Transcript Chem 400 Biochemistry I

What is biochemistry?
Advanced organic chemistry?
Cell biology?
Molecular biology?
The most fun and interesting subject in
science (personal bias)?
The study of life on a molecular level.
Or, the formal term of bios = life
meaning biochemistry is the science
concerned with the chemistry of
various molecules that occurs in living
cells
•Biochemistry encompasses large areas of cell biology, molecular biology,
and molecular genetics
•Biochemistry is essential to all of the life sciences (biomedical and
plant sciences) All advanced degrees require that biochemistry is one of
the first courses
•This class will be taught not - as an advanced organic but as an
encompassing science that should help tie several of your classes
together
Biochemistry I
We will be studying the four macro-biomolecules proteins, DNA/RNA, lipids and carbohydrates, and
whenever possible putting them into biomedical
context
What are YOUR expectations of this class?
– Ask yourself why you need this course
What are my expectations of this class?
– Work hard but have fun with the semester/year
– Push you intellectually and make you think about
how life works around you - like a mechanic
understands an engine, you will understand how a
cell/tissue/organ/body works
What is Critical
Thinking?
What is Critical Thinking?
The critical habit of thought, if usual in society, will
pervade all its mores, because it is a way of taking up the
problems of life. Men educated in it cannot be stampeded
by stump orators ... They are slow to believe. They can
hold things as possible or probable in all degrees,
without certainty and without pain. They can wait for
evidence and weigh evidence, uninfluenced by the
emphasis or confidence with which assertions are made
on one side or the other. They can resist appeals to their
dearest prejudices and all kinds of cajolery. Education in
the critical faculty is the only education of which it can be
truly said that it makes good citizens. William Graham
Sumner, Folkways, 1906
What is Critical Thinking?
Critical thinking is the intellectually disciplined
process of actively and skillfully
conceptualizing, applying, analyzing,
synthesizing, and/or evaluating information
gathered from, or generated by, observation,
experience, reflection, reasoning, or
communication, as a guide to belief and action.
In its exemplary form, it is based on universal
intellectual values that transcend subject matter
divisions: clarity, accuracy, precision,
consistency, relevance, sound evidence, good
reasons, depth, breadth, and fairness
What is Critical Thinking?
My down and dirty version:
Thinking about what and why rather than just
accepting some fact or comment.
Asking questions to answer “does this make
sense”? And answering that based on fact not
“feelings or blind faith”.
Study Tips
– Do not cram, too much material and topics build on the
next from the first day.
– Read the study tips on my homepage
– Write an outline, ask yourself what does all of this mean
in a few words
Test Tip
– The tests are multiple guess, short answer and essay
– DO NOT read the question and then look for and answer.
Think of the answer and then find if. Looking for a likely
answer will nearly always cause problems
This semester:
pH, buffers and amino acids
Protein structure and function
Enzymes and kinetics
Carbohydrates
Lipids and fats
Metabolism
– Biochemical source of
diseases
– Real life and interesting
examples
Next semester: More metabolism,
Diabetes, Cancer,
Nutrition, Signal Transduction
… and now the fun begins...
Functional Groups - One of the reasons why organic chemistry is
a prerequisite for the class
Just for review – know and be able to draw each of the
structures in fig 1-2..
Disulfide
Also know…
Thioester
Anhydride (2 carboxylic acids)
Guanidino
Imidizole
Disulfide
Also know…
R1-S-S-R2
Thioester
Anhydride (2 carboxylic acids)
Guanidino
Imidizole
Also know…
Disulfide
R1-S-S-R2
Thioester
R1-C-S-R2
=
O
Anhydride (2 carboxylic acids)
Guanidino
Imidizole
Also know…
Disulfide
R1-S-S-R2
Thioester
R1-C-S-R2
=
O
Anhydride (2 carboxylic acids)
R1-C-O-C-R2
Imidizole
=
=
Guanidino
O
O
Also know…
Disulfide
R1-S-S-R2
Thioester
R1-C-S-R2
=
O
Anhydride (2 carboxylic acids)
R1-C-O-C-R2
HN=C
NH2
Imidizole
=
=
R
NH
- - -
Guanidino
O
O
Also know…
Disulfide
R1-S-S-R2
Thioester
R1-C-S-R2
=
O
Anhydride (2 carboxylic acids)
R1-C-O-C-R2
HN=C
NH2
Imidizole
=
=
R
NH
- - -
Guanidino
O
O
R -C=CH
N
HN
C
H
Prokaryotic Cellular Organization
Eukaryotic Cellular Organization
The Plasma Membrane
Composed of a
phospholipid bilayer
and proteins.
The phospholipid sets up
the bilayer structure
Phospholipids have
hydrophilic heads and
fatty acid tails.
The plasma membrane is
fluid--that is proteins
move in a fluid lipid
background
The Plasma Membrane
Phospholipids:
Two fatty acids covalently linked
to a glycerol, which is linked to
a phosphate.
All attached to a “head group”,
such as choline, an amino acid.
Head group POLAR – so
hydrophilic (loves water)
Tail is non-polar -hydrophobic
The tail varies in length from 14 to
28 carbons.
The Plasma Membrane
Proteins:
Integral proteins:
– Embedded in lipid bylayer – serve as “ion pumps”
– They pump ions across the membrane against their
concentration gradient
Peripheral proteins:
– Bound to membrane surface by ionic bonds.
– Interact with components of the cytoskeleton
Anchored proteins:
– Bound to surface via lipid molecules
The nucleus
Contains almost all of the genetic
material
What it contains is called the nuclear
genome – this varies greatly between
plant species.
Surrounded by nuclear envelope- double
membrane - same as the plasma
membrane.
The nuclear pores allow for the passage
of macromolecules and ribosomal
subunits in and out of the nucleus.
The Endoplasmic reticulum
Connected to the nuclear envelope
3D-network of continuous tubules that
course through the cytoplasm.
Rough ER: Synthesize, process, and sort
proteins targeted to membranes, vacuoles,
or the secretory pathway.
Smooth ER: Synthesize lipids and oils.
Also:
– Acts as an anchor points for actin
filaments
– Controls cytosolic concentrations of
calcium ions
The Endoplasmic reticulum
Proteins are made in the Rough
ER lumen by an attached
ribosome.
Protein detaches from the
ribosome
The ER folds in on itself to form a
transport vesicle
This transport vesicle “buds off”
and moves to the cytoplasm
Either:
– Fuses with plasma
membrane
– Fuses with Golgi Apparatus
The Golgi Network
Proteins or lipids made in the ER
contained in transport vesicles fuse
with the Golgi.
The Golgi modifies proteins and lipids
from the ER, sorts them and
packages them into transport vesicles.
This transport vesicle “buds off” and
moves to the cytoplasm.
Fuse with plasma membrane.
The Golgi Network
The Mitochondria
Contain their own DNA and proteinsynthesizing machinery
– Ribosomes, transfer RNAs,
nucleotides.
– Thought to have evolved from
endosymbiotic bacteria.
– Divide by fusion
– The DNA is in the form of
circular chromosomes, like
bacteria
– DNA replication is independent
from DNA replication in the
nucleus
The Mitochondria
Site of Cellular Respiration
This process requires oxygen.
Composed of three stages:
– Glycolysis--glucose splitting,
occurs in the cell. Glucose is
converted to Pyruvate.
– Krebs cycle--Electrons are
removed--carriers are charged
and CO2 is produced. This
occurs in the mitochondrion.
– Electron transport--electrons are
transferred to oxygen. This
produces H2O and ATP. Occurs
in the mito.
The Chloroplast
Contain their own DNA and
protein-synthesizing
machinery
– Ribosomes, transfer RNAs,
nucleotides.
– Thought to have evolved
from endosymbiotic bacteria.
– Divide by fusion
– The DNA is in the form of
circular chromosomes, like
bacteria
– DNA replication is
independent from DNA
replication in the nucleus
The Chloroplast
Membranes contain chlophyll
and it’s associated proteins
– Site of photosynthesis
Have inner & outer membranes
3rd membrane system
– Thylakoids
Stack of Thylakoids = Granum
Surrounded by Stroma
– Works like mitochondria
During photosynthesis, ATP
from stroma provide the
energy for the production of
sugar molecules
Cellular Organization - Simple
comparison of prokaryotes and
eukaryotes
Prokaryotes
Eukaryotes
Eubacteria,
Animal, plants,
archabacteria
fungi, yeast
Organization
Simple
Complex
Cell Size
Small 2 Š5 µm
Large 10 Š 100
Organisms
µm
Membranous
No
Many
Cytoskeleton
No
Yes
Peptidoglycan cell
Yes Š helps with
No
walls
rigidity
Endo- and
No
organelles
exocytosis
Chromosomes
Yes yeast ->
mammals
Circular and few
Linear and many
Organelles with their principle
function
Organelle:
Nucleus
Mitochondria
Endoplasmic reticulum
Golgi apparatus
Lysome
Chloroplast
Function:
Contains genetic material
Aerobic energy metabolism
Synthesis of phospholipids; synth
of membrane and secretory
proteins
Modification and sorting of
proteins
Intracellular digestion
Photosynthesis
The End
Any Questions?