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

Section A: Cell structure

0.2 m
0.002 m

Microscopic observations of cells

Electron Micrograph

Structures that appear as separate objects in the electron micrograph may actually be continuous structures

Rat Liver cell

Eukaryotic Cell (true-nucleus cells)

Cell Organelles: membrane-bound compartments

Each organelle performs its specific functions that contribute to the cell survival

Comparison of cytoplasm and cytosol

Cell = nucleus + cytoplasma Cytoplasma= organelles + cytosol (fluid surrounding the organelles) Intracellular fluid = cytosol + fluid inside all of the organelles

Membrane Structure Amphipathic molecules

Fluid-mosaic model of cell membrane structure No chemical bonds link the phospholipids to each other or to the membrane proteins Cell membrane is flexible

The amino acids along the membrane section are likely to have non-polar side chains

Transmembrane protein

Glycocalyx

Phospholipid = Polar head + Non-polar fatty acid tail (Amphipathic) Integral membrane proteins = Polar region + Non-polar region (Amphipathic)

Peripheral membrane proteins = Polar region (Non-Amphipathic)

Membrane Asymmertries

Human red blood cell membrane

6-10 nm thick

Asymmertries

(1) Lipids (2) Proteins (3) Carbohydrates

Membrane Junctions
20 nm Protein channel

Anchoring junction

1.5 nm

Skin

Epithelial cells cover the inner surface of the intestinal tract

This forces nutrients to pass through the cells, rather than between them

Muscle cells of the heart

selective barrier

Receptors

Cell Organelles
Little Organs

Cell Organelles

Nucleus
(RNA + components of ribosomal subunits)

Chromosome (at the time of cell division)

mRNA

protein

Skeletal muscle cell = multiple nuclei Mature red blood cell = non-nucleus Storage and transmission of genetic information to the next generation of cells

Cell Organelles

Ribosome & Endoplasmic Reticulum

Golgi apparatus

Cytosol

Ribosomes = attached to endoplasmic reticulum + free = the protein factories of a cell

Cell Organelles

Endoplasmic Reticulum (ER)

packaging proteins

lipid synthesis & calcium storage

ER = rough (granular) + smooth (agranular)

Cell Organelles

Golgi Apparatus

Secretory vesicles

Carbohydrates are linked to proteins (glycoproteins) Golgi Apparatus = protein modifications Removing a terminal portion of the polypeptide chain

Cell Organelles

Mitochondria (Mitochondrion)

Mitochondria = outer membrane + inner membrane = cellular respiration ATP production = synthesis of steroid hormone (estrogen & testosterone) (Fig 11-5 )

Fig 11-5 Steps involved in steroid synthesis

Fig. 11.04a

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

Cytoskeleton (Cytoskeletal Filaments)

contractile protein

size
desmosomes

nerve cell or Cilia

Cytoskeleton = maintain and change cell shape and produce cell movements Microfilament & Microtubule = be assembled and disassembled rapidly

movements of organelles within the cytoplasm

Intermediate filament = once assembled, are less readily disassembled

Proteins
Genetic Code

Human genome -> Chromosome -> nucleosomes -> DNA sequence +Histones -> Gene -> Nucleotides (A,G,C,T)

A,T,C,G

()

Gene

ATCGC

[30-nm fiber]

ATCGATCGCCCGGTAT

[Histones]

[]

genome

[23]

Three-letter code words in a gene determines the 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

Transcription & Translation: mRNA & protein synthesis

Exon

Intron

Ribosome

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)

Protein Synthesis by a Ribosome (rRNA)

tRNA

rRNA interacts with tRNAs

during translation by providing

Ribosome peptidyl transferase activity

a number of ribosomes, as many as 70, may be moving along a single strand of mRNA

Posttranslational Splitting of a protein

One Gene, several proteins

The flow through DNA to Protein

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
Cytosolic proteins Signal sequence

Secreted proteins Integral membrane proteins

Section C Protein Binding Sites

(Ligand & Receptor)

How proteins interact with other molecules ?

1. Sharp (Conformation) [protein folding] 2. Binding Forces

several binding sites

Reversible

Binding Forces: (1) Electric attractions (charged ionic or polarized groups) (2) Van deer Waals force (nonpolar regions)

Protein Folding

Unfolding Amino acids at the binding site Folding

Chemical Specificity
Different Ligands

Sharp (Conformation)

Various Binding Proteins

Protein Y has a greater chemical specificity than Protein X Side Effects of therapeutic drugs

Chemical Affinity

Sharp (Conformation) + Binding Forces

Affinity = how likely it is that a ligand will leave the binding protein and return to its unbounded state

Potency of therapeutic drugs

Saturation

Concentration + Affinity

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

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)

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)

Ligand A Binding site C Ligand B

binding affinity ??
Ligand A High Affinity

Ligand B

Low Affinity

Competition of Ligands = many drugs produce their effects by competing with

bodys natural ligands for the same binding site

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

Cooperative

Allosteric proteins

Altering protein shape (Conformational Change)

Phosphoproteins

Section D Enzymes and Chemical energy

Chemical Reactions
Anabolism + Catabolism Metabolism

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

Collision Theory

ClNO2(g) + NO(g)

NO2(g) + ClNO(g)

Activation Energy (Ea) of Chemical Reactions

(Enzymes function)
Transient State

Activation energy = Threshold energy of chemical reactions

Chemical reaction rate = measuring the change in the conc. of reactants or products per unit of time

Reversible and Irreversible Reactions

Every chemical reaction is in theory reversible

Law of Mass Action = These effects of reactant and product concentrations on the
direction in which the net reaction proceeds are known as

For the reversible reaction:

A+B

C+D

the law of mass action applies, meaning that an increase in the amount of reactants will increase the rate of product formation, i.e.,

A+B

C+D

Alternatively, an increase in the the amount of products will decrease the rate of product formation. i.e.,

A+B

C+D

Two Models of Interaction of an enzyme with its substrates

(reactants)

(catalyst)

Allosteric modulation

Regulation of Enzyme-mediated reactions

(1) Substrate conc.

(2) Enzyme conc.

(3) Enzyme activity

Regulation of Enzyme-mediated reactions (I)

(1) Substrate conc.

Maximal Rate

(1)

Regulation of Enzyme-mediated reactions (II)

(2) Enzyme conc.

In most metabolic reactions, the substrate concentration is much higher than the concentration of enzyme available to catalyze the reaction

Regulation of Enzyme-mediated reactions (III)

(3) Enzyme activity

Allosteric modulation & Covalent modulation

One enzyme, Multiple Regulatory sites

A Functional Site

Multiple Regulatory Sites

Factors that affect the rate of enzyme-mediated reactions

In Living Organism

Multienzyme reactions

A Metabolic Pathway Multienzyme reactions

End-Product Inhibition
Rate-Limiting reaction = the step is likely to be slower than others

Metabolic Pathways
Transfer the energy released from the breakdown of fuel molecules to ATP (1) Carbohydrates (in the absence and presence of Oxygen)

(2)

(3) Carbohydrates + fats + Proteins (in the presence of Oxygen)

Glycolytic Pathway (Glycolysis)

Oxygen Dept

The Linkage between Glycolysis and Krebs Cycle

Krebs Cycle = Tricarboxylic acid (TCA) Cycle = Citric Acid Cycle

Krebs Cycle

Hans Adolf Krebs

Mitocondrial Matrix

Oxidative Phosphorylation (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
Rotenone Cyanide, carbon monoxide Oligomycin

H+ H+

H+

H+ H+ H+ H+ H+ H
+

ATP Synthase

DNP

FADH2

FAD 1 O2

NADH

NAD+ H+ H
+

+ 2 H+

H2O H
+

ADP

+ P

ATP

Three different categories:

Electron Transport Chain

Chemiosmosis

(1)Rotenone Inhibits Protein Complex I Cyanide / 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

??

H+

H+

Our model assumes: (1) NADH generates 3 ATPs (2.5 ATPs) (2) FADH2 generates 2 ATPs (1.5 ATPs)

Glycogen Storage

Skeletal Muscles & Liver

Hexokinase

Gluconeogenesis (Glucogenesis)

Gluconeogenesis (Glucogenesis)

Fat Catabolism
3 Fatty acids + 1 Glycerol

Gluconeogenesis

Fatty Acid Catabolism Beta-Oxidation

Most fatty acids in the body contain 14 to 22 carbons, 16 and 18 being the most common

Amino Acid Catabolism Urea (1) Liver

(2)

Amino Acids can enter the carbohydrate pathway

Krebs Cycle

Glycolysis

 Amino Acids Poor

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

Inter-conversions of the molecules that serve as building blocks and as fuels