Vous êtes sur la page 1sur 30

BCHS 3304, 20104

General Biochemistry I
TuTh 11:30-1:00, SW102
James M. Briggs, Ph.D. Purdue University.
C
Computer modeling;
d li computer-aided
id d drug
d design;
d i
Protein structure/function
http://adrik.bchs.uh.edu/bchs3304
p ((course home ppage)
g )
Office Room 402D Houston Science Center
Office hours M:10:30-11:30, Tu:10:30-11:30 or by appointment
Office phone: 713-743-8366 E-mail jbriggs@uh
jbriggs@uh.edu
edu
E-mail is the best way to reach me!
3 Exams and a Comprehensive Final (See Syllabus)
100 90 A;
100-90 A 8989.9-89.0
9 89 0 A-;
A 88.9-88.0
88 9 88 0 B+;
B 87.9-80
87 9 80 B;
B 79.9-79.0
79 9 79 0 B-;
B 78.9-
78 9
78.0 C+; 77.9-70 C; 69.9-69.0 C-; 68.9-68.0 D+; 67.9-60 D; and < 60 F.
Weekly Homework - to be COMPLETED but not turned in!!!
Good performance on the Final Exam can reduce poorer 1
performance on ONE earlier exam
Letters of Recommendation

•Think about this NOW! From whom will you ask for letters in the
future?
•Asking for a letter from an instructor who does not know you hurts your
application!
•Make sure that your future potential letter writers know you,
you inside
AND outside of class.
•Discuss your future career plans with your potential letter writers.
I i
•Investigate the
h review
i criteria
i i forf applications
li i andd make
k sure that
h your
resume and your letter writers have information about you in those
categories,
g for example:
p
•Leadership
•Communication (written and verbal)
Professionalism
•Professionalism
•Ability to adapt
2
•I will NOT write a letter for a student whom I do not know.
The Exams are based on the book, class notes, and homework.

Those who do the homework honestly and persistently will earn the
better grades.

I encourage group homework and study sections (groups of 3-4 are the
best size). But each person in a group must pull their own weight.
C
Copying
i theh homework
h k andd not fully
f ll participating
i i i cheats
h yourself.
lf

You will need to know the material! You can not just be familiar with it.
it
You will need to study about 2-3 hours a day!
This is an upper-level PROFESSIONAL COURSE
Virtually all figures used in these class notes were taken from the
i t t CD provided
instructor id d with
ith the
th class
l textbook
t tb k (Voet,
(V t Voet,
V t andd Pratt).
P tt)
3
I am not, in any way, taking credit for having created these figures!
Scantron answer keys to the exams may be placed on the course web
site.
site
Worked exams may be placed in glass cabinets in the hallway on the way
to my office.
S
Scores ffor th
the exams will
ill be
b placed
l d on the
th course webb site.
it
Please take advantage of the tutoring and review services in the Dept. of
Biology and Biochemistry - visit the Advising Office located in the Old
Science Building, Room, 116.
Iw
will TRY,, bu
but do not
o promise,
p o se, too have
ve thee course
cou se notes
o es available
v b e on o thee
class web site by 5:00 in the afternoon the day before the lecture is given.
You MUST attend everyy lecture! Chronic lack of attendance will
severely impact your course grade.
You MUST take ALL exams. NO exams are dropped. There are NO
makeups. There is NO extra credit.
4
Chapter 1: Intro to the Chemistry of Life
Biochemistry is the study of the chemistry of life.
Biochemistryy is an interdisciplinary
p y science overlapping
pp g with chemistry,
y,
cell biology, genetics, immunology, microbiology, pharmacology, and
physiology.
Main issues of Biochemistry

1. What are the chemical and three-dimensional structures of biological


molecules?
l l ?
2. How do biological molecules interact with each other?
y
3. How does the cell synthesize and degrade
g biological
g molecules?
4. How is energy conserved and used by the cell?
5. What are the mechanisms for organizing biological molecules and
the coordinating of their activities?
6. How is genetic information stored, transmitted, and expressed? 5
Living organisms operate within the same physical laws that apply to
physics and chemistry:

•Conservation of mass, energy


•Laws of thermodynamics
•Laws of chemical kinetics
•Principles of chemical reactions

These physical laws describe several axioms that make up the Molecular
Logic of Life. These axioms define

•Energy converted to work


•Catalytic chemical transformations
•Assembly of molecules with great complexity from simple subunits.
•Complex molecules combine to form supra molecular components,
organelles and finally assemble into a cell.
•Store and pass on instructions for the assembly of all future generations
6
from simple non-living precursors
Prebiotic World
Living matter consists of a small number
of elements
Elemental composition of the human
body (97%)
•Trace: B,, F,, Si,, V,, Cr,, Mn,, Fe,, Co,, Cu,,
Zn, Se, Mo, Sn, I

•Most organisms are ca.


ca 70% water

•The earth is ca. 4.6 billion years old.

•Earliest known fossil is ca. 3.5 billion


yyears old ((filamentous bacterium).
)

7
Prebiotic World
Early atmosphere probably consisted of H2O, O N2, CO2,
with small amounts of CH4, NH3, SO2, and H2
Sparking of a mixture of CH4, NH3, H2O, and H2 for 1
weekk yielded
i ld d (Stanley
(St l Miller
Mill andd Harold
H ld Urey)
U )
•Acids (formic, glycolic, lactic, propionic, acetic,
succinic, aspartic, glutamic, etc.)
•Amino acids (glycine, alanine, aspartic, glutamic)
•Others (urea, sarcosine, N-methyl-alanine, N-methyl-
urea etc.)
urea, etc )

The above experiments were meant to mimic the effects


off lightening
li ht i on the
th prebiotic
bi ti atmosphere.
t h
This has been challenged by some scientists who propose
that early biological molecules were created in the dark
underwater at hydrothermal vents, where heat stable
bacteria live today. 8
Key Organic Functional Groups

• Organic Functional Groups - you must know these


• They will show up time and time again in Biochemistry
• Note that the charge state of some of the groups above will
differ in different environments/conditions (e.g., COOH9 and
COO-; NH3 and NH4+)
Key Organic Functional Groups. cont

• Organic Functional Groups - you must know these


• They will show up time and time again in Biochemistry
• Note that the charge state of some of the groups above will
differ in different environments/conditions (e.g., COOH
10
and
COO-; NH3 and NH4+)
Chemical Evolution
• Many enzymes catalyze hydrolysis
and condensation reactions
• In prebiotic times, clay may have
provided the environment for
catalytic reactions (zeolites are
used as chemical catalytic
environments today)
• In particular, the condensation
reaction has been very useful
throughout evolution for increasing
biological complexity
• Of course, the hydrolysis carries
out the
h reverse reaction,
i leading
l di to
a loss in biological complexity
• Complementarity
p y allows for ((self)) replication
p
through templating (e.g., COO-…NH4+)
11
• Base complementarity in DNA
Cellular Architecture

• Vesicles (fluid-filled sacs) are thought to be the precursors to cells


• These entities would have had the abilityy to shield self-replicating
p g
chemical reactions and catalyzed reactions so that they were taking
place in a sheltered environment, giving them a competitive
g
advantage
• This process is called compartmentation
• This compartment then has the opportunity to further evolve in
order to enhance its advantage.
advantage
– It may do so by hoarding nutrients and ions
• A typical animal cell contains as many as 100,000 different types of
molecules
• A common bacterium, E. coli, contains millions of molecules,
p g 3000-6000 different compounds.
representing p

12
E. coli

13
Prokaryotes and Eukaryotes

•All
All modern organisms are based on the same morphological unit,
unit the
cell

•Prokaryotes
P k t – lack
l k a nucleus
l (e.g.,
( b t i archaea)
bacteria, h )
•Eukaryotes – membrane enclosed nucleus encapsulating their DNA,
animals, plants, fungi

•Viruses are not cells and are not living since they lack the apparatus to
reproduce outside of their host cells

•Prokaryotes range in size from 1 to 10 M


•Eukaryotes
E k t range ini size
i from
f t 100 M
10 to M andd thus
th have
h a thousand
th d
to a million times as much volume as a prokaryotic cell 14
15
Representative Prokaryotes
Eukaryotic Cell

16
Eukaryotic Cell

17
Taxonomy:
biological
g
classification

Phylogeny:
evolutionary
18
history
How do organisms evolve?
1. Evolution is not directed toward a particular goal.
It proceeds via random changes. Organisms that are better suited
to their environment flourish.

2. Evolution requires
q some built-in sloppiness.
pp
This is the source of the “random changes”. It allows for
adjustment to unforeseen changes in the environment.

3. Evolution is constrained by its past.


The new arises from the old.

4. Evolution is ongoing.
Not always
y toward increasingg complexity.
p y

19
Physical Units of Space, Time, and Energy.
LENGTH
Y mustt know
You k thi andd be
this b comfortable
f t bl using
i them.
th

Length is very important!!


•C - C bond is 1.54 Å
•Hemoglobin 65Å
•Ribosomes
Ribosomes 300Å
•Viruses 100 - 1000Å
•Prokaryotic cells 1 - 10 m or 1 - 10 x 104 Å (10,000 –
100 000 Å)
100,000
•Eukaryotic cells 10 - 100 m or 10 - 100 x 104 Å (100,000 –
1,000,000 Å)

1Å 10Å 100Å 1000Å 104Å 105Å


10-10m 10-9m(1nm) 10-8m 10-7m 10-6m 10-5m
20
Limit of a light microscope = 2000 Å or 0.2 m
Life is in constant flux
Substrates  Products 10-3 sec - milli sec (ms)
U i di off DNA 10-66 sec - micro
Unwinding i sec (s)
( )

10-15 s 10-12 s 10-9 s 10-8 s 10-6 s 10-3 s 10 s 103s


femto pico nano micro milli sec

•femto, fs excitation of chlorophyll


•pico,
i ps charge
h separation
ti ini photosynthesis
h t th i
•nano, ns hinge protein action
•10-8 (10 ns) fluorescence lifetime
•micro, s DNA unwind
•milli, ms enzymatic reactions
103 s
•10 generation of bacteria
•2.3 x 109 s average human life span
21
Energy
Ultimate source of energy
gy is the SUN
E = h 57 kcal/mol of photons green light
or
238 k kJ/mol
238.k kJ/ l
1 kcal = 4.184 kJoules
0.239 kcal = 1 kJ
You must know how to convert between the two. (We will be using
(kJ/mol))
ATP energy carrier
carrier, for hydrolysis to ADP + Pi
= -7.3 kcal/mol or -30.5 kJ/mol
While vibrational energy infrared = 0.6 kcal/mol or 2.5 kJ/mol

C - C bond = 83 kcal/mol or 348 kJ/mol


the framework of a carbon skeleton is thermallyy stable
but
22
non-covalent bonds are only a few kcal/mol
Thermodynamics – First Law
• The First Law of Thermodynamics
 Energy (U) is conserved – it can be neither created nor
d t
destroyedd
• Most biological processes take place under constant
pressure (P) and variable volume (V)
• The Enthalpy (H) of a process is defined as follows:
 H = U + PV
 H = U + PV (under constant pressure, the volume
will change – like the expansion of a gas)
• The
Th volume
l changes
h in
i biological
bi l i l processes are
practically negligible so
 H ≈ U
23
Thermodynamics – Second Law
• The Second Law of Thermodynamics
– Spontaneous processes are characterized by the conversion of
order to disorder
• A process is spontaneous if it can occur without the input of
additional energy from the outside of the system
• Entropy (S) is the measure of the degree of disorder in a system

• In the system to the right, the first


system has higher order than the
second.
• The second is more disordered.
• The entropy increases on going from
the first to the second system.
• The
Th change
h in
i entropy
t is
i measuredd
by: S = H/T (T=temperature) 24
Gibbs Free Energy (G)
• The Free Energy (G) change of a spontaneous
process is negative
• Free energy is defined as follows:G = H – TS
• Normally,
N ll we are interested
i t t d in
i the
th change
h in
i free
f
energy so the following equation is more useful:
G = H – TS
• For a spontaneous process, G < 0.
• If the G is < 0,
0 the process is called exergonic
• If the G is > 0, the process is called endergonic
• If the G is = 0,
0 the process is called equilibrium
eq ilibri m
25
26
Equilibrium Constants
• Relationships between concentration and free energy
• G0 = -RT ln Keq, where G0 is the free energy change in
the standard state,
state R is the gas constant 8.3145
8 3145 J/K-mol

aA  bB  cC  dD
 [C ]c [ D ]d 
G  G 0  RT ln 
 [ A]a [ B ]b 
At equilibrium, G=0 so G0 = -RT ln Keq

[C ]ceq [ D]eq
d
K eq   e  G 0 / RT
[ A]eq
a [ B ]b
eq 27
Each step of a biochemical process is not
required
i d to be
b exergonic.
i
As long as the overall pathway is exergonic,
it will operate in a forward manner.

Thus, the free energy of ATP hydrolysis, a


highly exergonic reaction, is harnessed to
drive many otherwise endergonic biological
processes to completion!!
28
Standard state conventions in biochemistry
• The activity of pure water is assigned a
value
l off 1 even though
h h it
i concentration
i isi
really 55.5 M (M = Molar). Therefore, the
terms for
f the
h concentration
i off water, [H2O],O]
in equilibrium expressions can be ignored.
• The standard pH is 7.0 (10-7 M)
• Temperature
p is 25oC
• Pressure is 1 atm (atmosphere)
• Standard concentration is 1M
29
For next time

• Work assigned
g Chapter
p 1 pproblems.
– Book: 1, 5-14
Companion: 14, 16a, 16c
• We will work some of them next time in class
• Read Chapter 2 - We will cover most of it next
time in class.

30

Vous aimerez peut-être aussi