyr)

  • Nonpolar (Ala, Val, Leu, Ile, Met, Phe, Trp)

  • Unique properties (Gly, Cys, Pro)

Disulfide bridges

• form between 2 cysteines that are distant from one another in the polypeptide backbone or in separate polypeptides

• oxidation/reduction of bonds between two cysteine residues

• help stabilize the protein shape

Posttranslational modifications
(PTMS)

• incorporation into a polypeptide chain

• can generate dramatic changes in properties and function of protein

  • modifying 3D structure, level of activity, localization within the cell, life span, and/or interactions with other molecules

• ex. Phosphorylation

  • reversible addition of phosphate group to serine, theronine, or tyrosine residue

  • most important/widespread

The two ends of a fatty acid molecules have different properties; the hydrocarbon chain is hydrophobic, whereas the carboxyl group is hydrophiliic. Molecules having both properties are called:

a. amphipathic

b. saturated

c. unsaturated

d. polyunsaturated

a

In the Fernandez lab, a graduate student is exploring the influence of Beta-mercaptoethanol (BME) on partially purified proteins. Functioning as a powerful reducing agent, BME disrupts bonds between amino acids in protein structures, leading to the effective cleavage and reduction of these bonds. This process results in the unfolding of proteins, facilitating their purification. What types of bonds does BMA target? Which protein structures are more affected by BME?

a. Disulfide bonds; secondary and tertiary

b. Peptide bonds; tertiary and quaternary

c. glycosidic bonds; secondary and tertiary

d. disulfide bonds; only primary structure

a

Soluble protein construction

• nonmembrane proteins

• polar residues situated at surface of molecule

• nonpolar residues (hydrophobic AA) in core of molecule

  • driving force during folding. and contribute to protein stability

  • in enzymes, reactive polar groups project into the nonpolar interior, giving catalytic activity

Primary structure of proteins

• linear sequence of amino acids in the chain

• 20^n (n=# amino acids)

• peptide bonds

• genome of organism encodes the specific sequence of amino acids for every protein it can produce

Sickle Cell Anemia

• results solely from single change in amino acid sequence within hemoglobin (glutamic acid to valine)

Secondary Structure of Proteins

• conformation of portions of the polypeptide chain

• backbone of polypeptide can form alpha helix (cylindrical twisting spiral) or beta sheet (folded/pleated, several segments lying side by side)

  • stabilized by H-bonds

• some portions can consist of hinges, turns, loops, or finger-like extensions

  • most flexible portions of chain

  • sites of greatest biological activity

  • ex. Disulfide bonds (formed btwn thiol groups in 2 cysteine residues)

Tertiary structure of proteins

• conformation of entire polypeptide

• stabilized by array of noncovalent bonds among side chains

• seen by X-ray crystallography

• tells us interactions and enzymatic activity of protein

• sometimes similarities in tertiary structure can help decide whether 2 proteins have similar structure/function (actin and MreB)

Quaternary Structure of Proteins

• conformation of 2 or more polypeptide chains within a protein

• linked by covalent disulfide bonds or noncovalent bonds

• different proteins can become physically associated to form multiprotein complex

  • pyruvate dehydrogenase: 60 polypeptide chains comprosied of 3 different enzymes

Homodimer

• protein with 2 identical subunits

Heterodimer

• protein with 2 nonidentical subunits

Hemoglobin

• best studied multisubunit protein

• O2 carrying protein of red blood cells

• 2 alpha globins and 2 beta globin polypeptides, each binds single molecule of oxygen

Denaturation

• unfolding or disorganization of a protein (tertiary or quaternary)

• caused by detergents, organic solvents, radiation, heat, urea, BME

  • interfere with interactions that stabilize tertiary structure

• unfolded proteins lose enzymatic activity

• removing reducing agents lead to refolding of protein to correctly folded/ native conformation

Prions

• protein infection agents

• cause brain damage (memory impairment, personality changes, difficulty moving)

• PRNP gene expressed in normal brain tissue encodes PrP^C protein (prion protein cellular) at surface of nerve cells that is monomeric, soluble in solution, and can be destroyed by protein-digesting enzymes

• PrP^Sc (prion protein scrapie) is a modified version with different tertiary fold (consists largely of alpha helix vs. normal beta sheets) that accumulates within nerve cells, forming insoluble fibrils (aggregates) that are resistant to enzymatic digestion and kills the nerve cells

Molecular Chaperones

• helper proteins that bind to short stretches of hydrophobic amino acids to help unfolded proteins achieve their proper D3 conformation

Hsp70

• type of molecular chaperone

• Heat shock proteins

• bind to elongating polypeptide chains and prevent new polypeptides (nascent polypeptides) from binding to other proteins in the cysotol to prevent aggregation and misfolding

Chaperonins

• cylindrial protein complexes

• contain chamers for newly synthesized polypeptides to fold without interference form other macromolecules in cell

Nucleic acids

• polymers of nucleotides

• store and transmit genetic information

• DNA and RNA

DNA

• deoxyribonucleic acid

• holds genetic information in all cellular organisms and some viruses

• usually double stranded

RNA

• ribonucleic acid

• genetic material in some viruses

• usually single-sided

• may fold back on itself to form 3D structures (ribosomes)

• may have catalytic activity (ribozymes)

  • ability to catalyze specific biochemical reactions, including RNA splicing in gene expression

Nucleotides

made of

• 5 carbon sugar

• phosphate group

• nitrogenous base (purine or pyrimidine)

Purines

• double rings

• adenine

• guanine

Pyrimidines

• single ring

• cytosine

• thymine (DNA)

• uracil (RNA)