W1 - Intro & Amino Acids

8/3/2019 W1 - Intro & Amino Acids

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Biochemistry

Course website on Moodle (you need to login first):ilearn.mq.edu.au check regularly for announcementsCheck your Macquarie email we send you unit informationCheck www.timetables.mq.edu.au lecture room numbers maychange from next week.

Lecture 1:

Overview of courseLab and tutorial classesAssessmentText books

Assumed knowledgeAmino acids (also theory for Prac 1)

pH and its importance in biological systems


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Checking your Macquarie email We will contact you only via your MQ email :

this is the only email provided to us byeStudent

If you do not see this regularly, please add

your favourite email address here! This is specially important for any last minute

changes of rooms, tutor/demonstrator info,

exam date, etc.


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Lab format and expectations Essential items to bring to lab sessions

Lab coat and safety glassesPlease wear covered shoes (thongs/sandals: NO)

Practical Notes & Laboratory BookBuy from Co-Op BookshopThis is also your Lab notebook for evaluation.

Usually in two separate partsso expect to be there the full 4 hours

Read lab notes before the class there will be prac quizat each lab (2 marks/15 marks).

Absence from lab must be made up during othersessions if available, or backed up by a medicalcertificate to avoid getting a zero mark.


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Lab format and expectations Lab results must be written up in the practical

notes and lab. book BEFORE leaving the lab. Record all results and paste all graphs/spectra/

printouts in the space(s) indicated. The finished account of ALL the experiments

must be submitted to the lab , for grading as setout in the prac notes:

Pracs 1 & 2: 29 Mar, 30 Apr or 2 Apr afterT3/P3

Pracs 3-5: 31 May, 1 Jun or 4 Jun at thePrac test.


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Tutorial format and expectations Tutorials (2 hours) complement lectures and the practicals.

Mathematical problems and questionshow to complete your practicals will be covered during the tutorial class

Print the Tutorials notes from Moodle . Answer Part A before your scheduled tutorial session . You may have to

Work these out on the board orProvide the answers or the steps.

Your tutor will discuss Part A and provide clues as to how to solvePart B questions, a few of which may be completed in the class.

Additional marks (1 mark per tutorial) will be given to students whohave completed Part A problems and can explain the solutions to the

class.These marks are in addition to your prac book and prac test marks.

Absence from tutorial may must be made up during other sessions ifavailable (special consideration form), or backed up by a medicalcertificate (no bonus mark applicable).


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Course Assessment

5%Laboratory test (problems on practicals)

15%Mid semester test (multiple choice questions)

5% Tutorials (bonus marks: 1% x 5 tutorials)

60%Final exam

15%Completed Practical Notes & Laboratory Book(3% x 5 pracs)

5%Protein structure assignment (problem basedquestions)

Successful completion of each assessmenttask is required for passing the unit.


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Key Dates

Sem 1Exams

12/13

9

5/6

5

Week(s)

CBMS223 Exam (usually early!)(check exam timetables by mid-April)

June 12onwards

60%

Practical test during lab session Submit the practical notes and lab.

book to the lab. for grading P3-P5

May 31 (Thu),1 Jun (Fri) or4 Jun (Mon)

5% 9%

Mid-semester test during the scheduledlecture hour (C5C T1 + other rooms)

May 8 (Tue)15%

Submit the practical notes and lab. bookto the lab. for grading P1 and P2 upto5.55 pm, after scheduled P3/T3

29 Mar (Thu),30 Mar (Fri) or2 Apr (Mon)

6%

Assignment due on MoodleMarch 26 (Mon)5%

What is scheduled?Date(s)Weightage


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Textbooks BIOCHEMISTRY 4th Edition: Garret and Grisham:

Thomson Learning 2009 (recommended)

BIOCHEMISTRY 3rd Edition: Garret and Grisham:Thomson Learning 2007 BIOCHEMISTRY 3 rd or 4 th

Edition: Voet and Voet: Wiley Publishing 2003/2004 BIOCHEMISTRY 4th Edition: Zubay: WC Brown

Publishing 1997 (ONLY available second hand)

BIOCHEMISTRY Explained 1st Edition: Thomas Millar: Wiley Publishing 1999 (remedial text)


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Textbook for PG students lackingOrganic Chemistry background Organic Chemistry 9th Edition: T.W.

Graham Solomons & Craig B. Fryhle,Wiley, 2009 (recommended)

Tips on doing well Workload in the unit is fairly heavy. Youll need

to work steadily, because new material is basedon earlier material.

You will not be able to leave mastering thecontent until the last few weeks.


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Assumed Knowledge Chemistry

mole concept

carbon chemistrychirality - mirror image compoundspH and pKaproperties of functional groups

chemical equilibriumelements of thermodynamics

Biologydifference between a prokaryote and a eukaryote

ultrastructure i.e. organelles, etc.DNA to RNA to protein


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Chirality or handedness

Chiral compounds: non-superimposable mirror imageforms also known as enantiomers. This property ischaracterised by optical activity.

most biological molecules have mirror image forms and only oneof these forms usually occurs in nature.


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Course format Weeks 1-4

Properties of amino acids and proteins

importance of these properties in terms of protein structure (assignment)proteins as catalysts: enzymes

Weeks 4-9Metabolic pathways

energy metabolismanabolic and catabolic pathwayscompartmentalization of these pathwaysmetabolism of sugars (upto here for mid-sem test)making ATP: electron transport and oxidative phosphorylation


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Course format Weeks 9-13

Metabolism of other key biomoleculesNitrogen and amino acid metabolismNucleotide metabolismFats and fatty acid metabolism

Vitamins and coenzymes


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Water: the medium of life Water is essential for all forms of life. Every organism is 70-90% water! Normal metabolic activity requires min. 65%

water! Water is an excellent solvent. Water causes ionization of polar molecules,

critical for the function of:amino acids and proteins

nucleotides and nucleic acidseven phospholipids and membranes.


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Amino acid structure Amino acids are important because they are the

building blocks of proteins They both an amino group and an acidic

carboxyl group

All amino acids have the general structure (insolution near neutral pH)NH3+(CHR) CO 2-

This is called a zwitterion : carrying both apositive and a negative charge at the same time.


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Amino acid structure

Solid orgas phase

In aqueous solutionat pH 7


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Amino acids found in proteins 20 common amino acids with different R groups are

found in proteins.

Four main classes with different types of R groupshave been identified:

Non-polar amino acids (8)Polar, uncharged amino acids (7)Acidic amino acids (2)Basic amino acids (3)

Each amino acid has a one letter code and a three

letter code that are helpful when working withproteins that can contain hundreds of amino acids.


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Class I amino acids: Nonpolar (hydrophobic) - I


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Class I amino acids: Nonpolar (hydrophobic) - II


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Class II amino acids: Polar, neutral - I


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Class II amino acids: Polar, neutral - II


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Class III amino acids: Acidic

In solution, these amino acids are known as by the names oftheir ionic forms: aspartate and glutamate, respectively.


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Class IV amino acids: Basic


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Uncommon amino acids occur inproteins

Hydroxylysine, hydroxyproline - collagen Carboxyglutamate - blood-clotting proteins Pyroglutamate in bacteriorhodopsin Phosphorylated amino acids a signaling

device

Aminoadipic acid is found in proteins isolatedfrom corn


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Structures of some rare amino acids

Collagen

Blood-clottingproteins

Bacterio-rhodopsin

corn


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Acid-base properties of amino acidspH: a measure of the acidity of a solution

H2O H + + OH -

pH = -log 10 [H+] for pure water, [H +] and [OH -] equal 10 -7 M

For pure water, [H +] = [OH -] = 1 x 10 -7 M & pH = 7

Importance of pH pH determines the viability of biochemical reactions It affects ionization and hence the charge of molecules that have

acidic or basic groups (groups than can gain or lose protons).This can have significant effects on the biological, chemical andphysical properties of these molecules.

pH can thus have a significant effect on the properties of aminoacids and hence proteins.


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The most common equilibrium that biochemistsencounter is that of weak acids and bases, both ofwhich can affect the pH

HA H+ + A-

Strong acids dissociate completely in solution butweak acids only partially dissociate and theequilibrium constant for this reaction is called the K a

Ka = [H+

] [A-

][HA]

Amino acids are weak acids/bases

- dissociation based on pH of media


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pH of amino acids (weak acids/bases) fromHenderson-Hasselbalch equation

Taking logarithms of this equation gives us-log [H +] = -log K a + log ([A -]/[HA])

or

pH = pK a + log (base/acid) When there is an equal amount of base andacid then pH = pK a

also known as half-titration pointtitration is an effective way to determine the pK avalues


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pI pI is defined as the pH at which there is no NET

charge on the amino acid (also for a protein orpeptide).

For simple systems such as amino acids and smallpeptides, it can be calculated easily.

For more complex systems such as proteins, it canbe measured experimentally.

If the molecular structure is known, pI can bemeasured by

completely protonating the molecule,titrating the number of positive charge equivalents and thenmeasuring the pH.


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Most amino acids have two ionizable groups!

Acidic Neutral BasicpI

1. 2.


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At equilibrium Cationic and zwitterionic forms have equal concentration Equilibrium constant is called K 1: in pH scale, this is p K 1 Charge is +0.5 (average of the charges of the two ionic species)

Following the ionization of an amino acid:

1. Acidic to neutral pH

1.

Start: low pH COOH group uncharged

(weak acid!) Amino group is protonated: +1charge

With increasing pH (i.e. lessacidic or more basic solution):

COOH starts to lose its proton Equilibrium is getting

establishedAs pH increases: Zwitterion predominates


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At equilibrium Zwitterionic and anionic forms have equal concentration Equilibrium constant is called K 2 : in pH scale, this is p K 2 Charge is -0.5 (average of the charges of the two ionic species)

Following the ionization of an amino acid:

2. Neutral pH to basic pH

2.

From: neutral pH Both groups are charged

Molecule is essentially neutral pH at zero charge = pIWith increasing pH (i.e. less acidic

or more basic solution):

Amino group starts losing itsproton and thus, its charge A second equilibrium is getting

establishedAs pH increases: Negative charge predominates


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Ionic forms of an amino acid as pH changes


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pK values of amino acids are uniqueand can identify them! Backbone or -COOH group (p K 1) = ~2 Backbone or -NH2 group (p K 2 ) = ~9 pI is also unique for each amino acid

The pI of a protein, which is made up of aminoacids is thus dependent on its amino acidcomposition!

pI is used to separate different proteins

Some amino acids also have additionalionizable groups in their sidechains


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p K values


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So why the pK value of R group? Two amino acids have extra COOH groups in their

sidechains (i.e. R groups)The extra COOH is also a weak acid and can lose its proton!

Aspartic Acid, Asp, D: p K R

= 3.9 Glutamic Acid, Glu, E: p K R = 4.3

M li ti id h i ith


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More complications: sidechains with

amino groups!

Histidine, His, H: pK a = 6.0 Lysine, Lys, K: pK a = 10.5 Arginine, Arg, R: p K R

(guanidino group) = 12.5So, which amino acid is the

strongest base?


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Summary Revision

Mole concept

n = wt / Mwtn = c v

Chiral molecules: non-superimposable mirrorimage forms of compounds (handedness)

Amino acidsAcid-base properties of amino acids

Henderson-Hasselbalch equation

Introduction to pH and pIpK of all amino acidspK R for some!

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W1 - Intro & Amino Acids

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