Upload
shane-weinberg
View
217
Download
0
Embed Size (px)
Citation preview
8/3/2019 W1 - Intro & Amino Acids
1/40
8/3/2019 W1 - Intro & Amino Acids
2/40
2
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
8/3/2019 W1 - Intro & Amino Acids
3/40
3
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.
8/3/2019 W1 - Intro & Amino Acids
4/40
4
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.
8/3/2019 W1 - Intro & Amino Acids
5/40
5
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.
8/3/2019 W1 - Intro & Amino Acids
6/40
6
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).
8/3/2019 W1 - Intro & Amino Acids
7/40
7
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.
8/3/2019 W1 - Intro & Amino Acids
8/40
8
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
8/3/2019 W1 - Intro & Amino Acids
9/40
9
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)
8/3/2019 W1 - Intro & Amino Acids
10/40
10
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.
8/3/2019 W1 - Intro & Amino Acids
11/40
11
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
8/3/2019 W1 - Intro & Amino Acids
12/40
8/3/2019 W1 - Intro & Amino Acids
13/40
13
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.
8/3/2019 W1 - Intro & Amino Acids
14/40
14
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
8/3/2019 W1 - Intro & Amino Acids
15/40
15
Course format Weeks 9-13
Metabolism of other key biomoleculesNitrogen and amino acid metabolismNucleotide metabolismFats and fatty acid metabolism
Vitamins and coenzymes
8/3/2019 W1 - Intro & Amino Acids
16/40
16
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.
8/3/2019 W1 - Intro & Amino Acids
17/40
17
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.
8/3/2019 W1 - Intro & Amino Acids
18/40
18
Amino acid structure
Solid orgas phase
In aqueous solutionat pH 7
8/3/2019 W1 - Intro & Amino Acids
19/40
19
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.
8/3/2019 W1 - Intro & Amino Acids
20/40
20
Class I amino acids: Nonpolar (hydrophobic) - I
8/3/2019 W1 - Intro & Amino Acids
21/40
21
Class I amino acids: Nonpolar (hydrophobic) - II
8/3/2019 W1 - Intro & Amino Acids
22/40
22
Class II amino acids: Polar, neutral - I
8/3/2019 W1 - Intro & Amino Acids
23/40
23
Class II amino acids: Polar, neutral - II
8/3/2019 W1 - Intro & Amino Acids
24/40
24
Class III amino acids: Acidic
In solution, these amino acids are known as by the names oftheir ionic forms: aspartate and glutamate, respectively.
8/3/2019 W1 - Intro & Amino Acids
25/40
25
Class IV amino acids: Basic
8/3/2019 W1 - Intro & Amino Acids
26/40
26
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
8/3/2019 W1 - Intro & Amino Acids
27/40
27
Structures of some rare amino acids
Collagen
Blood-clottingproteins
Bacterio-rhodopsin
corn
8/3/2019 W1 - Intro & Amino Acids
28/40
28
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.
8/3/2019 W1 - Intro & Amino Acids
29/40
29
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
8/3/2019 W1 - Intro & Amino Acids
30/40
30
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
8/3/2019 W1 - Intro & Amino Acids
31/40
31
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.
8/3/2019 W1 - Intro & Amino Acids
32/40
32
Most amino acids have two ionizable groups!
Acidic Neutral BasicpI
1. 2.
8/3/2019 W1 - Intro & Amino Acids
33/40
33
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
8/3/2019 W1 - Intro & Amino Acids
34/40
34
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
8/3/2019 W1 - Intro & Amino Acids
35/40
35
Ionic forms of an amino acid as pH changes
8/3/2019 W1 - Intro & Amino Acids
36/40
36
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
8/3/2019 W1 - Intro & Amino Acids
37/40
37
p K values
8/3/2019 W1 - Intro & Amino Acids
38/40
38
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
8/3/2019 W1 - Intro & Amino Acids
39/40
39
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?
8/3/2019 W1 - Intro & Amino Acids
40/40
40
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!