Учебно-методический комплекс дисциплины " Basis of biochemistry " Для специальности

МИНИСТЕРСТВО ОБРАЗОВАНИЯ И НАУКИ РЕСПУБЛИКИ КАЗАХСТАН ГОСУДАРСТВЕННЫЙ УНИВЕРСИТЕТ имени ШАКАРИМА города СЕМЕЙ
Документ СМК 3 уровня	УММ	УММ 042-18-25.1.55/03-2016
Учебно –методические материалы "Basis of biochemistry "	Редакция №1 от 8 сентября 2016 г.

УЧЕБНО-МЕТОДИЧЕСКИЙ КОМПЛЕКС

ДИСЦИПЛИНЫ

"Basis of biochemistry "

Для специальности

5BB080100 – Agronomy

5B080700 – Forests and forestry

5B080300 – Hunting study and fur-farming

5B080200 – Technology of production animal products

5B060800 – Ecology

5B073100 – Health and safety and protection of environment

5B120100 – Veterinary medicine

5B120200 – Veterinary Sanitation

УЧЕБНО-МЕТОДИЧЕСКИЕ МАТЕРИАЛЫ


Семей

2016

СОДЕРЖАНИЕ

1 Глоссарий 3

2 Лекции 5

3 Практические и лабораторные задания 154

4 Самостоятельная работа студента 194

5 Лист регистрации 218

1. 
   The conceptual apparatus
   

"Rule of 10%" (rule of the pyramid energy R. Lindemann): from one trophic level ecological pyramid moves to another higher its level (the "ladder" producer - consumer), on average, about 10% received the previous uro¬ven energy .

Abiotic factors - factors of inanimate nature (cosmic, geophysical, climatic, spatial, temporal, etc.) that have a direct or indirect impact on living organisms.

Act of tolerance (V.Shelford): environmental factors, with specific conditions pessimal (unfavorable as a minimum, and excess) value that limits the ability of the species in these conditions, in spite of and in spite of the optimal combination of certain other conditions.

Agrocenoses - community of organisms cultured and accompanying them in agriculture.

Amensalizm - type of interspecies relationships, in which in a joint environment, one kind of organism suppresses susche¬stvovanie another species without experiencing resistance.

Anthropogenic factors - factors that have arisen as a result of human activity.

Autotrophs - organisms can synthesize or¬ganicheskoe agent of carbon dioxide, water and salts mine¬ralnyh. energy sources are used for the biosynthesis of light (in photoautotrophs) or oxidation of a number of inorganic substances (in chemoautotrophs).

Bio-accumulation - the accumulation of substances (man-made pollutants) in the body increasing trophic levels.

Biogen - a nutrient; nutrients, nutrients essential chemical elements that make up the substance of living organisms, carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus.

Boreal zone - the zone of temperate forests.

Chemosynthesis - synthesis of organic substances in chemoautotrophic bacteria using as power sources of certain inorganic oxidizing substances.

Co-evolution - in parallel, the joint conjugate evolution of mankind and nature.

Consuments - heterotrophic organisms (mostly animals) who consume organic matter other plant organisms (herbivores - herbivores) and animals (carnivores - zoophages).

Cryostasis - temporary total suspension of the body's vital functions associated with the onset of unfavorable conditions or with extreme phase of individual development.

Depopulation - a reduction in population, population.

Desertification (aridity) - the process of depletion of vegetation associated with a persistent reduction in moisture areas, its transformation in the arid zone, topically, followed by the previous member of the chain.

Detritophages - organisms that feed on detritus (saprophagous).

Detritus - dead organic matter, isolation and decay organisms products.

Disadaptation - violations of vital activity caused by the incompleteness of acclimation, the inability to fully adapt to changing environmental conditions.

Dissimilation - the disintegration of complex organic substances in the body, accompanied by the release of energy, which is used in the processes of life.

Ecological culture - system of scientific knowledge about the human interaction of society and nature; environmental value orientations, rules and regulations; moral and aesthetic attitude towards nature; skills for the study of nature and its protection.

Edafon - a set of soil animal population of the Earth's thermal radiation air.

Education - a relatively meaningful and purposeful nurturing person in accordance with the specific objectives of groups and organizations, in which it is carried out.

Ektotermy - organisms, the body temperature is a little different from the temperature of the environment and follow its changes: lower organisms, plants, cold-blooded animals.

Emergence - the emergence of completely new properties of the interaction of two or more objects or phenomena, properties that are not simply the sum of the original.

Endotherm - warm-blooded animals birds and mammals, are capable of using the internal mechanisms of thermoregulation to maintain a relatively constant body temperature, to a certain extent independent of the ambient temperature. "

Environmental - trudnosti crisis, environmental problems due to anthropogenic human activities.

Environmental education - the formation of the human conscious perception of the environment, the conviction of the need for respect for nature, rational use of its wealth of natural resources.

Environmental education - tselenapravlennaya specially organized, systematic educational activities aimed at the development of environmental education and upbringing of children, on the formation of environmental awareness and skills for the study of nature and its protection.

Environmental education and training of students - pedagogical process, which ultimately should provide insight into the importance of proper behavior in the natural environment, the ability to anticipate and assess the impact of its activities, the realization that the man part of nature /

Environmental upbringing - purposeful human development, including the formation of its ecological culture, the perception of not only the public, but also of environmental norms and values;

Eurybionts (evrieki) - organisms that exist in a wide range of changes in environmental conditions: temperature (evritermy), humidity (evrigidridnye organisms), food choices (euryphages), etc.

Eutrophication - the excessive enrichment of water with nutrients.

Gene flow - the process of undirected random changes in gene frequency in a population.

Heterotrophic organisms - organisms that feed on organic matter ready.

Hibernation - a significant reduction in the level of life upon the occurrence of adverse external conditions (for example, hibernating animals).

Homeostasis - the ability of an organism or organisms of the system to maintain stable dynamic equilibrium in a changing environment.

Humid Zone - area or natural-climatic zone with high

Law of constancy of the amount of living matter of the biosphere (Vernadsky): The number of living matter (biomass of all organisms) for the biosphere of the geological eras.

Noogenesis (noospherogenesis) - the process of formation of the noosphere.

optimality law: any system with the highest efficiency in the functioning of some specific spatio-temporal limits to her.

Phenotype - a set of genetically determined characteristics and properties of the organism.

Photoperiodism - change the state of biological systems due to the natural rhythm of light exposure, the change of day and night, seasonal changes in the length of daylight.

Phytocoenosis - multispecies plant community.

Phytophagy - herbivorous animals.

Phytoplankton - a set of micro-algae, small plant organisms that live in the water column

Rule D.Allena: increase protruding body parts of one species or closely related species of warm-blooded animals (limbs, tail, ears) when moving from north to south.

Rule K.Bergmana: warm-blooded animals, subject to geographical variation, the body size of individuals statistically (on average) more than in populations living in colder parts of its range.

Security Environment - the degree of protection of the territorial complex ecosystems, the human potential of the eco-logical lesions derived from the magnitude of environmental risk.

Technosphere - "technical envelope" - artificially transformed space of the planet, being under the influence of human industrial activity products.

The capacity of the ecosystem - the maximum size of the population of one species, this ecosystem which is capable of supporting in certain environmental conditions for a long time.

The law of irreversibility of evolution (L. Dollo): evolution is irreversible; organism (population, species) can not return to their previous state, already implemented in a number of his ancestors.

 The noosphere - the letters "thinking envelope", the scope of reason; according to Vernadsky - a qualitatively new, higher stage of development of the biosphere under the control of a reasonable human activity.

The ontogenesis - the individual development of the organism; multicellular egg from fertilization to aging and death.

Valence Environment - (tolerance limits) the characteristic type of ability, populations exist in different

Valeology - science for the preservation and strengthening of health, healthy lifestyles.

Zoophages - carnivorous organisms that feed on other animals or their species (cannibalism).

Environmental education - process of mastering by students the system of scientific knowledge about the natural environment as the reality of human life, about the impact of industrial activity on the environment of society, as well as the knowledge and skills of environmental activities.

Environmental awareness -environmental knowledge (information, conclusions and generalizations) about the natural environment and interacting with her man, ecological thinking, feeling and will.

Environmental science is a generic of the relation of organisms in the environment (Haeckel), the science of organization and functioning supraorganismal systems at various levels: the populations of species, biocenoses (communities), ecosystems and the biosphere.

2.Lectures
Module 1.Introduction.

Biochemistry subject

The main principles of chemical logic of a live condition. The concept about macro- and microelements.
I. Basic Chemical Concepts

1. 
   Atoms
   
   1. 
      Def.- the smallest unit of an element that can combine chemically with other elements
      

Structure                                      

1. 
   Proton (+) charged
   
2. 
   Neutron (not charged)
   
3. 
   Electron (-) charged
   
   1. 
      Electrons exist in distinct orbital clouds
      
   2. 
      s, p, and d orbitals
      
   3. 
      Orbitals combine to form energy levels: K, L, M, N, etc
      
4. 
   Protons and neutrons are the same mass and make up the nucleus
   
1. 
   Identification
   
   1. 
      Atomic number: number of protons
      
   2. 
      Atomic mass number: number of protons + neutrons
      
   3. 
      Atoms are organized into groups in the periodic table
      
2. 
   Isotopes
   
   1. 
      Two atoms with the same atomic number but different atomic mass numbers
      
   2. 
      Differ only in the number of neutrons
      
   3. 
      Some are radioactive (radioisotopes)
      

B. Compounds

4. 
   Def: a combination of two or more elements which are joined chemically
   
5. 
   Chemical bonding
   
   1. 
      Ionic: when an atom will either give or take an electron from another atom
      
      1. 
         Cation: positive ion
         
      2. 
         Anion: negative ion
         
      3. 
         Electrostatic forces hold the atoms together
         
   2. 
      Covalent: when atoms share electrons
      
      1. 
         Forms single or multiple bonds
         
      2. 
         Sharing of electrons hold the atoms together
         
   3. 
      Hydrogen bonds: weak links between the hydrogen (+) end of one polar molecule and the negative end of another polar molecule
      

C. Acids and Bases

6. 
   Acid: a substance which releases a H+ ion
   
7. 
   Base: a substance which releases an OH- ion
   
8. 
   pH scale
   
   1. 
      A method of determining how acidic or basic a solution is
      
   2. 
      Negative logarithmic scale: 0 (acidic) to 14 (basic) (alkaline)
      
   3. 
      pH 7.0 is neutral (water)
      
9. 
   Buffers: a substance which limits the change of pH
   

D. Basic chemical reactions

10. 
    Synthesis: two or more atoms or molecules are combined
    
11. 
    Decomposition: molecules are broken down into simpler forms
    
12. 
    Reduction
    
    1. 
       The addition of electrons to a molecule
       
    2. 
       Often accompanied by a gain of a hydrogen nucleus (proton)
       
13. 
    Oxidation
    
    1. 
       The removal of electrons from a molecule
       
    2. 
       Often accompanied by a loss of a proton
       
    3. 
       Oxidized atoms are more reactive than reduced atoms
       

II. Basic Biochemistry Concepts

A. Building Materials of Life

1. 
   Inorganic compounds
   
2. 
   Organic compounds
   
   1. 
      All contain some form of carbon
      
   2. 
      Biosynthesis: the manufacture of things by a living organism
      
3. 
   Carbohydrates
   
   1. 
      Structure
      
      1. 
         Contain only C, H, and O
         
      2. 
         Ratio of O:H is 1:2 (same as water H₂O)
         
   2. 
      Reactions involving carbohydrates
      
      1. 
         Dehydration synthesis: joining two molecules by removing water
         
      2. 
         Hydrolysis: splitting two molecules by adding water
         
   3. 
      Types
      
      1. 
         Monosaccharides (simple sugars)
         
         1. 
            5-carbon: ribose
            
         2. 
            6-carbon: C₆H₁₂O₆ (Glucose, Galactose, Fructose)
            
      2. 
         Disaccharides
         
         1. 
            Two monosaccharides joined together (dehydration synthesis)
            
         2. 
            Sucrose (table sugar): Glucose + Fructose
            
         3. 
            Maltose (malt sugar): Glucose + Glucose
            
         4. 
            Lactose (milk sugar): Glucose + Galactose
            
      3. 
         Polysaccharides
         
         1. 
            Starch: straight chain of glucose (food storage in plants)
            
         2. 
            Glycogen: branched chain of glucose (food storage in animals)
            
         3. 
            Cellulose: Zig-zag chain of glucose (non-digestible roughage)
            
4. 
   Lipids
   
   1. 
      Fats (triglycerides)
      
      1. 
         3 fatty acid molecules + 1 glycerol joined by dehydration synthesis
         
      2. 
         Saturated: no double bonds between carbons
         
      3. 
         Unsaturated: at least one double bond
         
   2. 
      Phospholipids
      
      1. 
         2 fatty acids + 1 glycerol + 1 phosphate
         
      2. 
         Hydrophobic end (fat): water fearing (non-polar)
         
      3. 
         Hydrophilic end (phosphate): water loving (polar)
         
      4. 
         Used extensively in cell membranes
         
   3. 
      Sterols: multi-ringed compounds
      
      1. 
         Cholesterol
         
         1. 
            HDL: High density lipoprotein ("good" cholesterol)
            
         2. 
            LDL: Low density lipoprotein ("bad" cholesterol)
            
      2. 
         Hormones: i.e. prostaglandins, cortisone, etc
         
5. 
   Proteins
   
   1. 
      Structure: composed of 20 basic amino acids
      
   2. 
      Protein synthesis
      
      1. 
         Two amino acids are brought together and dehydration synthesis between the amino acids forms a peptide bond
         
      2. 
         Protein = polypeptide chain
         
      3. 
         The order of the amino acids is critical to the function of a protein
         
   3. 
      Enzymes: large proteins which catalyze reactions
      
      1. 
         Structure
         
         1. 
            Active site: attachment site for substrates
            
         2. 
            Substrate: molecule which reacts with the enzyme and is changed
            
         3. 
            Coenzyme: non-protein which helps to complete the active site (vitamins)
            
      2. 
         Enzyme action
         
         1. 
            Enzyme & substrate bind at the active site
            
         2. 
            Reaction proceeds (lytic- splitting apart, synthetic - putting together)
            
         3. 
            Enzyme and product(s) separate
            
6. 
   Nucleic acids
   
   1. 
      Consist of long chains of repeating subunits (nucleotides)
      
   2. 
      Nucleotide structure
      
      1. 
         5-carbon sugar (ribose)
         
      2. 
         Phosphate group (PO₄)
         
      3. 
         Organic nitrogen-containing base
         
   3. 
      DNA: Deoxyribonucleic acid
      
      1. 
         Used to store biological information
         
      2. 
         DNA base pairs
         
         1. 
            Guanine - Cytosine (G - C)
            
         2. 
            Adenine - Thymine (A - T)
            
      3. 
         Double-stranded helix shape formed by hydrogen bonds
         
   4. 
      RNA: Ribonucleic acid
      
      1. 
         Used as working blueprints for protein synthesis
         
      2. 
         RNA base pairs
         
         1. 
            Guanine - Cytosine (G - C)
            
         2. 
            Adenine - Uracil (A - U)
            
      3. 
         Single strand
         

III. Energy and its Changes

A. Kinetic energy: energy of motion

B. Potential energy: energy of position (stored energy)

C. Kinetic and potential energy are interconvertable

D. Energy in chemical reactions

1. 
   Exothermic: reactions which release energy (heat)
   
2. 
   Endothermic: reactions which require energy
   
3. 
   Activation energy: energy needed to start a chemical reaction
   

Module 2.Aminoacids.

Amino acids: classification, structure, stereochemistry, physical and chemical properties and classification amino acids forming proteins.

• 
  Properties of the 20 amino acids that occur in peptides and proteins are crucial to the structure and function of proteins.
  
  • 
    stereochemistry
    
  • 
    relative hydrophobicity or polarity
    
  • 
    hydrogen bonding properties
    
  • 
    ionization properties
    
  • 
    other chemical properties 
    
• 
  Condensation of 2 amino acids forms the peptide bond, the amide linkage holding amino acid residues in peptide and protein polymers. 
  
• 
  Properties of the peptide bond have major consequences in terms of the 3-dimensional structures of proteins
  

There's an excellent website on amino acids being developed here in the Department of Biochemistry and Molecular Biophysics; parts of it are still under construction, but there are links to various very useful parts of it here in these notes, and indeed parts of it may be used in class.

BASICS

• 
  Proteins are polymers of -amino acids:  
  
• 
  There are 20 different amino acids found in proteins and they differ by the nature of the R group. 
  

• 
  Both the -amino group (amino group substituent on the C) and the -carboxyl group (carboxyl substituent on the C) are ionizable.
  
  • 
    -COOH group:  a weak acid, can DONATE its proton, with a pKa of about 2-3. What's the conjugate base form of the carboxyl group? Which form is charged, and is it a positive or a negative charge?
    
  • 
    -NH₂ group:  a weak base (there's an unshared pair of electrons on the N; the neutral amino group can ACCEPT a proton). What's the conjugate acid form of the amino group? Which form is charged, and is it a positive or a negative charge?
    
  • 
    pK_as of -amino and -carboxyl groups are different for different amino acids, and also are altered if they're the terminal groups on a chain of amino acids, i.e., a peptide or protein.
    

Predominant form in H₂O is the zwitterion:   .  

Stereochemistry of the amino acids

• 
  -carbon is asymmetric (has four different substituents) except for one amino acid, for which the R group is a hydrogen atom.
  
• 
  amino acids occur as enantiomers (nonsuperimposable complete mirror images)
  
• 
  L-amino acids are the naturally occurring enantiomers found in all proteins
  
• 
  There are naturally occurring D-amino acids, but not in proteins (found in some bacterial cell wall peptide structures, in some peptide antibiotics, etc.) (D_L)
  

• 
  Perspective formulas show stereochemistry; projection formulas CAN be written "correctly", with convention that horizontal bonds project out of paper and vertical bonds behind plane of paper, but often biochemists use projection formulas casually (inaccurately), knowing that if it's in a protein, it's always an L-amino acid.
  
• 
  Absolute configurations of D-glyceraldehyde as the reference compound for -amino acids.  D- and L- apply only to the absolute configuration around the chiral  carbon; 2 of the 20 amino acids (threonine and isoleucine) have a second chiral center, requiring the RS system to describe their structures accurately, but we aren't going to worry about using the RS system here.
  

 

Which of the amino acids does NOT have a chiral center, so has no D/L isomers?

Amino Acid Abbreviations

amino acid (or residue in protein)	3-letter abbreviation	1-letter abbreviation	Mnemonic for 1-letter abbreviation
Glycine	Gly	G	Glycine
Alanine	Ala	A	Alanine
Valine	Val	V	Valine
Leucine	Leu	L	Leucine
Isoleucine	Ile	I	Isoleucine
Proline	Pro	P	Proline
Methionine	Met	M	Methionine
Phenylalanine	Phe	F	Fenylalanine
Tryptophan	Trp	W	tWyptophan (or tWo rings)
Tyrosine	Tyr	Y	tYrosine
Serine	Ser	S	Serine
Threonine	Thr	T	Threonine
Cysteine	Cys	C	Cysteine
Aspartic Acid	Asp**	D	asparDic acid
Glutamic Acid	Glu*	E	gluEtamic acid
Asparagine	Asn**	N	asparagiNe
Glutamine	Gln*	Q	Q-tamine
Histidine	His	H	Histidine
Lysine	Lys	K	(before L)
Arginine	Arg	R	aRginine

* Glx = either acid or amide (when it isn't known which it is)
**Asx = either acid or amide (when it isn't known which it is)

Properties of Amino Acid Side Chains

Side chains ("R groups") provide proteins with unique structural and functional properties.
Additional C atoms in R groups (after the  C) designated by successive Greek letters:  as shown in the structure of the amino acid LYSINE (Nelson & Cox: Lehninger Principles of Biochemistry, 3rd ed., p. 116):

 

Side chain classes

• 
  The side chains of the amino acids play an essential role in determining the properties of proteins. 
  

There is a wide diversity in the chemical properties of amino acid side chains, but they can be grouped into classes, sometimes with overlapping "membership" (e.g., tyrosine is both aromatic and hydroxyl-containing). Other classifications are also possible (for example, the 5 classes in textbook, Fig. 5-5, discussed below).  You are expected to know all 20 amino acid structures and their R group properties, including ionization properties (see table below with "generic" pK_a values for groups in peptides and proteins and links to titration curves, and the PDF of proton dissociation reactions).

Side Chain Class	Amino Acids
Aliphatic	glycine, alanine, valine, leucine, isoleucine
Cyclic	proline
Aromatic	phenylalanine, tyrosine, tryptophan
Hydroxyl-Containing	serine, threonine, tyrosine
Sulfur-Containing	cysteine, methionine
Basic	histidine, lysine, arginine
Acidic and Their Amides	aspartic acid, glutamic acid, asparagine, glutamine

• 
  Nonpolar, aliphatic R groups
  
  • 
    Gly: quite water-soluble (as is Pro)
    
  • 
    Ala, Val , Leu and Ile: increasing hydrophobicity with increasing number of C atoms in hydrocarbon chain
    
  • 
    Pro: cyclic (--> unusual properties)
    
    • 
      shares many properties with the aliphatic group
      
    • 
      rigidity of ring plays critical role in protein structure (more about that later)
      
  • 
    Met: methyl thioether (S-containing)
    
    • 
      quite hydrophobic
      
    • 
      Met's terminal methyl group important in metabolism
      

• 
  Aromatic R groups
  
  • 
    Phe: phenyl group (linked to -CH₂, so Phe = alanine with a phenyl substituent on the methylene C)
    
    • 
      VERY hydrophobic.
      
  • 
    Trp: indole functional group on C
    
    • 
      electronegative atom in ring system
      
    • 
      not as hydrophobic as Phe
      
    • 
      hydrogen bonding capability (donor? acceptor? how many hydrogen bonds?)
      
  • 
    Tyr: phenylalanine with aromatic OH group (phenolic OH) = p-hydroxyphenylalanine
    
    • 
      ionizable (pK_a around 10; loss of proton gives phenolate anion)
      

• 
  hydrogen bonding capability (donor? acceptor? how many hydrogen bonds?)
  
• 
  Tyr R group is the least hydrophobic of the 3 aromatic amino acid side chains.
  

• 
  Polar, uncharged R groups
  
  • 
    Ser and Thr: aliphatic OH groups, not ionizable in pH range 1-13
    
    • 
      pKa values so high that under any biologically reasonable pH conditions they're polar but not ionizable.
      
    • 
      hydrogen bonding capability (donor? acceptor? how many hydrogen bonds?)
      
  • 
    Asn and Gln: amide functional groups
    
    • 
      VERY polar, but NOT ionizable
      
    • 
      hydrogen bonding capability (donor? acceptor? how many hydrogen bonds?)
      
  • 
    Cys: thiol (also called a sulfhydryl group) -- not very polar, and IS ionizable
    
    • 
      sulfur atom makes protonated -SH group more hydrophobic than an aliphatic OH group
      
    • 
      thiol DOES lose its proton in physiologically relevant pH range (pK_a about 8.5)
      
    • 
      generates -S^- (thiolate anion is quite hydrophilic due to the charge).
      
  • 
    
    

• 
  Positively charged R groups (sometimes called "basic" R groups)
  
  • 
    Arg: guanidino group
    
    • 
      VERY high pK_a (~12+), so a very weak acid (stronger base)
      
    • 
      carries + charge all across physiological pH range
      
    • 
      resonance forms of guanidino group stabilize protonated form (charge is delocalized)
      
    • 
      hydrogen bonding capability (donor? acceptor? how many hydrogen bonds?)
      
  • 
    Lys: -amino group (a primary amine)
    
    • 
      pK_a about 10
      
    • 
      protonated form (predominates at physiological pH) carries + charge
      
    • 
      hydrogen bonding capability (donor? acceptor? how many hydrogen bonds?)
      
  • 
    His: imidazole functional group (has 2 N atoms in 5-membered unsaturated ring)
    
    • 
      pKa about 6-6.5
      
    • 
      protonated form carries + charge, but at pH 7 predominant form is neutral (despite textbook's categorization as "positively charged")
      
    • 
      very important player in catalytic activity of many enzymes
      
    • 
      hydrogen bonding capability, and also proton donor/acceptor
      

• 
  Negatively charged R groups (sometimes called "acidic" R groups)
  
  • 
    Asp and Glu: side chain carboxyl groups
    
    • 
      pK_a values around 4
      
    • 
      predominant form at physiological pH = carboxylate anion
      
    • 
      hydrogen bonding capability (donor? acceptor? how many hydrogen bonds?)
      

Relative hydrophobicity/hydrophilicity of amino acid R groups

• 
  Table 12.2 : Polarity scale for amino acid residues based on free energy changes for moving a residue from a hydrophobic environment (dielectric constant = 2) into H₂O.
  
• 
  Similar trends for relative hydrophobicities in text Table 5-1 (diff. numerical scale, and not arranged in order of relative polarity)
  
• 
  Depending on how transfer experiments are done, different absolute numbers can be obtained, but the general trends of relative polarity are clear
  
  • 
    Phe, Met, Ile, Leu, Val are very hydrophobic
    
  • 
    Arg, Asp, Lys, Glu, Asn, Gln, and His are quite hydrophilic
    
  • 
    The rest are in between -- neither very polar nor very hydrophobic
    

• 
  Reversible oxidation of 2 cysteine side chain thiols to form cystine, or re-reduction to 2 thiols
  
  • 
    disulfide bonds between 2 Cys residues in a (usually extracellular) protein
    
  • 
    often a critical structural feature in extracellular proteins (stabilize folded structures, in interior of protein structure)
    
  • 
    When found in intracellular proteins, usually have a functional role.
    

Ionization Properties of Amino Acid Functional Groups (in PEPTIDES AND PROTEINS)

• 
  weak conjugate acid/base groups in peptides and proteins crucial to functions
  
  • 
    only one -amino and one -carboxyl group on a peptide or proteins (at the termini of the chain) because the rest of the -amino and -carboxyl groups are tied up in amide bonds holding monomers together in polymer (more later)
    
  • 
    side chain ionizable groups (only 7 of the 20 amino acids)
    
• 
  PDF of the acid dissociation reactions for functional groups of amino acid residues in peptides and proteins
  
• 
  ionization states of side chain weak acid groups control charges on protein
  
• 
  Note: local environment in peptide or protein determines actual pKa of that specific group, so the ranges shown below (and the rather arbitrary "generic" values, rounded off for simplicity) are only the usual expected ranges for pK_a values for the functional groups in peptides and proteins; the pKa of a specific group in a specific protein can lie significantly outside the expected range if the local environment is unusual.
  
• 
  links in table below are to titration curves for that amino acid or functional group
  

Group	usual pKa range, in peptides & proteins (approx."generic"pKa )
a-Carboxyl (terminal group of peptide or protein)	~3.0 - 4.0 (generic 3.0)
Asp, Glu (side chain carboxyl)	~4.0 - 4.5 (generic 4.0)
His (imidazole)	~6.0 - 7.4 (generic 6.5)
Cys (thiol, SH)	~8.5 - 9.0 (generic 8.5)
Tyr (phenolic OH)	~9.5 - 10.5 (generic 10.0)
a-Amino (terminal group of peptide or protein)	~8.0 - 9.0 (generic 8.0)
Lys (-amino)	~9.8 - 10.4 (generic 10.0)
Arg (guanidino)	~12.0 - 12.5 (generic 12.0)

 

Isoelectric point (pI)

• 
  pI = "isoelectric pH" = "isoelectric point" = pH at which the NET charge on a molecule is ZERO. 
  
  • 
    If pH < pI, net charge is positive (more + than - charges)
    
  • 
    If pH > pI, net charge is negative (more - than + charges)
    
• 
  pI = the pH exactly halfway between the two pK_a values surrounding the zero net charge equivalence point on the titration curve (examples to be analyzed in class: Gly and His)
  

• 
  Fig. 5-10. Titration curve of glycine (Nelson & Cox: Lehninger Principles of Biochemistry, 3rd ed.)
  

• 
  Molecular separations based on charge properties (paper electrophoresis of amino acids as an example)
  
• 
  paper strip soaked in buffer, in contact with 2 reservoirs with electrodes connected to a power supply
  

Buffer reservoir #1 + (anode; anions move toward it)

O

Buffer reservoir #2 ^_ (cathode; cations move toward it)

^
Ultraviolet absorbance of amino acid side chains

• 
  Aromatic amino acids (Trp, Tyr, Phe) absorb light in the near ultraviolet region of the spectrum (250-300 nm). 
  
• 
  Trp has highest molar absorptivity, followed by Tyr, with Phe making only a small contribution.
  
• 
  Disulfide bonds (between Cys residues in proteins) also absorb in the uv range, but much less than the aromatics.
  
• 
  Fig. 5-6 (Nelson & Cox, Lehninger Principles of Biochemistry, 3rd ed.): Absorbance of ultraviolet light by aromatic amino acids
  

Posttranslational modifications of amino acid side chains

• 
  chemical modifications AFTER biosynthesis of proteins
  
• 
  occur for a few amino acid residues in some proteins
  
• 
  Some examples (see also Fig. 5-8, Nelson & Cox: Lehninger Principles of Biochemistry, 3rd ed.)):
  

O-Phosphoserine	4-Hydroxyproline	5-Hydroxylysine	-carboxyglutamate

• 
  reversible phosphorylation and dephosphorylation of Ser, Thr, and Tyr residues very important in covalent regulation of activity of some enzymes and many biosignalling proteins, including some hormone receptors and transcription factors
  
• 
  4-hydroxyproline & 5-hydroxylysine important in structure of collagen (fibrous protein in connective tissue)
  
• 
  -carboxyglutamate important in a number of proteins whose function involves Ca²⁺ binding, including several proteins involved in blood clotting
  

Chemical Reactions of Amino Acids

• 
  All amino acids have at least two reactive groups: the amino and -carboxyl groups and these groups can react with a variety of reagents. Here are two examples:
  

• 
  
  

 

• 
  A particularly interesting example is the green fluorescent protein (GFP) from the Pacific Northwest jellyfish Aequorea victoria, which has generated intense interest as a marker for gene expression and localization of gene products.  The chromophore, which results from the spontaneous cyclization and oxidation of the sequence -Ser65-Tyr66-Gly67- , is unusual because it does not involve a non-protein chromophore, as is usually the case for colored proteins. The chromophore is buried in the interior of GFP.
  

• 
  
  

The Peptide Bond

• 
  Peptides and proteins:polymers of amino acids joined bypeptide bonds
  
• 
  amide linkages from condensation of -carboxyl group of one amino acid with -amino group of another amino acid
  

• 
  process repeated many times --> linear chain of amino acids, a polypeptide chain
  
• 
  convention: sequence written from left to right starting with residue with free -amino group (the N-terminal or amino terminal amino acid residue) and ending with the residue containing the free -carboxyl group (the C-terminal or carboxyl terminal residue), 
  e.g., NH₂-Glu-Gly-Ala-Lys-COOH = EGAK
  
• 
  average residue mass ~110 (average M_r of the 20 amino acids minus Mr of H₂O)
  
• 
  a polypeptide chain with 100 amino acid residues would have a M_r of about 11,000)
  
• 
  small peptides (a "few" amino acid residues) = oligopeptides
  

Peptide bond formation endergonic (G^o' ~21 kJ/mol)

• 
  (How would a cell make the reaction go in the direction of condensation in an aqueous environment? no details needed here for biochemical mechanism -- that's covered in BIOC 411)
  
• 
  peptide bonds metastable in aqueous environment -- equilibrium lies far in direction of hydrolysis, but RATE of hydrolysis very slow in absence of catalyst
  
• 
  Enzymes that catalyze peptide bond hydrolysis = peptidases or proteases, e.g., (specific examples of proteases) your digestive proteases like trypsin and pepsin
  

Ionization properties of peptides

• 
  analyzed the same way as for free amino acids
  
• 
  one -amino group (pK_a approx. 8) and one -carboxyl group (pK_a approx. 3), plus any ionizable side chains on residues in the peptide
  
• 
  To figure out approximate net charge of a peptide at a given pH:
  
  • 
    make yourself notes on the sequence to keep track of what you're doing
    
  • 
    add up charges on all the ionizable groups
    

Example: Fig. 5-14 (Nelson & Cox: Lehninger Principles of Biochemistry, 3rd ed.): pentapeptide SGYAL = Ser-Gly-Tyr-Ala-Leu 
= Serylglycyltyrosylalanylleucine 

Amino Acid Analysis

• 
  Sequence of amino acids in a protein is dictated by the sequence of nucleotides in the gene encoding that protein:
  

(from Berg, Tymoczko & Stryer, Biochemistry, 5th ed., p. 28)

• 
  Each protein (unique sequence) has unique amino acid composition.
  
• 
  Can chemically hydrolyze (hot 6N HCl) a pure protein to generate the free amino acids and determine its amino acid composition chromatographically
  
• 
  Because side chains of the amino acids have different properties, can separate and quantitate all 20 amino acids using a variety of chromatographic techniques, as illustrated below.
  

 

Peptide bond has resonance structures --> partial double bond character

• 
  Due to the partial double bond character of the peptide bond, the O, C, N and H atoms are nearly planar and there is no rotation about the peptide bond (peptide).  As we shall see later, the planarity of the these elements has important consequences for the three dimensional structure of proteins. 
  

• 
  Generally, the two C_ groups are in a trans configuration, which minimizes steric interaction (cis/trans).