CHEM-XL 153A
SUMMER 2023
UCLA EXTENSION
DR. KAREN LOHNES
GENERAL INFORMATION
• Please familiarize yourself with the policies on the
course syllabus
• Class will be structured in ~3 sessions with breaks in-between
• ~ One problem set/case study per class
• There are 2 midterms and 1 cumulative final
GENERAL INFORMATION
• Study guides distributed the week before the exam to
help you focus on the material covered on the midterm.
• A review session will be scheduled several days before the
midterm is “scheduled” to be released. I often times
release the midterm after the review session to give
students a little extra time to work on the exam.
• Individual journal projects; covering a current biochemistry
research publication. Choices are endless. Please speak
with me if you need assistance finding/choosing an article.
Biochemistry in the News
Biodegradable gel shows promise for cartilage regeneration
University of British Columbia. "Biodegradable gel shows promise for cartilage regeneration." ScienceDaily.
Journal Reference:
Linglan Fu, Lan Li, Qingyuan Bian, Bin Xue, Jing Jin, Jiayu Li, Yi Cao, Qing Jiang, Hongbin Li. Cartilage-like protein hydrogels engineered via
DOI: 10.1038/s41586-023-06037-0
TIPS FOR SUCCESS IN 153A
CHALLENGES
• A LOT OF MATERIAL!!
• Applying your knowledge!
(not just memorization!)
• Clearly communicating your
understanding.
SOLUTIONS
• MANAGE YOUR TIME WISELY
• KEEP UP WITH SLIDES/VIDEOS AND STUDY QUESTIONS
• DISCUSSION/PROBLEM SOLVING PRACTICE
• STUDY QUESTIONS (PREVIOUS EXAM QUESTIONS)
• HOW WOULD YOU TEACH THEM TO SOMEONE?
• PART I TO LEARN MATERIAL (PRACTICE)
• PART II TO TEST YOURSELF (MORE PRACTICE)
• YOUR CLASSMATES
• PRACTICE WRITING ANSWERS
• EXPLAIN REASONING TO OTHER PEOPLE
MEDICINE ASKS THE QUESTIONS…
…BIOCHEMISTRY ANSWERS THEM
WHAT YOU SHOULD ALREADY KNOW…
• GENERAL CHEMISTRY:
• EQUILIBRIUM
• THERMODYNAMICS (ΔG) (14B/20B)
• WEAK ACIDS/TITRATIONS/BUFFERING (14A/20B)
• ORGANIC CHEMISTRY:
• FUNCTIONAL GROUPS (14B/30A)
• REACTIONS (14B-D/30A-C)
What you might already know…
• Biology (high school)
– General protein structure (LS3)
– Cells/Organelles/Membranes (LS2)
– Carbohydrates/Lipids (14C/30C)
Composition, Structures, and Functions of Biomolecules
Core Learning Goal: Understand the Relationship between
Macromolecular structure and function:
– The physical basis of interactions
– Thermodynamics of macromolecular structure formation
Smaller Molecules
H2O
CO2
Macromolecules
ATP
Coenzyme A
NAD+
O2
153B
Enzymes
Core Learning Goal: Explain and apply the Principles of Enzyme Catalysis
Core Learning Goals
for Metabolism
1. Understand the meaning and
consequences of Organisms being at
Steady state (Homeostasis)
2. Understand how organisms process
Matter and perform Energy
transformations
– Free energy
– Biochemical pathway dynamics and regulation
– How pathways gain directionality and
organisms control flux
Free Online Textbook
•
•
•
•
•
•
Biochemistry Free For All, Ahern, Rajagopal, Tan (Oregon State U)
A good, accessible overview of the topics in this class
On Windows, view as PDF (downloaded to your PC)
On Mac or iPad, view as iBook (downloaded to your mac or iPad)
Reading assignments will be given as page numbers to read
Optional: if you want more info than given in lecture or BFFA, can
use Lehninger, Voet, Voet, and Pratt (both available on reserve)
Amino Acids Quiz
• Posted online; as many attempts as you would
like! In other words, practice makes perfect
and you should start the quiz as SOON AS
POSSIBLE! Your highest score is the one you
keeps. IT MUST BE COMPLETED BY THE LAST
DAY OF CLASS!!
• Identify basic components of amino acids:
• Identify an amino acid:
– Full name
– Three letter code
– 1 letter code
• List Categories
– which aa are in each category
BIOCHEMISTRY
Chemistry of Life
• What are the chemical and three-dimensional structures of
biological molecules?
• How is energy conserved and used in the cell?
• How does the cell degrade and synthesize biological molecules?
• How do biological molecules interact with each other?
• What are the mechanisms for organizing biological molecules
and coordinating their activities?
• How is genetic information stored, transmitted, and expressed?
CELL: THE UNIVERSAL BUILDING BLOCK
• LIVING ORGANISMS ARE MADE OF CELLS
• SIMPLEST LIVING ORGANISMS ARE SINGLE-CELLED
• LARGER ORGANISMS CONSIST OF MANY CELLS WITH
DIFFERENT FUNCTIONS
• NOT ALL OF THE CELLS ARE THE SAME
All cells share some common features
All cells share some common features
TABLE 1-1
Molecular Components of an E. coli Cell
Percentage of total
weight of cell
Approximate number of
different molecular species
Water
70
1
Proteins
15
3,000
DNA
1
1–4
RNA
6
>3,000
Polysaccharides
3
20
Lipids
2
50a
Monomeric subunits and intermediates
2
2,600
Inorganic ions
1
20
Nucleic acids
Source: A. C. Guo et al., Nucleic Acids Res. 41:D625, 2013.
aIf all permutations and combinations of fatty acid substituents are considered; this number is much
larger.
Cross-section of E. coli
The Cytosol Is Very Crowded
Folded proteins
Translated peptide
30 Elements Essential for Life
• Other than carbon, elements H, O, N, P, and S are also common.
• Metal ions (e.g., K+, Na+, Ca++, Mg++, Zn++, Fe++) play important
roles in metabolism.
COMMON FUNCTIONAL GROUPS OF BIOLOGICAL
MOLECULES
BIOLOGICAL MOLECULES TYPICALLY HAVE
SEVERAL FUNCTIONAL GROUPS
The ABCs of Life
Chemistry review: pH
Learning Outcomes:
Student will be able to:
• Explain the chemical basis for pH
• Define pKa
• Predict the protonation state and charge of a functional group given pKa
and pH data.
• Explain how a buffer works, and why it is important for biological systems.
BIOLOGICAL BUFFER SYSTEMS
• MAINTENANCE OF INTRACELLULAR PH IS VITAL TO ALL CELLS.
• ENZYME-CATALYZED REACTIONS HAVE OPTIMAL PH.
• SOLUBILITY OF POLAR MOLECULES DEPENDS ON H-BOND DONORS AND
ACCEPTORS.
• EQUILIBRIUM BETWEEN CO2 GAS AND DISSOLVED HCO3– DEPENDS ON PH.
• BUFFER SYSTEMS IN VIVO ARE MAINLY BASED ON:
• PHOSPHATE, CONCENTRATION IN MILLIMOLAR RANGE
• BICARBONATE, IMPORTANT FOR BLOOD PLASMA
• HISTIDINE, EFFICIENT BUFFER AT NEUTRAL PH
• BUFFER SYSTEMS IN VITRO ARE OFTEN BASED ON SULFONIC ACIDS OF
CYCLIC AMINES.
• HEPES
• PIPES
• CHES
HO
N
N
SO3Na
Biological Fluids are Heavily Buffered H CO
CO2 + H2O
2
3
so biochemical experiments must be in buffers
Bicarbonate is the
blood buffering system
H2CO3
CO2 + H2O
H+ + HCO3–
H2CO3
Oxygen binding to
hemoglobin+
H + HCO3–
H2CO3
Main importance is for proper
protein function.
Changes in pH affect the:
protonation state of amino acids, which can alter
protein structure, and therefore protein function.
Lehninger Fig 5-16
Case Study
A 78-year-old woman, found by her caregiver, is confused, hyperventilating,
and vomiting. The caregiver finds an empty bottle of aspirin tablets and
calls 9-1-1. She is brought to the hospital because of suspected aspirin
overdose. She has taken aspirin for joint pain for many years without
incident, but during the past year, she has exhibited many signs of cognitive
decline.
In the emergency department, samples of venous and arterial blood are
obtained while the airway, breathing, and circulation are evaluated. An
intravenous (IV) drip is started, and gastrointestinal decontamination
begins. After blood gas results are reported, sodium bicarbonate is
administered via the IV. What is the purpose of the sodium bicarbonate?
Disruptions to the Blood Buffer system
Physiological pH ≈ 7.4
• Acidosis: Blood pH < 7.1
– High CO2 , overproduction of acids , or the over removal of base
– Symptoms: shortness of breath, or rapid breathing, confusion,
fatigue, headache, seizures, shock
– Treatment: help improve lung function, or base supplements.
• Depend on the underlying cause
• Alkalosis: Blood pH >7.6
– Low CO2 or excessive bicarbonate, due to a number of causes.
– Symptoms: muscle pain, weakness, spasms, vomiting, coma
– Treatment: Oxygen treatment, restoring electrolyte balance.
pH Scale Is Logarithmic:
1 unit = 10-fold
TABLE 2-6
The pH Scale
[H+] (M)
pH
[OH–] (M)
pOHa
100 (1)
0
10–14
14
10–1
1
10–13
13
10–2
2
10–12
12
10–3
3
10–11
11
10–4
4
10–10
10
10–5
5
10–9
9
10–6
6
10–8
8
10–7
7
10–7
7
10–8
8
10–6
6
10–9
9
10–5
5
10–10
10
10–4
4
10–11
11
10–3
3
10–12
12
10–2
2
10–13
13
10–1
1
10–14
14
100 (1)
0
expression pOH is sometimes used to describe the basicity, or OH–
concentration, of a solution; pOH is defined by the expression pOH = -log [OH-],
which is analogous to the expression for pH. Note that in all cases, pH + pOH = 14.
aThe
Relationship of pH, [H+], and [OH-]
pH of Some Common Liquids
pKa Measures Acidity
pKa = –log Ka
BUFFERS ARE MIXTURES OF WEAK
ACIDS AND THEIR ANIONS (CONJUGATE
BASE)
• Buffers resist change in pH.
• At pH = pKa, there is a 50:50 mixture of acid and
anion forms of the compound.
• Buffering capacity of acid/anion system is greatest
at pH = pKa.
• Buffering capacity is lost when the pH differs from
pKa by more than 1 pH unit.
Chemical Properties of Water
Water Ionizes to Form H+ and OH–
H3O+ + OH-
H2O + H2O
Acid
Hydronium
Ion
Base
Hydroxide
Ion
OR:
H2O
H+ + OH-
Dissociation Constant: K =
[H+][OH-]
[H2O]
Ionization (Ion Product) of Water (Kw)
Kw = K[H2O] = [H+][OH–] = 1 x 10–14 M2
pH = -log [H+]
Neutrality
[H+] = [OH-]
[H+] = 1 x 10–7 M
[OH-] = 1 x 10-7 M
pH = 7
pOH = 7
Note: pOH = 14-pH
Ionization of a Weak Acid
H3O+ + A-
HA + H2O
Acid
Base
Conjugate Conjugate
+][A–]
[H
O
Acid
3 Base
K =
[HA][H2O]
Strength of an Acid
(Acid Dissociation Constant, Ka)
K =
[H3O+][A–]
Ka = K[H2O] =
[HA][H2O]
pKa = –log Ka
+
–
[H+][A–]
[HA]
Buffers:
Solutions that can Resist Changes in pH
Adding Strong base
NaOH
Na+ +
H+ + Cl-
HCl
Adding Strong Acid
weak acids can be buffers
HENDERSON–HASSELBALCH EQUATION:
DERIVATION
[H  ][ A - ]
Ka 
[HA]
HA 
 H+ + A-
[HA]
[H ]  K a
[A - ]
+
[HA]
- log[H ]  -logK a  log
[A-]
-
[A ]
pH  pK a  log
[HA]
Henderson-Hasselbach Equation
 [A–] 
pH = pKa + log[HA]


If you have a solution of 0.5M H2PO4- (pKa =7.2)
and 0.5M HPO42- what is the pH?
pKa is the pH of the solution when [HA] = [A-]

-
[H ][A ]
Ka 
[HA]
Henderson–Hasselbalch Equation:
Example
Henderson–Hasselbalch Equation:
Example
Titration Curves
and Buffers
1 molar equivalent of NaOH
is equal to the
total moles of buffer in solution
(both weak acid and conjugate base forms)
Figure 2-17
Equivalents of
strong base added
WEAK ACIDS HAVE DIFFERENT PKAS
Titration of a Polyprotic Acid
Figure 2-18
Titration curves
• The pKas of the ionizable groups of lysine are
2.2, 9.0 and 10.0
– Sketch a titration curve for Lysine
– Draw the primary species of Lysine in each
buffering region and equivalents points.
• Define buffering region
– How could you locate it on a titration curve?
• Define equivalence point
– How could you locate it on a titration curve?
What would be the most efficient way to increase
the total buffering capacity of a 1 M acetic
acid/acetate (pKa 4.76) solution, if its initial pH is 4.9?
A.
B.
C.
D.
Add more acetate.
Add more acetic acid.
Add water.
Add both acetate and acetic acid.
Group Activity
In Breakout rooms, I will now have you work on a
simulation. You are welcome to continue this at
home;
https://edu.rsc.org/resources/titration-screenexperiment/2077.article
Proceed to the website above and begin the titration
screen experiment.
For Extra credit in the class, you can download the
pdf of the lab notebook from the simulation or
photograph the completion page after each level.