molecules

Solving Feedback Regulation Problems

b) Given that 3-phosphoglycerate is used by several other cellular pathways, while the other molecules

b) Given that 3-phosphoglycerate is used by several other cellular pathways, while the other molecules

MIT Biology Hypertextbook: Chemistry Review

Hydrogen bonds are formed when a hydrogen atom is shared between two molecules.

Hydrogen bonds have polarity. A hydrogen atom covalently attached to a very electronegative atom (N, O, or P) shares its partial positive charge with a second electronegative atom (N, O, or P). One example, shown above, involves the hydrogen bonding between water molecules.

Van der Walls interactions are very weak bonds (generally no greater than 1 kcal/mol) formed between nonpolar molecules or non-polar parts of a molecule. The weak bond is created because a C-H bond can have a transient dipole and induce a transient dipole in another C-H bond.

1.5 Hydrophobic Interactions Nonpolar molecules cannot form H-bonds with H2O, and are therefore insoluble in H2O. These molecules are known as hydrophobic (water hating), as opposed to water loving hydrophilic molecules which can form H-bonds with H2O. Hydrophobic molecules tend to aggregate together in avoidance of H2O molecules; hydrophobic interactions are clearly demonstrated when you put an oil drop on water. This attraction/repulsion is known as the hydrophobic (fear of water) force. To understand the energetics driving this interaction, visualize the H2O molecules surrounding a "dissolved" molecule attempting to form the greatest number of hydrogen bonds with each other. The best energetic solution involves forcing all of the nonpolar molecules together, thus reducing the total surface area that breaks up the H2O H-bond matrix.

Prokaryotic Gene Regulation

are grown in the presence of lactose or related molecules. In nature,

its regulation. Usually, protein molecules bind to these regions of

Large Molecules

Large Molecules

Large Molecules Chapter Directory

Large Molecules Practice Problems

E. coli

molecules of DNA and 15,000-30,000 ribosomes.

2 Sugars

molecules for living organisms. Their carbon rings contain

Amylose and cellulose, composed of long chains of glucose molecules, are examples of polysaccharides. The only structural difference between them is the linkage between the glucose molecules, yet the compounds have very different properties. Cellulose is a tough material found in plant cell walls, whereas amylose (a form of starch) is water soluble and used by plants as a carbon storage compound.

Lipids

meaning that most molecules are excluded but some molecules are allowed to pass freely (diffuse) through the

Control of the Cell Cycle

build-up of new molecules by a cell and the associated increase in its

Immunology Encyclopedia

class I MHC molecules

class II MHC molecules

Cell Basics

molecules

Cells are 90% water. Of the remaining molecules present, the dry

that are significant constituents of biological molecules are P,

Membrane Proteins Introduction

It must keep its molecules of life ( DNA , RNA , and its assortment of

It must keep out foreign molecules that damage or destroy the cells

components and molecules.

impermeable to most types of molecules. This barrier enables the cell

Membrane Transport Mechanisms

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

holes are only large enough to allow the passage of small molecules

Simple diffusion means that the molecules can pass directly through the

molecules (which otherwise could not diffuse across the cell membrane) to

type of transport that can actually take molecules up their concentration

Receptors

surface of a given cell. Second these receptor molecules, while tethered in

receptors molecules into close juxtaposition. The tyrosine kinase (TK) of

3 Enzyme Kinetics

limiting - all enzyme molecules are 'busy' operating on the substrate

Chemical Energetics

proceed very quickly because very few molecules overcome the energy

In a population of molecules there is a distribution of energies,

because individual molecules are subject to collisions with other

molecules, atomic vibrations, and external energy sources (such as

light). Most molecules have energy near the average energy, not enough

molecules have enough energy to make the transition over the barrier.

of large molecules are endothermic. For example, the conversion of

properties of the substrate and product molecules; second, their

the prototype of a group of molecules with high group donor potential,

that is, molecules that release much energy when they donate some parts

of themselves to water or to other acceptor molecules. (Remember that

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

Culturing cells in vitro

checks whether or not it has accumulated enough of the macromolecules

3.4 Competitive and Noncompetitive Inhibition

and Vo approaches Vmax. Vmax is unchanged because all of the enzyme molecules

the remaining active enzyme molecules are unaltered, Km is unchanged.

Title not found for link

Functional Groups Functional Groups This is a chart of the most common chemical functional groups. These functional groups will turn up in later chapters in the biological molecules we study. We recommend studying this chart so you can recognize the functional groups when they appear. R stands for any group of atoms--C,H,N,S--that is attached by a covalent bond to a chemical functional group. hyperbio@mit.edu last modified: 16 April 1997

1.1 Membrane Structure and Composition

This bilipid layer is semipermeable, meaning that some molecules are allowed

impermeable to large molecules, relatively impermeable to molecules

and quite permeable to lipid soluble low molecular weight molecules. Its

substantial permeability to water molecules is not well understood. Molecules

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

Notice that there are molecules of cholesterol embedded in the membrane.

Title not found for link

Chemical Models Chemical Models Models are key to our visual understanding of chemical molecules. Different types of models use different symbolism to represent the same information. Each type of model has advantages and disadvantages. For example, space-filling models are the most realistic representation possible of a molecule, but are time-consuming and moderately difficult to make. In contrast, a ball-and-stick model can quickly give you essential (but necessarily simplified) information about the spatial organization of a molecule. NIH Guide to Molecular Modeling that is worth checking out.--> hyperbio@mit.edu last modified: 16 April 1997

3 Proteins

Check out the Amino Acid Repository, maintained by the Image Library of Biological Macromolecules, for an excellent summary of amino acid properties and great graphic images of the twenty amino acids.

G Protein Receptors

membrane. Instead, single receptor molecules will change their 3

molecules made by the adenylate cyclase during its brief period of

Once made, the cAMP molecules act as intracellular glycogen, the high cAMP concentrations enable A kinase to

glucose-l-phosphate molecules; and

in turn will synthesize hundreds of cAMP molecules. Each of these in

modify hundreds of target molecules in the cell.

Biological Macromolecules

Biological Macromolecules

Other biologically important molecules (prosthetic groups, vitamins, steroids)

Structure and Function of Organelles

The ER is the transport network for molecules

as opposed to molecules that are destined to float freely in the

This organelle modifies molecules and packages them into small

breaking down molecules into their base components with strong

Membrane Transport Problem Answers

which two molecules/ions move together across the membrane is called

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

These are techniques for analyzing cellular macromolecules: DNA,

to identify the macromolecules of interest among a large number of other

molecules. Complementarity is the sequence-specific or shape-specific

molecular recognition that occurs when two molecules bind together. For

then be located if the probe molecules are tagged with radioactivity or

quantities of molecules similar but not identical to the target.

zillions of related but non-complementary molecules.

molecule in a complex mixture containing many similar molecules.

hybrids from the non-hybridized molecules. For this reason, you must

first physically separate the mixture of molecules to be probed on the

These molecules must then be immobilized on a solid support, so

initial separation of molecules is done on the basis of molecular

This is a technique that separates molecules on the basis of

matrix of long thin molecules forming sub-microscopic pores. The size

molecules being separated carry a net (-) charge so that they will me

gel, the larger molecules will be held up as they try to pass through

the pores of the gel, while the smaller molecules will be impeded less

molecules nearer the well and the smaller molecules farther away.

molecules, one of which is fully extended as a long chain (A);

As they migrate through the gel, both molecules behave as though they

of molecular weight, the molecules to be separated must be in a long

Although RNA is single-stranded, RNA molecules often have small

If these conditions are satisfied, the molecules will be separated by

molecular weight, with the high molecular weight molecules near the

wells and the low molecular weight molecules far from the wells. The

migration downwards. This leaves the large molecules at the top and the

smaller molecules at the bottom. Molecular weights are measured with

protein molecules of known molecular weight. These 'molecular weight

binds to a specific class of macromolecules in a sequence-independent

of macromolecules:

1) Electrophoresis, which takes advantage of the molecules'

2) Capillary blotting, where the molecules are transferred in a

Note: In a Southern Blot, the DNA molecules in the gel are

single-stranded molecules. RNA an protein are run in the gels in a state

molecules on it, as well as many spaces between the lanes, etc., where

no molecules have yet bound. If we added the probe directly to the

like the molecules transferred from the gel did. This would result in a

protein molecules and are not themselves radioactive.

labeled by chemically cross-linking the antibody molecules to molecules

molecules to find their targets.

the target molecules. Because the nitrocellulose is absorbent, some of

molecules with similar but not necessarily identical sequences (For

bound wherever the probe molecules could form hybrids with their

Hypertextbook Chapters

Large Molecules

Feedback Inhibition

major molecules in cells: nucleotides, amino acids, sugars, and lipids.

molecules.