MCAT bio/biochem

What is the function of the spleen?

* blood formation
* destruction of pathogens and damaged RBCs by phagocytic cells
* immune response mounted by phagocytes

What is the function of the thymus

It is the maturation site for T cells

What is the function of lymph nodes?

* lymph filtration
* pathogen destruction by phagocytic cells
* immune response mounted by lymphocytes

What aer the 3 stop codons?

UAA, UAG, UGA

How does the gallbladder play a role in bile production?

Bile is produced in the liver but it is stored in the gallbladder

What is the function of adiponectin in humans?

Increases the activity of sebaceous glands that produce oil in the skin

What are the products of glycolysis?

2 ATP and 2 NADH per molecule of glucose

What are the products of the Krebs Cycle?

1 ATP, 3 NADH, and 1 FADH2 per molecule of Acetyl-CoA

What are the products of the electron transport chain?

ATP, consumes NADH and FADH2

What are the products of fatty acid oxidation?

NADH and Acetyl-CoA

Water-soluble vitamins

Contain several hydrophilic groups that easily dissolve in aqueous environments. Not stored in the body and are usually excreted in the urine. Must be frequently replenished by diet

Fat-soluble vitamins

They are highly hydrophobic molecules that dissolve in lipids rather than aqueous environments and are not usually excreted in urine. Accumulated in adipose tissue

What are the aromatic amino acids?

Tryptophan (W), phenylalanine (F), tyrosine (Y)

What are the acidic amino acids?

Glutamic acid (E) and aspartic acid (D)

Condensation reactions

Release water when bonds are formed. An example is peptide bond formation

Hydrolysis reaction

Breaks peptide bonds by adding water

What is the direction of solid-phase peptide synthesis?

Occurs from C-terminus to N-terminus. BE CAREFUL! This is the opposite direction in which peptides are usually written. Synthesis will start on the right side and move towards the left

What is required for a disulfide bond to occur?

Since it is an oxidation-reduction reaction, the sulfur atoms in cysteine are in a reduced form and become oxidized which requires an oxidizing agent. Adding an oxidation agent helps increase the amount of disulfide bond formation

Is protein folding a spontaneous reaction?

Under conditions that mimic physiological settings, most proteins spontaneously fold into a conformation that minimizes interactions between hydrophobic residues and water (hydrophobic effect)

What happens to enzymes at low temperatures?

At low temperatures, molecular motion slows down and the active site becomes inflexible. If the active site in inflexible, then the induced fit model doesn’t work as well because the active site cannot easily change shape to accommodate the transition state

What happens to enzymes at high temperatures?

Molecular motion speeds up and the intramolecular bonds that maintain the enzyme’s tertiary structure are broken. High temperatures cause protein denaturation while low temperatures just cause enzyme stiffness

Cation exchange chromatography

Has negative residues in the column so that positively charged molecules stick to the column. Give all the molecules a positive charge and then slowly increase the pH so that they selectively get deprotonated and elute through the column

What is the stereochemistry for almost all amino acids except for glycine?

Almost all exclusively L-amino acids which corresponds to an S absolute configuration

What is an ionizable amino acid?

Amino acids with side chains that can be ionized at certain pH levels between 0 and 14. These are amino acids with a titration curveW

What are the 7 ionizable amino acids?

Arginine (R), Lysine (K), Tyrosine (Y), Cysteine (C), Histidine (H), Glutamic acid (E), and Aspartic acid (D)

What is the pKa of Lysine’s side chain?

10\.5

What is the pKa of the C-terminus of an amino acid?

2\.2

What is the pKa of the N-terminus of an amino acid

9\.5

Which is the only amino acid with a primary alcohol?

Serine

What does a nucleotide triphosphate consist of?

A nitrogenous base, a sugar (ribose), and triphosphate

What is the difference between furanose and pyranose?

Furanoses are five membered sugar rings and pyranoses are six membered sugar rings

When can carbohydrates participate in glycosidic linkages?

Only when they are in their cyclic forms (furanose or pyranose)

Steps of apoptosis pathway that is caused by oxidative stress

1. Initiated when the mitochondrial membrane is permeabilized in response to these environmental cues
2. Cytochrome C is released from the mitochondria into the cytosol
3. Cytochrome C causes proteolysis
4. Activates caspase proteases

What is the activity of Complex V dependent on?

Depends on the number of protons that are available to flow through it. The protein concentration in the intermembrane space is dependent on the number of NADH and FADH2 molecules that enter the ETC

What is the average weight of a single amino acid?

100 Da

What are histones?

Nuclear proteins that serve as structural support for DNA to wind tightly around which allows genomic DNA to be condensed into the nucleus of each cell

Which part of the DNA backbone does histone bind to?

Histones interact with the backbone of DNA, not the nitrogenous bases

What is Circular Dichroism?

A classic method of determining a protein’s secondary structure based on its ellipticity at different wavelengths

Which amino acids are good for stacking to stabilize secondary structures?

Aromatic side chains such as phenylalanine, tyrosine, and tryptophan

Which amino acid is flexible for turning?

Glycine

Which amino acid is used for tight turns?

Proline because its ability to adopt the cis-conformation

What is the hydrophobic effect?

Phenomenon that drives protein folding as it causes proteins to adopt a conformation that hides as many hydrophobic residues in the interior of the protein as possible

What does aggregation cause?

A significant decrease in the solubility of the protein

Parallel strands of beta sheets

Parallel strands run in the same direction so the N-terminal portion of one strand aligns with the N-terminal portion of another strand

Antiparallel strands in beta sheets

Run in the opposite direction to each other so the N-terminal aligns with the C-terminal portion of the neighboring strand

What links parallel strands

Since there is no reverse in directionality, neighboring strands must be linked by longer loops that makes 360 degree turns

What links antiparallel strands in beta sheets?

Beta turns link antiparallel sheets that cause a 180 degree turn

What are molecular chaperones?

Proteins that facilitate the proper folding of other proteins

How do molecular chaperones facilitate proper folding?

They bind to the hydrophobic parts of the wrongly folded proteins and stop them from being exposed to the solvent. This prevents and reverses aggregation by blocking interactions between hydrophobic regions of separate polypeptides

Quaternary structure

Result of intermolecular interactions between multiple polypeptides. This only exists for multimeric proteins

Is the hydrolysis of macromolecule favorable?

It is generally a spontaneous reaction but it will not proceed if it is kinetically unfavorable

What affects the isoelectric point values?

Protein structure and posttranslational modifications

Competitive enzyme mechanism

Competitive inhibitors bind the free enzyme E exclusively and prevent substrate from binding

Chemotaxis

The process by which mobile cells both sense and move toward or away from an increasing concentration of a specific chemical

What are the 3 parts of the flagellum?

A basal body, a hook, and a long helical tube called a filament

What is the function of the basal body in the flagellum?

It generates torque for movement

What is the function of the hook in the flagellum?

It is a flexible structure that connects the basal body and the filament. It transmits torque generated by the basal body but does not generate any rotation itself

Is the pH in the right ventricle lower or higher compared to the left ventricle?

It is lower. Blood coming into the right ventricle is deoxygenated so it has more CO2 which means the bicarbonate buffer reaction moves towards the right to produce more H+ which lowers the pH

What are macrophages?

Phagocytic immune cells that engulf and destroy foreign pathogens and damaged cells

Cascade of events after injury:

1. Formation of platelet plug: Platelets bind to collagen fibers and create a platelet plug which prevents blood flow out of the vessel
2. Strengthening of the clot: clotting factors are activated that leads to the formation of thrombin to reinforce the clot

Where are clotting factors formed?

Mainly synthesized in the liver

What is the function of thrombin?

Thrombin induces protein strands (fibrin) to form an adhesive mesh-like structure over the platelet plug

Where does majority of gas exchange occur?

Happens at the alveoli which are at the end of the respiratory tract branches

What is emphysema?

Breakdown of alveolar walls that results in less efficient gas exchange

Forced vital capacity (FVC)

The total volume of air exhaled in a single breath

How does asthma affect breathing?

Asthma exhibits decreased airway diameter and increased resistance to flow, resulting in a decreased volumetric rate of forcibly exhaled air

What is the regulation of the respiratory rate most sensitive to?

Indirectly respond to the PCO2 in the blood and brain by directly sensing changes in H+

What does prolonged bronchoconstriction during an asthma attack lead to?

Respiratory acidosis and increased respiratory rate

What happens during inhalation?

The diaphragm contracts, the intrapleural space drops pressure, and the ribs elevate

What is the function of cilia in the upper respiratory tract?

Ciliated cells beat synchronously to sweep foreign bodies trapped in mucus up the respiratory tract to the pharynx

What is found in plasma?

Water, electrolytes, respiratory gases, hormones, nutrients, metabolic waste, blood proteins (albumin)

What is the function of albumin?

Maintains capillary oncotic pressure

What happens if diaphragm contraction is impaired?

It causes reduced ability to decrease pressure in the lungs

Steps of inhalation

1. Inspiratory muscles contract
2. thoracic cavity volume increases and allows lungs to stretch
3. volume increases and pressure decreases within the lungs
4. intrapulmonary pressure falls below atmospheric pressure
5. air flows down pressure gradient into lungs

Enteric nervous system

Neurons that govern the function of the GI system

Peristalsis

Rhythmic contractions of the gut tube

How does chewing help digestion?

Helps increase the surface area to volume ratio of the food, creating more surface area for enzymatic digestion as it passes through the gut tube

What is the function of salivary amylase

Capable of hydrolyzing starch into smaller sugars (maltose and dextrins)

What is the function of lipase?

Catalyzes the hydrolysis of lipidsP

Pharynx

Cavity that leads from the mouth and posterior nasal cavity to the esophagus

Esophagus

Muscular tube that connects the pharynx to the stomach

What is the function of mucous cells?

The bicarbonate-rich mucous that protects the muscular wall from the harshly acidic (pH = 2) and proteolytic environment of the stomach

What is the function chief cells?

Secrete pepsinogen which is the zymogen form of pepsin

What is the function of parietal cells?

Secretes hydrochloric acid, whose hydrogen ions cleave pepsinogen to pepsin

What is the function of pepsin

Digests proteins by cleaving peptide bonds near aromatic amino acids, resulting in short peptide fragments

What are the 6 products that are secreted by the stomach?

HCl, pepsinogen, mucus, bicarbonate, water, intrinsic factor

What is the function of pyloric glands?

Contains G-cells that secretes gastrin

What is the function of gastrin?

It induces parietal cells in the stomach to secrete more HCl and signals the stomach to contract, mixing its contents

What is chyme?

Acidic, semifluid mixture

What are the 3 segments of the small intestine?

Duodenum, jejunum, and the ileum

What is the function of disaccharidases

It digests disaccharides

What is the function of maltase?

It digests maltose

Enteropeptidase

An enzyme critical for the activation of trypsinogen to trypsin

What is the function of secretin?

It is a peptide hormone that causes pancreatic enzymes to be released into the duodenum

What is the function of aminopeptidase

It is a peptidase secreted by glands in the duodenum that removes the N-terminal amino acid from a peptide

What is the function of cholecystokinin (CKK)

Secreted in response to the entry of chyme in the duodenum

What is the function of bile salts?

Serves as a bridge between aqueous and lipid environments. Bile salts emulsify fats and cholesterol into micelles which helps increase the rate that lipase can act

What is the function of pancreatic juices?

Complex mixture of several enzymes that digests all 3 nutrients of carbohydrates, fats, and proteins

What is the major pigment in bile

Bilirubin which is a byproduct of the breakdown of hemoglobin

What is the function of albumin

A protein that maintains plasma oncotic pressure and also serves as a carrier for many drugs, hormones, and clotting factors