Medical School - Semester 1 - Medical Biochemistry I - Lectures - Lecture. 2 - Protein Structure, Function and Regulation

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What are proteins? <ul><li>Proteins are the main buildingblocks from which
cells are assembled, and they constitute most of the cell’s dry mass<br></li><li>In
addition to providing the cell with shape and structure, proteins also execute
nearly all its myriad of functions<br></li></ul>
What are examples of the functions of proteins? <ul><li>Enzymatic proteins:
selective acceleration of chemical reactions. Example: Digestive enzymes catalyze
the hydrolysis of bonds in food molecules</li><li>Defensive proteins: protection
against disease. Example: Antibodies inactive and help destroy viruses and
bacteria</li><li>Storage proteins: Storage of amino acids. Example: Casein, the
protein of milk is the major source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an
amino acid source for the developing embryo. </li><li>Transport Proteins:
Transport of substances. Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to other parts of the body.
Other proteins transport molecules across membranes as shown
here. </li><li>Contractile and motor proteins: motor proteins are responsible
for the undulations of cilia and flagella. Actin and myosin proteins are
responsible for the contraction of muscles. </li><li>Structural proteins:
Example: Keratin, is the protein of hair, horns, feathers, and other skin
appendages, insects, and spiders use silk fibers to make their cocoons and webs
respectively. Collagen and elastin proteins provide a fibrous framework in animal
connective tissues. </li></ul>
What are amino acids? <ul><li>Proteins are all contstructed from the same set of
20 amino acids, linked in unbranched (linear) polymers. </li></ul>
What is the structure of the amino acid "<img src=""Screen Shot 2023-10-24 at
9.57.33 AM.png""><br><ul><li>Amino acids are define as small organic molecules that
possess one amino group, one carboxylic acid group, and a side chain.</li><li>The
identity of the side chain R is what distinguishes one amino acid from
another. </li></ul><div><img src=""Screen Shot 2023-10-24 at 9.59.05
AM.png""><br></div>"
Are Amino acids Chiral molecules? Yes they are, they contain optical isomers,
whereby the α-carbon is asymmetric allowing for 2 mirror-images or
stereoisomers: L and D. However proteins contain exclusively L-amino acids.
What is the basis for the preference for L amino acids? <div>The answer has been
lost to evolutionary history. It is possible that the preference for L over D amino
acids was a consequence of a chance selection. However, there is evidence that L
amino acids are slightly more soluble than a racemic mixture of D and L amino
acids, which tend to form crystals. This small solubility difference could have
been amplified over time so that the L isomer became dominant in solution<br></div>
How do Amino acids exist in different pH solutions? "<ul><li>Amino acids in
solution at neutral pH exist predominantly as dipolar ions (also called
zwitterions).<br></li><li>In the dipolar form, the amino group is protonated (-
NH3+) and the carboxyl group is deprotonated (-COO- ). The ionization state of an
amino acid varies with pH. In acid solution (e.g., pH 1), the amino group is
protonated (-NH3+) and the carboxyl group is not dissociated (-COOH). As the pH is
raised, the carboxylic acid is the first group to give up a proton. The dipolar
form persists until the pH approaches 9, when the protonated amino group loses a
proton<br></li></ul><div><img src=""Screen Shot 2023-10-24 at 10.03.43
What are Acidic and Basic Proteins? <ul><li>Acidic --> negatively charged R -
Side chain</li><li>Basic --> postively charged R - Side chain</li></ul>
How do we sort amino acids? <ol><li>Hydrophobic amino acids with nonpolar R
groups<br></li><li>Polar amino acids with neutral R groups but the charge is not
evenly distributed<br></li><li>Positively charged amino acids with R groups that
have a positive charge at physiological pH<br></li><li>Negatively charged amino
acids with R groups that have a negative charge at physiological pH<br></li></ol>
What is the covalent bond between 2 adjacent amino acids? Peptide bond
Explain the structure of the amino acids: <ul><li>They all possess a carboxylic
acid group and an amino group, both linked to their α-carbon atom (previous slide).
Each amino acid also has a side chain attached to its α-carbon. The identity of
this side chain is what distinguishes one amino acid from
another.<br></li><li>Regardless of the specific amino acids from which it is made,
the polypeptide always has an amino (-NH2) group at one end—its N-terminus—and a
carboxyl (-COOH) group at its other end—its C-terminus. This difference in the two
ends gives a polypeptide a definite directionality—a structural (as opposed to
electrical) polarity.Twenty types of amino acids are commonly found in proteins,
each with a different side chain attached to the α-carbon atom<br></li></ul>
How are amino acids joined together? <ul><li>Amino acids are joined together
by peptide bonds.</li><li>Peptide bond formation is a condensation reaction. In
cells, a similar reaction is catalyzed by ribosomes. Peptide bond cleavage is a
hydrolysis reaction. In cells, peptide bond cleavage is catalyzed by enzymes called
proteases. <br></li><li>Each polypeptide chain consists of a backbone that is
adorned with avariety of chemical side chains. </li><li>This polypeptide
backbone is formed from a repeating sequence of the core atoms (–N–C–C–) found in
every amino acid </li><li>Because the two ends of each amino acid are
chemically different—one sports an amino group (NH3+, also written NH2) and the
other a carboxyl group (COO–, also written COOH)—each polypeptide chain has a
directionality: the end carrying the amino group is called the amino terminus, or
N-terminus, and the end carrying the free carboxyl group is the carboxyl terminus,
or C-terminus<br></li><li>The side chains give each amino acid its unique
properties: some are nonpolar and hydrophobic (“water-fearing”), some are
negatively or positively charged, some can be chemically reactive, and so
on.<br></li></ul>
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Define a Heterotrimeric protein complex? "<img src=""Screen Shot 2023-10-24 at
10.18.46 AM.png""><br>Each subunit has individual structural and chemical
properties"
Define Homodimeric protein complex? "Two identical protein subunits<br><img
src=""Screen Shot 2023-10-24 at 10.19.18 AM.png"">"
What determines amino acid sequences? Amino acid sequences of proteins are
determined by the nucleotide sequences of genes. The sequence of nucleotides in DNA
specifies a complementary sequence of nucleotides in RNA, which in turn specifies
the amino acid sequence of a protein.
What are the 4 types of noncovalent interactions that help proteins fold?
"<ul><li>The shape of each of these folded chains, however, is constrained by
many sets of weak noncovalent bonds that form within proteins. These bonds involve
atoms in the polypeptide backbone, as well as atoms in the amino acid side
chains.</li><li>The noncovalent bonds that help proteins fold up and maintain their
shape include hydrogen bonds, electrostatic attractions, hydrophobic interactions
and van der Waals attractions<br></li><li>Because a noncovalent bond is much weaker
than a covalent bond, it takes many noncovalent bonds to hold two regions of a
polypeptide chain tightly together. The stability of each folded shape is largely
influenced by the combined strength of large numbers of noncovalent
bonds <br></li><li>A fourth weak force, hydrophobic interaction, also has a
central role in determining the shape of a protein. In an aqueous environment,
hydrophobic molecules, including the nonpolar side chains of particular amino
acids, tend to be forced together to minimize their disruptive effect on the
hydrogen-bonded network of the surrounding water molecules. Therefore, an important
factor governing the folding of any protein is the distribution of its polar and
nonpolar amino acids<br></li><li>The nonpolar (hydrophobic) side-chains tend to
cluster in the interior of thefolded protein. Tucked away inside the folded
protein, hydrophobic side chains can avoid contact with the aqueous cytosol that
surrounds them inside a cell.<br></li><li>polar side chains tend to arrange
themselves near the outside of the folded protein, where they can form hydrogen
bonds with water and with other polar molecules. When polar amino acids are buried
within the protein, they are usually hydrogen-bonded to other polar amino acids or
to the polypeptide backbone<br></li></ul><div><img src=""Screen Shot 2023-10-24 at
10.26.40 AM.png""><br></div><div><img src=""Screen Shot 2023-10-24 at 10.26.53
Which technique helps portrays the structure of the proteinX-ray Crystallography
Why is protein structure important to medicine? <ul><li>In the 1980s, it was
discovered that a single defective protein (BCR-Abl, atyrosine kinase enzyme) could
cause chronic myelogenous leukemia (CML)<br></li><li>By the mid-to-late 1990s, a
powerful, specific inhibitor of the abnormal cell pathway was developed from a
promising but weak-acting inhibitor class of molecules<br></li><li>Blocking the
pathway prevents the uncontrolled proliferation of white blood
cells<br></li><li>The drug is Gleevec/Glivec<br></li></ul>
What are the 4 levels of protein structure <ul><li>Proteins share three levels
of structure: Primary, secondary, tertiary</li><li>The 4th level, quaternary arises
when the protein consists of 2 or more polypeptide chains.</li></ul>
What is the primary protein structure <ul><li>The primary structure of a
protein is its sequence of amino acids<br></li><li>The final Shape of a Protein Is
Specified by Its Amino Acid Sequence</li></ul>
What is the secondary protein structure? "<ul><li>The secondary structure of a
protein comes about, when the polypeptide takes on a certain orientation in
space. </li><li>The secondary structure is the result of Hydrogen bonding
between the C ═ O of one amino acid and the N — H of another amino acid in the
polypeptide backbone<br></li><li>Coiling of the chain results in an α (alpha) helix
(a right-handed spiral), while a folding of the chain results in a β (beta) pleated
sheet.<br></li><li>Hydrogen bonding between atoms of the peptide bonds holds the
shape in place<br></li></ul><div><img src=""Screen Shot 2023-10-24 at 10.32.18
AM.png""><br></div><div><ul><li>Regions of amino acid sequences stabilized in
specific conformations or structures by hydrogen bonds between atoms of the
polypeptide backbone</li></ul></div>"
What is the alpha helix <div>Coiling of the chain results in an α (alpha) helix (a
right-handed spiral)<br></div>
What is a Beta pleated sheet <div><div><div>Folding of the chain results in a β
(beta) pleated sheet</div><div></div></div></div><div><div><div><br></div></div></
div>
What are the two variaties of Beta Pleated sheets? "<ol><li>Antiparallel β
sheet<br></li></ol><div><img src=""Screen Shot 2023-10-24 at 10.37.24
AM.png""> 2. Parallel Beta Pleated
Sheet: <br></div><div><img src=""Screen Shot 2023-10-24 at 10.38.17
AM.png""><br></div><div>Both of these structures are common in proteins. By
convention, the arrows point toward the C-terminus of the polypeptide
chain<br></div>"
Explain the alpha helix? a delicate coil held together by hydrogen bonding
between every <b>fourth</b> amino acid. Although each transthyretin polypeptide has
only one helix region, other globular proteins have multiple stretches of helix
separated by nonhelical regions. Some fibrous proteins, such as keratin, the
structural protein of hair, have the alpha helix formation over most of their
length.
Explain the Beta Pleated Sheets? <ul><li>In this structure two or more segments
of the polypeptide chain lying side by side are connected by hydrogen bonds between
parts of the two parallel segments of polypeptide backbone. </li><li>Beta
pleated sheets make up the core of many globular proteins, as is the case for
transthyretin (see Tertiary Structure), and dominate some fibrous proteins,
including the silk protein of a spider’s web. The teamwork of so many hydrogen
bonds makes each spider silk fiber stronger than a steel strand of the same
weight.</li></ul>
How are the domains of the proteins comprised? <ul><li>Many proteins are composed
of separate functional domains.<br></li><li>Elements of secondary structure such as
α helices and β sheets pack together into stable, independently folding, globular
elements called protein domains<br></li><li>A typical protein molecule is built
from one or more domains, linked by a region of polypeptide chain that is often
relatively unstructured.</li></ul>
What is a Tertiary Protein Structure <ul><li>The tertiary structure of a
protein is its final, 3D shape. In most proteins, the hydrophobic portions are
packed on the inside and the hydrophilic portions are on the outside, where they
can make contact with water. The tertiary structure determines the types of
molecules with which proteins will interact<br></li><li>The tertiary shape of a
polypeptide is maintained by various types of bonding between the R groups;
covalent, electrostatic, hydrophobic, van der Waals and hydrogen bonding all
occur<br></li></ul><div><br></div>
What is a disulfide bond The formation of a disulfide bond (disulfide bridge)
from two cysteine residues in a polypeptide chain stabilizes the tertiary structure
as well as quaternary structure.
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What is the quaternary structure? <ul><li>Some proteins have more than one
polypeptide, each with its own primary, secondary, and tertiary structures. These
separate polypeptides are arranged to give these proteins a fourth level of
structure, termed the quaternary structure<br></li></ul>
How does Misfolded proteins cause diseases? <ul><li>It has been estimated that
up to 30% of proteins that are synthesized in cells need to be refolded or degraded
to prevent the accumulation of non-functional proteins.<br></li><li>If these
misfolded proteins are not refolded or removed, they can interfere with the
function of normal proteins through the formation of protein
aggregates<br></li><li>Numerous human diseases have now been associated with
defects in protein folding <br></li><li>Many of these protein-folding diseases
are due to mutations in the protein-coding sequence of the gene, whereas others
have been shown to be the result of accumulated misfolded proteins that contain no
amino acid changes<br></li></ul>
What are some diseases caused by misfolded proteins? "<img src=""Screen Shot 2023-
10-24 at 10.47.52 AM.png"">"
How is Sickle Cell disease caused by misfolded proteins? <ul><li>Sickle cell is
caused by a change in the primary structure.</li><li>Even a slight change in
primary structure can affect a protein’s shape and ability to
function<br></li><li>Sickle-cell disease: an inherited blood disorder, is caused by
the substitution of one amino acid (valine) for the normalone (glutamic acid) at
the position of the sixth amino acid in the primary structure of
hemoglobin<br></li></ul>
How are Proteins controlled? <div><ol><li>Protein Production (gene
regulation)<br></li><li>Protein Degradation<br></li><li>Protein
localization/transport in specific subcellular compartments<br></li><li>Direct and
rapid inhibition/activation of proteins at the level of polypeptide chain itself
(by modifications or interactions with other molecules)<br></li></ol></div>
What is Protein Production (gene regulation) steps? <ol><li>Activator
Proteins bind to distal control elements grouped as an enhancer in the DNA. This
enhancer has 3 binding sites, each called distal control elements.</li><li>A DNA
Binding protein brings the bound activators closer to the promoter. General
transcription factors, mediator proteins, and RNA Polymerase II are
nearby. </li><li>The activators bind to certain mediator proteins and general
transcription factors, helping them form an active transcription initiation complex
on the promoter. </li></ol>
What are the steps for protein degredation Via
Lysosomes: <br><ol><li>Lysosomes contains active hydrolytic
enzymes </li><li>Lysosomes fuses with vacuole </li><li>Hydrolytic enzymes
digest food, waste, etc. particles </li></ol><div>Via
Proteosomes:</div><div><div><div>Proteins are targeted for proteasomal degradation
by a two-part degron, which consists of a proteasome binding signal and a
degradation initiation site.</div></div></div>
Proteins Are Transported into Organelles by Three Mechanisms:
"<ol><li>Transport through nuclear pores</li><li>Transport across
membranes</li><li>Transport by vesicles</li></ol><div>The fate of any protein
molecule
synthesized in the
cytosol depends on its
amino acid sequence,
which can contain a
sorting signal that
directs the protein to
the organelle in
which it is required<br></div>"
Explain the three mechanisms of transport for proteins: "<ol><li>Proteins moving
from the cytosol into the nucleus are transported through the nuclear pores, which
penetrate both the inner and outer nuclear
membranes. The pores function as selective gates that actively transport specific
macromolecules but also allow free diffusion of smaller
molecules<br></li><li>Proteins moving from the cytosol into the ER, mitochondria,
or chloroplasts are transported across the organelle membrane by protein
translocators
located in the membrane. Unlike transport through nuclear pores, the transported
protein must usually unfold in order to snake across the membrane
through the translocator. Bacteria have similar protein translocators in their
plasma membrane, which they use to export
proteins from the cytosol to the cell exterior<br></li><li>Proteins moving onward
from the ER—and from one compartment of the endomembrane system to another—are
transported by a mechanism that is
fundamentally different. These proteins are ferried by transport vesicles, which
pinch off from the membrane of one compartment and then fuse with the
membrane of a second compartment. In this process, transport vesicles deliver
soluble cargo proteins, as well as the
proteins and lipids that are part of the vesicle membrane.<br></li></ol>"
"<span class=""cloze"" data-cloze=""Sorting signals"" data-
ordinal=""1"">[...]</span> in
the amino acid
sequence of
proteins direct
their <span class=""cloze-inactive"" data-ordinal=""2"">transport and
localization</span> in
specific organelles" "<span class=""cloze"" data-ordinal=""1"">Sorting
signals</span> in
the amino acid
sequence of
proteins direct
their <span class=""cloze-inactive"" data-ordinal=""2"">transport and
specific organelles<br>
"
"<span class=""cloze-inactive"" data-ordinal=""1"">Sorting signals</span> in
the amino acid
sequence of
proteins direct
their <span class=""cloze"" data-cloze=""transport and
localization""
data-ordinal=""2"">[...]</span> in
specific organelles" "<span class=""cloze-inactive"" data-ordinal=""1"">Sorting
signals</span> in
the amino acid
sequence of
proteins direct
their <span class=""cloze"" data-ordinal=""2"">transport and
specific organelles<br>
"
How do enzymes work? "<img src=""Screen Shot 2023-10-25 at 9.09.01
AM.png""><br><img src=""Screen Shot 2023-10-25 at 9.09.13 AM.png"">"
"<span class=""cloze"" data-cloze=""Covalent modifications"" data-
ordinal=""1"">[...]</span>
can control Protein
activity by <span class=""cloze-inactive"" data-ordinal=""2"">regulating
structural
conformation, location
and interaction
repertoire</span>" "<span class=""cloze"" data-ordinal=""1"">Covalent
modifications</span>
can control Protein
activity by <span class=""cloze-inactive"" data-ordinal=""2"">regulating
structural
and interaction
repertoire</span><br>
"
"<span class=""cloze-inactive"" data-ordinal=""1"">Covalent modifications</span>
can control Protein
activity by <span class=""cloze"" data-
cloze=""regulating
structural
and&#
x20;interaction
repertoire"" data-ordinal=""2"">[...]</span>" "<span
class=""cloze-inactive"" data-ordinal=""1"">Covalent modifications</span>
can control Protein
activity by <span class=""cloze"" data-ordinal=""2"">regulating
structural
and interaction
repertoire</span><br>
"
Discuss the set of hydrophilic and hydrophobic amino acids "<img src=""Screen Shot
2023-10-30 at 10.29.11 AM.png"">"

Medical School - Semester 1 - Medical Biochemistry I - Lectures - Lecture. 2 - Protein Structure, Function and Regulation

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<button id=""io-revl-btn"" onclick=""toggle();"">Toggle Masks</button>

// Prevent original image from loading before mask

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