Introduction to Molecular Biology zMolecular biology is interdisciplinary (biochemistry, genetics,...

Introduction to Molecular Biology

Molecular biology is interdisciplinary (biochemistry, genetics, cell biology)

Impact of genome projects (human, bacteria, fungi, plants, etc.)….”postgenomics era”

Integration with other fields (e.g. computer science) leading to interdisciplinary career paths (Bioinformatics)

Molecular Biology syllabus web site

http://a32.lehman.cuny.edu/webwurtzel/course/CURRIC99j.htm

Model Organisms

Central Dogma

DNA is transcribed to mRNA

mRNA is translated to protein

Proteins play many roles

Lecture 1

Protein Structure and Function

Reading: Chapters 1-3

Protein Structure & Function

- protein structure

- protein purification & analysis

- protein structure determination

Protein structure determines function

Proteins are single, unbranched chains of amino acid monomers

There are 20 different amino acidsA protein’s amino acid sequence

determines its three-dimensional structure (conformation)

In turn, a protein’s structure determines the function of that protein

Copyright (c) by W. H. Freeman and Company

All amino acids have the same general structure but the side chain (R group) of each is different


Hydrophilic amino acids

Figure 2-13


Hydrophobic & “special” amino acids

Figure 2-13


Peptide bonds connect amino acids into linear chains

Fig 3-2

Amino acids are the repeating units in proteins, but it is the 3-D protein structure that underlies function.

How is 3-D structure obtained?


Four levels of structure determine the shape of proteins

Primary: the linear sequence of amino acidsSecondary: the localized organization of parts

of a polypeptide chain (e.g., the helix or sheet)

Tertiary: the overall, three-dimensional arrangement of the polypeptide chain

Quaternary: the association of two or more polypeptides into a multi-subunit complex

Secondary structure: the helix

Figure 3-4

The spiral is held by hydrogen bondsbetween nearly adjucent backbone O and H atoms


Secondary structure: the beta sheet

Hydrogen bonds occur between backbone O and H of separate ajucent strands


Motifs are regular combinations of secondary structures

A coiled coil motif is formed by two or more heliceswound around one another


Other examples of motifs

Tertiary structure // quaternary structure

hemagglutinin

Regions of proteins form domains: functional, topological or structural (like in case of HA)

Hydrophobic, hydrophylicinteractions anddisulfide bondshelp to keep the structure

The structure is stabilized by Interactions between domains

Sequence homology suggests functional and evolutionary relationships between proteins

Figure 3-10

Folding, modification, & degradation of proteins

A newly synthesized polypeptide chain must undergo folding and often chemical modification to generate the final protein

All molecules of any protein species adopt a single conformation (the native state), which is the most stably folded form of the molecule

The information for protein folding is encoded in the sequence

Folding of proteins in vivo is promoted by chaperones


Aberrantly folded proteins are implicated is slowly developing diseases

An amyloid plaque in Alzheimer’s disease is a tangle of protein filaments


Chemical modifications and processing alter the biological activity of proteins


Protein degradation via the ubiquitin-mediated pathway

Cells contain several other pathways for protein degradation in addition to this pathway


Functional design of proteins

Protein function generally involves conformational changes

Proteins are designed to bind a range of molecules (ligands) Binding is characterized by two properties: affinity

and specificityAntibodies exhibit precise ligand-binding specificityEnzymes are highly efficient and specific catalysts

An enzyme’s active site binds substrates and carries out catalysis


Kinetics of an enzymatic reaction are described by Vmax and Km


Mechanisms that regulate protein function

Allosteric transitions Release of catalytic subunits, active / inactive

states, cooperative binding of ligandsPhosphorylation / dephosphorylationProteolytic activationCompartmentalization


Purifying, detecting, and characterizing proteins

A protein must be purified to determine its structure and mechanism of action

Molecules, including proteins, can be separated from other molecules based on differences in physical and chemical properties


Centrifugation can separate molecules that differ in mass or density


Electrophoresis separates molecules according to their charge:mass ratio

SDS-polyacrylamidegel electrophoresis


Two-dimensional electrophoresis separates molecules according to their charge and their mass


Separation of proteins by size: gel filtration chromatography


Separation of proteins by charge: ion exchange chromatography


Separation of proteins by specific binding to another molecule: affinity chromatography


Highly specific enzymes and antibody assays can detect individual proteins


Time-of-flight mass spectrometry measures the mass of proteins and peptides


X-ray crystallography is used to determine protein structure

Other techniques such as cryoelectron microscopy and NMR spectroscopy may be used to solve the structures of certain types of proteins

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Introduction to Molecular Biology zMolecular biology is interdisciplinary (biochemistry, genetics,...

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