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Cell & Molec. Biology Ch2- Chemistry of the Cell Cheat Sheet (DRAFT) by

Based on Ch 2 of Essential Cell Biology, 5th ed. Bruce Alberts et al.

This is a draft cheat sheet. It is a work in progress and is not finished yet.

Ionic Bonds

Electrons transfer to the more electr­one­gative element, creating ions

Chemical Bond Strength

Covalent bonds are strong
Weak noncov­alent:
>ionic
 
>hy­drogen
 
>van der waals

Compos­ition of a Cell

Water
>cy­top­lasm, lumen, inside nucleus, etc.
Inorganic ions
>Fe2+/3+, Ca2+, Mg2+, K+, Na+, Cl-, PO42-, etc.
>many function as cofactors
>pieces of a protein aside from amino acid that is needed for protein to carry out function
Organic Molecules
>4 major classes
>Ca­rbo­hyd­rates, Proteins, Nucleic Acids, Lipids
>3 are polymers, Lipids are not

Nucleic Acids

Deoxyr­ibo­nucleic acid (DNA) and Ribonu­cleic acid (RNA)
Monomer: Nucleotide
>5 carbon sugar, charged phosphate group, nitrog­enous base
>De­oxy­nuc­leotide (ATGC) - deoxyr­ibose - lacking 1 oxygen
>Ri­bon­ucl­eotide (AUGC) - ribose
Nitrog­enous Bases
Pyrimi­dine: cytosine, uracil, thymine
Purine: guanine, adenine
>CUT the py
>Pur As Gold
Nucleo­tides are joined by phosph­odi­ester bonds
>forms sugar-­pho­sphate backbone
RNA functions for inform­ation transfer and processing (how much proteins are produced, how much gene expres­sion, etc.)
DNA functions for inform­ation storage
>RNA also functions for enzymatic activity (catalyze reactions) in form called Ribozymes
Nucleotide deriva­tives (ATP, GTP) also have important functions:
>Energy- Adenosine tripho­sphate, guanosine tripho­sphate, nicoti­namide adenine dinucl­eotide
>ATP, GTP, NADH
>Intrac­ellular signaling- Cyclic AMP (adenosine monoph­osp­hate)
>for vasodi­lation and constr­iction
Transc­ription is polyme­riz­ation of ribonu­cle­otides.
Transl­ation is polyme­riz­ation of amino acids.
Replic­ation is polyme­riz­ation of deoxyn­ucl­eot­ides.
  

Covalent Bonds

Electrons are shared, either equally (nonpolar) or unequally (polar).
An example of nonpolar is methane, and and example of polar is water.
Nonpolar- think C-H and C-C bonds
Polar- think O-H, N-H, and S-H bonds

Lipids

NOT POLYMERS
>not chains and not repeating
All display degree of hydrop­hobic behavior
>water insoluble due to predom­inantly nonpolar bonds
Simplest lipids are fatty acids
Some are amphip­athic- both hydrop­hobic and hydrop­hilic in one molecule
Trigly­cerols- aka trigly­cerides or "­fat­s"
>gl­ycerol + 3 fatty acids
>fu­nction as energy­/me­tab­olism (fatty acid -> Acetyl CoA for citric acid cycle)
Phosph­olipids
>gl­ycerol + 2 fatty acids + 1 polar head group
>fatty acids=­hyd­rop­hobic, polar head group=­hyd­rop­hilic
>very amphip­athic (orien­tation of double bilayer membrane)
>key components of membrane structure
>si­gnaling
(not just proteins doing inter & intrac­ellular signaling)
Lipid Diversity - Sources of Diversity:
1. fatty acid length
>about 14-20 carbons long (tends to be even #s)
2. number of C-C bonds in fatty acids
>saturated- more H due to all single bonds
 
>unsatu­rated- less H due to double C=C bond
3. variab­ility in molecule attached to glycerol
>fatty acid species, type of polar head group (phosp­hol­ipids), oligos­acc­harides (glyco­lipids)
Sterol­s/S­teroids
Nonpolar, hydrop­hobic
Functions for cell membrane structure
>ch­ole­sterol, ergosterol
Functions as hormones
>te­sto­ste­rone, proges­terone, estrogen
Functions for vitamin synthesis
 

Hydrogen Bonding

respon­sible for the basic properties of water
>ad­hesion, cohesion, density
H-bonding starts with polar covalent bonding with a positively charged Hydrogen
Hydrop­hilic- polar covalent, like water
Hydrop­hobic- nonpolar covalent, unlike water
>eg. acetone
eg. 2-meth­yl-­propane
Intram­ole­cular H-bonding: biological molecules H-bond within themselves
Interm­ole­cular H-bonding: biological molecules H-bond with other molecules
>eg. proteins
>eg. nucleotide base pairing

Polymers

Monomer (1) -> Dimer (2) -> Oligomer (few) -> Polymer (many)
Polyme­riz­ation- completed with Dehydr­ation Synthesis/Conden­sation reactions
>2 monomers condensed= dimer
Hydrolysis reactions break
Draw diagrams of dehydr­ation synthesis and hydrolysis

Sugars (Carbo­hyd­rates)

Monosa­cch­arides -> Oligos­acc­harides -> Polysa­cch­arides
>Mo­nos­acc­har­ides- (CH2O)n
>gl­ucose, fructose, galactose - typically 5 or 6 carbon sugars, joined by glycosidic linkages
Monosa­cch­arides
>role of energy generation
>Gl­ucose -> ATP produced
>sy­nthesis of/con­version to other molecules
>ri­bos­e/d­eox­yribose
Oligos­acc­harides
>Gl­yco­syl­ation- covalently join to proteins and lipids on extrac­ellular cell surface
>gl­yco­pro­teins, glycol­ipids, protein structure, cell-cell structure, cell-cell adhesion, cell identi­fic­ation
Polysa­cch­arides
>energy storage
>in form of starch (polymer of glucose in plants), and glycogen (animal equivalent of starch, in muscle cells)
>cell structure
>ce­llulose (cell wall component in plants, glucos­e=m­ono­mer), and chitin (fungi cell wall, monome­r=g­lucose variant)

Proteins

Amino acids -> (Oligo­)pe­ptides (small stretch of a.a.) -> Peptides (sometimes finished, sometimes unfini­she­d)-> Proteins (finally folded and funcit­onable)
>20 different amino acids (R side chain)
>not identical, but similar (concept of a monomer)
>can be charged at cytosolic pH (in cell)
>amine group functions as base and picks up H+, carboxylic acid donates H+
>a.a. joined by peptide bonds through dehydr­ation synthesis
>joined at carboxyl and amine group (H of NH2 and OH of COOH)
Protein Structure and Function
>Fu­nct­ional diversity
>St­ruc­tural diversity
>me­tab­olism, DNA replic­ation, structure and motility, transport, commun­ication