Video Lecture Notes: Amino Acids, Peptides, Polypeptides, and Proteins
Amino Acids, Peptides, and Polypeptides
Anything over 40 amino acids is considered a protein.
Peptide bond: the bond between amino acids.
N terminus: corresponds to the 5' end of DNA and RNA.
C terminus: corresponds to the 3' end of DNA and RNA.
Enkephalins: Pentapeptides as Painkillers
Enkephalins are pentapeptides, meaning they consist of five amino acids.
Function: they signal to the brain and act as painkillers.
Mechanism: they bind to pain receptors, preventing stimuli transmission from nerve to nerve.
Runner's High: Enkephalins bind to pain receptors in the brain, reducing pain and fatigue and inducing euphoria after long runs.
Peptide Hormones: Oxytocin and Vasopressin
Oxytocin
Nine amino acid peptide (nonapeptide).
Produced by the posterior pituitary gland.
Functions:
Stimulates uterine contractions (used to induce labor).
Helps shrink the uterus back to normal size post-birth.
Signals to the breasts to contract, facilitating lactation.
Vasopressin
Antidiuretic hormone; nine amino acids in length.
Produced by the posterior pituitary gland.
Function:
Signals to the kidneys to retain fluid, reducing urine output and preventing dehydration.
Proteins: Polypeptides with Secondary Structures
Proteins are polypeptides greater than 40 amino acids in length that adopt secondary structures.
Two main types:
Fibrous proteins
Globular proteins
Fibrous Proteins
Long, linear proteins that wrap around each other (like a French braid).
Water insoluble; essential for structural components.
Examples:
Keratin
Alpha-keratin
Collagen
Globular Proteins
Compact, tangled structures.
Water soluble, allowing them to move throughout the body.
Examples:
Hemoglobin
Myoglobin
Protein Shape and Function
Every protein has a unique three-dimensional shape that dictates its function.
Fibrous proteins are long and water-insoluble.
Globular proteins are compact and water-soluble, facilitating transport throughout the body.
Alpha-Keratin: Structure and Function
Fibrous protein found in hair, nails, and skin.
Composed of two alpha-keratin chains forming a superhelix.
Provides strength and toughness to hair and nails.
Collagen: Structure, Function, and Vitamin C
Found in connective tissues such as bones, tendons, and blood vessels.
Formed from three helix structures that wrap around each other like a French braid.
Vitamin C stabilizes the structure.
Scurvy:
Caused by vitamin C deficiency.
Leads to breakdown of blood vessels, causing bleeding (e.g., gum bleeding).
Rare in developed countries due to vitamin C availability.
Hemoglobin and Myoglobin: Conjugated Globular Proteins
Conjugated proteins: contain protein and non-protein components (heme).
Heme molecule:
Contains Fe^{2+} (iron(II) cation), which binds oxygen.
Gives blood its red color.
Myoglobin:
Tertiary structure
Stores oxygen in cardiac and muscle cells.
Composed of a single polypeptide chain and a single heme molecule.
Hemoglobin:
Quaternary protein with four tertiary subunits (two alpha and two beta).
Each subunit contains a heme molecule, allowing it to transport four oxygen molecules.
Delivers oxygen throughout the body.
Heme and Oxygen Binding
Heme is chelated, holding iron in the center.
Iron (Fe2+) binds a single oxygen molecule (O_2).
Myoglobin releases oxygen when muscles are depleted, causing the burning sensation during workouts.
Red blood cells (erythrocytes) contain millions of hemoglobin molecules.
Insulin: A Globular Protein Hormone
Synthesized in the pancreas (islets of Langerhans) and released into the blood.
Regulates blood glucose levels.
Globular protein made of two polypeptide chains (A and B) held together by disulfide bonds.
Water solubility is essential to prevent precipitation and clot formation in the blood.
Insulin Production:
Transcription: DNA to mRNA.
Translation: mRNA to protein.
Preproinsulin: precursor molecule.
Proinsulin: converted to insulin and C-peptide in the Golgi apparatus.
Insulin is secreted into the bloodstream and binds to cells, facilitating glucose uptake.
Enzymes: Biological Catalysts
Catalysts speed up reaction rates without being changed themselves.
Enzymes are proteins that act as biological catalysts.
Identification: Enzymes often have names ending in "-ase".
Classification of Enzymes
Oxidoreductases
Transferases
Hydrolases
Isomerases
Lyases
Ligases
Enzyme Functions
Oxidases: oxidize molecules.
Dehydrogenases: remove hydrogen.
Transaminases: move amino groups.
Kinases: move phosphate groups (important in ATP production).
Lipases: hydrolyze lipids.
Nucleases: hydrolyze RNA and nucleic acids.
Proteases: degrade proteins by breaking peptide bonds.
Mechanisms of Enzyme Action
Enzymes favor reactions in one direction but can go back and forth.
Active Site: unique region on the enzyme where the substrate binds.
Enzyme-Substrate Complex: formed when enzyme and substrate are bound.
The enzyme remains unchanged after the reaction, while the substrate is converted to products.
Enzymes increase reaction rates by bringing reactants into close proximity.
Enzyme Models
Lock and Key Model: rigid active site with high specificity.
Induced Fit Model: flexible active site that changes shape to accommodate the substrate.
Factors Affecting Enzyme Activity
Temperature and pH: can alter enzyme function by affecting the bonds that hold the protein together.
Optimal temperature and pH ranges exist for maximum enzyme activity.
High temperatures can break apart proteins, causing them to lose function.
Changes in pH can also affect enzyme function.
Allosteric Control: Turning Enzymes On and Off
Regulators: molecules that bind to enzymes and can either turn them on or off.
Negative Allosteric Control:
A regulator binds to a site other than the active site, causing a conformational change.
The active site changes shape, preventing the substrate from binding, and turning the enzyme off.
Positive Allosteric Control:
A regulator binds to a site other than the active site, causing a conformational change.
The active site opens up, allowing the substrate to bind, and turning the enzyme on.
Enzyme Inhibitors: Competitive and Noncompetitive
Bind to enzymes and inhibit their activity.
Irreversible inhibitors: permanently destroy enzymatic activity.
Reversible inhibitors: temporarily turn off enzyme activity.
Competitive Inhibition:
Inhibitor competes with the substrate for the active site. The inhibitor binds to the active site first, preventing the substrate from binding.
Noncompetitive Inhibition:
Inhibitor binds to a site other than the active site, inducing a conformational change. The active site changes shape, preventing the substrate from binding.
Zymogens: Inactive Enzyme Precursors
Proenzymes: inactive enzymes that are activated when needed.
Enzymes ending in "-gen" are zymogens.
Example: Trypsinogen is an inactive form of trypsin.
Trypsin: An enzyme that breaks down proteins. It's found in the stomach and only activated when protein is present, to not damage the cells that have proteins.
Trypsinogen is converted to trypsin when protein is present.
Enzymes in Diagnostics
Enzymes can leak into the circulatory system, lymphatic system, or interstitial tissue when cells are damaged or die.
Measuring enzyme levels can indicate potential injury within the body.
Examples:
Creatine Phosphokinase: Elevated levels in the blood can signal a heart attack. It is normally not present within the circulatory system.
Acid Phosphatase: Can be a sign of prostate cancer.
Amylase and Lipase: Elevated levels in the blood can signal pancreatitis.
Enzymes as Drug Targets: ACE Inhibitors
Angiotensin-Converting Enzyme (ACE): increases blood pressure.
ACE Inhibitors: block the conversion of angiotensin I to angiotensin II, lowering blood pressure.
Renin-Angiotensin System:
Renin is released from the kidneys in response to low blood pressure or fluid volume.
Renin acts on angiotensinogen (released from the liver) to convert it to angiotensin I.
ACE (released from the lungs) converts angiotensin I to angiotensin II.
Angiotensin II stimulates aldosterone release from the adrenal gland.
Aldosterone increases water and salt retention in the kidneys, raising blood pressure.
Angiotensin II also causes vasoconstriction, increasing blood pressure.
ACE inhibitors prevent the conversion of angiotensin I to angiotensin II, blocking vasoconstriction and water retention, and thereby lowering blood pressure.
Amino Acids, Peptides, and Polypeptides
Anything over 40 amino acids is considered a protein.
Peptide bond: the bond between amino acids.
N terminus: corresponds to the 5' end of DNA and RNA.
C terminus: corresponds to the 3' end of DNA and RNA.
Enkephalins: Pentapeptides as Painkillers
Enkephalins are pentapeptides, meaning they consist of five amino acids.
Function: they signal to the brain and act as painkillers.
Mechanism: they bind to pain receptors, preventing stimuli transmission from nerve to nerve.
Runner's High: Enkephalins bind to pain receptors in the brain, reducing pain and fatigue and inducing euphoria after long runs.
Peptide Hormones: Oxytocin and Vasopressin
Oxytocin
Nine amino acid peptide (nonapeptide).
Produced by the posterior pituitary gland.
Functions:
Stimulates uterine contractions (used to induce labor).
Helps shrink the uterus back to normal size post-birth.
Signals to the breasts to contract, facilitating lactation.
Vasopressin
Antidiuretic hormone; nine amino acids in length.
Produced by the posterior pituitary gland.
Function:
Signals to the kidneys to retain fluid, reducing urine output and preventing dehydration.
Proteins: Polypeptides with Secondary Structures
Proteins are polypeptides greater than 40 amino acids in length that adopt secondary structures.
Two main types:
Fibrous proteins
Globular proteins
Fibrous Proteins
Long, linear proteins that wrap around each other (like a French braid).
Water insoluble; essential for structural components.
Examples:
Keratin
Alpha-keratin
Collagen
Globular Proteins
Compact, tangled structures.
Water soluble, allowing them to move throughout the body.
Examples:
Hemoglobin
Myoglobin
Protein Shape and Function
Every protein has a unique three-dimensional shape that dictates its function.
Fibrous proteins are long and water-insoluble.
Globular proteins are compact and water-soluble, facilitating transport throughout the body.
Alpha-Keratin: Structure and Function
Fibrous protein found in hair, nails, and skin.
Composed of two alpha-keratin chains forming a superhelix.
Provides strength and toughness to hair and nails.
Collagen: Structure, Function, and Vitamin C
Found in connective tissues such as bones, tendons, and blood vessels.
Formed from three helix structures that wrap around each other like a French braid.
Vitamin C stabilizes the structure.
Scurvy:
Caused by vitamin C deficiency.
Leads to breakdown of blood vessels, causing bleeding (e.g., gum bleeding).
Rare in developed countries due to vitamin C availability.
Hemoglobin and Myoglobin: Conjugated Globular Proteins
Conjugated proteins: contain protein and non-protein components (heme).
Heme molecule:
Contains Fe^{2+} (iron(II) cation), which binds oxygen.
Gives blood its red color.
Myoglobin:
Tertiary structure
Stores oxygen in cardiac and muscle cells.
Composed of a single polypeptide chain and a single heme molecule.
Hemoglobin:
Quaternary protein with four tertiary subunits (two alpha and two beta).
Each subunit contains a heme molecule, allowing it to transport four oxygen molecules.
Delivers oxygen throughout the body.
Heme and Oxygen Binding
Heme is chelated, holding iron in the center.
Iron (Fe^{2+}) binds a single oxygen molecule (O_2).
Myoglobin releases oxygen when muscles are depleted, causing the burning sensation during workouts.
Red blood cells (erythrocytes) contain millions of hemoglobin molecules.
Insulin: A Globular Protein Hormone
Synthesized in the pancreas (islets of Langerhans) and released into the blood.
Regulates blood glucose levels.
Globular protein made of two polypeptide chains (A and B) held together by disulfide bonds.
Water solubility is essential to prevent precipitation and clot formation in the blood.
Insulin Production:
Transcription: DNA to mRNA.
Translation: mRNA to protein.
Preproinsulin: precursor molecule.
Proinsulin: converted to insulin and C-peptide in the Golgi apparatus.
Insulin is secreted into the bloodstream and binds to cells, facilitating glucose uptake.
Enzymes: Biological Catalysts
Catalysts speed up reaction rates without being changed themselves.
Enzymes are proteins that act as biological catalysts.
Identification: Enzymes often have names ending in "-ase".
Classification of Enzymes
Oxidoreductases
Transferases
Hydrolases
Isomerases
Lyases
Ligases
Enzyme Functions
Oxidases: oxidize molecules.
Dehydrogenases: remove hydrogen.
Transaminases: move amino groups.
Kinases: move phosphate groups (important in ATP production).
Lipases: hydrolyze lipids.
Nucleases: hydrolyze RNA and nucleic acids.
Proteases: degrade proteins by breaking peptide bonds.
Mechanisms of Enzyme Action
Enzymes favor reactions in one direction but can go back and forth.
Active Site: unique region on the enzyme where the substrate binds.
Enzyme-Substrate Complex: formed when enzyme and substrate are bound.
The enzyme remains unchanged after the reaction, while the substrate is converted to products.
Enzymes increase reaction rates by bringing reactants into close proximity.
Enzyme Models
Lock and Key Model: rigid active site with high specificity.
Induced Fit Model: flexible active site that changes shape to accommodate the substrate.
Factors Affecting Enzyme Activity
Temperature and pH: can alter enzyme function by affecting the bonds that hold the protein together.
Optimal temperature and pH ranges exist for maximum enzyme activity.
High temperatures can break apart proteins, causing them to lose function.
Changes in pH can also affect enzyme function.
Allosteric Control: Turning Enzymes On and Off
Regulators: molecules that bind to enzymes and can either turn them on or off.
Negative Allosteric Control:
A regulator binds to a site other than the active site, causing a conformational change.
The active site changes shape, preventing the substrate from binding, and turning the enzyme off.
Positive Allosteric Control:
A regulator binds to a site other than the active site, causing a conformational change.
The active site opens up, allowing the substrate to bind, and turning the enzyme on.
Enzyme Inhibitors: Competitive and Noncompetitive
Bind to enzymes and inhibit their activity.
Irreversible inhibitors: permanently destroy enzymatic activity.
Reversible inhibitors: temporarily turn off enzyme activity.
Competitive Inhibition:
Inhibitor competes with the substrate for the active site. The inhibitor binds to the active site first, preventing the substrate from binding.
Noncompetitive Inhibition:
Inhibitor binds to a site other than the active site, inducing a conformational change. The active site changes shape, preventing the substrate from binding.
Zymogens: Inactive Enzyme Precursors
Proenzymes: inactive enzymes that are activated when needed.
Enzymes ending in "-gen" are zymogens.
Example: Trypsinogen is an inactive form of trypsin.
Trypsin: An enzyme that breaks down proteins. It's found in the stomach and only activated when protein is present, to not damage the cells that have proteins.
Trypsinogen is converted to trypsin when protein is present.
Enzymes in Diagnostics
Enzymes can leak into the circulatory system, lymphatic system, or interstitial tissue when cells are damaged or die.
Measuring enzyme levels can indicate potential injury within the body.
Examples:
Creatine Phosphokinase: Elevated levels in the blood can signal a heart attack. It is normally not present within the circulatory system.
Acid Phosphatase: Can be a sign of prostate cancer.
Amylase and Lipase: Elevated levels in the blood can signal pancreatitis.
Enzymes as Drug Targets: ACE Inhibitors
Angiotensin-Converting Enzyme (ACE): increases blood pressure.
ACE Inhibitors: block the conversion of angiotensin I to angiotensin II, lowering blood pressure.
Renin-Angiotensin System:
Renin is released from the kidneys in response to low blood pressure or