USABO QUESTIONS AND ANSWERS SET A+
✔✔Glycosaminoglycans (GAG's) - ✔✔Also known as mucopolysaccharides these are
long unbranched polysaccharides consisting of a repeating disaccharide unit. The
repeating unit consists of a hexose (six-carbon sugar) or a hexuronic acid, linked to a
hexosamine (six-carbon sugar containing nitrogen). These are the major component of
the 'gel' found in the extracellular matrix of tissue. They are negatively charged and thus
attract ions, especially sodium which aids diffusion of water in to the tissue, giving tissue
it's compression resistance.
✔✔Extracellular Matrix - ✔✔This matrix is secreted by cells and laid down externally
and it's properties vary enormously depending on it's chemical composition and which
tissue is being examined. In some cells it acts as cement or scaffolding. In plants it can
be associated with individual cells.
✔✔Elastin - ✔✔An flexible protein found in the extra cellular matrix of blood vessels.
✔✔Collagen - ✔✔A strong protein which can provide strength and/or flexibility found in
animal tissue.
✔✔Connective Tissue - ✔✔The name often given to tissue that contain a large
proportion of extracellular matrix. In this tissues the cells that are secreting the materials
are often quite far from each other.
✔✔Gap junction - ✔✔A specialised type of cell junction, an example of which is the
smooth muscle of the intestine. The gap's allow for effective transmission of molecules
and electrical activity between the cells.
✔✔Tight junctions - ✔✔These cell junctions are linked very closely and prevent
movement of membrane proteins, in the skin for example or in the role mainting the
polarity of the cells of the intestine.
,✔✔Cytoskeleton - ✔✔A system of specialised long filament like proteins found in the
cytosol of eukaryote cells which forms the constantly changing 'scaffolding'. They have
many roles such as movement of motile cells, transport of organelles around the cell
and intracellular movement of chromosomes during mitosis.
✔✔Microfilaments - ✔✔Also known as actin filaments,one of three protein sub units that
make up the eukaryote cytoskeleton. Found in highest concentration around the edges
of the cell just below the cell membrane, they tend to form bundles. Actin polymers have
the ability to disassemble and re-assemble meaning they are particulary useful for cell
locomotion and in the microvilli of absorptive epithelial cells.
✔✔Tubulin - ✔✔The protein of which the microtubules of the eukaryote cytoskeleton are
formed.
✔✔Microtubules - ✔✔Hollow tubes composed of thirteen parallel filaments of
polymerized tubulin, measuring about 25 nm in external diameter. Part of the
cytoskeleton of ALL eukaryote cells radiating from the centrosome in the nucleas
towards the edges of the cell. They are very unstable and are constantly disassembling
and reassembling so most do not reach the cell cortex. These tubules play a crucial role
in cell organisation, movement of organelles and the reorganization of chormosomes in
to daughter cells during mitosis.
✔✔Gel Filtration - ✔✔This form of filtration chromatography seprarates proteins,
peptides, and oligonucleotides on the basis of size. Molecules move through a bed of
porous beads, diffusing into the beads to greater or lesser degrees. Smaller molecules
diffuse further into the pores of the beads and therefore move through the bed more
slowly, while larger molecules enter less or not at all and thus move through the bed
more quickly. Both molecular weight and three-dimensional shape contribute to the
degree of retention. This technique may be used for analysis of molecular size, for
separations of components in a mixture, or for salt removal or buffer exchange from a
preparation of macromolecules.
✔✔Gel Electrophoresis - ✔✔In simple terms: This is a procedure which enables the
sorting of molecules based on size and charge. Using an electric field, molecules (such
as DNA) can be made to move through a gel made of agar. The molecules being sorted
are dispensed into a well in the gel material. The gel is placed in an electrophoresis
chamber, which is then connected to a power source. When the electric current is
applied, the larger molecules move more slowly through the gel while the smaller
molecules move faster. The different sized molecules form distinct bands on the gel.
✔✔SDS-PAGE - ✔✔SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel
electrophoresis, is a technique widely used in biochemistry, forensics, genetics and
molecular biology to separate proteins according to their electrophoretic mobility (a
function of length of polypeptide chain or molecular weight). SDS gel electrophoresis of
samples that have identical charge per unit mass due to binding of SDS results in
,fractionation by size. This method can be used to separate all types, even those that are
not water soluble.
✔✔Two Dimensional PAGE - ✔✔Also known as 2-D electrophoresis, begins with 1-D
electrophoresis but then separates the molecules by a second property in a direction 90
degrees from the first. In 1-D electrophoresis, proteins (or other molecules) are
separated in one dimension, so that all the proteins/molecules will lie along a lane but
that the molecules are spread out across a 2-D gel. Because it is unlikely that two
molecules will be similar in two distinct properties, molecules are more effectively
separated in 2-D electrophoresis than in 1-D electrophoresis.
✔✔Western Blotting - ✔✔This protein seperation technique (sometimes called the
protein immunoblot) is a widely used analytical technique used to detect specific
proteins in the given sample of tissue homogenate or extract. It uses gel electrophoresis
to separate native or denatured proteins by the length of the polypeptide (denaturing
conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions).
The proteins are then transferred to a membrane (typically nitrocellulose or PVDF),
where they are probed (detected) using antibodies specific to the target protein.
There are now many reagent companies that specialize in providing antibodies (both
monoclonal and polyclonal antibodies) against tens of thousands of different proteins.
Commercial antibodies can be expensive, although the unbound antibody can be
reused between experiments. This method is used in the fields of molecular biology,
biochemistry, immunogenetics and other molecular biology disciplines.
✔✔Tertiary Structure - ✔✔In biochemistry and molecular biology, this structure of a
protein or any other macromolecule is its three-dimensional structure, as defined by the
atomic coordinates.[6] Proteins and nucleic acids are capable of diverse functions
ranging from molecular recognition to catalysis. Such functions require a precise three-
dimensional tertiary structure. While such structures are diverse and seemingly
complex, they are composed of recurring, easily recognizable tertiary structure motifs
that serve as molecular building blocks. Tertiary structure is considered to be largely
determined by the biomolecule's primary structure, or the sequence of amino acids or
nucleotides of which it is composed. Efforts to predict tertiary structure from the primary
structure are known generally as structure prediction.
✔✔Primary Structure - ✔✔This is the name given to the sequence of amino acid
monomer units, or residues of which a compound is composed.
✔✔Alpha carbon - ✔✔The carbon bonded to the carboxyl group in an amino acid.
✔✔R Group - ✔✔This is the group which varies in proteins and can be any of twenty
amino acids, the polarity of this Group dictates how a protein will behave in certain pH
conditions. This explains why enzymes require a certain pH to function.
, ✔✔Peptide Bond - ✔✔This bond occurs when the amino group from one protein joins
with the carboxyl group of another, forming a dipeptide.
✔✔Dipeptide - ✔✔A protein formed by two amino acids linked by a peptide bond,
✔✔Amino Terminus - ✔✔The name by which the -NH₂ free end of a peptide is known.
✔✔Carboxyl Terminus - ✔✔The name by which the -COOH (carboxyl) free end of a
peptide is known.
✔✔Peptide - ✔✔Small chains of amino acids.
✔✔Mr - ✔✔Shorthand for molecular mass.
✔✔Hydrophobic residues/amino acid - ✔✔Amino acids which are non polar and are
repelled by water example are Alanine, Valine, Leucine, Isoleucine, Proline, Methionine,
Phenylalanine, Tryptophan and Cystine. Hydrophbicity is also affected by pH levels in
some cases.
✔✔Hydrophillic residues/amino acid - ✔✔Amino acids which are polar and are attracted
to water examples are Glutamine, Serine,Theronine, Histodine, Lysine. Hydrophbicity is
also affected by pH levels in some cases.
✔✔Polar - ✔✔Pertaining to a compound exhibiting polarity or dipole moment, that is a
compound bearing a partial positive charge on one side and a partial negative charge
on the other.
✔✔Non Polar - ✔✔Molecule which has no separation of charge, so no positive or
negative poles are formed.
✔✔α Helix - ✔✔A common motif in the secondary structure of proteins, the alpha helix
(α-helix) is a right-handed coiled or spiral conformation, in which every backbone N-H
group donates a hydrogen bond to the backbone C=O group of the amino acid four
residues earlier (i+4 \rightarrow i hydrogen bonding). This secondary structure is also
sometimes called a classic Pauling-Corey-Branson alpha helix . Among types of local
structure in proteins, the α-helix is the most regular and the most predictable from
sequence, as well as the most prevalent.
✔✔β sheet - ✔✔The β sheet (also β-pleated sheet) is the second form of regular
secondary structure in proteins, only somewhat less common than alpha helix. Beta
sheets consist of beta strands connected laterally by at least two or three backbone
hydrogen bonds, forming a generally twisted, pleated sheet. A beta strand (also β
strand) is a stretch of polypeptide chain typically 3 to 10 amino acids long with
backbone in an almost fully extended conformation. The higher-level association of β
✔✔Glycosaminoglycans (GAG's) - ✔✔Also known as mucopolysaccharides these are
long unbranched polysaccharides consisting of a repeating disaccharide unit. The
repeating unit consists of a hexose (six-carbon sugar) or a hexuronic acid, linked to a
hexosamine (six-carbon sugar containing nitrogen). These are the major component of
the 'gel' found in the extracellular matrix of tissue. They are negatively charged and thus
attract ions, especially sodium which aids diffusion of water in to the tissue, giving tissue
it's compression resistance.
✔✔Extracellular Matrix - ✔✔This matrix is secreted by cells and laid down externally
and it's properties vary enormously depending on it's chemical composition and which
tissue is being examined. In some cells it acts as cement or scaffolding. In plants it can
be associated with individual cells.
✔✔Elastin - ✔✔An flexible protein found in the extra cellular matrix of blood vessels.
✔✔Collagen - ✔✔A strong protein which can provide strength and/or flexibility found in
animal tissue.
✔✔Connective Tissue - ✔✔The name often given to tissue that contain a large
proportion of extracellular matrix. In this tissues the cells that are secreting the materials
are often quite far from each other.
✔✔Gap junction - ✔✔A specialised type of cell junction, an example of which is the
smooth muscle of the intestine. The gap's allow for effective transmission of molecules
and electrical activity between the cells.
✔✔Tight junctions - ✔✔These cell junctions are linked very closely and prevent
movement of membrane proteins, in the skin for example or in the role mainting the
polarity of the cells of the intestine.
,✔✔Cytoskeleton - ✔✔A system of specialised long filament like proteins found in the
cytosol of eukaryote cells which forms the constantly changing 'scaffolding'. They have
many roles such as movement of motile cells, transport of organelles around the cell
and intracellular movement of chromosomes during mitosis.
✔✔Microfilaments - ✔✔Also known as actin filaments,one of three protein sub units that
make up the eukaryote cytoskeleton. Found in highest concentration around the edges
of the cell just below the cell membrane, they tend to form bundles. Actin polymers have
the ability to disassemble and re-assemble meaning they are particulary useful for cell
locomotion and in the microvilli of absorptive epithelial cells.
✔✔Tubulin - ✔✔The protein of which the microtubules of the eukaryote cytoskeleton are
formed.
✔✔Microtubules - ✔✔Hollow tubes composed of thirteen parallel filaments of
polymerized tubulin, measuring about 25 nm in external diameter. Part of the
cytoskeleton of ALL eukaryote cells radiating from the centrosome in the nucleas
towards the edges of the cell. They are very unstable and are constantly disassembling
and reassembling so most do not reach the cell cortex. These tubules play a crucial role
in cell organisation, movement of organelles and the reorganization of chormosomes in
to daughter cells during mitosis.
✔✔Gel Filtration - ✔✔This form of filtration chromatography seprarates proteins,
peptides, and oligonucleotides on the basis of size. Molecules move through a bed of
porous beads, diffusing into the beads to greater or lesser degrees. Smaller molecules
diffuse further into the pores of the beads and therefore move through the bed more
slowly, while larger molecules enter less or not at all and thus move through the bed
more quickly. Both molecular weight and three-dimensional shape contribute to the
degree of retention. This technique may be used for analysis of molecular size, for
separations of components in a mixture, or for salt removal or buffer exchange from a
preparation of macromolecules.
✔✔Gel Electrophoresis - ✔✔In simple terms: This is a procedure which enables the
sorting of molecules based on size and charge. Using an electric field, molecules (such
as DNA) can be made to move through a gel made of agar. The molecules being sorted
are dispensed into a well in the gel material. The gel is placed in an electrophoresis
chamber, which is then connected to a power source. When the electric current is
applied, the larger molecules move more slowly through the gel while the smaller
molecules move faster. The different sized molecules form distinct bands on the gel.
✔✔SDS-PAGE - ✔✔SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel
electrophoresis, is a technique widely used in biochemistry, forensics, genetics and
molecular biology to separate proteins according to their electrophoretic mobility (a
function of length of polypeptide chain or molecular weight). SDS gel electrophoresis of
samples that have identical charge per unit mass due to binding of SDS results in
,fractionation by size. This method can be used to separate all types, even those that are
not water soluble.
✔✔Two Dimensional PAGE - ✔✔Also known as 2-D electrophoresis, begins with 1-D
electrophoresis but then separates the molecules by a second property in a direction 90
degrees from the first. In 1-D electrophoresis, proteins (or other molecules) are
separated in one dimension, so that all the proteins/molecules will lie along a lane but
that the molecules are spread out across a 2-D gel. Because it is unlikely that two
molecules will be similar in two distinct properties, molecules are more effectively
separated in 2-D electrophoresis than in 1-D electrophoresis.
✔✔Western Blotting - ✔✔This protein seperation technique (sometimes called the
protein immunoblot) is a widely used analytical technique used to detect specific
proteins in the given sample of tissue homogenate or extract. It uses gel electrophoresis
to separate native or denatured proteins by the length of the polypeptide (denaturing
conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions).
The proteins are then transferred to a membrane (typically nitrocellulose or PVDF),
where they are probed (detected) using antibodies specific to the target protein.
There are now many reagent companies that specialize in providing antibodies (both
monoclonal and polyclonal antibodies) against tens of thousands of different proteins.
Commercial antibodies can be expensive, although the unbound antibody can be
reused between experiments. This method is used in the fields of molecular biology,
biochemistry, immunogenetics and other molecular biology disciplines.
✔✔Tertiary Structure - ✔✔In biochemistry and molecular biology, this structure of a
protein or any other macromolecule is its three-dimensional structure, as defined by the
atomic coordinates.[6] Proteins and nucleic acids are capable of diverse functions
ranging from molecular recognition to catalysis. Such functions require a precise three-
dimensional tertiary structure. While such structures are diverse and seemingly
complex, they are composed of recurring, easily recognizable tertiary structure motifs
that serve as molecular building blocks. Tertiary structure is considered to be largely
determined by the biomolecule's primary structure, or the sequence of amino acids or
nucleotides of which it is composed. Efforts to predict tertiary structure from the primary
structure are known generally as structure prediction.
✔✔Primary Structure - ✔✔This is the name given to the sequence of amino acid
monomer units, or residues of which a compound is composed.
✔✔Alpha carbon - ✔✔The carbon bonded to the carboxyl group in an amino acid.
✔✔R Group - ✔✔This is the group which varies in proteins and can be any of twenty
amino acids, the polarity of this Group dictates how a protein will behave in certain pH
conditions. This explains why enzymes require a certain pH to function.
, ✔✔Peptide Bond - ✔✔This bond occurs when the amino group from one protein joins
with the carboxyl group of another, forming a dipeptide.
✔✔Dipeptide - ✔✔A protein formed by two amino acids linked by a peptide bond,
✔✔Amino Terminus - ✔✔The name by which the -NH₂ free end of a peptide is known.
✔✔Carboxyl Terminus - ✔✔The name by which the -COOH (carboxyl) free end of a
peptide is known.
✔✔Peptide - ✔✔Small chains of amino acids.
✔✔Mr - ✔✔Shorthand for molecular mass.
✔✔Hydrophobic residues/amino acid - ✔✔Amino acids which are non polar and are
repelled by water example are Alanine, Valine, Leucine, Isoleucine, Proline, Methionine,
Phenylalanine, Tryptophan and Cystine. Hydrophbicity is also affected by pH levels in
some cases.
✔✔Hydrophillic residues/amino acid - ✔✔Amino acids which are polar and are attracted
to water examples are Glutamine, Serine,Theronine, Histodine, Lysine. Hydrophbicity is
also affected by pH levels in some cases.
✔✔Polar - ✔✔Pertaining to a compound exhibiting polarity or dipole moment, that is a
compound bearing a partial positive charge on one side and a partial negative charge
on the other.
✔✔Non Polar - ✔✔Molecule which has no separation of charge, so no positive or
negative poles are formed.
✔✔α Helix - ✔✔A common motif in the secondary structure of proteins, the alpha helix
(α-helix) is a right-handed coiled or spiral conformation, in which every backbone N-H
group donates a hydrogen bond to the backbone C=O group of the amino acid four
residues earlier (i+4 \rightarrow i hydrogen bonding). This secondary structure is also
sometimes called a classic Pauling-Corey-Branson alpha helix . Among types of local
structure in proteins, the α-helix is the most regular and the most predictable from
sequence, as well as the most prevalent.
✔✔β sheet - ✔✔The β sheet (also β-pleated sheet) is the second form of regular
secondary structure in proteins, only somewhat less common than alpha helix. Beta
sheets consist of beta strands connected laterally by at least two or three backbone
hydrogen bonds, forming a generally twisted, pleated sheet. A beta strand (also β
strand) is a stretch of polypeptide chain typically 3 to 10 amino acids long with
backbone in an almost fully extended conformation. The higher-level association of β
