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References

Huse, M. and Kuriyan, J. (2002) The conformational plasticity of protein kinases, Cell, 109, pp. 275–282.
Lipscomb, W. N., Reeke, G. N. Jr, Hartsuck, J. A., Quiocho, F. A. and Bethge, P. H. (1970) The structure of carboxypeptidase A. 8. Atomic interpretation at 0.2 nm resolution, a new study of the complex of glycyl-L-tyrosine with CPA, and mechanistic deductio
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6.6 Summary of Section 6

  1. The majority of proteins of known function are enzymes. Enzymes are biological catalysts, increasing the rates of reactions. Enzymes are not permanently altered by catalysis of a reaction.

  2. The transition state is an unstable intermediate enzyme–substrate complex in which the enzyme and the substrate are in highly strained conformations.

  3. There are a number of different catalytic mechanisms employed by enzymes including general
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5.5 Summary of Section 5

  1. Proteins are dynamic molecular machines. All proteins bind to other molecules, whether ions, small molecules or macromolecules, and these interactions are critical to the protein's function. The activity of proteins is regulated by changes in conformation.

  2. In allosterically regulated proteins, binding of one ligand affects the conformation of a remote part of the protein, thereby regulating interaction with a second ligand. Cooperative binding
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5.3.2 Cooperative binding

A feature of some proteins comprising more than one subunit is that binding of a ligand to its binding site on one subunit, can increase the affinity of a neighbouring subunit for the same ligand, and hence enhance binding. The ligand-binding event on the first subunit is communicated, via conformational change, to the neighbouring subunit. This type of allosteric regulation is called cooperative binding.

Haemoglobin, as we have already discussed, is a tetramer consisting of two
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5.2 All proteins bind other molecules

All proteins bind to other molecules (generically termed ligands). Ligands that can bind to proteins include:

  • ions, e.g. Ca2+;

  • small molecules, e.g. H2O, O2 and CO2, glucose, ATP, GTP, NAD;

  • macromolecules, i.e. proteins, lipids, polysaccharides, nucleic acids.

These interactions are specific and key to the protein's function and, of course, are critically d
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5.1 Introduction

In some ways, proteins can be thought of as molecular machines, that through evolution have become highly specialised and efficient. Despite the somewhat static representations of proteins that you have met so far, proteins are in fact dynamic molecules. Not only are there internal movements, with conformational changes that are integral to protein function and regulation of function, but proteins, by virtue of their specific interactions with other cellular components, are essential to all t
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3.4 The functional domains of Src

To illustrate some of the principles of multidomain protein function, we will use as an example, the Src protein, a very well-characterised tyrosine kinase. As described earlier, Src contains four domains: two kinase domains, which together comprise the catalytic component of this protein, and two distinct binding/regulatory domains. The binding domains are of the SH2 and SH3 types. The identification of domains in other proteins, homologous to those in Src, led to the ‘Src ho
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1.6 Fibrous proteins

Most of the proteins described so far have been globular proteins. There are, however, some distinctive features that characterise fibrous proteins and we present here a general overview of these. Elongated fibrous proteins frequently play a structural role in the cell. They do not readily crystallise but tend to aggregate along their long axis to form fibres. X-ray diffraction studies of these fibres, in contrast to analysis of protein crystals, provides only very limited information on the
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1.4.4 Covalent cross-linkages stabilise protein structure

Proteins that are secreted by the cell, or are attached to the extracellular surface of the plasma membrane, can be subject to more extreme conditions than those experienced by intracellular proteins. Often, covalent cross-linkages stabilise these proteins by connecting specific amino acids within a polypeptide or between polypeptide chains in multisubunit proteins (see below). Typically such a linkage will be a covalent sulfur–sulfur bond which forms between the –SH groups of two cystein
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1.4.2 Protein fold

Protein folds are often very extensive arrangements, combining elements of secondary and supersecondary structure. Some of the most common protein folds are described in Table 4: view document with examples of proteins that contain them. Notice that proteins can be conveniently divided into three classes, on the basis of the elements of secondar
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1.4.1 Motifs and supersecondary structures

Supersecondary structures or motifs are particular arrangements and combinations of two or three secondary structures, often with defined topology (or connectivity). Table 3: view document describes some of the most common of these.

The term ‘motif’ is also used to describe a consensus sequence of amino acids, i.e. a partial sequence c
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1.1 Introduction

Proteins are made up of one or more polypeptide chains, polymers of amino acid residues found in all proteins. The structure that a polypeptide adopts is determined by the component amino acid units – both their chemical properties and the order in which they occur in the polymer – and by the structure of the peptide bond that links them.

Protein structure is described in terms of four levels of organisation: primary, secondary, tertiary and quaternary. The linear sequence of amino
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Introduction

Proteins are the ‘doers’ of the cell. They are huge in number and variety and diverse in structure and function, serving as both the structural building blocks and the functional machinery of the cell. Just about every process in every cell requires specific proteins.

Let us begin by listing some of the basic cellular processes and the role that proteins play.

  • Chemical catalysis Enzymes, which are responsible for catalysing biological
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1.3 Adding observations, images and locations to iSpot

Observations are the main thing on the site. To make an observation, you need to provide this information:

  • A photo and/or description of your observation
  • where you saw it (the location)
  • when you saw it (date)
  • what you saw (the identification, if you are able to suggest one - this is optional)

If you don't have a photograph just describe what you saw in as much detail as possible, including size, colour, behaviour etc. Y
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8.7 Luminosity functions

Samples of galaxies can be biased due to the flux limit of the sample that is observed. This is the so called Malmquist bias.

Activity 9: Radio-quiet quasars

0 hours 20 minutes

Read Pe
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8.6 Line spectra: Activity 8 Quasar redshifts

Activity 8: Quasar redshifts

Read Peterson section 1.3.5 (pages 16 and 17) by clicking the link below.

7.9 Compton scattering

Electromagnetic radiation interacts strongly with electrons. If a photon encounters an electron, there is a high probability that a scattering interaction will occur. In the low-energy non-relativistic regime, i.e. where h Author(s): The Open University

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7.7 Radiation detection

In astronomy we detect the radiation from large numbers of electrons, rather than being able to distinguish the contributions of individual electrons. The electrons will have a range of velocities and of orientations with respect to the magnetic field, so the synchrotron spectrum we observe will be the sum of lots of individual spectra with varying values of
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7.5 Emission from spiralling electrons: synchrotron radiation

In the very first reading (Activity 1) we encountered the term ‘non-thermal’ describing the spectrum of light emitted from AGN. In this subsection we will learn more about the most important type of non-thermal radiation: synchrotron emission.

When a charged particle moves in the presence of a magnetic field it experiences a Lorentz force, which produces an acceleration whose direction is perpendicular to both the magnetic field line and the velocity of the particle,
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7.3 Polarization of electromagnetic radiation

So far we have described electromagnetic radiation in terms of its wavelength, frequency and speed. It has another, sometimes important, property: polarization. Figure 10 shows the electric and magnetic field in a plane-polarized electromagnetic wave. In any electromagnetic radiation, the electric an
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