1014NSC Fundamentals of Biochemistry Semester Summary

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1 1014NSC Fundamentals of Biochemistry Semester Summary Griffith University, Nathan Campus Semester 1, 2014 Topics include: - Water & ph - Protein Diversity - Nucleic Acids - DNA Replication - Transcription - Translation - Protein Structure & Function - Enzymes - Enzyme Kinetics - Enzyme Inhibitors - Carbohydrates - Lipids - Membranes - Membrane Transport

2 Module 1.1- Water and ph - Water plays a central role in the chemistry of all life - Proteins, polysaccharides, nucleic acids and membranes all assume their characteristic shapes in response to water - Chemical properties of water are related to the functions of biomolecules, entire cells and organisms The structure of Water Important properties arise from its angled shape: - Angle of o between two covalent bonds o Bonding orbital- sp 3 - Polar O-H bonds due to electronegativity of oxygen o Oxygen nucleus attracts electron more strongly o Electrons are more often in the vicinity of the oxygen atom (2δ - ) than hydrogen (δ + ) - Angled arrangement of polar bonds creates permanent dipole o Negative O dipole is equal in magnitude to the two positive H dipoles Weak interactions in aqueous solutions Hydrogen Bonding Between water molecules Due to their polarity, water molecules attract each other - Hydrogen bond formed between positive H dipole and negative O dipole of two water molecules o Relatively weak- bond dissociation energy of 23 kj/mol (470kJ/mol for O-H covalent bond) - Water molecule can form up to 4 H-bonds For liquid water - Molecules are disordered and in constant motion - Each forms H-bonds with average of 3.4 other water molecules For ice - Molecules form maximum of 4 H-bonds o Creates regular lattice (uniform structure) o Makes ice less dense than liquid water Between water and polar solutes Hydrogen bonds are not unique to water - Form between any hydrogen bond donor and hydrogen bond acceptor o H-bond donor= electronegative atom covalently bound to hydrogen o H-bone acceptor= electronegative atom (usually oxygen or nitrogen) - H-bonds strongest when molecules are orientated to maximise electrostatic attraction o Straight line so that acceptor atom is in line with covalent bond between donor atom and H

3 Examples of biologically important hydrogen bonds Polar, nonpolar and amphipathic molecules Water is a polar solvent (only forms H-bonds with polar molecules) - Hydrophilic- generally charged or polar, readily dissolved - Hydrophobic- non-polar, poor solvents

Ionic Interactions Water dissolves crystalline salts by hydrating and stabilizing component ions For example NaCl: - NaCl crystal lattice is disrupted as water molecules cluster about the Cl - and Na

Hydrophobic Interactions Nonpolar gases Biologically important gases (CO 2, O 2, N 2) are nonpolar - Hydrophobic and poorly soluble in water - Change from disordered gas phase into aqueous solution

in entropy (energetically unfavourable) Nonpolar compounds Nonpolar compounds interfere with H-bonding among water molecules - Water molecules in immediate vicinity of nonpolar solute are constrained

4 Ionic Interactions Water dissolves crystalline salts by hydrating and stabilizing component ions For example NaCl: - NaCl crystal lattice is disrupted as water molecules cluster about the Cl - and Na + ions o Ionic charges of ions partially weakened electrostatic attractions between ions reduces - Ions acquire greater freedom of motion- increase in entropy (favourable free-energy change) Hydrophobic Interactions Nonpolar gases Biologically important gases (CO 2, O 2, N 2) are nonpolar - Hydrophobic and poorly soluble in water - Change from disordered gas phase into aqueous solution reduces motion o Decrease in entropy (energetically unfavourable) Hydrophilic and are poorly soluble in water o Transitioning from disordered gas phase into aqueous solution reduces motion Decrease in entropy (energetically unfavourable) Nonpolar compounds Nonpolar compounds interfere with H-bonding among water molecules - Water molecules in immediate vicinity of nonpolar solute are constrained in possible orientation o Solute becomes surrounded by highly ordered water molecules decrease in entropy For amphipathic compounds: - Polar, hydrophilic region interacts favourably with water - Nonpolar, hydrophilic region tends to avoid contact o Will form micelles (held together with hydrophobic interactions) Disruption of ordered water molecules is driving force in formation of polar enzyme-substrate complexes o Causes entropy increase as water molecules can become more disordered

van der Waals Interactions Occur between two uncharged atoms in close proximity - Surrounding electron clouds influence each other - Random variations in electron position creates transient electric

5 van der Waals Interactions Occur between two uncharged atoms in close proximity - Surrounding electron clouds influence each other - Random variations in electron position creates transient electric dipole o Induces transient, opposite electric dipole in nearby atom - Weak electrostatic attraction brings two atoms closer Ionization of water, weak acids, and weak bases Pure water is slightly ionized - Ionization expressed by an equilibrium constant (K w) K = [H+ ][OH ] [H 2 O] = products reactant - ph scale designates H + and OH - concentrations ph = - log10[h + ] - Weak acids have characteristic dissociation constants o Titration curves reveal pk a of weak acids Water is a neutral molecule with a very slight tendance to ionize - H 2 O H + + OH - - Free protons (H + ) don t actually exist, rather they exist as hydronium ions, H 3 O + o For simplicity- often represented as H + Proton movement between water molecules Proton of a hydronium ion is highly mobile ( proton hopping ) - H + and OH - ions therefore much more mobile than other ions o Reason why acid/base reactions are so fast Acids and bases Acid = proton donors - Once acid has lost proton, it becomes the conjugate base Base = proton acceptor - Once base has accepted proton, it becomes the conjugate acid Strong acids and bases completely dissociate HA H + + A - Weak acids and bases partially associate as described by their dissociation constant (K a) - The larger K a, the stronger the acid - The smaller pk a, the stronger the acid HA H + + A - Titration Curves Titration is used to determine amount of acid in solution - Strong base is added until solution is neutralised (ph7) Plot of ph against amount of base added (titration curve) reveals pk a - At midpoint, half of original acid has dissociated o At this point concentration of acid is equal to concentration of conjugate base ph=pk a Stronger acids have midpoint at low ph whereas weaker acids have theirs at high ph

6 Buffering against ph changes in Biological Systems Buffers are mixtures of weak acids and their conjugate bases - Buffer cells and tissues against changes in ph - Concentrations of acid and conjugate base should be equal such that ph=pka - Tend to resist changes in ph where small amounts of acid/base are added o Result of the acid-conjugate base equilibrium shifting as described by Le Chatelier's principle Decreasing ph causes an increase in acid Increasing ph causes a decrease in conjugate base o Buffer region ~pka +/- 1 Henderson-Hasselbalch equation relates ph, pka and buffer concentration ph = pk a + log [A ] [HA] Three important points 1. ph depends on pk a and [A ] [HA] 2. [A ] [HA] depends on ph and pka o log [A ] [HA] = ph pk a 3. At half-equivalence (midpoint) ph = pk a o [acid]=[conjugate base] log [A ] = 0 [HA]

biological molecules occurring in all cells and all parts of cells - Range in size from relatively small peptides to huge polymers of molecular weights in the millions - Occur in great variety and

7 Module 1.2- Protein Diversity Define protein: a macromolecule composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by peptide bonds Proteins - Most abundant biological molecules occurring in all cells and all parts of cells - Range in size from relatively small peptides to huge polymers of molecular weights in the millions - Occur in great variety and exhibit enormous diversity in biological function o Enzymes o Transport proteins o Nutrient & storage proteins o Contractile & motile proteins o Structural proteins o Defence proteins o Regulatory proteins o Specialized proteins Amino acids 20 amino acids linked through peptide bonds give rise to the entire array of proteins - Amino acid= α-amino-substituted carboxylic acids - Peptide bond= a substituted amide linkage between the α-amino group of one amino acid and the α-carboxylic group of another All amino acids have a carboxyl and amino group bonded to a α-carbon - The α-carbon also has a hydrogen and a side chain (R-group) - Each amino acid differs in the side chain which vary in charge, size, structure, water solubility and chemical properties Chirality of amino acids Amino acids consist of four substituents around a α-carbon, thus they have two possible stereoisomers - Since they are non-superimposable they are enantiomers Formation of stable repeating structures requires constituent amino acids to the same enantiomer - Exclusively L isomers are synthesised due to the asymmetric binding sites of enzymes

Nonpolar, aliphatic - Nonpolar and hydrophobic - Become more hydrophobic as side chain length increases - Usually cluster together within proteins, avoiding aqueous environments o Stabilizing

8 Nonpolar, aliphatic - Nonpolar and hydrophobic - Become more hydrophobic as side chain length increases - Usually cluster together within proteins, avoiding aqueous environments o Stabilizing structure by means of hydrophobic interactions Proline - Cyclic amino acid - Shares many properties of aliphatic (straight chain) amino acids - Rigid bond-angles of proline make it difficult to fold into proteins - Generally introduces a kink into polypeptide chain

Polar, uncharged amino acids - More soluble in water and hydrophilic - Polarity due to: o Hydroxyl groups of serine and threonine o Sulfhydryl group of

Side chain can ionize at moderately high ph - Can from a covalently linked dimeric amino acid (cysteine) o Two cysteine residues joined by disulphide bond -

Positively charged (basic) amino acids Lysine and Arginine - R groups carry positive charges and are strongly polar at ph7 - Very hydrophilic, usually found

imidazole group - Only common amino acid ionisable with a pka near neutrality - Residues facilitate many enzyme-catalysed reactions by serving as a proton

9 Polar, uncharged amino acids - More soluble in water and hydrophilic - Polarity due to: o Hydroxyl groups of serine and threonine o Sulfhydryl group of cysteine o Amide groups of asparagine and glutamine Asparagine and glutamine are the amide derivatives of aspartate and glutamate, respectively Cysteine - Side chain can ionize at moderately high ph - Can from a covalently linked dimeric amino acid (cysteine) o Two cysteine residues joined by disulphide bond - Plays special role in structures by covalently linking different parts of a protein/polypeptide - Disulphide linkages are strongly hydrophobic (nonpolar) Positively charged (basic) amino acids Lysine and Arginine - R groups carry positive charges and are strongly polar at ph7 - Very hydrophilic, usually found on exterior of proteins - Lysine- secondary amino group on aliphatic side chain - Arginine- positively charged guanidino group Histidine - Contains a imidazole group - Only common amino acid ionisable with a pka near neutrality - Residues facilitate many enzyme-catalysed reactions by serving as a proton donor/acceptor Negatively charged (acidic) amino acids - R groups carry a net negative charge at ph7 - Very hydrophilic Aspartate and glutamate have a second carboxylic acid group

Aromatic amino acids - R groups are relatively nonpolar and participate in hydrophobic interactions - Tyrosine and tryptophan are significantly more polar than phenylalanine due to tyrosine hydroxyl

10 Aromatic amino acids - R groups are relatively nonpolar and participate in hydrophobic interactions - Tyrosine and tryptophan are significantly more polar than phenylalanine due to tyrosine hydroxyl group and tryptophan indole ring - Able to absorb ultraviolet light- allows us to study proteins. Modified amino acids There are a number of modified amino acids which are formed from the common amino acids Examples: Selenocysteine Introduced during protein synthesis rather than created through a post-synthetic modification - Cysteine but with sulphur replaced by selenium Other properties of Amino Acids Amino acids are ionised in aqueous solution. - pka for substituents will vary For amino acids without ionisable side chains, at ph 7 zwitterions are formed (dipolar ion) - Amino group is largely protonated (NH3+) - Carboxyl group is largely deprotonated (COO-)

Amino Acid titration curves Distinct stages correspond to the deprotonation of carboxyl and amide

point (pi)= ph at which molecule has net charge of zero - Average of pka values ph < pi amino acid has

are also ionisable: - ph > pka the proton tends to be off - ph < pka the proton tends to be on Peptide

Properties of peptide bonds - Planar and prefer to be in the trans form - Have an unreacted amino

11 Amino Acid titration curves Distinct stages correspond to the deprotonation of carboxyl and amide groups and any ionisable side chain - At these stages regions of buffering power exist Isoelectric point (pi)= ph at which molecule has net charge of zero - Average of pka values ph < pi amino acid has net positive charge ph > pi amino acid has net negative charge The side chains of some are amino acids are also ionisable: - ph > pka the proton tends to be off - ph < pka the proton tends to be on Peptide bond Formed when two amino acids are covalently linked between an amino group and a carboxyl group Properties of peptide bonds - Planar and prefer to be in the trans form - Have an unreacted amino group at one terminus (amino N terminus) and an unreacted carboxyl group at the other terminus (carboxyl C terminus)

Module 2.1- Nucleic Acids Four Functions of Genetic Material 1. Must contain complex information o Capable of storing instructions for the traits/functions of an organism 2.

Must encode the phenotype o Genotype must have capacity to be expressed/code for traits (phenotype) 4.

linkages Nucleotides Sugar Pentose sugar containing 5 carbons, numbered 1, 2, 3 RNA- sugar is called ribose - Has a hydroxyl group (-OH) attached to the 2 -carbon - Additional oxygen makes RNA

12 Module 2.1- Nucleic Acids Four Functions of Genetic Material 1. Must contain complex information o Capable of storing instructions for the traits/functions of an organism 2. Must replicate faithfully o Capacity to be copied accurately and transmitted to descendant cells 3. Must encode the phenotype o Genotype must have capacity to be expressed/code for traits (phenotype) 4. Must have the capacity to vary o Different species/individuals of a species differ in their genetic make up Nucleic Acids Primary structure String of nucleotides joined together by phosphodiester linkages Nucleotides Sugar Pentose sugar containing 5 carbons, numbered 1, 2, 3 RNA- sugar is called ribose - Has a hydroxyl group (-OH) attached to the 2 -carbon - Additional oxygen makes RNA nucleotide more reactive/ less chemical stable DNA- sugar is called deoxyribose - Has hydrogen atom (-H) attached to the 2 -carbon - More stable, therefore better suited as long-term repository of genetic information Nitrogenous base Purines- six-member ring attached to a five-member ring - Adenine (A) and guanine (G) Pyrimidines- six-membered ring only - Cytosine (C), thymine (T) and uracil (U) o Cytosine present in both DNA and RNA however, thymine only present in DNA and uracil only present in RNA Nucleoside= deoxyribose/ribose sugar and a nitrogenous base Chargaff s rule- for DNA, A=T and G=C Phosphate group - Phosphorus atom bonded to four oxygen atoms - Frequently carry a negative charge which makes DNA acidic Polynucleotide strands Phosphodiester linkages= strong covalent bonds connecting nucleotides - Join the 5 -phosphate group of one nucleotide to the 3 -hydroxyl group of the next nucleotide - Backbone consists of alternative sugars and phosphates Polynucleotide stands have direction/polarity 5 end- free phosphate group attached to the 5 -carbon 3 end- free hydroxyl group attached to the 3 -carbs

2: CHEMICAL COMPOSITION OF THE BODY

1 2: CHEMICAL COMPOSITION OF THE BODY Although most students of human physiology have had at least some chemistry, this chapter serves very well as a review and as a glossary of chemical terms. In particular,