Bio/Biochem

Question 1

• Microtubules
• Microfilaments
• Intermediate Filaments

-Golgi operation hypotheses

• Lysosomes
• Peroxisome
• Proteasome
• COPI
• COPII
• Clathrin
• Lytic
• Lysogenic

Answer 1

-Microtubules: Made of actin. Provide structure to the cytoskeleton and function in cytokinesis.

• Microfilaments: Organized in the centrosome. Several functions:
  1) form spindle fibers during mitosis
  2) used by molecular transport proteins like kinesin and dynein
  3) key component of motility components like flagella and cilia

-Intermediate Filaments: Maintain cell shape and structure. Unlike the other fibers, does not function in motility. Classic examples are keratin and desmin.

-Golgi operation hypotheses:
Two hypotheses for how the Golgi apparatus works:
• Cisternal maturation hypothesis: Proteins remain in cisternae of the Golgi with fixed locations, but the cisternae evolve over time
• Vesicular transport hypothesis: The cisternae are static and do not evolve, but proteins get shuttled to different parts of the Golgi through vesicles

• Cytochrome c of mitochondria signals to capases during oxidative stress*
• Lysosomes: Breaks down cells through hydrolytic enzymes activated by acidic pH. Can help trigger apoptosis.
• Peroxisome: Breaks down and detoxifies hydrogen peroxide and ethanol. Also helps metabolize fatty acids through beta oxidation.
• Proteasome: Degrades proteins that are tagged by ubiquitin.
• *Note that a proteasome is a protein complex (not an organelle).**

-COPI: Retrograde transport from Golgi apparatus to ER.
Mnemonic: the earliest cop has a retro style = COPI does retrograde transport

-COPII: Anterograde transport from ER to Golgi apparatus
Mnemonic: COP two returns proteins to the Golgi where they were packaged

• Clathrin: Transports proteins from Golgi apparatus to plasma membrane
• Lytic: Forces host cell to use its replicative resources until it lyses, but does not integrate into genome.
• Lysogenic: Integrates into genome and stays dormant until activated.

Question 2

• Transformation
• Conjugation
• Transduction
• Transposons
• Episomes
• Flagella Motion
• Reproductive System:
• Spermatogenesis
• Prostate gland
• Bulbourethral gland
• Oogonium
• Primary oocyte
• Primary follicle
• Secondary oocyte
• Estrogen
• Progesterone

Answer 2

• Transformation: Bacteria integrates external DNA from environment
• Conjugation: Plasmid transfer between two bacteria, connected by a sex pilus encoded by F plasmid.
• Transduction: DNA transfer through viral vector (bacteriophage).
• Transposons: Regions of DNA that can insert/remove themselves in a bacterial chromosome, jumping around. They contribute to genetic variation.
• Episomes: A piece of genetic material that can either exist independently of the main chromosome or at other times be integrated into a genome. Transposons and viral vectors are both examples of episomes.
• Flagella motion: Counterclockwise movement of a bacteria’s flagella results in forward motion while clockwise movement results in change of direction
• Reproductive System
• Spermatogenesis: Sperm is produced in the seminiferous tubules and is nourished by Sertoli cells, which are stimulated by FSH
• Prostate gland: Produces seminal fluid, which is alkaline and neutralizes the acidic female reproductive environment.
• Bulbourethral gland: Function: Produces viscous fluid that clears out and lubricates urethra.
• Oogonium: Divides into two primary oocytes during the time before birth. This first step occurs by mitosis
• Primary oocyte: Remain arrested at birth in prophase I until menstrual cycle of puberty. After completing meiosis I, one daughter cell becomes polar body and the other a secondary oocyte. This step marks the transition from diploid to haploid.
• Primary follicle: Houses the primary oocyte. Growth and maturation is stimulated by FSH.
• Secondary oocyte: Begins meiosis II and arrests at metaphase II. Then finishes meiosis II after fertilization. End products after fertilization are fertilized egg and second polar body.
• Estrogen: Released by the ovaries. Made in response to FSH and results in increase in LH. Causes buildup/thickening of endometrium (uterine lining).
• Progesterone: Released in response to LH. Results in maintenance of the endometrium (uterine lining).

Question 3

• Embryogenesis:
• Cleavage
• Morula
• Blastulation
• Gastrulation
• Neurulation
• Germ Layers:
• Ectoderm
• Mesoderm
• Endoderm
• Stem cell potency:
• -> Totipotent
• -> Multipotent
• -> Pluripotent
• Communication: electrical synapse vs chemical synapse
• Sympathetic vs parasympathetic system: pre- and post-ganglionic neurons
• Action Potential:
• Resting Membrane Potential
• Depolarization
• Repolarization
• Hyperpolarization

Answer 3

• Embryogenesis:
• Cleavage: Fertilized egg undergoes rapid division through 8-cell stage, with cells being totipotent.
• Morula: Solid mass of cells that enters the uterine cavity.
• Blastulation: The cell mass becomes a hollow cavity and implants into the endometrium (uterine lining). The outer cells become the placenta and inner cells become embryo.
• Gastrulation: The germ layers and notochord form. First step is formation of primitive streak, which determines midline of body.
• Neurulation: The ectoderm is induced by the notochord. The ectoderm then forms the neural tube, which develops into the brain and spine (central nervous system), and the neural crest cells, which develop into the peripheral nervous system.
• Germ Layers:
• Ectoderm: Ectoderm = Attract-oderm.
• —-> Develops into attractive features such as outer appearance (skin, eyes, hair, nails), external orifices (mouth, anus), and “personality” (nervous system).
• Mesoderm: Mesoderm = Movement.
• —> Develops into things that move externally (bone, muscle) and internally (lymph, blood, steroid hormones, urinary system including kidneys and gonads).
• Endoderm: Endoderm = Inner tubing or IN-doderm.
• —–> Develops into internal organs such as GI system, respiratory system, endocrine glands.
• Stem cell potency:
• Totipotent: “total” freedom to develop into any cell.
• Multipotent: “multiple.” Can develop into several different types. Adult stem cells are multipotent.
• Pluripotent: “plural”. Can develop into any cell except placental structures.
• Communication: electrical synapse vs chemical synapse
• -> Electrical synapse is a direct physical connection through a gap junction between neurons. Chemical synapse is when neurons communicate through neurotransmitters released from synaptic vesicles
• Sympathetic: Preganglionic neurotransmitter is acetylcholine and postganglionic is norepinephrine.
• Parasympathetic: Both preganglionic and postganglionic neurotransmitter is acetylcholine
• Action Potential:
• Resting Membrane Potential: embrane potential of -70 mV. At rest K+ ions are concentrated inside of the cell and Na+ ions are outside, due to greater membrane permeability for K+. The concentration gradients are maintained by Na+-K+ pump which moves 3 Na+ from inside to outside and 2 K+ from outside to inside per unit of ATP.
• Depolarization: Upon reaching threshold potential, Na+ ions move inside of the cell through voltage-gated Na+ channels. –> Peaks at +30 mV.
• Repolarization: Occurs as K+ ions move outside of the cell. Returns membrane potential in direction of resting potential.
• Hyperpolarization: Cell “overshoots” its resting membrane potential because of delayed closing of K+ channels. While returning to resting state, cell is in a refractory period and cannot fire.

Question 4

• Glial Cells:
• Astrocytes
• Ependymal cells
• Microglia
• Satellite Cells
• Schwann cells versus oligodendrocytes

-Temporal vs spatial summation

• Inhibitory neurotransmitters
• Excitatory neurotransmitters
• Synaptic release
• Total lung volume
• Tidal volume
• Functional residual capacity Residual volume
• Inspiratory and expiratory reserve volume
• Vital capacity
• Pharynx
• Larynx
• Blood acidosis
• Blood alkalosis

-Differential pressure: Intrapulmonary and intrapleural pressure

• Inhalation
• Exhalation
• Surface tension
• Regulation
• Respiratory quotient

Answer 4

• Glial Cells:
• Astrocytes: Help form the blood-brain barrier. Regulate solute and ion balance.
• Ependymal cells: Form lining between cerebrospinal fluid (CSF) and interstitial fluid.
• Microglia: Immune cell. Functions to break down waste and repair damage.
• Satellite Cells: Injury and Inflammation
• Schwann cells versus oligodendrocytes: Both coat axons with myelin
• –> Oligodendrocytes: myelinate many cells in the central nervous system (CNS)
• —-> Schwann cells: myelinate the axon of one cell in the peripheral nervous system (PNS)
• *Mnemonic: COPS drive fast like myelin. CNS Oligodendrocytes PNS Schwann cells.**
• Temporal Summation: Multiple excitatory signals from a single neuron sum together to trigger a threshold action potential.
• Spatial summation: Excitatory signals from many neurons sum together to trigger a threshold action potential.
• Inhibitory neurotransmitters: Primary inhibitory neurotransmitter in brain is GABA. Primary inhibitory neurotransmitter in spinal cord is glycine.
• Excitatory neurotransmitters: Primary excitatory neurotransmitter in the central nervous system is glutamate.
• Synaptic release: Calcium influx triggers neurotransmitter release into the synaptic cleft. Neurotransmitters are often released in vesicle form through exocytosis.
• Total lung volume: Sum of all volumes in the lungs.
• *Note that this can not be measured by spirometry (only lung capacity can be measured).**
• Tidal volume: Volume of a normal breath.
• Functional residual capacity: Volume left in lungs after a natural exhalation
• Residual volume: Volume left in lungs after a full forced exhalation. In order to keep alveoli open, the lung cannot fully deflate, resulting in residual volume
• Inspiratory and expiratory reserve volume: Additional volume that can be inhaled after a natural breath in, or exhaled after a natural breath out.
• Vital capacity: Volume of a full forced inhalation and exhalation. Equals the total lung capacity minus the residual volume.
• Pharynx: Connects the mouth to the esophagus. Allows passage of both air and food.
• Larynx: Connects the mouth to the trachea. Allows air, but food is blocked by the epiglottis.
• Blood acidosis: If the blood pH is too low, the body will compensate by increasing respiration rate to blow off more CO2.
• Blood alkalosis: If the blood pH is too high, the body will compensate by decreasing respiration rate to blow off less CO2.
• Differential Pressure: Intrapulmonary pressure: same as atmospheric pressure because lung is open to outside.
• -> Intrapleural pressure: lower than atmospheric pressure to keep lung from collapsing.
• Inhalation: Occurs through negative pressure mechanism. The diaphragm muscle pulls downward, decreasing intrapleural pressure and causing lung expansion.
• Exhalation: Usually a passive process due to muscle relaxation. Active exhalation recruits the intercostal muscles to help force air out.
• Regulation: Respiratory control center of brain is the medulla oblongata. When blood pH is acidic, respiration increases to blow off CO2 and increase bicarbonate buffer.
• Respiratory quotient: Amount of CO2 produced per O2 consumed.

Question 5

• Small Intestine produces which enzymes?
• Secretin
• Cholecystokinin (CCK)
• Where does food enter and leave the stomach?
• Parietal cells
• G-cells
• Chief cells
• Goblet cells
• Trypsin
• Pancreas: Exocrine function and pH regulation
• Esophagus
• Large Intestine

Answer 5

• Small Intestine: Functions in digestion and absorption. Divided into duodenum, jejunum, then ileum (think DJ Ileum). Also produces the enzymes secretin and CCK.
• Secretin: Stimulates release of pancreatic bicarbonate in response to acidic chyme from stomach.
• Cholecystokinin (CCK): Stimulates release of bile from the gallbladder.
• In the stomach, food enters through gastroesophageal sphincter and exits through pyloric sphincter.
• Parietal cells: Secrete hydrochloric acid (maintain pH of 2 in stomach) and intrinsic factor (IF) (vitamin B12 absorption).
• G-cells: Produce gastrin which stimulates secretion of gastric juices.
• Chief cells: Secrete pepsinogen which is converted to pepsin, an enzyme which breaks down food and is activated by acidic environment.
• Goblet cells: Produce mucus lining to protect the wall of the stomach from self-digestion.
• Trypsin: Catalyzes the breakdown of peptide bonds in proteins. Converted from inactive form of trypsinogen to active form by enteropeptidase.
• Pancreas: Exocrine function and pH regulation
• -> Produces digestive enzymes including amylase, lipase, proteases.
• -> Produces bicarbonate.
• Trypsin: Catalyzes the breakdown of peptide bonds in proteins. Converted from inactive form of trypsinogen to active form by enteropeptidase.*
• Esophagus: Top third has skeletal muscle and is under somatic control.
• Bottom third has smooth muscle and is under autonomic control.
• Middle third has mixed skeletal and smooth muscle and is under autonomic control.
• Large Intestine: Three subdivisions: Cecum, Colon, and Rectum.
• *Bacterial flora produce vitamin K and B7 (biotin).**

Question 6

• Circulatory Pathway
• Systole
• Diastole
• Blood pressure regulation
• Blood osmolarity regulation
• Cardiac output
• Blood pressure
• Bohr shift
• Myoglobin vs Hemoglobin
• 2,3-bisphosphoglycerate (2,3- BPG)
• Fetal Circulation: Shunts
• Sequence of conduction
• Sinoatrial (SA) Node
• Atrioventricular (AV) Node
• Bundle of His
• Purkinje fibers

Answer 6

-Circulatory Pathway: Right atrium → tricuspid valve → right ventricle → pulmonary valve → pulmonary artery → lungs → pulmonary veins → left atrium → mitral valve → left ventricle → aortic valve → aorta → systemic circulation (arteries → veins)
Remember: right heart → pulmonary circulation & left heart → systemic circulation

• Systole: “Pumping phase.” Both ventricles contract, pushing blood out through the aortic and pulmonary valves. Tricuspid and mitral valves are closed. –> This is the phase of highest arterial blood pressure.
• Diastole: “Filling phase.” Ventricles relax, allowing filling from the atria. Pulmonary and aortic valves are closed. –> This is the phase of lowest arterial blood pressure.
• Blood pressure regulation: Low blood pressure leads to activation of the renin-angiotensin-aldosterone hormone system which works by increasing sodium re-absorption. –> High blood pressure leads to secretion of ANP (atrial natriuretic peptide)
• Blood osmolarity regulation: High blood osmolarity leads to increased release of ADH leading to increased water resorption.
• Cardiac output: Cardiac output = Stroke volume x Heart rate
• Blood pressure: Blood pressure = Q x R = (cardiac output) x (resistance)
• -> Example: if there is vasoconstriction, then resistance increases, therefore blood pressure increases.
• Bohr shift: Refers to the decrease in oxygen binding affinity due to a rightward shift of the binding curve, under conditions of high CO2 or high H+
• Myoglobin (found in muscle cells) has a higher binding affinity that hemoglobin
• 2,3-bisphosphoglycerate (2,3- BPG): 2,3-BPG is a molecule that affects heme-oxygen binding affinity. –> Increased 2,3-BPG causes heme to release O2, decreasing binding affinity and shifting the curve rightward. Myoglobin only has one subunit and therefore is not affected by 2,3-BPG.
• Fetal Circulation: Shunts: There are three major shunts, two that allow blood to skip the lungs of a fetus and one that skips the liver
• -> Foramen ovale: from right atrium to left atrium.
• -> Ductus arteriosus: from pulmonary artery to aorta, skipping the lungs.
• -> Ductus venosus: skips the liver.
• Sequence of conduction: SA node → AV node → Bundle of His → Purkinje fibers → Ventricles
• *Mnemonic: Suck A Big Pecker**
• Sinoatrial (SA) Node: Primary pacemaker of the body. Heart rate is increased by sympathetic and decreased by parasympathetic nervous system tone.
• -> Located at the upper right atrium.
• Atrioventricular (AV) Node: Secondary pacemaker, receives signal from SA node. –> Located at the junction of the atria and ventricles.
• Bundle of His: A delay in conduction occurs between the AV node and Bundle of His to allow for atrial contraction and ventricle filling. The bundle of His then conducts the signal from the AV node to the ventricles.
• Purkinje fibers: Fast conduction. Final connection directly to the ventricles.

Question 7

• Genetics and Evolution:
• Inclusive fitness
• Adaptive radiation
• Molecular clock model
• Inclusive fitness
• Hardy-Weinberg principle
• Hardy-Weinberg conditions (5)
• SRY gene
• Urinary System:
• Proximal convoluted tubule
• Distal convoluted tubule
• Collecting duct
• Aldosterone
• Renal Cortex vs Renal Medulla
• Glomerular filtration rate
• Hydrostatic pressure
• Osmotic pressure
• Afferent and efferent arterioles

Answer 7

• Inclusive fitness: Evolutionary fitness that includes both individual fitness (propagation of one’s own genes) and indirect fitness (cooperative behavior to help propagate genes of close relatives).
• Adaptive radiation: A single common ancestor species diverges (or “radiates”) into several new species that fill different niches.
• Molecular clock model: Estimates time of divergence from a common ancestor based on differences between species. The more different two species are, the further back they diverged.
• Inclusive fitness: Theory that evolutionary fitness includes close relatives as well as an individual’s own offspring.
• -> Example: altruism.

-Hardy-Weinberg principle: In equilibrium state, allele frequencies remain constant and no evolution occurs.

• Hardy-Weinberg conditions: Five conditions:
  1) Large population
  2) No natural selection
  3) Random mating
  4) No genetic drift
  5) No migration

-SRY gene: The sex-determining gene. Found on the Y chromosome and leads to male characteristics like development of testicles.

• Urinary System:
• Proximal convoluted tubule: Reabsorbs water, sodium, nutrients. Excretes H+, NH3, K+, urea.

-Countercurrent multiplier system: The vasa recta of the nephron runs counter to the loop of Henle. This acts to multiply the resorption of H2O.

• Distal convoluted tubule: The hormone aldosterone will act on the distal convoluted tubule to increase sodium reabsorption.
• *Aldoesterone also acts on the collecting duct**

-Collecting duct: The hormone ADH will increase water permeability through aquaporin increase. Also responsive to aldosterone similar to the distal convoluted tubule.

-Aldosterone: Synthesized in adrenal cortex.
Main function: regulates sodium and potassium ion balance by increasing Na+ re-absorption and K+ excretion in the distal convoluted tubule –> This will also lead to increase in blood pressure due to Na+ and water reabsorption.

• Renal Cortex vs Renal Medulla: Cortex contains Bowman’s capsule, proximal and distal convoluted tubules. Medulla contains the Loop of Henle and collecting duct.
• Glomerular filtration rate: A measure of the volume of fluid being filtered through the kidney.
• Hydrostatic pressure: The pressure in the blood vessels that “pushes” filtrate into the kidney through the glomerulus.
• *Higher hydrostatic pressure leads to increased GFR.**
• Osmotic pressure: The Osmotic Pressure in the tubule “sucks” filtrate into the kidney. Higher solute concentration in the tubule increases osmotic pressure and increases GFR. (Basically fluid pressure aka like “blood” pressure)
• Afferent and efferent arterioles: Blood flow goes into the kidney through the afferent arteriole and exits through the efferent arteriole. Vasoconstriction of the afferent arteriole decreases GFR whereas vasoconstriction of the efferent arteriole increases GFR.

Question 8

• Musculoskeletal and Skin System:
• Osteon
• Lamellae
• Haversian Canal
• Canaliculi
• Stretch reflex
• Fasciculations
• Clonus
• Mechanoreceptors of the skin:
• Merkel cells
• Meissner’s corpuscles
• Pacinian corpuscles
• Ruffini endings
• Parathyroid hormone
• Vitamin D
• Calcitonin
• H-Zone
• A-Band
• I-band
• Z-disc
• Contraction
• Creatine phosphate
• Sarcolemma
• Sarcoplasmic reticulum

Answer 8

• Musculoskeletal and Skin System:
• Osteon: Structural unit of compact bone.
• Lamellae: Rings of bone matrix that surround a central canal.
• Haversian Canal: Central canal in bone containing blood vessels and nerves.
• Canaliculi: Microscopic channels in bone that connect lacunae, allowing nutrient exchange and waste disposal.
• Stretch reflex: The afferent stimulus comes from muscle spindles, stretch receptors within the muscles. The efferent reflex gets activated, causing the stretched muscles to contract and antagonist muscles to relax.
• Fasciculations: Involuntary twitch of a muscle, associated with diseases that cause lower motor neuron problems.
• Clonus: Involuntary and rhythmic contraction/relaxation of a muscle, usually in response to stretching of a muscle. –> Seen in some neurologic pathologies.
• Mechanoreceptors of the skin:
• Merkel cells: Receptors for light touch and pressure sensation located in the base of the epidermis.
• *Mnemonic: Miss Meissner Merkel handles minor touches.**
• Meissner’s corpuscles: Nerve ending for light touch sensation in the dermis. Mnemonic: Miss Meissner Merkel handles minor touches.
• Pacinian corpuscles: Nerve ending for vibration and deep pressure in the dermis. Mnemonic: “Pack it in deep” = Pacinian corpuscles.
• Ruffini endings: Nerve endings for stretch in the dermis.
• *Mnemonic: “Doing the splits (“stretching”) is rough = Ruffini endings.**
• Parathyroid hormone: Increase in parathyroid hormone leads to increasing blood calcium due to increase in calcium reabsorption in the GI tract, decrease in calcium excretion in the kidneys, and increased activity of osteoclasts.
• Vitamin D: Activated by parathyroid hormone. Leads to increase in calcium resorption.
• Calcitonin: Made by parafollicular C cells in thyroid. –> Leads to decreased blood calcium due to increased bone formation (osteoblast activity).
• H-Zone: Contains only myosin filaments (no overlap with actin filaments).
• A-Band: Defined as the length of the myosin filament. This is the region of overlap that contains both myosin and actin filaments.
• I-band: Contains only actin filaments.
• Z-disc: Dividing point between sarcomeres. Contained within the I-band.
• Contraction: Muscle contraction causes shortening of the H-zone and I-band, with no change in the A-band. –> There is no change in the length of the actin or myosin filaments.
• Creatine phosphate: Source of ATP in the muscle tissues. –> Adds phosphate group to ADP, regenerating ATP.
• Sarcolemma: Cell membrane of a muscle cell. –> Forms into T-tubules which propagate action potentials.
• Sarcoplasmic reticulum: The muscle version of the endoplasmic reticulum –> Contains calcium that starts the muscle contraction process.

Question 9

• Sarcomere Contraction:
• Step 1
• Step 2
• Step 3
• Step 4
• Step 5
• Step 6

*Muscle fibers: Slow-oxidative fibers (Type 1) vs Fast-glycolytic fibers (Type 2X)

Answer 9

• Sarcomere Contraction:
• Step 1: At the neuromuscular junction, the neurotransmitter acetylcholine is released.
• Step 2: Depolarization is transmitted through the T-tubules and triggers release of calcium from the sarcoplasmic reticulum.
• Step 3: Calcium binds to troponin and triggers uncovering of the actin filament. (Troponin is the small protein on the tropomyosin chain).
• Step 4: Myosin binds to actin causing shortening of the sarcomere as the actin filament slides along the myosin filament.
• Step 5: The neurotransmitter is degraded by the enzyme acetylcholinesterase ending the signal.
• Step 6: ATP binds to the myosin head and causes the binding to be released. Calcium returns to the sarcoplasmic reticulum through active transport Ca2+ pumps.
• Muscle fibers:
• Slow-oxidative fibers (Type 1):
• -> Red color, High myoglobin and mitochondria content, Slow contraction
• ->Primarily aerobic respiration

-Fast-glycolytic fibers (Type 2X):

White color

• -> Low myoglobin and mitochondria content Fast contraction
• -> Primarily anaerobic glycolysis

Question 10

• Hormones
• Adrenal Cortex
• -> Aldosterone
• Other Hormones:
• -> Cortisol
• -> Leptin
• -> Ghrelin
• -> Erythropoietin
• -> Melatonin
• -> Somatostatin
• Adrenal Medulla
• -> Catecholamines
• -> Epinephrine and norepinephrine
• Anterior Pituitary
• -> Hormones and action
• Thyroid and Parathyroid Hormones
• Thyroid hormones (T3 and T4)
• Calcitonin
• Parathyroid hormone
• Posterior pituitary Hormones
• Hypothalamus
• Peptide vs Steroid Hormone Mechanism

Answer 10

-Adrenal cortex releases the corticoids: aldosterone (mineralocorticoids) and cortisol (glucocorticoids). Also releases androgens which are converted to testosterone and estrogen in gonads.

• Aldosterone: Part of the renin-angiotensin II-aldosterone system in the kidneys –> ↑ blood pressure by ↑ water absorption from kidneys.
• *Key role in electrolyte balance: ↑ Na+ absorption and ↓ K+ absorption**

-Cortisol: Key regulator of the stress response. ↑ gluconeogenesis (↑ blood glucose) ↓ immune system activity

• Other Hormones:
• Leptin: After a meal, adipocyte cells release leptin to trigger appetite suppression.
• Ghrelin: Fasting state triggers Gastric cells to release ghrelin, triggering hunger.
• Erythropoietin: The kidneys produce EPO which triggers production of red blood cells.
• Melatonin: Made in the pineal gland –> Controls circadian rhythm and sleep-wake cycle.
• Somatostatin: Made in the pancreas –> Inhibits the release of growth hormone (GH) from the anterior pituitary.

-Adrenal medulla releases catecholamines: epinephrine and norepinephrine. Catecholamines activate the fight-or-flight response.

• Catecholamines: A class of hormones that is hydrophilic and derived from the molecule tyrosine.
• *Important distinction: the adrenal cortex makes steroid hormones while the medulla makes catecholamines.
• Epinephrine and norepinephrine: Induce the fight-or-flight response of the sympathetic nervous system that aims to maximize blood flow, blood glucose, and oxygen delivery.
• -> ↑ blood pressure
• -> ↑ heart rate
• -> ↓ glycogenesis ↑ airway flow
• Hormones produced by the anterior pituitary: FSH, LH, ACTH, TSH, prolactin, endorphins, GH. Mnemonic: FLAT PEG.
• FSH: In females: stimulates ovarian follicle growth. In males: stimulates spermatogenesis.
• LH: In females: stimulates ovulation. In males: stimulates production of testosterone.
• *High estrogen leads to ↑ LH and ↓FSH.**
• ACTH: Stimulates production of cortisol as part of the hypothalamic-pituitary- adrenal axis: CRH (hypothalamus) → ACTH (anterior pituitary) → cortisol (adrenal cortex)
• TSH: Stimulates the thyroid to produce triiodothyronine (T3) and thyroxine (T4), which help regulate basal metabolic rate.
• Prolactin: Stimulates production of breast milk and will shut down sexual desire after orgasm. –> Prolactin release is inhibited by dopamine.
• Endorphins: Block the sensation of pain while inducing feelings of euphoria and pleasure.
• GH: Stimulates bone growth during childhood/adolescence –> Stimulated by GHRH from the hypothalamus and inhibited by somatostatin.
• Thyroid and Parathyroid Hormones:
• -> Thyroid hormones regulate metabolism.
• -> Thyroid and parathyroid together regulate calcium metabolism in the body
• Thyroid hormones (T3 and T4): Thyroid hormones control the basal metabolic rate.
• *Note: thyroid hormones are their own class of hormones (distinct from catecholamines, peptide, or steroid hormones). They are hydrophobic**
• Calcitonin: Made by parafollicular C cells in the thyroid. Decreases calcium in the blood.
• *Mechanism: ↓ bone resorption and ↑ renal excretion.**

-Parathyroid hormone: ↑ calcium and ↓ phosphorus in the blood. Mechanism: ↑ osteoclast activity for bone breakdown.

• Hormones of the posterior pituitary: oxytocin and ADH.
• *Important difference from the anterior pituitary: these hormones are made in the hypothalamus and released from the posterior pituitary.**

-Oxytocin: Stimulates milk ejection in the breasts and uterine contractions during childbirth.

• ADH: Leads to an increase in water absorption in kidneys and a decrease in water lost through urine.
• *Purpose: help the body hold onto water by concentrating urine.**
• Hypothalamus: A small region in the brain. Can be thought of as a regulatory control center.
• -> Plays many roles in homeostasis through regulating the release of hormones from the pituitary gland.
• Tropic hormones: Hormones that induce the release of other hormones from endocrine glands.
• -> Many are produced in the hypothalamus and act on the pituitary, examples: GnRH, CRH.
• Gonadotropin-releasing hormone (GnRH): GnRH (hypothalamus) → FSH and LH (anterior pituitary) → gonads
• Corticotropin-releasing hormone (CRH): CRH (hypothalamus) → ACTH (anterior pituitary) → cortisol (adrenal cortex)
• Dopamine : Inhibits release of prolactin from the pituitary and plays a role in the reward pathway.
• Homeostasis functions: Hypothalamus plays a critical role in regulating hunger, temperature, thirst. Mnemonic: HTTP = Hunger, Temperature, Thirst, Pituitary control
• Peptide vs Steroid Hormone Mechanism: Peptide vs Steroid Hormone Mechanisms:
• Peptide: Triggers signaling cascade of a second messenger inside the cell
• Steroid: Induces changes in gene expression

Question 11

• Enzymes:
• -> Ligase
• -> Isomerase
• -> Oxidoreductase
• -> Hydrolases
• -> Lyases
• Lineweaver-Burke Plots:
• -> Principles
• -> Axes
• -> Intercepts
• -> Michaelis-Menten equation
• ———> Assumptions about Michaelis-Menten
• Subclasses of transferases:
• Kinase
• Phosphatase
• Phosphorylase
• Cooperative Enzymes:
• Effect on activity curves
• Hill coefficient
• Other enzyme concepts:
• Suicide inhibition
• Feedback inhibition
• Allosteric effector
• Zymogen

Answer 11

• Enzymes:
• Ligase: Catalyze joining of two molecules.
• *Example: DNA ligase catalyzes phosphodiester bond formation between Okazaki fragments.**
• Isomerase: Catalyze conversion between isomeric forms.
• *Example: Conversion between glucose-6-phosphate and fructose-6- phosphate in the glycolysis pathway.**
• Oxidoreductase: Catalyze redox (reduction-oxidation) reactions.
• *Example: NADH dehydrogenase catalyzes the NADH → NAD+ reaction in the electron transport chain.**
• Hydrolases: Catalyze hydrolysis reactions.
• *Example: proteases cleave peptide bonds.**
• Lyases: Catalyze cleavage reactions other than hydrolysis reactions (handled by hydrolases) and oxidation reactions (handled by oxidoreductases). These reactions form double bonds. –> Enzymes ending in the suffix -lase are lyases.
• *Example: Fructose-1,6-bisphosphate → GADP + DHAP is catalyzed by an aldolase in glycolysis.**

-Lineweaver-Burk Plots: These are linear graphs derived from rearrangement of the Michaelis-Menten equation.
Michaelis-Menten graphs record observed values while Lineweaver-Burk curves describe theoretical values which are more precise.

-Axes: • X-axis: 1 / [S]. Inverse of substrate concentration. • Y-axis: 1 / V. Inverse of reaction rate.

-Intercepts: • X-intercept: - 1 / Km. Negative reciprocal of Michaelis constant Km.
• Y-intercept: 1 / Vmax. Reciprocal of maximal reaction rate.
• Slope: Ratio of Km / Vmax

-Michaelis-Menten equation: Vo = (Vmax [S]) / (Km + [S])
• Vmax represents the maximum reaction rate.
• Km represents the substrate concentration necessary to achieve half the maximum reaction rate.
• Km is also a measure of enzyme-substrate binding affinity. A higher Km indicates a lower binding affinity.
The point on the x-axis at half the maximum height of the curve represents Km.

Three major assumptions of the Michaelis-Menten equation:
• Irreversibility assumption: Product concentration [P] and reverse reaction rate are negligible.
• Steady state assumption: Concentration of enzyme- substrate complex [ES] is constant throughout reaction. Rate of formation = rate of consumption.
• Free ligand assumption: Concentration of substrate must be much higher than concentration of enzyme; otherwise enzyme cannot be saturated. In other words [S]&raquo_space;»> [E].

-Subclasses of transferases: Class of catalyst that catalyzes the transfer of functional groups between molecules. Kinases and phosphatases are subclasses of transferases.

-Kinase: Catalyzes the addition of a phosphate group from ATP.
Example: Phosphofructokinase catalyzes the committed step of glycolysis, fructose-6-phosphate → fructose 1,6-bisphosphate.

-Phosphatase: Catalyzes the removal of a phosphate group.
Example: Dephosphorylation of the PDC in the citric acid cycle.

-Phosphorylase: Catalyzes the addition of an inorganic phosphate group, like HPO4.
Example: glycogen phosphorylase in glycogenolysis.

• Cooperative Enzymes: Cooperative enzymes have multiple active sites, and binding to one changes the affinity of others for the substrate
• Effect on activity curves: Enzymes with positive cooperativity have sigmoidal-shaped activity curves. Enzymes with negative or no cooperativity have hyperbolic-shaped activity curves.

-Hill coefficient: A quantitative measure of cooperativity, derived from the Michaelis-Menten equation.
Hill coefficient > 1 indicates positive cooperativity.
Hill coefficient < 1 indicates negative cooperativity.

• Other enzyme concepts:
• Suicide inhibition: Binds to active site by a covalent bond, causing irreversible inhibition. Generally slower compared to reversible inhibition.

-Feedback inhibition: The product of a reaction pathway “feeds backwards” and inhibits an enzyme.
Also called end-product inhibition.

-Allosteric effector: A substance that binds to the allosteric site of an enzyme (away from the active site) and changes the conformation of an enzyme and its active site. This changes the kinetics of the reaction (e.g. the Michaelis-Menten curve).

-Zymogen: An inactive precursor to an enzyme which can be activated under certain conditions.
Example: pepsinogen is activated to pepsin at low pH in the stomach.

Question 12

• Enzyme inhibition: Binding, kinetics, and notes
• Competitive inhibition
• Uncompetitive inhibition
• Noncompetitive inhibition
• Mixed Inhibition
• Principles of kinetics:
• > Kcat (turnover number)
• > Catalytic efficiency
• > Relation to Vmax

Answer 12

• Enzyme inhibition:
• Competitive inhibition
• > Binding: Resembles substrate and binds to active site
• > Km ↑ and Vmax no change
• Overcome by adding substrate*
• Uncompetitive inhibition
• > Binding: Binds only to enzyme-substrate complex
• > Km ↓ and Vmax ↓
• Most effective at high substrate concentration since enzyme-substrate complex must form first*
• Noncompetitive inhibition
• > Binds equally to enzyme and enzyme-substrate complex at separate allosteric site
• > Km no change and Vmax ↓
• Allosteric inhibition is a form of this*
• Mixed Inhibition
• > Binding: Binds unequally to enzyme and enzyme-substrate complex
• > Km is variable and Vmax ↓ always
• When favoring the complex will decrease Km*
• Principles of kinetics:
• > Kcat (turnover number): Represents rate of substrate conversion to product under conditions of saturation.
• • kcat = Vmax / [E] **

-> Catalytic efficiency: Given by the equation: Efficiency = kcat / Km
↓ Km results in ↑ efficiency

-> Relation to Vmax: Vmax = kcat * [E]

Question 13

• *Biologically significant proteins:
• Collagen
• Actin
• Tubulin
• Kinesin and Dynein
• Myosin
• Three main mechanisms of biological signaling
• Endocrine versus paracrine
• Second messenger systems
• Ligand-gated ion channels
• Structural proteins
• Motor proteins
• Cell adhesion molecules
• ->Cadherin
• ->Integrins
• ->Selectins
• Protein electrophoresis
• -> Native PAGE
• -> SDS-PAGE
• -> Isoelectric focusing
• Protein laboratory techniques:
• -> Isolating or purifying a protein
• -> Determining sequence
• -> Determining structure
• -> Determining concentrations
• -> Determining absorbance

-G-protein coupled receptor (GPCR) signaling (5 steps)

• Binding affinity:
• Equilibrium dissociation constant (Kd)
• Cooperative binding
• Positive cooperativity

Answer 13

• *Biologically significant proteins:
• Collagen: A structural protein that provides elastic strength.
• -> Remember that it is a critical component of the extracellular matrix. Can be found in connective tissues like dermis and cartilage.
• Actin: A structural protein that forms microfilaments. Plays a key role in muscle cells.
• Tubulin: A structural protein that helps form microtubules. Play a key role in mitosis as they form spindle fibers.
• Kinesin and Dynein: These are motor proteins that slide along microtubules.
• —> Kinesin goes away (anterograde) from the nucleus while dynein goes toward (retrograde) the nucleus (think dynein toward)

-Myosin: A motor protein that plays a key role in muscle contraction.

• *Three main mechanisms of biological signaling:
  1) Altering channel permeability of ion channels
  2) Using the second messenger system (ie GPCR)
  3) Changes in gene expression

-Endocrine versus paracrine: Endocrine messengers are delivered by bloodstream while paracrine signals act locally between cells.

-Second messenger systems:
Two-step process
1) First messenger: initial interaction between a receptor and ligand.
2) Second messenger: downstream effect that is triggered by the initial receptor-ligand-binding.
Common example: GPCR**

-Ligand-gated ion channels: Channels that let ions through and change their permeability in response to a signaling molecule such as a neurotransmitter.

• Structural proteins: Fibrous proteins that provide structure and strength to cytoskeleton, extracellular matrix, etc.
• *Examples: collagen, actin, tubulin**
• Motor proteins: Proteins that generate force and motion, generally through the conformation change of a head.
• *Examples: myosin, kinesin, dynein**
• Cell adhesion molecules: Proteins that bind things together.
• Examples: cadherins, integrins, selectins.*
• Cadherin: A cell adhesion molecule that adheres cells together and are dependent on calcium.
• *Mnemonic: Cadherin = “Ca” + “Adhering”**
• Integrins: Cell adhesion molecules that bind to the extracellular matrix.
• Selectins: Cell adhesion molecules that play a role in immune function.
• Protein electrophoresis: Proteins are run through an electric field in a gel matrix to separate them based on size or charge.
• *Note: proteins can also be separated by other properties using chromatography techniques.**

-Native PAGE: Electrophoresis technique that maintains shape of protein but is limited due to the effect of charge.

• SDS-PAGE: Electrophoresis technique that denatures proteins using SDS. –> More accurately separates proteins by size because this removes the confounding factor of charge.
• Note that after SDS-PAGE, the proteins are no longer usable.*
• Isoelectric focusing: Proteins are placed between an acidic (+ charge) anode and a basic (- charge) cathode.
• -> They then migrate and separate based on their isoelectric point. Utilizes the amphoteric nature of amino acids.
• Protein laboratory techniques:
• Isolating or purifying a protein: Use chromatography or electrophoresis.
• Determining sequence: Use Edman degradation
• Determining structure: Use crystallography
• Determining concentrations: Use colorimetric techniques such as Bradford protein assay.
• -> Western blot can also be used with comparison to a reference protein.

-Determining absorbance: Use Beer’s law to calculate absorbance
Absorbance = ε C L
ε = extinction coefficient, C = concentration, L = path length

• G-protein coupled receptor (GPCR) signaling (5 steps): GPCRs are located on the cell membrane.
• *Special receptors are associated with G-proteins, which relay extracellular signals inside the cell through a second messenger system.**
• Step 1: The G-protein coupled receptor binds to its corresponding ligand and induces a conformational change. The ligand is the first messenger.
• Step 2: The alpha subunit gets activated as GDP is swapped with GTP (active form).
• Step 3: The active subunit comes off and initiates the second reaction, the conversion of ATP to cAMP by adenylyl cyclase .
• Step 4: The “second messenger”, commonly cAMP, triggers downstream effect inside the cell.
• Step 5: GTP gets hydrolyzed back to GDP and subunit then rejoins the receptor to get ready to go again.
• Binding affinity
• Equilibrium dissociation constant (Kd): Can be used as a measure of binding affinity, where lower values of Kd indicate greater binding affinity.
• Cooperative binding: Ligand binding induces a conformational change in one subunit of a protein, that increases or decreases binding affinity in other subunits. Classic example: the binding of one oxygen molecule to hemoglobin increases its affinity for other oxygen molecules.
• Positive cooperativity: Results in a sigmoidal-shaped binding curve.

Question 14

• Carbohydrate Bonding
• Reducing sugars
• Reducing saccharides
• Key monosaccharides:
• Glucose
• Galactose
• Fructose
• Key disaccharides and polysaccharides:
• Maltose
• Lactose
• Sucrose
• Cellulose

-Carb stereochemistry and Anomer configurations

• Properties of carbohydrates:
• Structure
• Nomenclature
• Cyclic carbohydrates

Answer 14

• Carbohydrate Bonding: Glycosidic bonds form from nucleophilic attack onto the anomeric carbon of a sugar. These bonds can be α or β. To determine this, look at whether the -OH group of the anomeric carbon is pointing up (β) or down (α).
• Reducing sugars: Sugars with a ketone or aldehyde group containing a free anomeric carbon that can be oxidized are capable of serving as reducing agents. In cyclic form, reducing sugars have hemiacetal or hemiketal configurations.
• Reducing saccharides: Remember that a sugar must have a free anomeric carbon to act as a reducing sugar. All free monosaccharides are reducing, whereas disaccharides are reducing if they have a free anomeric carbon not participating in a glycosidic bond.
• For example, sucrose has a glycosidic bond between anomeric carbons and therefore is nonreducing.
• Key monosaccharides:
• Glucose: Most common monosaccharide
• Galactose: A monosaccharide that is an epimer of glucose at C4 –> Comes from milk and is converted to glucose in the liver.
• Fructose: A monosaccharide found in foods like honey. Converted to glucose in the liver –> Be able to recognize glucose, galactose, and fructose.
• Key disaccharides and polysaccharides:
• Maltose: Disaccharide made of glucose and glucose linked by a α-1,4-glycosidic bond.
• Lactose: Disaccharide made of galactose and glucose linked by a β-glycosidic bond.
• Sucrose: Disaccharide made of glucose and fructose linked by a α-1,2-glycosidic bond.
• Cellulose: A polysaccharide connected by β-glycosidic bonds, functions as the main component of plant cell walls.
• Carb stereochemistry and Anomer configurations:
• Stereochemistry: Carbohydrates are generally structures with enantiomers and can be in D- or L- configurations. To find the configuration, look at the C furthest from the carbonyl group (highest chiral number). The -OH group on the left means L-configuration. In nature, carbohydrates are found in the D-configuration.

-Anomer Configurations: Anomers are epimers formed by ring closure and can have α or β stereochemistry. α-anomers have the -OH on the anomeric carbon trans to the CH2OH group. The -OH group will be pointing down. β-anomers have the -OH on the anomeric carbon cis to CH2OH group. The - OH group will be pointing up.

• Properties of carbohydrates:
• Structure: Carbohydrates must have a carbon backbone, at least 2 hydroxyl groups, and a ketone or aldehyde group.
• Nomenclature: All sugars use the suffix -ose. Sugars with aldehyde group are aldoses; with a ketone group are ketoses.
• Cyclic carbohydrates: Straight chain carbohydrates can form into rings. The carbon of the carbonyl group (C=O) is called the anomeric carbon; this is the stereocenter of a cyclic carbohydrate.

Question 15

• Lipids:
• Steroids
• Fat-soluble vitamins
• Cholesterol
• Steroid hormones
• Terpenes
• Lipid storage:
• Adipocytes
• Chylomicrons
• Saponification reaction
• Soaps
• Types of lipids:
• Waxes
• Sphingolipids
• Lipid rafts
• Saponification
• Transportation
• Phospholipid structure:
• ->Head
• ->Tail
• ->Backbone

Answer 15

• Lipids:
• Steroids: Ringed lipids that help regulate metabolic activities. Examples: cholesterol, steroid hormones, vitamins

-Fat-soluble vitamins: The four fat-soluble vitamins are A, D, E, K.

• Cholesterol: Plays two key roles:
  1) Structure and fluidity in the cell membrane
  2) Precursor to steroid hormones
• Steroid hormones: Key properties of steroid hormones:
  1) They act more slowly because their mechanism affects gene transcription and expression.
  2) They have a long half-life so they work at low concentrations.
  3) They can diffuse freely but act only on cells with their specific high-affinity receptor.

-Terpenes: These are precursors of steroids that are non-cyclic and contain double bonds. They form into steroids through a cyclization reaction.

• Lipid storage:
• Adipocytes: Cells that store lipids inside their smooth endoplasmic reticulum. Also known as lipocytes or fat cells.
• Chylomicrons: These are lipoproteins that function in transport of triacylglycerols. They are similar structurally to a micelle but also contain proteins.
• Saponification reaction: Refers to the ester hydrolysis of triacylglycerols, with the nucleophilic attack performed by a strong base. This results in free fatty acids which travel in the bloodstream.
• Soaps: Salt forms of free fatty acids
• Types of lipids:
• Waxes: Contain long-chain alcohol esters connected to a fatty acid. Provide waterproofing and defense. Mainly present in plants
• Sphingolipids: A lipid with a sphingosine backbone. Most are phospholipids and are found in the cell membrane. Glycosphingolipids are attached to a sugar rather than a phosphate.
• Lipid rafts: Regions of the cell membrane with glycoprotein, cholesterol, and receptors organized into a unit. The lipid component allows the unit to move around the membrane.
• Saponification: The ester hydrolysis of lipids using a strong base.
• Transportation: Because lipids are insoluble in blood, they are surrounded and transported by lipoproteins.
• Phospholipid structure:
• Head: The head consists of a phosphate group connected to an alcohol and is polar.
• Tail: The tail consists of two fatty acids and is nonpolar.
• Backbone:The backbone is made of glycerol (glycerophospholipid) or sphingosine (sphingophospholipid).

Question 16

• DNA:
• Primers in PCR (3 steps)
• Nucleic acid structure:
• Nucleoside
• Nucleotides
• Nucleotide bonds
• DNA Repair:
• Mismatch repair
• Nucleotide excision repair
• Base excision repair
• Oncogene precursors:
• Proto-oncogene
• Tumor suppressor genes
• Centromeres
• Restriction sites
• Organization of DNA:
• Nucleosomes Histones
• Histone acetylation
• DNA methylation
• Chromatin

Answer 16

-DNA:
-Primers in PCR: The primers used in PCR must have high G-C base pair content with a G or C on either end.
Step 1. Denaturation: High temperature is used to denature the template DNA in a tube

Step 2. Annealing: Cool temperature allows for the DNA primers to anneal.
–> Note that either DNA or RNA primers could be used, although DNA primers are more commonly used

Step 3. Extension: Moderate temperature (e.g. 72°C) allows for activity of Taq polymerase

• Nucleic acid structure:
• Nucleoside: Composed of a 5-carbon sugar and a nitrogenous base. Unlike nucleotides, they do not have phosphates.
• Nucleotides: The structural unit of DNA and RNA. Consist of a nucleoside plus phosphate groups.
• Nucleotide bonds: Nucleotides are joined by phosphodiester bonds. The link between the sugar and the base within a nucleotide is a glycosidic bond.
• DNA Repair:
• Mismatch repair: Repairs an erroneous pairing (e.g. G-T). A segment of the DNA is removed → DNA polymerase replaces it with correct sequence → sealed with DNA ligase
• Nucleotide excision repair: Fixes structural issues, for example thymine dimers caused by UV radiation. Removes the segment of DNA and replaces it.
• Base excision repair: Fixes base mutations, for example when a cytosine gets deaminated into uracil. Removes a single nucleotide and replaces it with the correct nucleotide.
• Oncogene precursors:
• Proto-oncogene: Genes that stimulate growth. If mutated with gain of function, they can become oncogenes and cause cancer.
• Tumor suppressor genes: Genes that suppress growth. If mutated with loss of function, this can cause tumors.
• Centromeres: The middle portion of chromosomes. Function to keep sister chromatids together until separation during anaphase. Need to maintain a strong bond so have higher proportion of C-G base pairs.
• Restriction sites: Cut by restriction enzymes–> at palindromic sequences
• For a nucleotide sequence to be considered as a palindrome, its complementary strand must read the same in the opposite direction [2]. For example, the sequence 5’-CGATCG-3’ is considered a palindrome since its reverse complement 3’-GCTAGC-5’ reads the same. Palindromes can be exact or approximate.*

-DNA stability:
-Structural interactions: Two main interactions contribute to stabilizing the double helix structure in DNA:
• Hydrogen bonding between nitrogenous bases in opposite strands
• Base stacking interactions between aromatic rings of bases

-Denaturation: Under disruptive conditions, the double-strand helix can come apart, called denaturation.
At the melting point (Tm), half of the DNA is denatured and single-stranded, half is double-stranded.

-Factors in stability:
• Higher G-C base pair content results in higher stability
• Acidic or basic pH can denature DNA
• High salt concentration will stabilize DNA due to ionic interactions
• DNA molecules that have greater length take longer to denature

• Organization of DNA:
• Nucleosomes: A unit of DNA wrapped around a core of histone proteins.
• Histones: Proteins that can affect the expression of DNA. If DNA is more tightly wound around a histone, expression will decrease because their DNA is less accessible. Histones are positively charged whereas DNA is negatively charged.
• Histone acetylation: The process of adding an acetyl group to lysine residues in the histone. This results in a decrease in the positive charge of the histone, loosening the coupling and increasing DNA expression.
• DNA methylation: Methylation of base pairs will increase the coupling between histones and DNA and result in decreased expression.
• Chromatin: Composed of a mass of DNA plus histones. Heterochromatin is dense and inactive while euchromatin is uncondensed and expressed.

Question 17

• Small nuclear RNA (snRNA)
• Small interfering RNA (siRNA)
• Micro RNA (miRNA)

Ribosomal sites
Step 1. Initiation
Step 2. Elongation
Step 3. Termination
Step 4. Post-translational modifications

• RNA enzymes:
• Helicase
• RNA polymerase II
• RNAse H
• Primase

-Degenerate

• Operons:
• Lac operon
• Lac operon regulation
• Lac operon induction
• Lac operon activation
• Jacob-Monod model
• Alternative splicing
• Polycistronic genes
• Central Dogma:
• Location
• Sense and Antisense
• Eukaryotic gene expression:
• Transcription factors
• Promotors and enhancers
• Activators and repressors

Answer 17

• Small nuclear RNA (snRNA): Component of spliceosomes.
• Small interfering RNA (siRNA) : Functions in RNA interference by marking a mRNA sequence for breakdown.
• Micro RNA (miRNA): Functions in RNA interference by blocking a mRNA sequence.
• Ribosomal sites: Three sites: E site (exit site), P site (peptidyl site), A site (aminoacyl site) oriented in the 5’ to 3’ direction.
• Step 1. Initiation: In prokaryotes, the 30S ribosomal subunit attaches to the Shine-Dalgarno sequence. In eukaryotes, the 40S subunit attaches to the 5’ cap of the mRNA transcript and looks for Kozak sequence and the start codon
• Step 2. Elongation: In a stepwise process, tRNAs (attached to amino acids) in the A site will get attached to the growing chain in the P site. The “empty” tRNA then exits through the E site.
• Step 3. Termination: Translation stops from the signal of a stop codon. The protein gets released from the ribosome.
• Step 4. Post-translational modifications: Structures called chaperones help fold the protein into its final shape and add in other covalently bonded molecules if needed.
• RNA enzymes:
• Helicase: Starts off transcription as it “unzips” and separates the strands of DNA. Breaks hydrogen bonds between base pairs.
• RNA polymerase II: Binds to a promoter region and uses the antisense strand of the DNA as a template. Then synthesizes RNA in the 5’ to 3’ direction, while moving along the DNA in the 3’ to 5’ direction.
• RNAse H: Removes RNA primers during DNA replication.
• Primase: Creates the RNA primer during DNA replication.
• Degenerate: Refers to the ability of multiple codons to redundantly code for the same amino acid.
• Operons: Found in prokaryotes. A group of genes that are transcribed together. Their expression is regulated (activated or repressed) together as well by the binding of specific proteins to regulatory regions.
• Lac operon: Classic example of an operon. Found in E. Coli, codes for proteins that transport lactose.
• Lac operon regulation: By default, the lac repressor protein is bound to the operator site, meaning that expression is repressed. Under conditions of low glucose and available lactose, it becomes active.
• Lac operon induction: Allolactose binds to the repressor region and detaches the lac repressor protein. This results in induction (e.g. initiation of expression).
• Lac operon activation: cAMP can bind upstream to the promoter region to activate the catabolite activator protein.
• *When there is high amounts of lactose –> the repressor protein comes off
• *When there is low amounts of glucose –> cAMP binds to CAP site to activate CAP protein
• —>BOTH need to happen to activate lac operon
• Jacob-Monod model: Describes the structure of an operon. Consists of an operator, promotor, and coding region.
• Alternative splicing: A process that allows for different variations of introns and exons to be spliced from the same transcript sequence. This allows multiple product variations, called protein isoforms, to come out of the same coding sequence.
• Polycistronic genes: These are found in prokaryotic cells and have similar purpose to alternative splicing. The same gene has multiple possible translation sites, allowing for variable gene products.
• Central Dogma: States that DNA → RNA → Protein. DNA to RNA occurs through transcription, then RNA to protein occurs through translation.
• Location: In eukaryotes, transcription and post-transcriptional processing takes place in the nucleus. Translation takes place in the cytoplasm on a ribosome.
• Sense and Antisense: In DNA, the template strand is antisense and the coding strand is sense. The transcribed mRNA is sense.
• Eukaryotic gene expression:
• Transcription factors: Bind to promotor or enhancer sequences in the DNA to initiate transcription.
• Promotors and enhancers: Sequences to initiate and upregulate transcription. Promotors are close to the transcription start site while enhancers are far.
• Activators and repressors: Bind close to the promoter region and affect the activity of RNA polymerase.

Question 18

• Glucose Metabolism:
• ->GLUT 2 and GLUT 4
• Key enzymes of gluconeogenesis: Which one is in the rate-limiting step?
• —> Glucose 6-phosphatase
• —> Fructose-1,6-bisphosphatase
• ———> Activated by two and limited by two
• —-> Pyruvate carboxylase
• ———> Activated by what?
• —–> Phosphoenolpyruvate carboxykinase (PEPCK)
• Key enzymes of glycolysis:
• -> Glucokinase
• -> Hexokinase
• -> Phosphofructokinase-1
• -> Phosphofructokinase-2
• -> Pyruvate kinase
• -> Glyceraldehyde-3-phosphate (G3P) dehydrogenase
• Principles of gluconeogenesis:
• Bypassing glycolysis
• Hormone regulation
• Rate-limiting step
• Location

Answer 18

• Glucose Metabolism:
• *Active transport of glucose in the gut and facilitated diffusion elsewhere
• GLUT 2: glucose transporter located in pancreas and liver tissues –> Has a high Km (low affinity).
• ——> Only transporter that is bidirectional (glucose going both into and out of cells).
• GLUT 4: Found in adipose and muscle tissues –> Has a low Km (high affinity).
• ——–> The only transporter that requires stimulation by insulin.

-Gluconeogenesis: The production of glucose from carbon substrates (like pyruvate).

• Key enzymes of gluconeogenesis:
• Glucose 6-phosphatase: Converts glucose 6-phosphate to glucose through a hydrolysis reaction. Bypasses the glucokinase/hexokinase step from glycolysis.
• *Found only in the liver.**
• Fructose-1,6-bisphosphatase: Converts fructose 1,6-bisphosphate to fructose 6-phosphate, bypassing PFK-1 –> Activated by ATP, glucagon and inhibited by AMP, insulin.
• *This is the rate-limiting step of gluconeogenesis.**
• Pyruvate carboxylase: Converts pyruvate to oxaloacetate which leaves the mitochondria. Activated by acetyl-CoA. Pyruvate carboxylase and fructose-1,6-bisphosphatase are the main regulatory enzymes.
• Phosphoenolpyruvate carboxykinase (PEPCK): Converts oxaloacetate to PEP. Works with pyruvate carboxylase to bypass pyruvate kinase from glycolysis.

-Key enzymes of glycolysis:
-Glucokinase: Catalyzes conversion of glucose to G6P in the pancreas and liver. The initial step of glycolysis.
Prevents glucose from escaping through its conversion.

-Hexokinase: Catalyzes conversion of glucose to G6P in the peripheral tissues. Inhibited by feedback from G6P (its product).

-Phosphofructokinase-1: Catalyzes conversion of F6P → F-1,6BP with ATP → ADP.
Inhibited by signals of high energy: ATP and citrate. Activated by low energy signal AMP or F-2,6BP.
The rate-limiting step of glycolysis.

• Phosphofructokinase-2: Catalyzes production of F-2,6BP which allows continued activation of PFK-1 in the liver even with abundance of ATP. Activated by insulin and inhibited by glucagon.
• Pyruvate kinase: Performs substrate-level phosphorylation, specifically conversion of phosphoenolpyruvate (PEP) to pyruvate with ADP to ATP. This enzyme is a transferase that transfers an inorganic phosphate onto ADP. Activated by F-1,6BP whose production is catalyzed by PFK-1. Inhibited by its product ATP.
• Glyceraldehyde-3-phosphate (G3P) dehydrogenase: Produces NADH which is the substrate for the electron transport chain under aerobic conditions.

-Principles of gluconeogenesis::
-Bypassing glycolysis: The reversible reactions of glycolysis use the same enzymes in gluconeogenesis while the irreversible reactions of glycolysis are bypassed by different enzymes.
• Pyruvate kinase is bypassed by PEPCK and pyruvate carboxylase.
• PFK-1 is bypassed by fructose 1,6-bisphosphatase.
• Hexokinase is bypassed by glucose-6-phosphatase.

• Hormone regulation: Activated by glucagon and cortisol. Inhibited by insulin.
• Rate-limiting step: Catalyzed by fructose 1,6-bisphosphatase.
• Location: Within the cell, occurs in the cytoplasm and mitochondria. In terms of organ location, primarily in the liver with some occurring in kidneys.

Question 19

• Principles of Glycolysis:
• -> Overall reaction
• -> Enzymes of irreversible steps
• -> Link to other pathways
• -> Key step
• -> Anaerobic conditions
• -> Overall pathway

-10 steps of glycolysis

• General Metabolism:
• -> Reaction pathway locations
• -> Reactions occurring in the cytoplasm
• -> Reactions occurring in the mitochondria
• Metabolic organs:
• -> Liver
• -> Adipocytes

-Regulation of appetite

• Urea cycle
• -> Location and link to other pathways
• -> Link to other pathways
• Postabsorptive state
• Postprandial state

Answer 19

• Principles of Glycolysis:
• Overall reaction: Glucose + 2NAD+ + 2ADP + 2P → 2 Pyruvate + 2 ATP (net) + 2 NADH + 2 H+

-Enzymes of irreversible steps: The kinases glucokinase, hexokinase, PFK-1, and pyruvate kinase catalyze irreversible reactions.
Mnemonic: Go Help one Persistent Person

• Link to other pathways: Glucose-6-phosphate from the glycolysis pathway is the primary substrate for glycogenesis. DHAP is used for fatty acid synthesis.
• Key step: Fructose-6-phosphate → fructose-1,6-bisphosphate, catalyzed by PFK-1. This is the rate-limiting step as well as the committed step (can no longer be redirected to glycogenesis pathway).
• Anaerobic conditions: In absence of oxygen, pyruvate must be converted to lactic acid to regenerate NAD+.
• Overall pathway: Glucose → G6P → F6P → F1,6BP → GADP + DHAP → 1,3BPG → 3PG → 2PG → PEP → Pyruvate

-10 steps of glycolysis:
Step - Conversion –> Coupled rxn - Key enzyme
1 - Glucose → G6P –> ATP → ADP - Hexokinase
2 - G6P → F6P
3 - F6P → F-1,6BP –> ATP → ADP - PFK-1
4 - F-1,6BP → GADP + DHAP
5 - DHAP → GADP
6 - GADP → 1,3 BPG —> NAD → NADH
7 - 1,3 BPG → 3-PG —> ADP → ATP
8 - 3-PG → 2-PG
9 - 2-PG → PEP —-> Produces H2O - Enolase
10 - PEP → Pyruvate —> ADP → ATP - Pyruvate kinase

• General Metabolism:
• Reaction pathway locations:
• Reactions occurring in the cytoplasm: Glycolysis, glycogenolysis, fatty acid synthesis, PPP, part of the urea cycle.

-Reactions occurring in the mitochondria: Citric acid cycle, oxidative phosphorylation, β-oxidation, part of the urea cycle, pyruvate oxidation (mitochondrial matrix). The highest energy pathways occur in the mitochondria; everything else in the cytoplasm. Urea cycle is unique in that it spans both.

Metabolic organs:
-Liver: Primary site of glucose regulation through gluconeogenesis and glycogen formation/breakdown, in response to insulin and glucagon.

-Adipocytes: These store lipids which are released in response to catecholamines.

• Insulin: Secreted by β-islet cells in the pancreas –> Overall effect is to lower blood sugar
• —> Promotes glucose uptake at cellular level and Promotes glycolysis in all tissues and glycogenesis in liver/adipocytes
• Glucagon: Secreted by α-cells in the pancreas –> Overall effect is to raise blood sugar
• Promotes glucose release at cellular level and Promotes gluconeogenesis and glycogenolysis in the liver

-Regulation of appetite: Ghrelin and orexin increase appetite while leptin decreases appetite.

• Urea cycle: Amino acid metabolism results in NH3 –> converted to urea by the urea cycle and then excreted by the kidneys
• -> Location: A series of reactions that occurs in both the cytoplasm and mitochondria of the cell –> Occurs in the liver.

Link to other pathways: The urea cycle produces oxaloacetate and fumarate which are part of the citric acid cycle as well.

• Postabsorptive state: The “between meals” fasting state –> Insulin is decreased and glucagon is increased. Catabolism is dominant.
• Postprandial state: The “after meals” full state –> Insulin is increased. Anabolism is dominant.

Question 20

• Lipid Metabolism:
• -> Fatty Acid Activation
• ——–> Initial step
• ——–> Subsequent step
• Lipoproteins:
• VLDL
• LDL
• HDL
• Lipid breakdown:
• Mechanical breakdown
• Chemical breakdown
• Bile salts
• Lipid synthesis:
• Fatty acid synthesis
• Cholesterol synthesis
• Ketogenesis
• Lipid transport:
• Micelles
• Direct bloodstream absorption
• Chylomicrons
• Fatty acid synthesis:
• Location
• Rate-limiting step
• Fatty acid synthase
• Fatty acid oxidation (β-oxidation):
• Products
• Examples
• Location
• Initial step
• Link to other pathways
• Saturated versus unsaturated fatty acids

-Protein catabolism: Gluconeogenesis vs ketogenesis

Answer 20

• Lipid Metabolism:
• Fatty Acid Activation: Entrance into the mitochondrial matrix is highly regulated. –> In order to cross the inner mitochondrial membrane where fatty acid oxidation occurs, fatty acids must be activated.
• Initial step: The enzyme acyl-CoA synthetase catalyzes the formation of acyl-CoA from fatty acids and coenzyme A. –> This reaction is energetically unfavorable and requires coupling to ATP hydrolysis.
• Subsequent step: Acyl-CoA reacts with carnitine in the intermembrane space, forming acylcarnitine. Acylcarnitine is recognized by inner mitochondrial membrane transport proteins and passes into the matrix.
• Lipoproteins: Primary transport mechanism for lipids.
• VLDL: Very-low-density lipoproteins. Transport triglycerides from the liver out to the peripheral tissues.
• LDL: Low-density lipoproteins. This is the “bad cholesterol”. Transports cholesterol to the peripheral tissues. VLDL gets converted to IDL and then to LDL.
• HDL: High-density lipoproteins. This is “good cholesterol.” –> Transports cholesterol to the liver where it gets processed and exits the body.
• Lipid breakdown:
• Mechanical breakdown: Occurs in the mouth and stomach.
• Chemical breakdown: Multiple enzymes (called lipases) help digest lipids. The primary site of lipase production is the pancreas.
• Bile salts: In the small intestine, bile will emulsify the fat by mixing it with water. This results in increased surface area which increases the rate of digestion.
• Lipid synthesis:
• Fatty acid synthesis: Synthesized in the cytoplasm of cells from acetyl-CoA molecules.
• Cholesterol synthesis: Synthesized in the liver. –> The rate-limiting step is the production of mevalonate, catalyzed by HMG- CoA reductase.
• Ketogenesis: During prolonged fasting, excess acetyl-CoA in the liver gets converted to ketone bodies. –> The brain can use ketone bodies as a major energy source (ketosis) in starvation or prolonged fasting environments.
• Lipid transport:
• Micelles: Spherical structures with hydrophilic heads facing the exterior and hydrophobic tails on the interior. –> This allows micelles to be absorbed like a polar molecule but break down nonpolar molecules in the interior.
• Direct bloodstream absorption: Short-chain fatty acids are absorbed directly in the intestine. Long-chain fatty acids get absorbed as micelles.
• Chylomicrons: Micelles can form into chylomicrons which transport cholesterol and fatty acids through the lymphatic system.
• Fatty acid synthesis: Synthesis of fatty acids starting from acetyl-CoA.
• Location: Takes place in the cytoplasm.
• Rate-limiting step: In the initial and rate-limiting step, the enzyme acetyl CoA-carboxylase (ACC) converts acetyl-CoA to malonyl-CoA.
• Fatty acid synthase: The subsequent steps are catalyzed by fatty acid synthase. Know that it uses reduction with NADPH to link malonyl-CoA units.
• Fatty acid oxidation (β-oxidation): Breakdown of fatty acids resulting in Acetyl CoA and electron carriers (NADH, FADH2).
• Products: The products in β-oxidation depend on the # of carbons in the original fatty acid. Fatty acids go through rounds of oxidation. Each round takes off the 2- carbon acetyl-CoA, produces 1 NADH and 1 FADH2. This continues until only a 2-carbon acetyl-CoA or a 3-carbon propionyl-CoA remains.
• Examples: Starting with a 18-carbon fatty acid, there are 8 rounds of oxidation, resulting in 9 acetyl-CoA and 8 NADH and FADH2. Starting with a 17-carbon fatty acid, there are 7 rounds of oxidation, resulting in 7 acetyl CoA, 7 NADH and FADH2, and 1 propionyl-CoA.
• Location: Occurs in the mitochondria within the cell. Occurs in all tissues in the body.
• Initial step: Fatty acid is converted to acyl-CoA, consuming one ATP molecule.
• Link to other pathways: The product acetyl-CoA can feed into the citric acid cycle or fatty acid synthesis.
• Saturated versus unsaturated fatty acids: Unsaturated fatty acids require an additional isomerization step in β- oxidation to convert double bonds in the cis conformation to the trans conformation.
• Protein catabolism: Breakdown of proteins as an energy source, happens during prolonged starvation state.
• Gluconeogenesis: Glucogenic amino acids can be converted into intermediates of gluconeogenesis. This includes all amino acids other than leucine and lysine.

-Ketogenesis: Ketogenic amino acids can be converted into ketone bodies to be used as an energy source. The two amino acids that can only be used for ketogenesis are leucine and lysine.

Question 21

-Key enzyme of fermentation

• Pentose phosphate pathway (PPP):
• ->Location
• ->Regulation
• ->Phases
• ->Key enzymes
• ->Link to glycolysis
• ->Glucose 6-phosphate dehydrogenase (G6PD)
• Glycogenolysis:
• ->Location
• ->Regulation
• ->Key enzymes
• ->Glycogen phosphorylase
• ->Debranching enzyme
• ->Link to other pathways
• Citric acid cycle principles
• ->Reactants and products
• ->Location
• ->Rate-limiting step
• ->Checkpoint steps
• ->Key steps

Answer 21

• Key enzyme of fermentation: Lactate dehydrogenase converts pyruvate to lactate and converts NADH to NAD+.
• Pentose phosphate pathway (PPP): Conversion of glucose 6-phosphate to NADPH and ribose-5-phosphate (5-carbon sugar used for nucleic acid synthesis).
• Location: Occurs in the cytoplasm of the cell. In terms of organs, occurs mainly in the liver and other lipid-synthesizing tissues.
• Regulation: Activated by insulin and inhibited by NADPH.

-Phases:
• Oxidative phase: irreversible reaction that starts with G6P and produces NADPH and ribulose-5- phosphate.
• Non-oxidative phase: reversible reactions that produce ribose-5-phosphate for nucleic acid synthesis.

-Key enzymes: Rate-limiting enzyme is glucose-6-phosphate dehydrogenase (G6PD) which produces NADPH.

-Link to glycolysis: Because the non-oxidative phase is reversible, products from this phase can be shared in both directions with glycolysis.
In other words, glycolysis can feed into the PPP, and PPP can feed into glycolysis. These products include fructose 6-phosphate and glyceraldehyde 3-phosphate.

-Glucose 6-phosphate dehydrogenase (G6PD): Catalyzes the conversion of glucose 6-phosphate to 6-phosphogluconate with production of NADPH.
The rate-limiting step of the pentose phosphate pathway.

• Glycogenolysis:
• Location: Glycogen breakdown occurs in the liver or muscle tissues where glycogen is stored.
• Regulation: Glycogenolysis is stimulated by catecholamines in peripheral tissues or by glucagon in the liver.
• Key enzymes: Glycogen phosphorylase and debranching enzyme.
• Glycogen phosphorylase: The rate limiting reaction. Breaks α-1,4 glycosidic bonds between glucose molecules by adding inorganic phosphate (Pi) in a phosphorolysis reaction.
• Debranching enzyme: Breaks α-1,6 glycosidic branches in glycogen through hydrolysis.
• Link to other pathways: Glycogenolysis results in glucose-6-phosphate which feeds into glycolysis and fermentation.
• Glycogenesis:
• Location: Glycogen production occurs in liver and muscle cells. Glycogen is then stored in the liver and skeletal muscle cells.

-Regulation: Stimulated by insulin.

• Key enzymes: Remember glycogen synthase and branching enzyme.
• ->Glycogen synthase: Synthesizes α-1,4 glycosidic bonds between glucose molecules.
• ->Branching enzyme: Creates α-1,6 glycosidic branches in glycogen.

-Citric acid cycle principles: Also known as the TCA cycle or Krebs cycle. Overall purpose is to oxidize acetyl-CoA and produce electron carriers (NADH, FADH2) to feed into the electron transport chain.

-Reactants and products: Note: need to fully memorize this for the MCAT
• Reactants: 1 Acetyl CoA, 3 NAD+, 1 FAD, 2 H2O, 1 GDP + Pi
• Products: 3 NADH, 1 FADH2, 2 CO2, 1 GTP, 3 H+

• Location: Occurs in the mitochondrial matrix in eukaryotes and the cytoplasm in prokaryotes.
• Rate-limiting step: Rate limiting step is isocitrate dehydrogenase, which catalyzes conversion of isocitrate to α-ketoglutarate. Results in conversion of NAD+ to NADH and production of CO2.
• Checkpoint steps: The three regulatory enzymes (or checkpoints) of the citric acid cycle are:
• ->Citrate synthase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase complex.
• ***These are irreversible reactions that are allosterically regulated.

-Key steps: Know which enzyme steps result in production of:
• NADH: isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, malate dehydrogenase
• FADH2: succinate dehydrogenase
• GTP: succinyl-CoA synthetase

Question 22

• Citric acid cycle steps:
• Citrate synthase
• cis-Aconitase
• Isocitrate dehydrogenase
• α-ketoglutarate dehydrogenase
• Succinyl-CoA synthetase
• Succinate dehydrogenase
• Fumarase
• Malate dehydrogenase
• Acetyl CoA production:
• Regulation
• Enzymatic regulation
• Pyruvate dehydrogenase

-Electron Transport Chain (Oxidative Phosphorylation):
Chemiosmotic coupling
ATP synthase
ATP yield

-Complexes

• ETC Principles
• ->Location
• ->Coenzyme Q (CoQ)
• ->Q cycle

Electron shuttle mechanisms: Glycerol 3-phosphate shuttle vs Malate-aspartate shuttle

Answer 22

• Citric acid cycle steps:
• Citrate synthase: Convert acetyl-CoA to CoA with coupled conversion of oxaloacetate to citrate. Enzyme is regulated by negative feedback from downstream products like ATP, NADH, citrate.

-cis-Aconitase: Part of the isomerase class of enzymes. Converts citrate to isocitrate.

• Isocitrate dehydrogenase: Catalyzes conversion of isocitrate to α-ketoglutarate. The rate-limiting step. Results in conversion of NAD+ to NADH and production of CO2.
• • Isocitrate + NAD+ → α-ketoglutarate + CO2 + NADH + H+ **
• α-ketoglutarate dehydrogenase: Converts α-ketoglutarate to succinyl-CoA, generating CO2 and NADH. Inhibited by negative feedback from products ATP, NADH, succinyl-CoA. Activated by ADP and Ca2+.
• Succinyl-CoA synthetase: Converts succinyl-CoA to succinate, generating one GTP.
• Succinate dehydrogenase: Converts succinate to fumarate through oxidation. This produces FADH2. Succinate dehydrogenase is a flavoprotein, meaning it binds to FAD found in the inner mitochondrial membrane.
• Fumarase: Converts fumarate to malate through a reversible hydration reaction.
• Malate dehydrogenase: Converts malate to oxaloacetate through oxidation, producing NADH.
• Acetyl CoA production: The pyruvate dehydrogenase complex converts pyruvate to acetyl-CoA prior to entry into the citric acid cycle.
• Regulation: Stimulated by insulin and inhibited by acetyl-CoA.
• -> The general principle is to activate this pathway when the body wants to breakdown more glucose into energy.
• Enzymatic regulation: Activated through dephosphorylation by pyruvate dehydrogenase phosphatase. Deactivated through phosphorylation by pyruvate dehydrogenase kinase.
• Pyruvate dehydrogenase: Key enzyme of this reaction. Converts pyruvate to acetyl-CoA. Cofactors are lipoic acid and thiamine.
• Electron Transport Chain (Oxidative Phosphorylation): Refers to the combination of
  1) Proton translocation from the electron transport chain.
  2) Chemiosmotic coupling producing ATP.

Chemiosmotic coupling: The ETC results in movement of protons (H+ ions) across the membrane. This creates an electrochemical gradient which can be harnessed for energy. Also called proton-motive force.

• ATP synthase: Harnesses the proton-motive force from diffusion of H+ ions through an ion channel to convert ADP to ATP. –> Activity depends on # of NADH and FADH2 molecules in the mitochondrial matrix.
• *Also called complex V of the electron transport chain.

-ATP yield: Oxidative phosphorylation yields 1.5 ATP per FADH2 and 2.5 ATP per NADH

• Complexes:
• Complex I aka NADH dehydrogenase –> Oxidizes NADH and reduces CoQ (4H+)
• Complex II aka Succinate dehydrogenase –> (succinate + FAD → FADH2 + fumarate → CoQH2) : Part of the Citric Acid Cycle (0H+)
• Complex III aka Cytochrome c reductase –> The heme in cytochrome c gets reduced (Fe3+ → Fe2+) by CoQH2: Part of the q cycle which moves electrons from CoQH2 to cytochrome c (4H+)
• Complex IV aka Cytochrome c oxidase –> Transfers electrons from cytochrome c to oxygen, reducing it to water (2H+)
• ETC Principles: Each complex of the electron transport chain oxidizes an electron donor, starting with NADH. The reduction potential increases until the final electron acceptor, oxygen, is reached.
• Location: Occurs in the inner mitochondrial membrane.
• Coenzyme Q (CoQ): Also called ubiquinone. Important role in the electron transport chain as an electron acceptor for complexes I and II and delivering electrons to complex III.
• Q cycle: Describes the process of electrons moving from CoQH2 to cytochrome C. Occurs through complex III of the ETC.
• Electron shuttle mechanisms: NADH is unable to cross the inner mitochondrial membrane. –> Mechanisms to circumvent this are glycerol 3-phosphate and malate-asparatate
• Glycerol 3-phosphate shuttle: Electrons get transferred from NADH to DHAP, forming glycerol 3- phosphate. –> The electrons then get transferred to FAD in the mitochondria forming FADH2.
• Malate-aspartate shuttle: Electrons get transferred from NADH to oxaloacetate, forming malate. After the malate moves into the mitochondria, the electrons get transferred to NAD+ forming NADH.

Question 23

• Amino Acid Stereochemistry
• Chirality
• Isoelectric point (pI)
• Solving for the isoelectric point
• Proline (Pro / P)
• Glycine (Gly / G)
• Glutamine (Gln / Q)
• Phosphorylation
• Nucleophilicity
• Deamidation
• Ketogenecity

-Group:
Guanidinium
Indole
Imidazole

Answer 23

-Amino Acid Stereochemistry: Stereochemistry of α-carbon in amino acids is L- configuration, as opposed to D-configuration in carbohydrates.

• Chirality: All amino acids are chiral except glycine.
• *All chiral amino acids are in (S) configuration except cysteine.

-Isoelectric point (pI): At the isoelectric point (pI), amino acids are in zwitterion form, meaning it has opposite charges that cancel out.

-Solving for the isoelectric point:
• Acidic side chain: average the pKa of the side chain and the carboxylic acid functional group.
• Basic side chain: average the pKa of the side chain and the amine functional group.
• Neutral side chain or glycine: average the pKa of carboxylic acid and amino functional groups.

**The amino acid proline has disrupted α-helices due to rigid cyclic structure.

-Proline (Pro / P): Unique because the ring of its R group includes the amino group of the amino acid.
This means the N has bonds to two different C atoms so the N cannot participate in hydrogen bonding.
In protein secondary structure, proline will disrupt α-helices but is useful for inducing turns in β-sheets, both due to its rigid cyclic structure.

-Glycine (Gly / G): Unique for having the smallest R group.
This gives glycine a “floppy” quality meaning that it disrupts α-helices and can induce sharp turns in β-sheets and linker regions.

-Glutamine (Gln / Q): Can simultaneously act as a hydrogen acceptor and donor, meaning it can form a network of hydrogen bonds.
This property stabilizes the β-sheet secondary structure.

• Phosphorylation: Addition of a phosphate to an amino acid.
• -> Occurs exclusively to amino acids which are alcohols, specifically serine, threonine, and tyrosine.

-Nucleophilicity: Amino acids containing -SH or -OH groups are good nucleophiles.
These include serine, threonine, tyrosine, and cysteine. –> Deprotonation of these groups results in a negative charge that can increase nucleophilicity.

-Deamidation: Amino acids containing amide groups can undergo deamidation, a process which produces ammonia.
These include asparagine (Asn / N) and glutamine (Gln / Q).

-Ketogenecity: Lysine and leucine can be broken down into ketone bodies for energy.

-Group:
Guanidinium –> Arginine (Arg / R)
Indole –> Tryptophan (Trp / W)
Imidazole –> Histidine (His / H)