Chapter 4: Protein Structure and Function
THE SHAPE AND STRUCTURE OF PROTEINS
• The noncovalent bonds that help proteins maintain their shape include hydrogen bonds,
electrostatic attractions and van der Waals attractions. Hydrophobic interaction also plays a
role in the shape of a protein.
• The final folded structure (conformation) is determined by energetic considerations: a
protein generally folds into the shape in which the free energy in minimized.
• In living cells proteins are generally assisted in folding into its correct conformation by special
proteins called molecular chaperones.
• α-helix: hydrogen bond between every fourth amino acid, linking the C=O from one bond to
the N-H of another. All the side chains of α-helices are pointed outward. If all side chains are
hydrophobic, an α-helix can be present in a layer of lipids.
• β-sheets are made when hydrogen bonds form between segments of polypeptide chains
lying side by side. When neighboring polypeptide chains run in the same orientation (both
from N-terminus to C-terminus for example), it is considered a parallel β-sheet. If not, it is
considered an antiparallel β-sheet. Both form a rigid, pleated structure. In β-sheets, side-
chains alternately point upwards and downwards. This means β-sheets can have a
hydrophilic and a hydrophobic side.
• Primary structure: amino acid sequence. Secondary structure: α-helices and β-sheets, or
elemental folds. Tertiary structure: the full, 3-dimensional conformation formed by an entire
polypeptide chain. Quaternary structure: multiple chains that together form a protein
molecule (not always the case).
• Protein domain: any segment of a polypeptide chain that can fold independently into a
compact, stable structure. Different domains are often associated with different functions.
• Larger protein molecules often consist of multiple polypeptide chains. Any region on a
protein’s surface that interacts with another molecule through sets of noncovalent bonds is
termed a binding site. Each polypeptide chain in such a protein is called a subunit. A chain of
identical protein molecules can be formed if the binding site on one protein molecule is
complementary to another region on the surface of another protein molecule of the same
type.
• Much of the structure of a cell is self-organizing: if the required proteins are produced in the
right amounts, the appropriate structures will form.
• Globular proteins: proteins in which the polypeptide chain folds up into a compact shape
with an irregular surface. Enzymes are often globular proteins. Fibrous proteins have a
relatively simple, elongated 3-dimensional structure (e.g. extracellular matrix).
• Proteins that are directly exposed to extracellular conditions often have covalent crosslinks
between chains or in the same protein. The most common of these cross-links are disulfide
bonds (SH-group → S-S).
,HOW PROTEINS WORK
• All proteins bind to other molecules: in some cases very tight, in others weak. The ability of a
protein to bind selectively is due to the formation of weak, noncovalent bonds: effective
interaction requires many weak bonds to be formed simultaneously. This is possible only if
the surface contours of the ligand (a substance that is bound by a protein) molecule fit very
closely to the protein.
• The binding site of a protein usually consists of a cavity in the surface.
• Our bodies are capable of producing antibodies that are able to recognize and bind tightly to
any molecule possible. When binding to a particular target molecule they either inactivate
this target (called an antigen)or mark it for destruction. Antibodies are Y-shaped with two
identical binding sites at the end of the arms.
• Enzymes bind to one or more ligands, called substrates, and speed up reactions without
themselves being changed. Enzymes act as catalysts that permit cells to make or break
covalent bonds at will.
• Sometimes proteins make use of non-protein molecules, because it would be difficult or
impossible to perform functions with amino acids alone. Example: heme groups,
noncovalently bound to hemoglobin, gives blood it red color and enables hemoglobin to pick
up oxygen and release it later.
HOW PROTEINS ARE CONTROLLED
• Protein activities are regulated in a coordinated fashion so that the cell can maintain itself in
an optimal state, generating only those molecules it requires to thrive under the current
conditions.
• The cell controls how many molecules of each enzyme it makes by regulating the expression
of the gene that encodes that protein.
• The cell controls enzymatic activities by confining sets of enzymes to particular subcellular
compartments.
• A molecule other than a substrate can bind to an enzyme at a special regulatory site outside
of the active site, altering the rate at which the enzyme converts its substrates to products.
This is often the case in feedback inhibition: an enzyme acting early in a reaction pathway is
inhibited by a late product of the pathway (negative regulation). The binding of the product
leads to conformational changes: it causes a shift in the structure and might for example lead
to a slightly less accommodating active site, thereby slowing down its working rate.
Many proteins are allosteric: they can adopt multiple conformations, and by a shift from one
to another, their activity can be regulated.
• Positive regulation: a product in one branch stimulates the activity of an enzyme in another
pathway.
• A method commonly used by eukaryotic cells involves attaching a phosphate group
covalently to one of the protein’s amino acid side chains. Because each phosphate group
carries two negative charges, this can lead to major conformational changes (e.g. by
attracting a cluster of positively charged amino side chains). This reversible protein
phosphorylation involves the enzyme-catalyzed transfer of one of the phosphate groups of
ATP to the hydroxyl group on a side chain of the protein. This reaction is catalyzed by a
protein kinase, the reversed reaction, dephosphorylation is catalyzed by a protein
phosphatase. Phosphorylation can either stimulate or inhibit protein activity. There are
many different protein kinases and phosphatases, each responsible for (de)phosphorylating a
different protein or set of proteins.
• There is another way to regulate protein activity by phosphate addition and removal. In this
case, the phosphate is part of a guanine nucleotide (GTP or GDP) that is bound tightly to the
protein. Such GTP-binding proteins are active with GTP bound. The protein itself then
hydrolyzes GTP to GDP and flips to an inactive conformation. This process is reversible. A
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GDP
to GTP is often stimulated in response to a signal received by the cell. The GTP-binding
proteins bind to other proteins to control their activities.
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• Conformational changes enable proteins whose major function is to
move other molecules, the motor proteins, to generate the forces
for muscle contraction and many of the dramatic movements of
Upload
cells. To make the series of conformational changes unidirectional it
is enough to make any of the steps irreversible. This is done, for
example, by shape changes due Share your
to ATP documents
or GTP hydrolysis.to unlock
• Each central process in a cell is catalyzed by a highly coordinated,
linked set of 10 or more proteins. In such protein machines the
hydrolysis of bound ATP or GTP drives an ordered series of
conformational changes in some of the individual protein subunits,
enabling the ensemble of proteins to move coordinately.
HOW PROTEINS ARE STUDIED
Free Trial
• Getcells
Proteins are often isolated from 30 that
days areofgrown
free in
Premium
a laboratory. Often these cells have
been tricked into making large quantities of a given protein.
• The first step in a purification procedure is to break open the cells to release their contents.
The resulting slurry is called a cell homogenate. This is followed by an initial fractionation
procedure to separate out the class of molecules of interest. To isolate the desired protein, a
series of chromatography steps are used. After each such step, one uses some sort of assay
to determineLearn moretheabout
which fractions protein ofStudocu Premium
interest, and so on. The most popular forms of
protein chromatography separate polypeptides on the basis of size, charge, or their ability to
bind to a particular chemical group (for example other proteins).
• Proteins can also be separated by electrophoresis. A mixture of proteins is loaded onto a
polymer gel and subjected to an electric field. The polypeptides will migrate through the gel
and different speeds depending on size and net charge.
• Many future advances may come from proteomics, the large-scale stud of cellular proteins in
which the activities or structures of hundreds (even thousands) of proteins are analyzed by
highly sensitive automated techniques.
, Chapter 7: From DNA to Protein: How Cells Read the Genome
• Before RNA exits the nucleus it must go through several RNA processing steps. These take
place as RNA is being transcribed. The enzymes responsible for RNA processing ride on the
‘tail’ of RNA polymerase as it transcribes RNA. Depending on which type of RNA is being
produced, the transcripts are processed in various ways. Two steps that only occur on
transcripts destined to become mRNA are capping and polyadenylation
o RNA capping involves a modification of the 5’ end of the mRNA transcript. The RNA is
capped by the addition of a G nucleotide with a methyl group, and occurs after RNA
polymerase has produced about 25 nucleotides.
o Polyadenylation: the 3’ ends of RNAs are first trimmed by an enzyme that cuts the
RNA chain at a particular sequence and are then finished off by an enzyme that adds
a series of A nucleotides. This poly-A-tail is 100s of nucleotides long
It is thought that these modifications increase the stability of mRNA, and to identify the RNA
molecule as mRNA.
• Most RNA undergoes an additional processing step. Most genes have their coding sequences
interrupted by noncoding intervening sequences, called introns. The coding sequences
(expressed sequences) are called exons and are shorter.
• After capping, and as RNA polymerase continues to transcribe the gene, RNA splicing begins,
in which the intron sequences are removed. Polyadenylation happens either after splicing or
before splicing has finished.
A cell determines which parts of the RNA transcript to remove by short nucleotide sequences
that act as cues. These sequences are found at the end of the intron and are the same or
similar in all introns. The intron sequence is cut out in the form of a ‘lariat’ structure.
RNA splicing is carried out largely by RNA molecules instead of proteins. RNA molecules
recognize intron-exon boundaries through complementary base-pairing and participate in
the chemistry of splicing. These RNA molecules (small nuclear RNAs or snRNAs) are
packaged with additional proteins to form small nuclear ribonucleoprotein particles (snRNPs).
The snRNPs form the core of the spliceosome, the assembly of RNA and proteins that carry
out RNA splicing.
• The transcripts of many genes can be spliced in different ways, which can produce a different
protein (alternative splicing). The intron-exon structure of genes is thought to have speeded
up the emergence of new and useful proteins in evolution.
• Of the total mRNA that is synthesized, only mature mRNA is useful to the cell. The remaining
RNA fragments (introns, broken RNAs) could be dangerous for the cell if not destroyed. The
cell needs to distinguish between mature mRNA and debris. It does this by having highly
selective transport of mRNA from the nucleus to the cytoplasm. This is regulated by the
nuclear pore complex. To be exported, mRNA must be bound to an appropriate set of
proteins, each of which signals the mRNA has been correctly processed. These proteins
include poly-A-binding proteins, a cap-binding complex and proteins that mark completed
RNA splices.
• A single mRNA molecule can be translated many times. mRNA is eventually degraded into
nucleotides by RNases, but the lifetimes of mRNAs differ (30mins – 10hrs), depending on the
nucleotide sequence and the type of cell in which the mRNA is produced. These lifetimes are
controlled by nucleotide sequences often present in the portion of the RNA called the 3’
untranslated region between the 3’ end of the coding sequence and the poly-A-tail. In
general, proteins made at high levels are translated from mRNAs that have long lifetimes.
FROM RNA TO PROTEIN
• Each group of 3 consecutive nucleotides in RNA is called a codon, specifying for one amino
acid.
THE SHAPE AND STRUCTURE OF PROTEINS
• The noncovalent bonds that help proteins maintain their shape include hydrogen bonds,
electrostatic attractions and van der Waals attractions. Hydrophobic interaction also plays a
role in the shape of a protein.
• The final folded structure (conformation) is determined by energetic considerations: a
protein generally folds into the shape in which the free energy in minimized.
• In living cells proteins are generally assisted in folding into its correct conformation by special
proteins called molecular chaperones.
• α-helix: hydrogen bond between every fourth amino acid, linking the C=O from one bond to
the N-H of another. All the side chains of α-helices are pointed outward. If all side chains are
hydrophobic, an α-helix can be present in a layer of lipids.
• β-sheets are made when hydrogen bonds form between segments of polypeptide chains
lying side by side. When neighboring polypeptide chains run in the same orientation (both
from N-terminus to C-terminus for example), it is considered a parallel β-sheet. If not, it is
considered an antiparallel β-sheet. Both form a rigid, pleated structure. In β-sheets, side-
chains alternately point upwards and downwards. This means β-sheets can have a
hydrophilic and a hydrophobic side.
• Primary structure: amino acid sequence. Secondary structure: α-helices and β-sheets, or
elemental folds. Tertiary structure: the full, 3-dimensional conformation formed by an entire
polypeptide chain. Quaternary structure: multiple chains that together form a protein
molecule (not always the case).
• Protein domain: any segment of a polypeptide chain that can fold independently into a
compact, stable structure. Different domains are often associated with different functions.
• Larger protein molecules often consist of multiple polypeptide chains. Any region on a
protein’s surface that interacts with another molecule through sets of noncovalent bonds is
termed a binding site. Each polypeptide chain in such a protein is called a subunit. A chain of
identical protein molecules can be formed if the binding site on one protein molecule is
complementary to another region on the surface of another protein molecule of the same
type.
• Much of the structure of a cell is self-organizing: if the required proteins are produced in the
right amounts, the appropriate structures will form.
• Globular proteins: proteins in which the polypeptide chain folds up into a compact shape
with an irregular surface. Enzymes are often globular proteins. Fibrous proteins have a
relatively simple, elongated 3-dimensional structure (e.g. extracellular matrix).
• Proteins that are directly exposed to extracellular conditions often have covalent crosslinks
between chains or in the same protein. The most common of these cross-links are disulfide
bonds (SH-group → S-S).
,HOW PROTEINS WORK
• All proteins bind to other molecules: in some cases very tight, in others weak. The ability of a
protein to bind selectively is due to the formation of weak, noncovalent bonds: effective
interaction requires many weak bonds to be formed simultaneously. This is possible only if
the surface contours of the ligand (a substance that is bound by a protein) molecule fit very
closely to the protein.
• The binding site of a protein usually consists of a cavity in the surface.
• Our bodies are capable of producing antibodies that are able to recognize and bind tightly to
any molecule possible. When binding to a particular target molecule they either inactivate
this target (called an antigen)or mark it for destruction. Antibodies are Y-shaped with two
identical binding sites at the end of the arms.
• Enzymes bind to one or more ligands, called substrates, and speed up reactions without
themselves being changed. Enzymes act as catalysts that permit cells to make or break
covalent bonds at will.
• Sometimes proteins make use of non-protein molecules, because it would be difficult or
impossible to perform functions with amino acids alone. Example: heme groups,
noncovalently bound to hemoglobin, gives blood it red color and enables hemoglobin to pick
up oxygen and release it later.
HOW PROTEINS ARE CONTROLLED
• Protein activities are regulated in a coordinated fashion so that the cell can maintain itself in
an optimal state, generating only those molecules it requires to thrive under the current
conditions.
• The cell controls how many molecules of each enzyme it makes by regulating the expression
of the gene that encodes that protein.
• The cell controls enzymatic activities by confining sets of enzymes to particular subcellular
compartments.
• A molecule other than a substrate can bind to an enzyme at a special regulatory site outside
of the active site, altering the rate at which the enzyme converts its substrates to products.
This is often the case in feedback inhibition: an enzyme acting early in a reaction pathway is
inhibited by a late product of the pathway (negative regulation). The binding of the product
leads to conformational changes: it causes a shift in the structure and might for example lead
to a slightly less accommodating active site, thereby slowing down its working rate.
Many proteins are allosteric: they can adopt multiple conformations, and by a shift from one
to another, their activity can be regulated.
• Positive regulation: a product in one branch stimulates the activity of an enzyme in another
pathway.
• A method commonly used by eukaryotic cells involves attaching a phosphate group
covalently to one of the protein’s amino acid side chains. Because each phosphate group
carries two negative charges, this can lead to major conformational changes (e.g. by
attracting a cluster of positively charged amino side chains). This reversible protein
phosphorylation involves the enzyme-catalyzed transfer of one of the phosphate groups of
ATP to the hydroxyl group on a side chain of the protein. This reaction is catalyzed by a
protein kinase, the reversed reaction, dephosphorylation is catalyzed by a protein
phosphatase. Phosphorylation can either stimulate or inhibit protein activity. There are
many different protein kinases and phosphatases, each responsible for (de)phosphorylating a
different protein or set of proteins.
• There is another way to regulate protein activity by phosphate addition and removal. In this
case, the phosphate is part of a guanine nucleotide (GTP or GDP) that is bound tightly to the
protein. Such GTP-binding proteins are active with GTP bound. The protein itself then
hydrolyzes GTP to GDP and flips to an inactive conformation. This process is reversible. A
, This is a preview
Do you want
large numberfull access?
of GTP Go function
-binding proteins Premium andswitches:
as molecular unlockthe all 36from
change pages
GDP
to GTP is often stimulated in response to a signal received by the cell. The GTP-binding
proteins bind to other proteins to control their activities.
Access to all documents
Get Unlimited Downloads
Improve your grades
• Conformational changes enable proteins whose major function is to
move other molecules, the motor proteins, to generate the forces
for muscle contraction and many of the dramatic movements of
Upload
cells. To make the series of conformational changes unidirectional it
is enough to make any of the steps irreversible. This is done, for
example, by shape changes due Share your
to ATP documents
or GTP hydrolysis.to unlock
• Each central process in a cell is catalyzed by a highly coordinated,
linked set of 10 or more proteins. In such protein machines the
hydrolysis of bound ATP or GTP drives an ordered series of
conformational changes in some of the individual protein subunits,
enabling the ensemble of proteins to move coordinately.
HOW PROTEINS ARE STUDIED
Free Trial
• Getcells
Proteins are often isolated from 30 that
days areofgrown
free in
Premium
a laboratory. Often these cells have
been tricked into making large quantities of a given protein.
• The first step in a purification procedure is to break open the cells to release their contents.
The resulting slurry is called a cell homogenate. This is followed by an initial fractionation
procedure to separate out the class of molecules of interest. To isolate the desired protein, a
series of chromatography steps are used. After each such step, one uses some sort of assay
to determineLearn moretheabout
which fractions protein ofStudocu Premium
interest, and so on. The most popular forms of
protein chromatography separate polypeptides on the basis of size, charge, or their ability to
bind to a particular chemical group (for example other proteins).
• Proteins can also be separated by electrophoresis. A mixture of proteins is loaded onto a
polymer gel and subjected to an electric field. The polypeptides will migrate through the gel
and different speeds depending on size and net charge.
• Many future advances may come from proteomics, the large-scale stud of cellular proteins in
which the activities or structures of hundreds (even thousands) of proteins are analyzed by
highly sensitive automated techniques.
, Chapter 7: From DNA to Protein: How Cells Read the Genome
• Before RNA exits the nucleus it must go through several RNA processing steps. These take
place as RNA is being transcribed. The enzymes responsible for RNA processing ride on the
‘tail’ of RNA polymerase as it transcribes RNA. Depending on which type of RNA is being
produced, the transcripts are processed in various ways. Two steps that only occur on
transcripts destined to become mRNA are capping and polyadenylation
o RNA capping involves a modification of the 5’ end of the mRNA transcript. The RNA is
capped by the addition of a G nucleotide with a methyl group, and occurs after RNA
polymerase has produced about 25 nucleotides.
o Polyadenylation: the 3’ ends of RNAs are first trimmed by an enzyme that cuts the
RNA chain at a particular sequence and are then finished off by an enzyme that adds
a series of A nucleotides. This poly-A-tail is 100s of nucleotides long
It is thought that these modifications increase the stability of mRNA, and to identify the RNA
molecule as mRNA.
• Most RNA undergoes an additional processing step. Most genes have their coding sequences
interrupted by noncoding intervening sequences, called introns. The coding sequences
(expressed sequences) are called exons and are shorter.
• After capping, and as RNA polymerase continues to transcribe the gene, RNA splicing begins,
in which the intron sequences are removed. Polyadenylation happens either after splicing or
before splicing has finished.
A cell determines which parts of the RNA transcript to remove by short nucleotide sequences
that act as cues. These sequences are found at the end of the intron and are the same or
similar in all introns. The intron sequence is cut out in the form of a ‘lariat’ structure.
RNA splicing is carried out largely by RNA molecules instead of proteins. RNA molecules
recognize intron-exon boundaries through complementary base-pairing and participate in
the chemistry of splicing. These RNA molecules (small nuclear RNAs or snRNAs) are
packaged with additional proteins to form small nuclear ribonucleoprotein particles (snRNPs).
The snRNPs form the core of the spliceosome, the assembly of RNA and proteins that carry
out RNA splicing.
• The transcripts of many genes can be spliced in different ways, which can produce a different
protein (alternative splicing). The intron-exon structure of genes is thought to have speeded
up the emergence of new and useful proteins in evolution.
• Of the total mRNA that is synthesized, only mature mRNA is useful to the cell. The remaining
RNA fragments (introns, broken RNAs) could be dangerous for the cell if not destroyed. The
cell needs to distinguish between mature mRNA and debris. It does this by having highly
selective transport of mRNA from the nucleus to the cytoplasm. This is regulated by the
nuclear pore complex. To be exported, mRNA must be bound to an appropriate set of
proteins, each of which signals the mRNA has been correctly processed. These proteins
include poly-A-binding proteins, a cap-binding complex and proteins that mark completed
RNA splices.
• A single mRNA molecule can be translated many times. mRNA is eventually degraded into
nucleotides by RNases, but the lifetimes of mRNAs differ (30mins – 10hrs), depending on the
nucleotide sequence and the type of cell in which the mRNA is produced. These lifetimes are
controlled by nucleotide sequences often present in the portion of the RNA called the 3’
untranslated region between the 3’ end of the coding sequence and the poly-A-tail. In
general, proteins made at high levels are translated from mRNAs that have long lifetimes.
FROM RNA TO PROTEIN
• Each group of 3 consecutive nucleotides in RNA is called a codon, specifying for one amino
acid.
