Download - Advanced organic chemistry? Cell biology? Molecular biology? The most fun and interesting subject in science (personal bias)? The study of life on a molecular

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

What is biochemistry?What is biochemistry?

•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

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

Biochemistry IBiochemistry I

What is What is Critical Critical Thinking?Thinking?

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


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


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 TipsStudy Tips– Do not cram, too much material and topics build Do not cram, too much material and topics build on the next from the first day.on the next from the first day.

– Read the study tips on my homepageRead the study tips on my homepage– Write an outline, ask yourself what does all of Write an outline, ask yourself what does all of this mean in a few wordsthis mean in a few words

Test TipTest Tip– The tests are multiple guess, short answer The tests are multiple guess, short answer andand essayessay

– DO NOT read the question and then look for and DO NOT read the question and then look for and answer. Think of the answer and then find if. answer. Think of the answer and then find if. Looking for a likely answer will nearly always Looking for a likely answer will nearly always cause problemscause problems

This semester:This semester:pH, buffers and amino acidsProtein structure and

functionEnzymes and kineticsCarbohydratesLipids and fatsMetabolism

– Biochemical source of diseases

– Real life and interesting examples

Next semester: More metabolism,

Diabetes, Cancer, Nutrition, Signal

Transduction

… … and now the fun begins...and now the fun begins...Functional Groups - One of the reasons why organic

chemistry is a prerequisite for the classJust for review – know and be able to draw each of

the structures in fig 1-2..

Also know…Also know…DisulfideDisulfide

ThioesterThioester

Anhydride (2 carboxylic acids)Anhydride (2 carboxylic acids)

GuanidinoGuanidino

ImidizoleImidizole


ThioesterThioester


GuanidinoGuanidino

ImidizoleImidizole

RR11-S-S-R-S-S-R22


ThioesterThioester


GuanidinoGuanidino

ImidizoleImidizole

RR11-S-S-R-S-S-R22

RR11-C-S-R-C-S-R22

==

OO


ThioesterThioester


GuanidinoGuanidino

ImidizoleImidizole

RR11-S-S-R-S-S-R22

RR11-C-S-R-C-S-R22

==

OORR11-C-O-C-R-C-O-C-R22

==OO

==

OO


ThioesterThioester


GuanidinoGuanidino

ImidizoleImidizole

RR11-S-S-R-S-S-R22

RR11-C-S-R-C-S-R22

==


==OO

==

OORRNHNH

HN=CHN=CNHNH22

----

--


ThioesterThioester


GuanidinoGuanidino

ImidizoleImidizole

RR11-S-S-R-S-S-R22

RR11-C-S-R-C-S-R22

==


==OO

==

OORRNHNH

HN=CHN=CNHNH22

----

--

R -C=CHR -C=CH

HNHN NN

CC

HH

Prokaryotic Cellular Prokaryotic Cellular OrganizationOrganization

Eukaryotic Cellular Eukaryotic Cellular OrganizationOrganization

The Plasma MembraneThe Plasma Membrane

Composed of a Composed of a phospholipid bilayer phospholipid bilayer and proteinsand proteins..

The phospholipid sets up The phospholipid sets up the bilayer structurethe bilayer structure

Phospholipids have Phospholipids have hydrophilic heads and hydrophilic heads and fatty acid tails.fatty acid tails.

The plasma membrane is The plasma membrane is fluid--that is proteins fluid--that is proteins move in a fluid lipid move in a fluid lipid backgroundbackground

The Plasma MembraneThe Plasma MembranePhospholipidsPhospholipids::

Two fatty acids covalently linked Two fatty acids covalently linked to a to a glycerolglycerol, which is linked to , which is linked to a a phosphatephosphate..

All attached to a “head group”, All attached to a “head group”, such as such as cholinecholine, an amino acid., an amino acid.

Head group POLAR – so Head group POLAR – so hydrophilichydrophilic (loves water) (loves water)

Tail is non-polar -Tail is non-polar -hydrophobichydrophobic

The tail varies in length from 14 to The tail varies in length from 14 to 28 carbons.28 carbons.

The Plasma MembraneThe Plasma Membrane

ProteinsProteins::

Integral proteinsIntegral proteins::

– Embedded in lipid bylayer – serve as “ion pumps”Embedded in lipid bylayer – serve as “ion pumps”

– They pump ions across the membrane against their They pump ions across the membrane against their concentration gradientconcentration gradient

Peripheral proteinsPeripheral proteins::

– Bound to membrane surface by ionic bonds.Bound to membrane surface by ionic bonds.

– Interact with components of the cytoskeletonInteract with components of the cytoskeleton

Anchored proteinsAnchored proteins::

– Bound to surface via lipid moleculesBound to surface via lipid molecules

The nucleusThe nucleusContains Contains almost allalmost all of the genetic of the genetic

materialmaterial

What it contains is called the What it contains is called the nuclear nuclear genomegenome – this varies greatly between – this varies greatly between plant species.plant species.

Surrounded by Surrounded by nuclear envelope-nuclear envelope- double double membrane - membrane - same as the plasma same as the plasma membranemembrane..

The The nuclear poresnuclear pores allow for the passage allow for the passage of macromolecules and ribosomal of macromolecules and ribosomal subunits in and out of the nucleus. subunits in and out of the nucleus.

The Endoplasmic reticulumThe Endoplasmic reticulumConnected to the nuclear envelopeConnected to the nuclear envelope3D-network of continuous tubules that 3D-network of continuous tubules that

course through the cytoplasm.course through the cytoplasm.

Rough ERRough ER: Synthesize, process, and sort : Synthesize, process, and sort proteins targeted to membranes, proteins targeted to membranes, vacuoles, or the secretory pathway.vacuoles, or the secretory pathway.

Smooth ER:Smooth ER: Synthesize lipids and oils. Synthesize lipids and oils. Also:Also:

– Acts as an anchor points for actin Acts as an anchor points for actin filaments filaments

– Controls cytosolic concentrations of Controls cytosolic concentrations of calcium ionscalcium ions

The Endoplasmic reticulumThe Endoplasmic reticulum

Proteins are made in the Rough Proteins are made in the Rough ER lumen by an attached ER lumen by an attached ribosome.ribosome.

Protein detaches from the Protein detaches from the ribosomeribosome

The ER folds in on itself to form a The ER folds in on itself to form a transport vesicletransport vesicle

This transport vesicle “buds off” This transport vesicle “buds off” and moves to the cytoplasmand moves to the cytoplasm

Either:Either:

– Fuses with plasma Fuses with plasma membranemembrane

– Fuses with Fuses with Golgi ApparatusGolgi Apparatus

The Golgi NetworkThe Golgi NetworkProteins or lipids made in the ER Proteins or lipids made in the ER

contained in transport vesicles fuse contained in transport vesicles fuse with the Golgi.with the Golgi.

The Golgi modifies proteins and lipids The Golgi modifies proteins and lipids from the ER, sorts them and from the ER, sorts them and packages them into packages them into transport vesiclestransport vesicles..

This transport vesicle “buds off” and This transport vesicle “buds off” and moves to the cytoplasm.moves to the cytoplasm.

Fuse with plasma membrane.Fuse with plasma membrane.

The Golgi NetworkThe Golgi Network

The Mitochondria The Mitochondria

Contain their own DNA and protein-Contain their own DNA and protein-synthesizing machinerysynthesizing machinery

– Ribosomes, transfer RNAs, Ribosomes, transfer RNAs, nucleotides.nucleotides.

– Thought to have evolved from Thought to have evolved from endosymbiotic bacteriaendosymbiotic bacteria..

– Divide by fusionDivide by fusion

– The DNA is in the form of The DNA is in the form of circular chromosomes, like circular chromosomes, like bacteriabacteria

– DNA replication is independent DNA replication is independent from DNA replication in the from DNA replication in the nucleusnucleus

The MitochondriaThe MitochondriaSite of Cellular RespirationSite of Cellular Respiration

This process requires oxygen.This process requires oxygen.Composed of three stages:Composed of three stages:

– GlycolysisGlycolysis--glucose splitting, --glucose splitting, occurs in the cell. Glucose is occurs in the cell. Glucose is converted to Pyruvate.converted to Pyruvate.

– Krebs cycle-Krebs cycle--Electrons are -Electrons are removed--carriers are charged removed--carriers are charged and CO2 is produced. This and CO2 is produced. This occurs in the mitochondrion.occurs in the mitochondrion.

– Electron transport-Electron transport--electrons are -electrons are transferred to oxygen. This transferred to oxygen. This produces H2O and ATP. Occurs produces H2O and ATP. Occurs in the mito.in the mito.

The ChloroplastThe Chloroplast

Contain their own DNA and Contain their own DNA and protein-synthesizing machineryprotein-synthesizing machinery

– Ribosomes, transfer RNAs, Ribosomes, transfer RNAs, nucleotides.nucleotides.

– Thought to have evolved Thought to have evolved from from endosymbiotic bacteriaendosymbiotic bacteria..

– Divide by fusionDivide by fusion

– The DNA is in the form of The DNA is in the form of circular chromosomes, like circular chromosomes, like bacteriabacteria

– DNA replication is DNA replication is independent from DNA independent from DNA replication in the nucleusreplication in the nucleus

The ChloroplastThe ChloroplastMembranes contain chlophyll Membranes contain chlophyll

and it’s associated proteinsand it’s associated proteins

– Site of photosynthesisSite of photosynthesis

Have inner & outer membranesHave inner & outer membranes

33rdrd membrane system membrane system

– ThylakoidsThylakoids

Stack of Thylakoids = Stack of Thylakoids = GranumGranum

Surrounded by Surrounded by StromaStroma

– Works like mitochondriaWorks like mitochondria

During photosynthesis, ATP During photosynthesis, ATP from stroma provide the from stroma provide the energy for the production of energy for the production of sugar moleculessugar molecules

Cellular Organization - Cellular Organization - Simple comparison of Simple comparison of

prokaryotes and prokaryotes and eukaryoteseukaryotes

Prokaryotes Eukaryotes

Organisms Eubacteria,

archabacteria

Animal, plants,

fungi, yeast

Organization Simple Complex

Cell Size Small 2 Š5 µm Large 10 Š 100

µm

Membranous

organelles

No Many

Cytoskeleton No Yes

Peptidoglycan cell

walls

Yes Š helps with

rigidity

No

Endo- and

exocytosis

No Yes yeast ->

mammals

Chromosomes Circular and few Linear and many

Organelles with their Organelles with their principle functionprinciple function

Organelle: Function:Nucleus Contains genetic materialMitochondria Aerobic energy metabolismEndoplasmic reticulum Synthesis of phospholipids; synth

of membrane and secretoryproteins

Golgi apparatus Modification and sorting ofproteins

Lysome Intracellular digestionChloroplast Photosynthesis

The EndThe End

Any Questions?Any Questions?

Download - Advanced organic chemistry? Cell biology? Molecular biology? The most fun and interesting subject in science (personal bias)? The study of life on a molecular

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