Lecture Notes in Biochemistry for Medical Laboratory Science Students PDF

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“Whatever you decide to do, make sure it makes you happy.”Note: Alcohol- OH group- Hydroxyl groupThe presence of this group makes the biomolecules abundant (can form hydrogen bonding) and polar.Biochemistry  Biological Chemistry  Study of chemistry of the living organism. Includes biomolecules, an...

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Biochemistry for Medical Laboratory Science Chapter 1: Introduction Biochemistry  

Biological Chemistry Study of chemistry of the living organism. Includes biomolecules, and biochemical reactions.

Four Biomolecules of the body 1. Proteins 2. Carbohydrates 3. ZxzLipids 4. Nucleic Acids

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Base on the illustration there is a part of Hydrophilic Hydrophilic are opposites of hydrophobic, they are water loving molecules they don’t repel water.  Because of the presence of hydrophilic and hydrophobic molecules on Palmitic Acid we can consider this molecule as an Amphipathic molecule which hydrophilic and hydrophobic are both present. Functional Groups are group of atoms that renders the chemical properties of an organic molecules and biomolecules.

Biomolecules-can be found in Plant and Animal cells Cytological composition 1. 50-95 % water 2. 1% ions- magnesium, potassium, calcium ions 3. Other organic molecules Organic Molecules  

Are Carbon based molecules Covalently bond to itself or other elements ex. H, O, N, S, and P Simplest organic molecule CH4 (methane)

Hydrocarbons   

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One of the most organic molecules Are derived from Hydrogen and Carbons If the hydrocarbons chains are longer the more it becomes Non-polar and insoluble in water whether there is the presence of OH. Note that hydrocarbons are useless inside the body, the only thing that important in this compound is the derivative Hydrogen and Carbon.

Hydrophobic and Hydrophilic Hydrophobic are molecules that repels water that usually are nonpolar molecules Example: Lipids/ fatty acids a monocarboxylic acid can be a component of fat/oil. A good example of this is a Palmitic acid

Note: Alcohol- OH group- Hydroxyl group The presence of this group makes the biomolecules abundant (can form hydrogen bonding) and polar. Aldehyde- usually have smell (not that really good) Acids- fatty acids are example of acids in lipids; some certain kind of acids are found in acidic amino acids- bears the carboxyl group (makes a weak acid)

Note: if H+ is easily remove it has a higher acidity; not all hydrogen are acidic because it only becomes acidic when it is beside an electronegative element. Amines- a weak basic; had a positive charge when it accepts proton; NH2 in amino acids.

“Whatever you decide to do, make sure it makes you happy.” Paulo Coelho

Biochemistry for Medical Laboratory Science Thiol- contains Sulfur; important in the proteins which it forms the disulfide bond. Esters- makes up fat and acid.  Double bond is important in fatty acids; reactive site or serve as like a dipole bond in fatty acids. 1. Saturated- single bond 2. Unsaturated- double bond

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Chapter 2. Water: The Solvent for Biochemical Reactions 

Polarity of Water   

Water is not a linear molecule. Water molecule is bent thus, asymmetric distribution of electron density occurs. Oxygen of water has a high electronegativity which pulls hydrogen electrons closer and creates a partial positive charge.

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When we add a non-polar substance in water, water forms a cage around the non-polar substances. This situation is not favorable to water, because non-polar substances interferes with the waters ability to interact with other water molecules. When we add to or more non-polar substances to water, the non-polar molecules will form together. This is favorable because it releases the trapped water molecules and allows them to once more form hydrogen bonds with other water molecules. This interaction between non-polar molecules in water are called hydrophobic interactions and this effect is called hydrophobic effect.

Intramolecular Bonds and Intermolecular Bonds

Strong Intermolecular Bonds   

By an electron forces water molecule can strongly interact with each other. The partial positive charge part of hydrogen allows it to get very close with other atoms oxygen atom. This intermolecular bond is called a hydrogen bond.

Hydrophobic Effect 

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Because of the high polarity characteristic and to hydrogen bond of water, it can easily dissolve other polar substances. In some situations, when we add sodium chloride in water, water can break the ionic bonds between Na and Cl, and form many other hydrogen bonds, this situation is favorable. Non-polar molecules don’t interact favorably with water.

Intramolecular Bonds – bonds that exist in any given molecules, atoms interact with one another via these bonds. 1. Non-polar Covalent- formed between 2 two atoms by the equal sharing of electrons. The electronegativity value of the two atoms is equal. 2. Polar Covalent- unequal sharing of electrons that arises due to different electronegativity values. 3. Ionic Bond- one atom with so much more electronegativity pulls away the electron completely to its side from the other atom. Intermolecular Bonds – Bonds that exist between atoms of different molecules. Considered as weaker than intermolecular bonds on a one to one basis, there are usually many intermolecular bonds at any given moment and this makes them a driving force in many biochemical processes. 1. Hydrogen Bonds (dipole-dipole) - hydrogen atom is shared by two electronegative atoms. Strongest intermolecular bond; the group that has the H- atom is called the H-bond donor, while the other group that accepts is the H-bond acceptor. 2. London-Dispersion Forces (van der Waals) - the electron density around atoms is not static but rather fluctuates with the time. The asymmetric distribution of one molecule can cause the electron density of a nearby molecules to change accordingly. The two molecules can then bond through the instantaneous dipole moments. Acids and Bases  

Determines what the pH of a solution is. pH is a factor that can influence the many different types of biological processes that take place inside our body.

“Whatever you decide to do, make sure it makes you happy.” Paulo Coelho

Biochemistry for Medical Laboratory Science 

pH can determine the final structure of a biological molecules.

Acid and Base reaction    

A hydrogen atom is exchanged between molecules. One covalent bond is broken and one is formed. Acid molecule donates H+ ion and a bond are broken Base molecule accepts H+ ion because it has a lone pair of electrons and it forms covalent bond. 𝑯𝑨 ↔ 𝑯+ + 𝑨− Acid dissociation 𝑯+ + 𝑯𝟐𝑶 ↔ 𝑯𝟐𝑶+𝑯

Base hydrogen in water exist as hydronium molecules

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The concentration of H ions is measured in terms of pH. 𝒑𝑯 = −𝒍𝒐𝒈[𝑯+]

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A pH of 7.0 means that [H+] =1.0x10-7 𝟕. 𝟎 = −𝒍𝒐𝒈[𝑯+] → 𝟕. 𝟎 = 𝒍𝒐𝒈[𝑯+] → 𝟏𝟎−𝟕 = [𝑯+]

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We can also use the pH to describe the concentration of OH- in solution 𝑯𝟐𝑶 ↔ 𝑯+ + 𝑶𝑯− [𝑯+][𝑶𝑯−] 𝑲=

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[𝑯𝟐𝑶]

At room temperature, K=1.8x10-16 and the concentration of H2O in pure water is always equal to a constant value of 55.5 [𝑯+][𝑶𝑯−] 𝟏. 𝟖𝒙𝟏𝟎−𝟏𝟔 = = 𝟏. 𝟎𝒙𝟏𝟎−𝟏𝟒 = [𝑯+][𝑶𝑯−] 𝟓𝟓. 𝟓 Therefore, at a pH=7, the concentration of hydroxide is also 1.0x10-7 𝟏. 𝟎𝒙𝟏𝟎−𝟏𝟒 = (𝟏. 𝟎𝒙𝟏𝟎−𝟕)[𝑶𝑯−] → [𝑶𝑯−] = 𝟏. 𝟎𝒙𝟏𝟎−𝟕

Amino Acid Structure and Properties  With the exception of glycine, all protein-derived amino acids have at least one stereo center (the a-carbon) and are chiral (stereoisomers) o the vast majority of a-amino acids have the L 

configuration at the a-carbon (Proline is usually D) Side-chain carbons in other amino acids designated with Greek symbols, starting at a carbon (…etc) Amino acids can be referred to by three-letter or oneletter codes.

Individual Amino Acids Group A: Nonpolar Side Chains 1. Alanine – Ala – A 2. Valine – Val – V 3. Leucine – Leu – L 4. Isoleucine – Ile – I 5. Proline – Pro – P 6. Phenylalanine – Phe – F 7. Tryptophan – Trp – W 8. Methionine – Met – M

Chapter 3. Amino Acids and Peptides Amino Acids Exist in a 3-D World Amino acid: a compound that contains both an amino group and a carboxyl group  c-Amino acid has an amino group attached to the carbon adjacent to the carboxyl group  -carbon also bound to side chain group, R  R gives identity to amino acid  Two stereoisomers of amino acids are designated L- or D-. Based on similarity to glyceraldehyde Important Structural Features: 1. 2. 3. 4. 5.

All 20 are a-amino acids For 19 of the 20, the a-amino group is primary; for proline, it is secondary With the exception of glycine, the a-carbon of each is a stereocenter Isoleucine and threonine contain a second stereocenter 3, and 1-letter codes (ex. Glycine – Gly – G)

Amino acids Ala, Val, Leu, Ile, Pro Pro Phe Trp Met

Features contain aliphatic hydrocarbon group Pro has cyclic structure hydrocarbon aromatic ring Indole ring side chain, aromatic Sulfur atom in side chain

Group B: Neutral Polar Side Chains 1. Serine – Ser – S 2. Threonine – Thr – T 3. Tyrosine – Tyr – Y 4. Cysteine – Cys – C 5. Glutamine – Gln – Q 6. Asparagine – Asn – N Amino acids Features Ser, Thr Side chain is polar hydroxyl group Tyr hydroxyl group bonded to aromatic hydrocarbon group Cys Side chain contains thiol group (-SH) Gln, Asn contain amide bonds in side chain

“Whatever you decide to do, make sure it makes you happy.” Paulo Coelho

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Biochemistry for Medical Laboratory Science

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Group C: Acidic Side Chains 1. Glutamic Acid – Glu – E 2. Aspartic Acids – Asp – D  Both have a carboxyl group in side chain  Can lose a proton, forming a carboxylate ion  These amino acids are negatively charged at neutral pH Group D: Basic Side Chains 1. Histidine – His – H 2. Lysine – Lys – K 3. Arginine – Arg – R  Side chains are positively charged at pH 7 Amino acids Features Arg side chain is a guanidino group His side chain is an imidazole group Lys side chain NH3 group is attached to an aliphatic hydrocarbon chain

Ionization of Amino Acids Remember, amino acids without charged groups on side chain exist in neutral solution as zwitterions with no net charge

Acidity: -COOH Groups The average pKa of a α-carboxyl group is 2.19, which makes them considerably stronger acids than acetic acid (pKa 4.76)  the greater acidity of the amino acid carboxyl group is due to the electron-withdrawing inductive effect of the -NH 3+ group Basicity α-NH 3+ groups: The average value of pK afor an a-NH +3 group is 9.47, compared with a value of 10.76 for a 2° alkylammonium ion Guanidine Group  The side chain of arginine is a considerably stronger base than an aliphatic amine o basicity of the guanido group is attributed to the large resonance stabilization of the protonated form relative to the neutral form Imidazole Group  The side chain imidazole group of histidine is a heterocyclic aromatic amine

Titration of Amino Acids When an amino acid is titrated, the titration curve represents the reaction of each functional group with the hydroxide ion

Uncommon Amino Acids Each derived from a common amino acid by a modification:  hydroxylysine and hydroxyproline are found only in a few connective tissues such as collagen  thyroxine is found only in the thyroid gland

Titration of Histidine with NaOH

“Whatever you decide to do, make sure it makes you happy.” Paulo Coelho

Biochemistry for Medical Laboratory Science

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Chapter 4. The Three-Dimensional Structure of Protein Primary Structure these are the sequence made up of specific amino acids.

 Ionization of Amino Acids  In amino acid, carboxyl group (-) and amino group (+) are charged at neutral pH.  In free amino acids -carboxyl, and a-amino groups have titratable protons. Some side chains do as well

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Isoelectric pH Isoelectric pH, pI: the pH at which the majority of molecules of a compound in solution have no net charge

The linear polymers of amino acids contain polarity. By contains polarity. By concentration, the beginning of any polypeptide chain is at the α-amino group and the end is at the end is at the α-carboxyl group. Each amino acid is called a residue. The polypeptide chain consists of separating units that makes up the backbone. The variable portions of the polypeptide are the side chains. The polypeptide chain has the ability to form more hydrogen bonds. a. Hydrogen-bond donor: N-H group b. Hydrogen-bond acceptor: C=O group

the pI for glycine, for example, falls midway between the pKa values for the carboxyl and amino groups

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The Peptide Bond  

Individual amino acids can be linked by forming covalent bonds. Peptide bond: the special name given to the amide bond between the a-carboxyl group of one amino acid and the a-amino group of another amino acid

Direction of Peptide Chain

Peptide bonds are resonance-stabilized, which means they have double-bond character.  The double bond nature of the peptide bond: 1. Makes the peptide bond planar. 2. Prevents any rotation about the peptide bond. Trans and Cis Configuration 

Majority of the cases, trans peptide bonds are energetically more favorable than cis because these is no bumping of atoms.

Geometry of Peptide Bond 

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the four atoms of a peptide bond and the two alpha carbons joined to it lie in a plane with bond angles of 120°about C and N to account for this geometry, a peptide bond is most accurately represented as a hybrid of two contributing structures (resonance structures) the hybrid has considerable C-N double bond character and rotation about the peptide bond is restricted

“Whatever you decide to do, make sure it makes you happy.” Paulo Coelho

Biochemistry for Medical Laboratory Science 

Secondary Structure Once the primary structure of the polypeptide is formed, is begins to twist into regular patterns that make up the secondary structure. These include the α-helix, the β-pleated sheet, the B-turn, and Ω loop. These twists are found as a result of the regular pattern of hydrogen bonds between NH and C=O groups on the polypeptide chain.

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In this arrangement, the NH and C=O groups of an amino acid on one strand form H bonds with C=O and N-H groups of the opposing amino acid on the other strand.

Parallel Beta Sheet  In the parallel beta sheet, the adjacent strands run in the same direction.  An amino acid on one strand connects to two amino acids on the opposing end via hydrogen bond.

Alpha Helix 

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The alpha-helix is a rod-like structure that contains the backbone on the inner portion of the helix and the side chains on the outer portion. Each amino acid uses its N-H group to form a hydrogen bond with the C=O of the amino acid that is four units ahead of it. The screw sense of the α-helix describes the direction in which the helix rotates with respect to its axis. A right-handed helix rotates clockwise while a left-handed helix rotates counter clockwise. The right-handed α-helix predominates because there is less steric hindrance between the side chains.

Beta Turns  The compact nature of proteins is in part due to the polypeptides ability to make sudden turns in their chain.  These turns, called B turns or reverse turns, are stabilized by hydrogen bonding. They allow polypeptide to make abrupt turns and are usually found on the surface of the protein.

Beta Pleated Sheets

Tertiary Structure The tertiary structure refers to the spatial arrangement of amino acids that are found far away from on another along the polypeptide chain Antiparallel Beta Sheet  In the antiparallel beta sheet, two linear polymers of amino acids run in opposite directions.

Hydrophobic Interactions 

Most proteins exist in an aqueous solution. We know that when non-polar molecules are placed into water, they will aggregate together because this will create a thermodynamically more stable system.

“Whatever you decide to do, make sure it makes you happy.” Paulo Coelho

Biochemistry for Medical Laboratory Science 

What does that tell us about the way in which the polypeptide will fold? 1. Those amino acids with hydrophobic side chains (i.e. valine, leucine, etc.) will tend to be found inside the protein. 2. Those amino acids that contain hydrophilic side chain (i.e. lysine, aspartate) will tend to be found on the outside of the protein,

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Fibrous proteins  These large proteins form long fibers and play a structural role. Keratin and collagen are two examples of these proteins.

Keratin  van der Waal’s Interaction The non-polar amino acids of the protein core interact with one another via their instantaneous dipole moments. Although these van der Waals forces are relatively weak on an individual base, the aggregate effect of the many non-polar amino acids creates a substantial binding effect.

α-Keratin is the major component of hair and it consists of two polypeptide subunits. These subunits consist of right-handed αhelices that intertwine to form a left-handed supercoil called the α-coiled coil.

These two subunits are held together by: 1. van der Waals forces 2. Ionic bonds 3. Disulfide bonds

Disulfide Bonds Globular Proteins – these proteins have a wide range of function and are relatively spherical in shape. Some examples include hemoglobin, insulin, DNA polymerase, etc. Hemoglobin

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In some proteins, usually the ones destined to be extracellular, the polypeptide chains can be cross-linked via disulfide bonds between cysteine residues. This cross-linked units are called cystines.

Hydrogen bonds – the polar and hydrophilic side chains on the surface interact with the water molecules via hydrogen bonds. Ionic Interactions – two oppositely charged side chain can interact via ionic bonds. For instance, Lysine can form an ionic bond with aspartate Quaternary Structure  

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Refers to the ways in which in these polypeptides interact with one another. A dimer is the simplest case of quaternary structure. In a dimer, there are two polypeptide that constitute the protein. Generally, each individual polypeptide is called subunit. These subunits are usually held together by non-covalent bonds but can also be held by covalent bonds such as disulfide bridge There are two major categories of proteins with quaternary structure globular and fibrous proteins.

Hemoglobin is a tetramer that consists of four individual subunits. Each subunit is equipped with a heme group that is capable of binding an oxygen molecule. Heme group consist of an organic component called protoporphyrin as well as an inorganic component that consist of an iron atom.

“Whatever you decide to do, make sure it makes you happy.” Paulo Coelho

Biochemistry for Medical Laboratory Science

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Carbonic Anhydrase catalyzes the conversion of non-polar carbon dioxide into carbonic acid, which dissociates into the polar bicarbonate. These enzymes speed up the reaction by a factor of one million. In the absence of this enzyme, we would not be able to dissolves CO3 in our blood.  Enzymes typically help transform one energy form into a more usable form.  Plants use a variety of enzymes to capture the energy stored in light and transform it into a more usable form. That is, into the energy store din chemical bonds (i.e. Glucose). This process is called photosynthesis. 𝑪𝑶𝟐 + 𝑯𝟐𝑶 + 𝒍𝒊𝒈𝒉𝒕 ↔ 𝑪𝟔𝑯𝟏𝟐𝑶𝟔 + 𝑶𝟐

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The iron atom lies at the center of the protoporphyrin and is boun...