PROTEINS
Amino acids Side chain -Carbon atom Amino group Carboxyl group
Amino acids
Primary structure Amino acid monomers Peptide bond
Peptide bond Amino group Carboxyl group Peptide bond N-terminal ( + H 3 N) C-terminal (COO )
Secondary structures -helix -sheet Hydrogen bond Hydrogen bond
Tertiary and quaternary structures Tertiary structure -sheet Quaternary structure Subunit 1 Subunit 2 Hydrogen bond -helix Disulphide bridge Subunit 3 Subunit 4
Disulphide bridge cysteine molecules side chains disulphide bridge
Denaturation Native protein Denatured protein
The subunits of hemoglobin -subunits red blood cells hem group -subunits
Macromolecular assemblies Transcription pre-initiation complex virus capsid
Types of proteins
ENZYMES
The First Law of Thermodynamics The laws of thermodynamics Energy before Energy transformation Energy after The Second Law of Thermodynamics Energy before Energy transformation Usable energy after (free energy) Unusable energy after Free energy Energy transformations Unusable energy after Entropy
Exergonic reaction Reactants Amount of energy released Products Endergonic reaction Products Amount of energy required Reactants
Activation energy Energy barrier Transition state Reactants (stable) E a G Products Stable state Less stable state (transition state)
Enzyme and substrate Active site Product Enzyme Enzyme substrate complex Enzyme
Enzymes lower the energy barrier E a Uncatalyzed reaction E a Reactants Catalyzed reaction G Products
Life at the Active Site Enzymes orient substrate molecules, bringing together the atoms that will bond Citrate synthase Lysozyme Enzymes can stretch the bonds in substrate molecules, making them unstable Chymotrypsin Enzymes can temporarily add chemical groups to substrates
Some enzymes change shape when substrate binds to them Empty active site Glucose substrate
Some examples of nonprotein partners of enzymes
Metabolic Pathways Metabolism of Cofactors and Vitamins Nucleotide Metabolism Carbohydrate Metabolism Lipid Metabolism Metabolism of Other Amino Acids Amino Acid Metabolism ATP production Metabolism of Other Substances
Irreversible Inhibition Active site DIPF Trypsin Hydrogen fluoride
Competitive inhibitor Competitive inhibition Active site Reversible Inhibition Substrate Noncompetitive inhibition Substrate Active site Noncompetitive inhibitor
Allosteric Regulation of Enzymes Inactive form Catalytic subunit Active form Active site Inhibitor site Regulatory subunits Substrate Activator site Allosteric inhibitor Allosteric activator No product formation Product formation
Allosteric Regulation of Enzymes Catalytic subunit INACTIVE FORM ACTIVE FORM Active site Inhibitor site Regulatory subunits Activator site The enzyme switches back and forth between the two forms. They are in equilibrium
Allosteric Regulation of Enzymes INACTIVE FORM When the enzyme is in the inactive form, it cannot accept substrate.
Allosteric Regulation of Enzymes INACTIVE FORM Allosteric inhibitor Binding of an inhibitor makes it less likely that the active form will occur.
Allosteric Regulation of Enzymes ACTIVE FORM Substrate When the enzyme is in the active form, it can accept substrate.
Allosteric Regulation of Enzymes ACTIVE FORM Substrate Allosteric activator Binding of an activator makes it more likely that the active form will occur.
Allosteric Regulation of Enzymes INACTIVE FORM ACTIVE FORM No product formation Product formation
Translation
12.8 Transfer RNA
12.9 Charging a trna Molecule (Part 1)
12.9 Charging a trna Molecule (Part 2)
12.10 Ribosome Structure
The Initiation of Translation
The Initiation of Translation
The Elongation of Translation
The Elongation of Translation
The Termination of Translation
The Termination of Translation
The Termination of Translation
Polysome
Post-translational regulation
Protein degradation proteasome Causes of degradation: - aberrant structure - Optimal life time - No need any more - Starvation for amino acids Life time: short-lived proteins: e.g. steroid receptor; long-lived proteins: pl. eye lens proteins - Amino acids at the N-terminus is correlated with: 1. stability 2. rate of ubiquitin binding - Arg, Lys, Phe, Leu, Trp 1/2 life: 3 min - Cys, Ala, Ser, Thr, Gly, Val, Pro, Met 1/2 life: 20 hrs Ubiquitin (a peptide composed of 76 amino acids) binds to proteins and identify them for degradation by proteolytic enzymes in proteasomes
Protein degradation
Protein modification 16. precursor peptide peptide variants 1. Proteolytic cleavage - Various peptides from a precursor molecule (e.g. neuropeptides) - Cleavage of inhibitory peptide (e.g. digestive enzymes) 2. Glycosylation: transport (control the final location of proteins) I 3. Phosphorylation: activation - inactivation 4. Methylation acetylation: histone regulation protein inactive kinase phosphatase protein active P N-acetilgluckosamine mannose glucose protein Carbohydrate group glycosylation: addition of glycosyl group