Theme B1-B2 Form and Function HL Test

1. amine groups/carboxyl groups -

2. R-groups -

1. link amino acids tg

2. gives each amino acid its unique characteristics

Hydrophobic R-groups

• non-polar

• repel water molecules

Hydrophilic R-groups

• polar or charges

• acidic or basic

• attract molecules

Polar R-groups

• contain partial charges that interact w/ water molecules

Charged R-groups

• positively charges (basic)

• negatively charged (acidic)

Primary Structure

• specific sequence of amino acids joined tg to form a polypeptide chain

unique sequence of animo acid determines..

how the polypeptide chain will fold

secondary structure

• local folding patterns that occur within the polypeptide chain

• alpha helices

• beta-pleated sheets

formation of alpha helices and beta-pleated sheets facilitated by

• ability of polypeptide chain to fold into coils and pleats

• achieved through hydrogen bonding btw carboxyl group and animo group

alpha helix

• hydrogen bond forms btw the amine hydrogen and the carboxyl oxygen that is 4 residues away in the sequence

beta-pleated

• sections of the polypeptide chain run parallel to each other, and hydrogen bonds form btw adjacent strands

tertiary structure

• further folding of the polypeptide

• dependent on the interaction between R-groups (could include formation of hydrogen bonds, ionic bonds, disulfide covalent bonds, and hydrophobic interactions) → stabilise structure of the protein

hydrogen bonds

• stabilising its 3D shape (tertiary structure) → holding distant regions of the polypeptide chain tg

• maintaining protein’s functional integrity and any slight deviations

Ionic bonds

• btw oppositely charged ions (R-group can undergo binding/dissociation of hydrogen ions → positively or negatively charged state)

• contribute to the overall stability/function of the protein

Disulfide covalent bonds

• form btw pairs of cysteine amino acid residues (contain sulfur atoms)

• critical for stabilising tertiary and quaternary structures → forming covalent bonds that help to maintain the protein’s overall 3D shape

Hydrophobic interactions

• occur btw non-polar amino acids

• non-polar AAs are unable to interact w/ water, they tend to clump tg into hydrophobic clusters in protein interior

• stabilise the protein’s tertiary structure and quaternary structure

Myoglobin

• protein found in muscle tissue that binds and stores oxygen

• globular protein w/ hydrophobic core

haemoglobin

• protein responsible for transporting oxygen throughout the body

• globular protein w/ hydrophobic core

Rhodopsin

• protein found in cell membrane of retinal cells responsible for absorbing light

• integral membrane protein that has hydrophobic regions

quanternary structure

• arrangement and interaction of 2 or more polypeptide chains to form a functional protein

• ex. haemoglobin

• haemoglobin

• consists of 4 individual polypeptide chains (2 a-chains, 2 b-chains)

• conjugated (non-protein component haem)

• 4 subunits held tg by non-covalent bonds

• interactions btw subunits allow conformational changes necessary for oxygen-carrying

Conjugated

• have non-protein components such as metal ions or carbohydrates in addition to having polypeptide subunits. 

• Non-protein components have ability to increase a proteins diversity and functionality (ex. Crucial role in many enzymes → help perform their catalytic functions) 

  • Ex. Haemoglobin contains Haem (contains iron) → responsible for binding of oxygen. 

Non-Conjugated

• consist only of polypeptide subunits 

• Ex. Insulin (composed of 2 polypeptide subunits)

Globular

• complex proteins that are usually spherical in shape with irregular fold. 

• Soluble in water → important roles as enzymes, transporters, and regulators 

• Ex. Insulin

• Arranged in a 3D shape held together by hydrogen bonds, hydrophobic interactions and disulfide bonds. 

Fibrous

• simpler than globular proteins in structure and have a long, narrow shape. 

• Composed of repeating structures that are designed for strength and stability + insoluble in water 

• Provide structural support/stability to cells/tissues 

• Ex. Collagen

Insulin 

Form 

• Consists of 2 polypeptide chains (a-chain and b-chain) 

• Arranged in specific 3D shape held tg by hydrogen bonds, hydrophobic interactions and disulfide bonds

• compact/globular w/ hydrophilic exterior (allows to interact w/ water in blood → travel) and hydrophobic interior (stabilize the shape of the protein)

Function 

• Regulates the amount of glucose in the blood

• Produced by pancreas → released into bloodstream (response to high blood sugar) 

• Binds to specific receptors → glucose to enter the cells + be used for energy/stored

Collagen 

Form

• Most abundant protein in the body → forming main component of connective tissue 

• Made up of 3 polypeptide chains that are twisted together in a triple helix structure 

  • Each chain → rich in amino acid glycine + proline + hydroxyproline residues

Function (allows chain to twist tg into tight helix held tg by hydrogen bonds + van der waals forces) 

• Fibres are strong and flexible 

Function 

• Provides structural support to tissues → maintain their shape and integrity 

All lipids have

• 2 long fatty acid chains

• Vary in lengths, number of double bonds, and degree of saturation 

Saturated fatty acids 

• Higher melting point → provide stability to the membrane 

• Fit tg snugly making membrane denser + more rigid

• Freeze more easily than unsaturated fatty acids 

Unsaturated fatty acids

• Lower melting points → ensure fluidity of the membrane 

• Kinks prevent membrane lipids from packing together closely, maintaining fluidity 

Cholesterol

• It is an amphipathic steroid (hydrophobic region → 4 steroid rings + hydrocarbon side chain | hydrophilic region → polar hydroxyl group) 

Role of cholesterol in membrane fluidity

• Plays an important role in the fluidity of biological membranes 

• Regions interact w/ the corresponding regions of adjacent phospholipid molecules 

• Interactions hold phospholipid molecules together

• Low temps - Prevents the fatty acid chains from fitting closely tg 

• High temps - stabilises the membrane and reduces fluidity 

Endocytosis 

• Bulk transport mechanism, particles are moved into the cell 

• Cell membrane engulfs the particles →  membrane then pinches off to form a vesicle with the particles

• ex. Phagocytosis and Pinocytosis

• Lipids and proteins are added 

Phagocytosis

• ingestion of large solid particles (seen in white blood cells) 

Pinocytosis

• ingestion of liquids (Vesicles that are formed are smaller )

Exocytosis 

• Bulk transport  of material to be secreted

•  material is enclosed in vesicles →  vesicles move to the plasma membrane and fuse with it  → discharging contents 

• Ex. glycolipids produced by ER and modified in golgi apparatus 

Gated Channels

• Respond to inputs given by either opening or staying closed 

• Transmembrane proteins present on cell membrane → form pores for the movement of ions across the membrane 

• Only specific ions can pass through them

4 types of gated channels

• voltage-gated channels

• ligand-gated channels

• mechanically gated channels (which respond to mechanical cues such as sound waves and vibrations).

neurons

• cells of the nervous system that transmit information in the form of electrical impluses

potential difference across the nerve cell membrane

-70 mV - inside of the neuron is more negatively charged than outside

electrochemical gradient

higher concentration of potassium ions inside the cell

stimulus

causes the generation of an electrical impulse

impulse

temporary reversal in the potential difference

Nerve signalling

• Change in potential is due to opening of voltage-gated sodium channels / potassium channels 

• When VGS opens → sodium ions diffuse into the neuron (+ charge) → action potential 

• When VGS closes and VGP opens → potassium ions diffuse out of the neurons  (less +) → resting membrane potential re-established

Ligand-gated channels 

• Open when a ligand binds to the transmembrane protein 

• Present at skeletal neuromuscular junctions

• Conformational change (from acetylcholine molecules binding) opens channel → sodium ions diffuse down their concentration → more + 

• Enzyme cholinesterase breaks down acetylcholine → closure of ion channels 

Sodium-Potassium Pump - Direct Active Transport

• Enzyme that generates energy by the breakdown of ATP 

• Energy released drives the transport of sodium and potassium ion against their concentration gradient 

• Asymmetric distribution of ions (electrochemical gradient → high concentration of K and low intracellular concentration of Na) is in part due to the Na/K pump

• re-establishes membrane potential after passage of nerve impulse

Na+/K+ Pumps

• transmembrane pumps with 3 binding sites (for sodium and 2 for potassium)

• initially open to inside of cell (way that sodium ions bind to all 3 sites)

• sodium ions binding triggers hydrolysis of ATP

• latter attaches to pump → conformational change (pump now opens to exterior)

• potassium ions attach now to sites → phosphate group detaches

• conformation change → original form

for every molecule of ATP hydrolyses

• 3 sodium ions are pumped out

• 2 potassium ions are pumped in

• builds higher concentration of K+ inside

Sodium-Potassium Pump - Indirect Active Transport   

• Involves transport of 2 solutes (ions or molecules) (on transported down, one transported against) → drives the latter

• Sodium ions bind to binding sites on outer surface → molecule of glucose binds to its site → results in conformational change (transports both sodium ions and glucose moles to inside of cell)

indirect active transport example

• reabsorption of glucose y the cells of the nephron

• as kindey filters blood large amounts of glucose are removed

• then glucose molecules are reabsorbed w/ help of the sodium-dependent glucose contransporters present on kidney cells (prevents loss of glucose)

What is biological cell adhesion

• The binding of cells with each other (or with the extracellular matrix) to form functional tissues.

What are Cell-Adhesion Molecules (CAMs) and what is their role

They are specialized glycoproteins that mediate the binding of cells to adjacent cells or to the extracellular matrix. They are essential for forming cell junctions.

What are the 4 main families/forms of Cell-Adhesion Molecules (CAMs)?

• Cadherins

• Integrins

• Selectins

• Immunoglobulin superfamily

What are the general functions of cell junctions?

• Connect cells to each other

• Allow intracellular transport and communication

• Regulate cell proliferation and cell migration

• Prevent unregulated movement of materials between cells

What are Adhesive Junctions (Anchoring Junctions)?

• Types: Adherens junctions and desmosomes.

• Location: Epithelial and cardiac cells.

• Function: Facilitate cell–cell adhesion to ensure structural stability and withstand mechanical stress.

What are Tight Junctions (Occluding Junctions)?

• Location: Epithelial cells.

• Function: Form a tight seal between neighboring cells acting as a barrier to prevent the unregulated movement of molecules across tissues.

What are Gap Junctions (Communicating Junctions)?

• Function: Intercellular channels connecting neighboring cells that allow the physical movement and direct cell–cell transfer of small molecules and signals.

What type of cell junction forms the blood–brain barrier?

Tight junctions — they wedge capillary endothelial cells tightly together to block harmful, unregulated substances from entering brain tissue.

Which cell junction is responsible for passing electrical impulses between cardiac muscle cells?

Gap junctions — disruption of gap junctions prevents electrical signal transmission between heart muscle cells.

Which cell junctions fail in Junctional Epidermolysis Bullosa?

Adhesive junctions (anchoring junctions / desmosomes) — without them, epithelial tissues cannot withstand normal everyday mechanical stress, causing skin sores and blisters.

What causes a "leaky gut" at the cellular level?

A decrease or impairment in tight junction function, allowing harmful substances from the intestinal gut to cross into the bloodstream.

What is the primary function of the mitochondrion?

To produce ATP through the breakdown of molecules, most commonly glucose (cellular respiration).

How do the permeability properties of the mitochondrial outer and inner membranes differ?

• Outer membrane: Permeable to many small molecules and ions; contains transport proteins for larger molecules.

• Inner membrane: Highly folded into cristae; holds key respiration enzymes and regulates molecule movement tightly.

What are cristae in mitochondria, and what is their structural advantage?

• Highly folded structures of the inner membrane that increase surface area. This allows more ATP-producing enzymes to be present, increasing the speed and efficiency of cellular respiration.

What is the mitochondrial matrix and what occurs there?

The fluid-filled enclosed space inside the inner membrane. It contains a high concentration of enzymes and molecules needed for the Krebs cycle.

What is the function of the mitochondrial intermembrane space?

It is a small space between the outer and inner membranes that allows molecules to accumulate rapidly to high concentrations, establishing a concentration gradient across the inner membrane to generate ATP.

What are the three distinct membranes and three distinct compartments of a chloroplast?

• Membranes: Outer membrane, inner membrane, and thylakoid membrane.

• Compartments: Intermembrane space, stroma, and thylakoid space.

What are thylakoids and grana?

• Thylakoids: Pancake-like membrane structures containing photosystems for light-dependent reactions.

• Grana (singular: granum): Stacks of thylakoids that maximize sunlight absorption as light passes through.

How do lamellae connect chloroplast structures?

They are thylakoid membranes that connect individual grana stacks, creating a continuous thylakoid space.

Why is the small volume of the thylakoid space biologically important?

1. Allows rapid accumulation of molecules to generate a high concentration gradient quickly.

2. Provides compartmentalization to isolate potentially dangerous chemical products from the rest of the cell.

What is the stroma and what chemical pathway takes place inside it?

The compartment between the inner membrane and thylakoid membranes. It contains all the enzymes and substrates required for the Calvin cycle to produce glucose

What are two primary functions of the nuclear double membrane?

1. Serves as a protective barrier to shield environmentally sensitive DNA from damage.

2. Regulates gene expression by controlling the passage of signaling molecules and transcription factors.

What structural feature is unique to the outer nuclear membrane?

It has ribosomes attached to its surface and is continuous with (joined to) the rough endoplasmic reticulum (rER).

What are nuclear pores and what do they transport?

• Integral/channel proteins spanning the nuclear envelope that regulate the exit of mRNA to ribosomes/rER and control the entry and exit of signaling proteins/transcription factors.

How does the nuclear membrane reassemble after cell division (mitosis/meiosis)?

• Small vesicles derived from the endoplasmic reticulum (ER) containing nuclear proteins and lipids bind to chromosomes.

• The vesicles join around the chromosomes.

• Vesicles fuse together to reform the continuous double nuclear membrane.

Where are free ribosomes located, and what is the destination of the proteins they synthesize?

Located in the cytoplasm. They synthesize proteins that remain and function inside the cell's cytoplasm.

Where are bound ribosomes located, and what is the destination of the proteins they synthesize?

Attached to the cytosolic side of the Rough Endoplasmic Reticulum (RER). They synthesize proteins that enter the RER lumen to be exported outside the cell or sent to specific organelles.

Are free and bound ribosomes structurally or functionally different?

No. They are structurally and functionally identical; only their location differs depending on the protein being made.

How does a cell know to direct a ribosome to the RER during protein synthesis?

The mRNA contains an ER signal sequence. When translated, this signal directs the ribosome to bind to the RER membrane.

Why do pancreatic cells contain a higher proportion of RER and bound ribosomes?

Pancreatic cells specialize in exporting large amounts of digestive enzymes and hormones (proteins) outside the cell, requiring extensive RER for synthesis and transport.

What is the difference between Rough ER (RER) and Smooth ER (SER)?

• RER: Has ribosomes bound to its cytosolic surface; involved in protein synthesis and modification.

• SER: Lacks ribosomes; involved in lipid synthesis and metabolic processes.

What is the ER lumen?

The internal space enclosed by the system of interconnected flattened sacs and tubes of the Endoplasmic Reticulum membrane.

What types of protein modifications occur inside the RER lumen?

• Addition of carbohydrates (forming glycoproteins)

• Addition of phosphate groups

• Assisted protein folding by enzymes

How do proteins move from the RER to the Golgi apparatus?

A piece of the RER membrane buds off around the modified protein to form a transport vesicle, which travels through the cytoplasm and fuses with the Golgi apparatus.

What is the primary function of the Golgi apparatus?

To modify, sort, package, and transport proteins and lipids produced in the cell.

Name the three main compartments of the Golgi apparatus in order of processing.

• cis compartment: Receiving side (fuses with vesicles from RER).

• Medial compartment: Middle processing zone.

• trans compartment: Shipping side (packages proteins into vesicles for final destinations —> outside)

What happens at the cis compartment of the Golgi apparatus?

It receives transport vesicles from the RER; the vesicle membrane fuses with the cis compartment to release proteins into the Golgi for sorting

Where are proteins sent after passing through the medial and trans compartments of the Golgi?

They are sorted and packaged into vesicles destined for:

• Lysosomes (internal use)

• Plasma membrane integration

• Secretion/export outside the cell

What is the biological benefit of compartmentalization in the RER and Golgi apparatus?

It isolates specific chemical environments, allowing the cell to concentrate necessary enzymes and molecules for specialized tasks (e.g., lysosome formation, targeted protein folding).

What is a vesicle?

A small, membrane-bound sac that transports, stores, or isolates materials (proteins, lipids, RNA) within a cell

What is the role of a Transport Vesicle?

Moves materials between organelles inside the cell (e.g., carrying newly made proteins from the RER to the Golgi apparatus).

What is the role of a Secretory Vesicle?

Stores and transports molecules (e.g., hormones, neurotransmitters, digestive enzymes) to the plasma membrane to be released outside the cell via exocytosis

What is a Lysosome and what is its function?

A specialized vesicle containing hydrolytic enzymes that break down cellular waste, macromolecules, and damaged organelles.

What is a Peroxisome?

A membrane-bound vesicle containing specialized enzymes involved in lipid metabolism and the detoxification of harmful compounds.

What is clathrin?

A protein that plays a key role in vesicle formation by assembling into a cage-like structure that helps shape and pinch off membrane segments.

How does clathrin assist in forming a vesicle?

• Multiple clathrin molecules polymerize around a membrane area.

• As the membrane invaginates, clathrin forms a coated pit (scaffold).

• It pulls together necessary proteins to shape and pinch off the vesicle.

What happens to the clathrin coat after a vesicle buds off into the cell?

The clathrin coat breaks down via hydrolysis back into individual clathrin molecules, leaving an uncoated vesicle.

List three cellular processes that rely on clathrin-coated vesicles.

• Endocytosis (and phagocytosis)

• Transport of cargo from the Golgi to the plasma membrane

• Formation of lysosomes

How is cellular protein transport analogous to a city public transport network?

Just like passengers choose buses, trains, or subways based on destination, proteins are routed via different pathways (free ribosomes, RER, Golgi, specialized vesicles) depending on where they need to go inside or outside the cell.

How does mutated Huntington (Htt) protein cause symptoms like involuntary tics in Huntington's Disease?

Mutated Htt sticks together and inhibits clathrin polymerization. This prevents the endocytosis of neurotransmitters back into neurons, leaving neurotransmitters active and causing continuous muscle signals.