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8/4/2019 Ch3- Cell Structure and Protein Function
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Chapter 3
Cell structure and protein function
Section A: Cell structure
Section B: Proteins
Section C: Protein Binding Sites
Section D: Enzymes and chemical energy
Section E: Metabolic pathways
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Section A: Cell structure
0.2 m
0.002 m
Microscopic observations of cells
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Electron Micrograph
Rat Liver cell
Structures that appear as separateobjects in the electron micrograph mayactually be continuous structures
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Eukaryotic Cell (true-nucleus cells)
Cell Organelles: membrane-bound compartments
Each organelle performs its specific functions that contribute to the cell survival
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Cell = nucleus + cytoplasma
Cytoplasma= organelles + cytosol (fluid surrounding the organelles)
Intracellular fluid = cytosol + fluid inside all of the organelles
Comparison of cytoplasm and cytosol
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Membrane Structure
Fluid-mosaic modelof cell membrane structure
No chemical bondslink the phospholipids to each other or to the membrane proteins
Cell membrane is flexible
Amphipathic molecules
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Transmembrane protein
T
heaminoacidsalong
themembranesection
arelikelytohave
non-polarsid
echains
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Phospholipid = Polar head + Non-polarfatty acid tail (Amphipathic)
Integral membrane proteins = Polar region + Non-polar region (Amphipathic)
Glycocalyx
Peripheral membrane proteins = Polar region (Non-Amphipathic)
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Membrane Asymmertries
(1) Lipids(2) Proteins(3) Carbohydrates
Asymmertries
Human red blood cell membrane
6-10 nm thick
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Membrane Junctions
Skin Epithelial cells cover
the inner surface of theintestinal tract
This forces nutrients to
pass through the cells,rather than between them
Muscle cells ofthe heart
20 nm
Protein channel
1.5 nm
Anchoring junction
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selective barrier
Receptors
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Cell Organelles
Little Organs
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Cell Organelles Nucleus
Skeletal muscle cell = multiple nuclei
Mature red blood cell = non-nucleus
Chromosome
proteinmRNA
Storage and transmission ofgenetic informationto the next generation of cells
(at the time ofcell division)
(RNA + components ofribosomal subunits)
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Cell Organelles Ribosome & Endoplasmic Reticulum
Ribosomes = attached to endoplasmic reticulum + free
= the protein factories of a cell
Golgi apparatus Cytosol
C O
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Cell Organelles Endoplasmic Reticulum (ER)
ER = rough (granular)+ smooth (agranular)
packaging proteins lipid synthesis & calcium storage
C ll O ll
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Cell OrganellesGolgi Apparatus
Secretory vesicles
Golgi Apparatus = protein modifications
Carbohydrates are linked to proteins (glycoproteins)
Removing a terminal portion of the polypeptide chain
C ll O ll Mit h d i (Mit h d i )
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Cell Organelles Mitochondria (Mitochondrion)
Mitochondria = outer membrane + inner membrane= cellular respirationATP production= synthesis of steroid hormone(estrogen & testosterone) (Fig 11-5 )
Fi 11 5
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Fig. 11.04a
Fig 11-5
Steps involved insteroid synthesis
C ll O ll
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Cell Organelles
Lysosomes= Cellular stomachs= The fluid within a lysosome is highly acid= Digestive enzymes
= Defense systems of the body
Peroxisomes= removing hydrogen from various organic molecules= hydrogen peroxide production
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Cytoskeleton (Cytoskeletal Filaments)
Cytoskeleton= maintain and change cell shape and produce cell movements
size
Microfilament & Microtubule = be assembled and disassembled rapidly
movements of organelleswithin the cytoplasm
Intermediate filament= once assembled are less readil disassembled
contractile protein
desmosomes
nerve cell orCilia
Proteins
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Proteins
Genetic Code
Human genome -> Chromosome -> nucleosomes -> DNA sequence +Histones ->
Gene -> Nucleotides (A,G,C,T)
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ATCGATCGCCCGGTAT
ATCGC
A,T,C,G
Gene
[23]
[]
[Histones]
[30-nm fiber]
()
genome
Three letter code words in a gene determines
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Three-letter code words in a gene determinesthe kind of amino acid in a polypeptide chain
Transcription + Translation
20 different amino acids that found in the proteins;
64 different three-letter code
Glycine is represented by C-C-A, C-C-G, C-C-T, C-C-C
Transcription: mRNA synthesis
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Transcription: mRNA synthesis
Transcription & Translation: mRNA & protein synthesis
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Transcription & Translation: mRNA &proteinsynthesis
Exon Intron
Ribosome
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Three different types of RNA:
(1) mRNA (messenger RNA)
(2) rRNA (ribosomal RNA): rRNA (nucleus) + ribosomal proteins (cytosol) cytosol
(3) tRNA (transfer RNA): tRNA (nucelus) cytosol
Translation: tRNA (protein synthesis)
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Translation: tRNA (protein synthesis)
Protein Synthesis by a Ribosome (rRNA)
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Protein Synthesis by a Ribosome (rRNA)
Ribosome
tRNA
rRNA interacts with tRNAs
during translation by providing
peptidyl transferase activity
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a number of ribosomes, as many as 70, may be moving along a single strand of mRNA
Posttranslational Splitting of a protein
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Posttranslational Splitting of a protein
One Gene, several proteins
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The flow through DNA to Protein
Regulation of Transcription
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Regulation of Transcription(Transcriptional factor)
Preinitiation Complex
Loop
The rate of a proteins synthesis can be regulated at various levels:(1) gene transcription to mRNA(2) the initiation of protein assembly on a ribosome
(3) mRNA degradation in the cytoplasm
Protein secretion
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Protein secretion
Signal sequence
Secreted proteins Integral membraneproteins
Cytosolic proteins
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Section C
Protein Binding Sites
(Ligand & Receptor)
How proteins interact with other molecules ?
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Binding Forces: (1) Electric attractions (charged ionic or polarized groups)(2) Van deer Waals force (nonpolar regions)
several binding sites
Reversible
1. Sharp (Conformation)[protein folding]
2. Binding Forces
How proteins interact with other molecules ?
Protein Folding
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ote o d g
Folding
Unfolding
Amino acids at the binding site
Chemical Specificity
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Chemical Specificity
Different Ligands
Various Binding Proteins
Protein Y has a greater chemical specificitythan Protein X
Side Effectsof therapeutic drugs
Sharp (Conformation)
Chemical Affinity
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y
Sharp (Conformation)+
Binding Forces
Affinity = how likely it is that a ligand will leave the binding protein and return to itsunbounded state
Potencyof therapeutic drugs
Saturation
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Saturation = the fraction of total binding sites that are occupied at any given time
50% saturation = Half of total binding proteins are occupied (The System)= A single binding site is occupied by a ligand 50% of the given time
Concentration+
Affinity
Measurement of binding affinity= the ligand concentration necessary to produce 50% saturation= the lower the ligand conc. required to bind to half the binding sites, the greater the
affinity of the binding sites
Competition for the binding sites (I)
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Competition for the binding sites (I)
Two different binding sites for the same ligand
binding affinity ??
Side Effects of therapeutic drugs
= the same drug molecule affects different tissues
Competition for the binding sites (II)
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p g ( )
Competition of Ligands= many drugs produce their effects by competing with
bodys natural ligands for the same binding site
Ligand A Ligand B
Binding site C
Ligand A
Ligand B
binding affinity ??
High Affinity
Low Affinity
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The Interactions Between Ligands and Binding Sites (of Proteins):
(1)Chemical Specificity
(2)Affinity
(3)Saturation
(4)Competition
(5)Allosteric Modulation
Modulation of a proteins binding site
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Altering protein shape(Conformational Change)
Allosteric proteins
Cooperative
Phosphoproteins
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S i D E d Ch i l
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Chemical Reactions
Anabolism + CatabolismMetabolism
Synthesis Breakdown
H2CO3(carbonic acid)
CO2(carbon dioxide)
H2O(water)
Heat+ +
Chemical Reactions: (1) Breaking of chemical bonds in reactant molecules
(2) Making new chemical bonds in product molecules
Section D Enzymes and Chemical energy
Collision Theory
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ClNO2(g) + NO(g) NO2(g) + ClNO(g)
A ti ti E (E ) f Ch i l R ti
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Activation Energy (Ea) of Chemical Reactions
Activation energy = Threshold energy of chemical reactions
Transient State
(Enzymes function)
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hemical reaction rate = measuring the change in the conc. of reactants or productsper unit of time
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Reversible and Irreversible Reactions
Law of Mass Action = These effects of reactant and product concentrations on the
direction in which the net reaction proceeds are known as
Every chemical reaction is in theoryreversible
For the re ersible reaction
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For the reversible reaction:
A + B C + D
the law of mass action applies,meaning that an increase in the
amount of reactants will increasethe rate of product formation, i.e.,
A + B C + DAlternatively, an increase in the
the amount of products will decreasethe rate of product formation. i.e.,
A + B
C + D
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(catalyst)
(reactants)
Two Models of Interaction of an enzyme with its substrates
Allosteric modulation
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Regulation of Enzyme-mediated reactions
(1)Substrate conc.
(2)Enzyme conc.
(3)Enzyme activity
Regulation of Enzyme-mediated reactions (I)
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(1)
Maximal Rate
(1)Substrate conc.
Regulation of Enzyme-mediated reactions (II)
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In most metabolic reactions, the substrate concentration is much higher than theconcentration of enzymeavailable to catalyze the reaction
(2) Enzyme conc.
Regulation of Enzyme-mediated reactions (III)
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Allosteric modulation &Covalent modulation
(3) Enzyme activity
One enzyme, Multiple Regulatory sites
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A Functional Site
Multiple Regulatory Sites
Factors that affect the rate of enzyme-mediated reactions
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In Living Organism
Multienzyme reactions
A Metabolic Pathway Multienzyme reactions
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End-Product Inhibition
Rate-Limiting reaction = the step is likely to be slower than others
Metabolic Pathways
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Transfer the energy released from thebreakdown of fuel molecules to ATP
(1)
(2)
(3)
Carbohydrates(in the absence and presence of Oxygen)
Carbohydrates + fats + Proteins(in the presence of Oxygen)
Glycolytic Pathway (Glycolysis)
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Oxygen Dept
The Linkage between Glycolysis and Krebs Cycle
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The Linkage between Glycolysis and Krebs Cycle
Krebs Cycle = Tricarboxylic acid (TCA) Cycle = Citric Acid Cycle
Krebs Cycle
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Hans Adolf Krebs
Mitocondrial Matrix
Oxidative Phosphorylation(Electron transport chain reaction)
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(Electron transport chain reaction)
Inner Mitochondrial Membrane
Chemiosmotic hypothesis = the movement of Protons (H+)
Reactive Oxygen Species = several highly reactive transient oxygen derivatives can
be formed during this process
Respiratory Poisons
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H+
H+
H+
H+
H+
H+ H+ H+ H+
H+
H+
H+
H+
O2
H2OP ATP
NADH NAD+
FADH2 FAD
Rotenone Cyanide,carbon monoxide
Oligomycin
DNP
ATPSynthase
+ 2
ADP +
Electron Transport Chain Chemiosmosis
1
2
Three different categories:
(1)Rotenone Inhibits Protein Complex ICyanide / Carbon Monoxide Inhibits Protein Complex III
(2) Oligomycin Inhibits ATP Synthase (ATP)
(3) Dinitrophenol (Uncouplers) Increases membrane leak to Protons(Abolishes H+ Gradient)
mitrochondrial wheel-spinning
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??
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H+ H+
Our model assumes:
(1) NADH generates 3 ATPs(2) FADH2 generates 2 ATPs
(2.5 ATPs)(1.5 ATPs)
Glycogen Storage
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Skeletal Muscles & Liver
Gluconeogenesis(Glucogenesis)
Hexokinase
Gluconeogenesis(Glucogenesis)
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(G ucoge es s)
Fat Catabolism
3 Fatty acids + 1 Glycerol Gluconeogenesis
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Fatty Acid CatabolismBeta-Oxidation
3 Fatty acids + 1 Glycerol Gluconeogenesis
Most fatty acids in the body contain 14 to 22carbons, 16 and 18being the most common
Amino Acid Catabolism
Urea
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Liver
Urea
(1)
(2)
Amino Acids can enter the carbohydrate pathway
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Krebs Cycle
Glycolysis
Amino Acids Poor
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Negative Nitrogen Balance & Positive Nitrogen Balance= a net loss or gain of amino acids in the body over any period of time
Essential Amino Acids
Essential
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Inter-conversions of the molecules that serveas building blocks and as fuels
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g
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