Ch3- Cell Structure and Protein Function

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
http://en.wikipedia.org/wiki/Image:Hans_Krebs.gif


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Hans Adolf Krebs

Mitocondrial Matrix

Oxidative Phosphorylation(Electron transport chain reaction)
http://en.wikipedia.org/wiki/Image:Hans_Krebs.gif


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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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Ch3- Cell Structure and Protein Function