Biochem Quick Reference Review

A comprehensive set of 200 question-and-answer flashcards covering protein structure, membrane biochemistry, signal transduction, membrane transport, and physiological buffer systems.

What determines a protein's identity and folding behavior?

The linear sequence of amino acids, i.e., primary structure.

Which level of protein structure consists of alpha helices and beta sheets stabilized by hydrogen bonds?

Secondary structure.

What types of interactions stabilize tertiary protein structure?

Hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridges.

What is the assembly of multiple polypeptide subunits called?

Quaternary structure.

Give an example of a protein that has quaternary structure.

Hemoglobin.

What type of molecules assist in folding large or complex proteins?

Molecular chaperones.

Why is the final folded state of a protein typically favored?

It is the most stable and functionally active conformation.

What is a functional domain in a protein?

A region that folds independently and performs a specific biological function.

Which domain phosphorylates substrates?

The kinase domain.

Which domain binds DNA via zinc ions?

Zinc finger domain.

Which domain recognizes phosphorylated tyrosines?

SH2 domain.

List the six major classes of protein function.

Enzymes, structural proteins, transport proteins, receptors & signal proteins, motor proteins, immune proteins.

Give an example of a protein that catalyzes biochemical reactions.

DNA polymerase (or trypsin).

Which structural protein provides tensile strength in connective tissues?

Collagen.

What transport protein carries oxygen in the blood?

Hemoglobin.

Which receptor responds to insulin?

Insulin receptor (a receptor tyrosine kinase).

Name a motor protein involved in intracellular transport along microtubules.

Kinesin.

Which immune proteins recognize and neutralize pathogens?

Antibodies.

What is the primary function of ribosomes?

Synthesizing cellular proteins.

Which molecular machine converts proton gradients into ATP?

ATP synthase.

What cytoskeletal proteins form microfilaments?

Actin.

What term describes a membrane's ability to allow certain substances to pass while blocking others?

Selective permeability.

Describe the structure of a phospholipid.

An amphipathic molecule with a hydrophilic head and hydrophobic tails.

How do phospholipids arrange themselves in an aqueous environment?

In a bilayer with tails inward and heads facing outward.

What effect do unsaturated fatty acids have on membrane fluidity?

They increase fluidity.

How does cholesterol affect membrane fluidity at high temperatures?

It decreases fluidity by stabilizing the bilayer.

What type of membrane protein spans the entire bilayer?

Integral protein.

What type of membrane protein is loosely attached to the surface?

Peripheral protein.

Which small non-polar gases can diffuse directly through the lipid bilayer?

O2 and CO2.

What specialized channels facilitate rapid water movement across membranes?

Aquaporins.

What is the primary role of membrane receptors?

Detect external signals and initiate intracellular responses.

Give an example of an intracellular membrane-bound organelle.

Endoplasmic reticulum.

What is the definition of signal transduction?

The process by which a cell converts external signals into specific intracellular responses.

Which class of signaling molecules can cross the plasma membrane directly?

Hydrophobic signals such as steroid hormones.

Which class of signaling molecules binds to cell-surface receptors?

Hydrophilic signals like peptide hormones and neurotransmitters.

What family of receptors spans the membrane seven times?

G protein-coupled receptors (GPCRs).

What triggers activation of a heterotrimeric G protein?

GDP-GTP exchange on the alpha subunit.

In the Gs pathway, which enzyme converts ATP to cAMP?

Adenylate cyclase.

Which kinase is activated by cAMP?

Protein Kinase A (PKA).

In liver cells, which hormone uses the cAMP pathway to stimulate glycogen breakdown?

Norepinephrine (or epinephrine).

Which enzyme does a different GPCR pathway activate to produce IP3 and DAG?

Phospholipase C.

What second messenger causes calcium release from the endoplasmic reticulum?

IP3.

Which kinase is activated by DAG and calcium?

Protein Kinase C (PKC).

What happens to receptor tyrosine kinases (RTKs) upon ligand binding?

They dimerize and autophosphorylate.

Which small GTPase is recruited by phosphorylated RTKs in the MAPK pathway?

Ras.

Name the kinase cascade following Ras activation.

RAF → MEK → ERK.

Where does activated ERK migrate to regulate gene expression?

The nucleus.

Give one way signaling pathways are terminated.

GTP hydrolysis, receptor desensitization, or second messenger degradation.

What is passive transport?

Movement of substances down their electrochemical gradients without ATP expenditure.

Give two examples of molecules that cross the membrane by simple diffusion.

Oxygen and carbon dioxide.

How do polar or charged solutes cross membranes without energy?

By facilitated diffusion through channels or carriers.

What is osmosis?

Diffusion of water toward the side with higher solute concentration.

What happens to a cell placed in a hypotonic solution?

It swells and may lyse.

What pumps 3 Na⁺ out and 2 K⁺ in per ATP hydrolyzed?

Na⁺/K⁺-ATPase.

What type of transport directly uses ATP hydrolysis?

Primary active transport.

What type of transport uses the energy stored in an ion gradient?

Secondary active transport.

Give an example of a symporter driven by the sodium gradient.

Na⁺/glucose cotransporter.

Which antiporter removes calcium from cardiac myocytes using sodium entry?

Na⁺/Ca²⁺ exchanger.

Name the process by which cells engulf large particles.

Phagocytosis.

What is receptor-mediated endocytosis used for?

Selective internalization of ligands such as LDL cholesterol.

What process releases neurotransmitters and hormones from cells?

Exocytosis.

Which pump establishes the steep Na⁺ gradient used by many secondary transporters?

Na⁺/K⁺-ATPase.

How do ion gradients contribute to electrical excitability?

They create a negative resting membrane potential enabling action potentials.

Define pH.

The negative logarithm of hydrogen ion concentration.

What is the normal arterial blood pH range?

7.35–7.45.

Why are small pH changes dangerous for proteins?

They alter charge states, disrupting structure and function.

What two components make up a buffer?

A weak acid and its conjugate base.

State the Henderson–Hasselbalch equation.

pH = pKₐ + log([A⁻]/[HA]).

Within how many pH units of its pKₐ does a buffer work best?

±1 pH unit.

What is the pKₐ of the carbonic acid/bicarbonate system?

6.3.

What ratio of HCO₃⁻ to H₂CO₃ exists in blood at pH 7.4?

About 20:1, favoring the base.

Which organs adjust the components of the bicarbonate buffer?

Lungs and kidneys.

What is metabolic acidosis characterized by?

Decreased bicarbonate and blood pH below 7.35.

Give a common cause of metabolic acidosis.

Diabetic ketoacidosis or renal failure.

What causes respiratory acidosis?

Elevated CO₂ due to hypoventilation or COPD.

What is the immediate threat of respiratory acidosis?

Cerebral vasodilation and CNS depression.

What primary disturbance defines metabolic alkalosis?

Increased bicarbonate.

Name a cause of metabolic alkalosis.

Prolonged vomiting or diuretic use.

What is respiratory alkalosis?

Decreased CO₂ leading to pH above 7.45.

How can high altitude induce alkalosis?

Hyperventilation lowers CO₂.

Which buffer predominates inside cells and in renal tubules?

Phosphate buffer (H₂PO₄⁻/HPO₄²⁻).

What role does hemoglobin play in buffering?

Absorbs protons produced by CO₂ hydration in RBCs.

How quickly can the lungs compensate for acid-base disturbances?

Within minutes.

How long do the kidneys take to adjust bicarbonate levels?

Hours to days.

What is the effect of cAMP on the MAPK pathway?

It can inhibit MAPK signaling.

Why are proteins called macromolecules?

They are large polymers composed of amino acids.

Which chemical bond joins amino acids in the primary structure?

Peptide bond.

What determines the specificity of protein–protein interactions in signaling?

Recognition of functional domains such as SH2.

What is the fluid mosaic model?

Concept that membranes are dynamic bilayers with moving lipids and proteins.

How does cholesterol prevent membrane crystallization at low temperatures?

By inserting between phospholipids, disrupting tight packing.

Which type of transport is described as "downhill"?

Passive transport.

Which cellular process is known as "cell drinking"?

Pinocytosis.

What does the term amphipathic mean?

Having both hydrophilic and hydrophobic regions.

What is the chief energy currency produced by ATP synthase?

ATP.

Which structural protein makes up hair and nails?

Keratin.

Name two motor proteins that move along microtubules.

Kinesin and dynein.

What is the primary role of albumin in the blood?

Transporting molecules and maintaining osmotic pressure.

Which ion gradient often powers secondary active transport?

Sodium gradient.

What does the acronym GPCR stand for?

G protein-coupled receptor.

What second messenger activates Protein Kinase C along with DAG?

Calcium.