KA 2 Flashcards by Ella MacCulloch

What is the proteome?

The entire set of proteins expressed by a genome

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Why is the proteome larger than the number of genes? particularly in eukaryotes.

Because more than one protein can be produced from a single gene as a result of alternative RNA splicing

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What are all genes not expressed as?

Not all genes are expressed as proteins in a particular cell type.

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What are Genes that do not code for proteins called? What do they include and do?

Non-coding RNA genes and include those that are transcribed to produce tRNA, rRNA, and RNA molecules that control the expression of other genes.

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What can the set of proteins expressed by a given cell type do?

It can vary over time and under different conditions

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Some factors affecting the set of proteins expressed by..

a given cell type are the metabolic activity of the cell, cellular stress, the response to signalling molecules, and diseased versus healthy cells.

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What do Eukaryotic cells have? And what does this do because of..

A system of internal membranes, which increases the total area of membrane Because of their size, eukaryotes have a relatively small surface area to volume ratio.

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The plasma membrane of eukaryotic cells is too small an area to carry out what?

All the vital functions carried out by membranes.

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What does the endoplasmic reticulum (ER) do?

Forms a network of membrane tubules continuous with the nuclear membrane

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What is the Golgi apparatus?

It is a series of flattened membrane discs

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What are Lysosomes?

Membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates

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What do vesicles do?

Transport materials between membrane compartments

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Where are lipids and proteins synthesised?

In the ER (endoplasmic reticulum)

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What does Rough ER (RER) have? That Smooth ER (SER) lacks..

Ribosomes on its cytosolic face while smooth ER (SER) lacks ribosomes.

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What is the exact location of the synthesis of lipids? What happens to these after synthesis?

Lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane

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Where does the synthesis of all proteins begin and complete and where do these remain after?

In cytosolic ribosomes. The synthesis of cytosolic proteins is completed there, and these proteins remain in the cytosol.

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What do transmembrane proteins carry? And what does this do?

A signal sequence, which halts translation and directs the ribosome synthesising the protein to dock with the ER, forming RER

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What is a signal sequence? And what does this determine?

A short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell.

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What continues after docking? And what happens to the protein?

Translation and the protein is inserted into the membrane of the ER

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Once the proteins are in the ER what are they transported by?

Vesicles that bud off from the ER and fuse with the Golgi apparatus

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As proteins move through the Golgi apparatus what do they undergo?

Post-translational modification

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When molecules move through the Golgi discs what happens to them?

They move along in vesicles that bud off from one disc and fuse to the next one in the stack.

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Enzymes catalyse the addition of what?

Various sugars in multiple steps to form the carbohydrates.

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What is the addition of carbohydrate groups?

A major modification

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Where do vesicles that leave the Golgi apparatus take proteins?

To the plasma membrane and lysosomes

Vesicles move along what? To what?

Microtubules to other membranes and fuse with them within the cell

Secreted proteins are translated in what?

Ribosomes on the RER and enter its lumen.

Give 2 examples of secreted proteins

Peptide hormones and digestive enzymes

The proteins move through what and what happens to them after this?

The Golgi apparatus is then packaged into secretory vesicles.

Secretory vesicles move to and fuse with what? Which then releases…

The plasma membrane, releasing the proteins out of the cell

Many secreted proteins are synthesised as what? What do these require to become active?

Inactive precursors and require proteolytic cleavage to produce active proteins

Proteolytic cleavage is another type of?

Post translational modification.

Digestive enzymes are one example of ?

Secreted proteins that require proteolytic cleavage to become active.

Amino acid sequence determines what?

Protein structure

What can you use to distinguish between different amino acids?

Amino acid chromatography

What are proteins?

Proteins are polymers of amino acid monomers

What are Amino acids linked by?

peptide bonds to form polypeptides

Amino acids have the same? What differs about them?

Basic structure, differing only in the R group present R groups of amino acids vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity.

How are amino acids classified?

According to their R groups: basic (positively charged); acidic (negatively charged); polar; hydrophobic

What does the wide range of functions carried out by proteins result from?

The diversity of R groups

The primary structure is…

The sequence in which the amino acids are synthesised into the polypeptide

What does Hydrogen bonding along the backbone of the protein strand result in?

Regions of secondary structure — alpha helices, parallel or antiparallel beta-pleated sheets, or turns

What does the polypeptide fold into?

A tertiary structure

Tertiary structure is stabilised by?

Interactions between R groups: hydrophobic interactions; ionic bonds; London dispersion forces; hydrogen bonds; disulfide bridges

What are Disulfide bridges?

Covalent bonds between R groups containing sulfur.

Quaternary structure exists in proteins with?

Two or more connected polypeptide subunits

Quaternary structure describes?

The spatial arrangement of the subunits.

A prosthetic group is?

A non-protein unit tightly bound to a protein and necessary for its function

The ability of haemoglobin to bind oxygen is dependent upon?

The non-protein haem group.

Interactions of the R groups can be influenced by?

Temperature and pH.

Increasing temperature disrupts? What does this do to the protein?

The interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured.

The charges on acidic and basic R groups are affected by?

As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are?

Lost, which gradually changes the conformation of the protein until it becomes denatured.

Ligand binding changes?

The conformation of a protein

A ligand is?

A substance that can bind to a protein R groups not involved in protein folding can allow binding to ligands

Binding sites will have?

complementary shape and chemistry to the ligand

As a ligand binds to a protein-binding site?

The conformation of the protein changes

This change in protein conformation causes?

a functional change in the protein

Allosteric interactions occur between?

spatially distinct sites

The binding of a substrate molecule to one active site of an allosteric enzyme increases?

The affinity of the other active sites for binding of subsequent substrate molecules.

What is the biological importance of affinity changes after binding?

Because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration.

What do many allosteric proteins consist of?

Multiple subunits (have quaternary structure)

Allosteric proteins with multiple subunits show?

Cooperativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits

Allosteric enzymes contain?

A second type of site, called an allosteric site

Modulators regulate?

the activity of the enzyme when they bind to the allosteric site

Following binding of a modulator what changes and alters?

The conformation of the enzyme changes and this alters the affinity of the active site for the substrate

Positive modulators increase?

The enzyme’s affinity for the substrate

Negative modulators reduce?

the enzyme’s affinity.

The binding and release of oxygen in haemoglobin shows?

Cooperativity

Changes in binding of oxygen at one subunit alter?

the affinity of the remaining subunits for oxygen.

A decrease in pH or an increase in temperature does what to the affinity of haemoglobin for oxygen?

Lowers so the binding of oxygen is reduced.

Reduced pH and increased temperature in actively respiring tissue will?

Reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue

The addition or removal of phosphate can cause? What is this a common form of?

Reversible conformational change in proteins. This is a common form of post-translational modification

Protein kinases catalyse?

The transfer of a phosphate group to other proteins

The terminal phosphate of ATP is transferred to?

Specific R groups

Protein phosphatases catalyse?

The reverse reaction

Phosphorylation brings about?

Conformational changes, which can affect a protein’s activity

The activity of many cellular proteins, such as enzymes and receptors, is regulated?

By phosphorylation

Some proteins are …. By phosphorylation while others are?

Activated, inhibited

Adding a phosphate group adds?

Negative charges

Ionic interactions in the unphosphorylated protein can be?

Disrupted and new ones created.