proteins

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electrophoresis of DNA and proteins

The future of genetic research

correspond pretty closely to the two fundamental categories of proteins:

If the genetic defect affects structural proteins, however, for example,

analyzing how dystrophin functions, what other proteins it interacts

MIT Biology Hypertextbook: Chemistry Review

The study of biology requires an understanding of simple organic chemistry and simple biological chemistry. Carbohydrates, lipids, proteins, and nucleic acids, the players in molecular biology, are themselves composed of smaller building blocks. This chapter contains a review of important chemical interactions and concepts you will encounter in this course.

Hydrogen bonds are ~5 kcal/mol in strength. These bonds are frequently found in proteins and nucleic acids, and by reinforcing each other serve to keep the protein (or nucleic acid) structure secure. But, since the hydrogen atoms in the protein could also H-bond to the surrounding water, the relative strength of protein-protein H-bonds vs. protein-H2O bonds is smaller than 5 kcal/mol.

Prokaryotic Gene Regulation

these are regions of DNA that code for proteins. These genes produce

proteins. (Note: some structural genes produce RNAs that are themselves

sequences in these regions do not code for proteins.

regions) and genes that control the production of proteins (regulatory

(i) Proteins can diffuse throughout the cell and act all over the

structural genes which produce proteins and can therefore act in

proteins which can diffuse throughout the cell. Therefore the wild-type

proteins can complement the

sufficient amounts of functional proteins. Therefore, growth on

Large Molecules

The Structures and Functions of

Proteins in Biological Systems

3.1 Amino Acids

3.2 Peptide Bonds

3.3 pKa's

3.4 Primary through

3.5 Sequencing

E. coli

prokaryotic cell of E. coli makes thousands of specific proteins.

Control of the Cell Cycle

DNA together with associated proteins. This process of doubling the

Monoclonal Antibody Technology

agents are antibodies, proteins that seek out the antigens and help destroy

3.5 Sequencing

sequence of most proteins . This strategy is outlined below

in a polypeptide we must break the peptide bond . This can be accomplished

with strong acids (i.e. 6N HCl) or strong bases or by exhaustive enzymatic

However, there are proteins that are made up of two or more polypeptides,

Immunology Encyclopedia

proteins, produced by the immune system, that specifically recognizes a

complement system A group of eleven proteins that play a role in

some reactions of the immune system. The complement proteins are not

immunoglobulin A class of proteins,

interleukins Regulatory proteins, produced by

MIT Biology Hypertextbook: Enzyme Mechanisms

Most biological enzymes are proteins . They perform the chemical

reactions in cells. Not all proteins are enzymes, but most enzymes are

proteins (the exception is catalytic RNA). A catalyst is a molecule

Solving Enzyme Structure Problems

Yanofsky & co. collected more mutants and examined their proteins to determine which of

Membrane Proteins Introduction

Membrane Proteins Introduction

Membrane Proteins Introduction

proteins ) from dissipating away.

it begins synthesizing proteins to take in and metabolize the lactose. But,

environment it instead begins synthesizing proteins to take in and metabolize

proteins to gather information about the environment in various ways.

Therefore, cells have two major types of membrane proteins :

Some proteins serve both of these functions simultaneously, but most proteins

The cell has therefore evolved an array of proteins to cope with these

it. They are called intrinsic membrane proteins; yet others are adsorbed to

the surface of the lipid bilayer and are termed extrinsic membrane proteins

Cell Basics

50% protein

Membrane Transport Mechanisms

molecules in and out of itself. Imagine that a protein having multiple

In practice, given the structure of known membrane proteins , these

Receptors

transmembrane proteins termed receptors that function to acquire

and pass through mitosis, are themselves polypeptides , often 50-100 amino

GF factor receptor proteins. Outside the cell, they have a ligand-binding N-

substrate proteins. In the case of GF receptors, the phosphate groups are

attached to the tyrosine side chains of substrate proteins that communicate

a series of cytoplasmic substrate proteins that in turn become activated or

cytoplasmic substrate proteins that then pass signals further into the cell.

Chemical Energetics

Consider a reaction proceeding in the opposite direction, where the end products are at a higher energy level than the starting materials. As an example, suppose you want to convert a mixture of amino acids into a protein. Such a reaction requires

used to distort or rotate molecules of specific transporter proteins. See

Membrane transport proteins

Culturing cells in vitro

specific cell surface proteins that are termed growth factor receptors.

1.1 Membrane Structure and Composition

proteins, cholesterol, and other types of molecules besides phospholipids).

times the size of the phospholipid. Membrane proteins diffuse throughout the

Membrane Proteins

Membrane Proteins

Membrane Proteins

Transmembrane Proteins

Membrane proteins are either extrinsic or intrinsic. Extrinsic membrane

proteins are entirely outside of the membrane, but are bound to it by weak

Intrinsic membrane proteins, the class we are mainly interested in, are

to the other and are referred to as transmembrane proteins.

Cells contain proteins that are embedded in the lipid bilayer of their

the other. Such transmembrane proteins can function to effect ion

proteins, we see that they often have three different domains, two

transmembrane domains anchor many proteins in the lipid bilayer,these

proteins are not free-floating and cannot be isolated and purified

by the need to solubilize proteins that are embedded in lipid membranes

Glycoproteins

proteins are glycoproteins in the sense that sugar side chains are covalently

glycoproteins will have its extracellular domain glycosylated with a

asparagine side chains. Some glycoproteins may have 2 or 3 asparagine-

Multi-membrane-spanning proteins

depicting membrane proteins having single transmembrane domains

involves certain membrane proteins that have multiple transmembrane

domains. As one scans along the amino acid sequence of these proteins, it

between opposite sides of the plasma membrane. Some think such proteins

membrane proteins. A commonly used type of structure seen in many

hundreds of serpentine transmembrane proteins involves 7 hydrophobic

3.3 Acid-Base Equilibria

For example: You are studying a bottle full of valine amino acids and

3 Proteins

3 Proteins

3 Proteins

Proteins are very complicated moleucules. With 20

different amino acids that can be arranged in any order to make a polypeptide

extraordinary. This variety allows proteins to function as exquisitely

different proteins working at various times to catalyze the necessary

All proteins are linear chains composed of these 20 amino acids.

G Protein Receptors

of polypeptide mating factors. The cell surface receptors that recognize

dozens of alpha subunits of proteins. Each of these in turn will

Characteristics of Prokaryotes and Eukaryotes

large polymer of amino acids and sugar . Many types of eukaryotic cells

Basic Virus Structure

What you are seeing are the interlocking proteins of the virus capsid. Each

Biological Macromolecules

proteins, amino acids, and the pKa of amino acids

Structure and Function of Organelles

transported out of the nucleus through the nuclear pores. Proteins

organelles are quite small, made up of 50 proteins and several long

Enzyme Biochemistry

methods used to purify proteins

The Cytoskeleton

There are a great number of proteins associated with the

particularly interesting group of cytoskeletally-associated proteins

Cell Biology Chapter

Membrane proteins structures

Domains

Glycoproteins

Multi-membrane-spanning proteins

Membrane Transport Problem Answers

a) Explain.Transmembrane proteins don't generally `flip-flop'

module not yet titled

membrane-associated proteins and carbohydrates

Southerns, Northerns, Westerns, & Cloning: Molecular Searching Techniques

proteins) can form a complex with a target protein molecule if the

of different proteins. When the cell is broken open to extract DNA, RNA,

Preparing Proteins for Western Blots

Proteins have extensive 2' and 3' structures and are not always

negatively charged. Proteins are treated with the detergent SDS (sodium

7.012 Cloning Project: Agricultural Biotechnology

sequences were compared to known proteins in in the database, they got

and other sequences similar to proteins known to be permeases.

* translated ORF2 has regions similar to proteins known to use

encoding genes that produce proteins capable of helping the bacteria to

The Peptide Bond

The amino acids are linked linearly through peptide bonds. These bonds are formed via a dehydration

3.5 Solving Enzyme Kinetics Problems

in the membrane. The characteristics of the two transport proteins are as

3.4 Primary through Quartenary structure

This is a molecule of hexokinase, a metabolic protein found in almost all

amino acids . Note that this order is always written from amino end to

SCOP (Structural Classification of Proteins) and use the PDB reference number 1HKG.

structures found in proteins. There are two types of secondary structures:

amino acids. a-helices are found in almost all proteins to various extents.