Cell Biology Chemical Foundations/Macromolecules
4 elements make up 96% of living organisms
- C, O, H, N
Molecules
- particles consisting of 2 or more atoms held together by chemical
bonds (compound = different atoms)
- H2 (hydrogen gas); CH4
Chemical Bonds
Involve interactions between electrons of reacting atoms.
Valence (outermost) shell is most important.
In cells, most elements have an unfilled valence shell and will interact
with other elements to gain or lose electrons to achieve a complete
valence.
Can transfer or share electrons
E.g. C and H need 4 and 1 electrons, respectively. Share electrons to
form CH4
Types of Chemical Bonds
Ionic Bonds
- form when atoms lose or gain electrons to become charged ions.
- attraction between negatively charged ions (anion) and positively
charged ion (cation)
- most compounds formed by ionic bonds are called salts (Na+Cl-)
- in aqueous environment, ionic bonds become weak because ions
interact with water.
Covalent Bonds
- strongest chemical bonds
- sharing of a pair of valence electrons
- atoms can be joined by single (CH4), double (O2), or triple covalent
bonds (N2).
Nonpolar covalent bonds
- equal sharing of electrons between atoms (CH4).
Polar covalent bonds
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- unequal sharing of electrons between atoms (H2O).
- O and N are electronegative atoms (electron “hogs”)
- molecule left with a slightly negative (-) and positive (+) charge.
- biological molecules (e.g. proteins) with polar groups are often held
together by electrical attractions.
Hydrogen Bonds (H-bonds)
- very weak bonds
- when H is polar covalently bonded to an electronegative atom, its
partial negative charged is attracted to another electronegative
atom forming a bridge.
o e.g. H-bonding between polar water molecules.
- combined effect of many weak H-bonds is important in holding
biological molecules together and in determining their shape.
Biochemistry: chemical composition of living matter.
Inorganic compounds
- lack carbon (except CO2)
- e.g. water, salts, many acids and bases.
Water
- all cellular reactions take place in aqueous solution
- 70% of cells weight
- molecules of water join together in a H-bonded lattice.
- because of waters polarity, it is an excellent solvent
- can form H-bonds with other molecules.
Hydrophilic molecules
- dissolve in water (soluble)
- ionic substances (ions Na+Cl-) or polar molecules that form H-bonds
with water
Hydrophobic molecules
- uncharged molecules that do not dissolve in water (insoluble).
- form few or no H-bonds with water
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- e.g. hydrocarbons – contain only C and H
Hydrophobic interactions
- biological molecules containing hydrophobic groups are forced
together to minimize disruptive effect on water
Acids and Bases
Acids
- substances that release protons (H+)
- carboxyl group -COOH  -COO- + H+
Bases
- substances that reduce the [H+]
- amino group
-NH2 + H+  -NH3
- sodium hydroxide generates OH- that binds H+
o NaOH  Na+ + OH+
pH scale
- 0-14
< 7 is acidic
<7 is basic 7 is neutral
- change of 1 pH unit represents a 10-fold change in [H+]
Acid-Base Balance in Cells
- cells are very sensitive to changes in pH
- kept close to pH 7
- buffers are compound that interact with H+ or OH- to minimize
changes in pH
- cell cytoplasm is regulated by a phosphate buffer system
o H2PO4-  HPO42- + H+
Organic Compounds
- contain carbon
- 4 major families
o Carbohydrates, Lipids, Nucleic Acids, and Proteins
Macromolecules
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- carbohydrates, nucleic acids, and proteins
- large polymers polymeric constructed of monomer subunits
o condensation reaction (removal of water)
- 3D shape or conformation is determined by H-bonds, ionic bonds,
hydrophobic interactions, van der Waals bonds.
Carbohydrates
- Simple sugars and molecules made from sugars
- function
o chemical energy
o structural components
- classified according to size
Monosaccharides (simple sugars)
- contain C, H, and O
- 2 H atoms to 1 O atom
o glucose
C6H12O6
- mostly exist in ring form
- e.g. glucose, fructose, galactose
Disaccharides
- two monosaccharides linked together by covalent glycosidic bonds
o maltose = glucose + glucose
o lactose = galactose + glucose
o sucrose = glucose + fructose
- disaccharides can’t pass through cell membranes
o glycosidic bond must be broken by hydrolysis (addition of
water breaks bond)
Oligosaccharides
- a short chain of linked sugars
- often attached to lipids and proteins forming glycolipids and
glycoproteins
- ABO blood groups are glycolipids found on surface of RBCs
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Polysaccharides
- long polymers of linked sugars (100 to 1,000s)
- diverse shapes because of branching
Types of Polysaccharides
Nutritional Polysaccharides
- hydrolyzed to simple sugars for energy
- Glycogen
o Store of chemical energy for animals
o Stored in granules
o Branched polymer of glucose
- Starch
o Store of chemical energy in plants
o Polymer of glucose, less branched than glycogen
o Animals have enzyme amylase that hydrolyzes starch
Structural Polysaccharides
- Cellulose
o cell wall of plants
o most abundant organic chemical on earth
o unbranched polymer of glucose
o mammals lack enzyme that hydrolyzes the  glycosidic bonds
that link glucose units (other polysaccharides are linked by 
glycosidic bond)
- Chitin
o Insect exoskeleton and fungal cell walls
o Polymer of sugar N-acetylglucosamine
Lipids
- mostly hydrocarbon (C and H)
- insoluble in water; hydrophobic (nonpolar)
- energy source and component of cell membranes
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- 3 main types
Triglycerides (Triacylglycerols; fats)
- long-term energy storage
o stored in cells as lipid droplets
o when hydrolyzed, more energy than carbohydrate
- composed of glycerol linked to 3 fatty acids
o can contain different fatty acids
 vary in length
 saturated
 no db bonds
 more solid; fatty acid tails pack well
 unsaturated
 one or more db bonds
 more fluid; fatty acid tails pack less well
Phospholipids
- important component of cell membranes
- glycerol + 2 fatty acids + phosphate-containing group
- phosphate-containing group is charged (e.g. choline)
- phospholipids are amphipathic
o contain a polar hydrophylic “head” + nonpolar hydrophobic
fatty acid “tails”
o various types of phospholipids
o allows membranes to form lipid bilayers
 heads interact with aqueous environment inside and
outside cell; tails group together
Steroids
- flat molecules formed of 4 interlocking rings
- Cholesterol
o found mainly in animal cell membranes
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o precursor for many hormones (e.g. estrogen, testosterone)
o an –OH group makes amphipathic
Nucleic Acids
- store and transmit genetic information
- macromolecules made of long chains (stands) of monomers called
nucleotides
- composed of C, O, H, N, and P atoms
- DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
Nucleotides
- nitrogen-containing base + pentose sugar + one or more phosphate
groups
Bases
- purines
o 6 plus 5-membered ring
o adenine (A) and guanine (G)
- pyrimidines
o 6-membered ring
o thymine (T), cytosine (C), and uracil (U; RNA only)
Pentose sugars (5C)
- DNA – deoxyribose
- RNA – ribose
- Bases added at carbon #1
Phosphates
- 1, 2, or 3 phosphate groups at carbon #5
- 1st attached by phosphoester bond, 2nd and 3rd by
phosphoanhydride bond (high-energy)
Nucleotide nomenclature
o Adenosine (for adenine), guanosine (for guanine), cytidine (for
cytosine), and thymidine (for thymine)
 deoxyadenosine triphosphate (dATP)
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 guanosine triphosphate (GTP)
Phosphodiester Bonds
- covalent bond that links nucleotides together to form polymers
(strands)
- #3 C of one pentose with #5 on another
- gives strand polarity (5´ and 3´ ends)
- 5´ – CGATCCGA – 3´ (written as 1 letter codes)
DNA and RNA
- phosphate groups makes DNA and RNA negatively charged
- DNA typically double-stranded with strands running aniparallel and
held together by H-bonds between bases
o AT (2 H-bonds) and CG (3 H-bonds)
- RNA usually a single-stranded molecule
Proteins
- 50% of organic matter in cell
- carry out most of cells activities
- polymer of amino acids (50-1000s) linked together
- complex 3D structure or conformations
Amino Acids
- 20 different amino acids
- all have a carbon bounded to 4 different chemical groups
o amine group (-NH2)
o carboxyl group (-COOH)
o H atom
o R group or side chain
 distinguishes amino acids
 very in size and chemical properties
- 1 and 3 letter abbreviations
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Amino Acid Categories
- Polar
- Acidic – negatively charged; hydrophilic R groups
o Aspartic acid, Glutamic acid
- Basic – positively charged; hydrophilic R groups
o Lysine, Arginine, Histidine
- Uncharged Polar - hydrophilic R groups
o Asparagine, Gutamine, Serine, Threonine, Tyrosine
- Polar amino acids tend to be on protein surface in contact with
water
- Nonpolar
- Hydrophobic R groups (mostly hydrocarbon)
- Avoid water; protein core
o Ala, Val, Leu, Ile, Pro, Phe, Met, Trp, Gly, Cys
Peptide Bonds
- covalent bond that links amino acids together
- creates a polypeptide with N (amino) and C (carboxyl) terminus
- N-Phe-Ser-Glu-Lys-C
- Polypeptide backbone
o Repeating sequence of atoms (excludes R-groups)
Disulfide Bonds
- covalent
- can form between two cysteine R groups in proteins
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