Molecular Biology- Exam 2

Cell membrane function

• The primary function of the cell membrane is to separate the cell's interior from its exterior.

• This separation is crucial for maintaining distinct internal conditions (e.g., pH, temperature) necessary for protein function.

• Cell membranes enable selective interaction with the environment, allowing cells to selectively take in and expel substances.

• Selective permeability is vital; some toxic molecules can cross membranes easily without regulation.

• Membranes facilitate interactions between cells and their environment.

Cell membrane composition by mass

• By Mass: Cell membranes are composed of approximately 40% lipid, 50% protein, and 10% carbohydrate.

• Comparison to Whole Cell: The membrane has a significantly higher lipid proportion (four times more) and a similar carbohydrate percentage compared to the cell as a whole. Proteins, being denser and larger, account for a substantial mass percentage despite appearing less numerous than lipids.

• Whole cell: 50–60% protein, 20% DNA/RNA, 10%

  lipid, 10% carbohydrate

  • Membrane: 4× the lipid share, but still half

  protein

Cell Membrane Composition: inside vs outside

• Outside Surface: Predominantly features carbohydrates (glycocalyx) for interaction, recognition, and increased hydrophilicity.

• Inside Surface: Connects to the cytoskeleton, providing structural support and anchoring, essential for cell shape and movement.

• Lipid Asymmetry: The inner and outer leaflets have different lipid compositions. For example, the flipping of inner lipids (like phosphatidylserine) to the outer surface signals cell death (apoptosis), leading to the cell's reabsorption by other cells.

Glycocalyx: The carbohydrate coat

• The glycocalyx is the carbohydrate coating on the cell surface.

• Functions:

  • Attracts water molecules, making the cell surface highly hydrophilic.

  • Plays a critical role in self and non-self recognition, important for immune responses and interactions with other cells.

• It is a complex structure with many modifications, and its full details are still being researched.

• Differences in glycocalyx composition are a major reason why cross-species transplantation (e.g., pig to human) is challenging.

• carbohydrates are more polar than the phospholipid heads

Lipid properties and membrane fluidity: phospholipids

• Form a bilayer with polar phosphate head groups and hydrophobic fatty acid tails.

Lipid properties and membrane fluidity: fatty acid tails

• Saturated: Straight tails that pack densely, decreasing membrane permeability and fluidity. They are typically solid at room temperature.

• Unsaturated: Kinked tails that pack less densely, increasing membrane permeability and fluidity. They are typically liquid at room temperature.

Lipid properties and membrane fluidity: importance for fluidity

• Prevents cell lysis (bursting) if cell volume increases, acting like a flexible balloon rather than a rigid structure.

• Allows membrane proteins to move and function.

• Enables processes like cell division and membrane budding.

• Cells must maintain a balance between fluidity (to prevent rigidity) and stability (to prevent leakiness).

Lipid properties and membrane fluidity: temperature dependence

• Cells adapt their fatty acid composition to maintain appropriate fluidity in different temperature environments (e.g., more saturated in high temperatures, more unsaturated in cold temperatures).

Lipid properties and membrane fluidity: cholesterol

• Helps regulate fluidity by broadening the temperature range over which the membrane remains fluid, preventing excessive rigidity at low temperatures and excessive fluidity at high temperatures.

• Location: between phospholipids

• Function: membrane fluidity buffer

• When cold: prevents the membran from becoming too rigid

• When hot: prevents membrane from being too fluid

• without cholesterol, membrane fluidity becomes more sensitive to temperature changes

Membrane proteins: Integral Membrane Proteins

• Span the entire membrane, interacting with both the aqueous environments outside and inside the cell, as well as the hydrophobic core of the membrane.

• Are amphipathic, possessing both hydrophobic and hydrophilic regions

• emebedded in membrane

• may:

  • span entire membrane

  • act as a channel for transport

  • act as a carrier

  • function as a receptor

  • can cross membrane

Membrane proteins: peripheral membrane protiens

• Associate with the membrane surface but do not embed within the hydrophobic core.

• Membrane fluidity is essential for receptors to move, cluster, and interact effectively for cellular signaling.

• located on membrane surface

• function

  • cell regcognition

  • cytoskeleton attachement

  • enzyme activity

  • can not cross

Selective Permeability

• Molecules that can pass freely (without active transport):

  • Small, nonpolar molecules (e.g., steroids). Their passage can be somewhat hindered by the hydrophilic glycocalyx. Also lipid soluble. Ex. O2, CO2,

• Molecules that are blocked or require specific channels/transporters:

  • Polar molecules.

  • Large molecules.

  • Charged molecules.

• Membrane fluidity allows for medical procedures like in vitro fertilization (IVF), where a cell can be punctured with a needle and then reseal.

• Need help: glucose, amino acids, Na+, K+, Ca+2, Cl-

• ions can’t diffuse b/c they’re charged and the membrane interior is hydrophobic

Why would the cell surface need to be as hydrophilic as possible?

• Hydration layer stops nonspecific sticking — contact goes

through specific receptors

• Cushions and protects the bilayer

If you had a membrane that was mostly saturated fatty acids what would happen at low temperatures?

Tails lock into a gel: membrane stiffens, proteins stop moving, transport and signaling stall

• Fix: more unsaturated tails (cold-water fish, bacteria grown cold)

Why might fluidity be important for interacting with the environment?

• Receptors diffuse and cluster → signaling

• Membrane bends and re-seals → endo/exocytosis, migration, division

Phospholipids

• build membrane wall

• form bilayer by arranging with the hydrophobic tails facing each other and the heads facing outward

• hydropobic interior blocks many polar + charged moelcues allowing membrane to be selectively permeable and control what enters and exits cell

amphilic

hydrophobic and hydrophilic regions

describes phospholipids

What type of materials do you expect could go through the membrane without active transport?

• Polar? → small uncharged (H₂O, glycerol, ethanol) slowly; ions blocked

• Non-polar? → small (O₂, CO₂, steroids) freely

• Large molecules? → blocked (glucose, sucrose)

• Small molecules? → yes if uncharged; anything blocked needs a channel or transporter (Friday)

Diffusion

• movement from high to low

• does not use ATP

Factors that make diffusion faster

1. Larger gradient

2. higher temperature

3. lower molecular mass

4. larger surface area

5. shorter distance

6. thinner membrane

7. greater lipid solubility

Facilitated Diffusion

Passive = H to L concentration, no ATP, requires membrane protein

Diffusion across the plasma membrane through a transport protein that does not require energy (channel proteins or carrier proteins)

Channel proteins

• create pores

• do not force molecules through, provide a tunnel/ pathway

• ex. ion channels or aquaporins (specifically for H2O, meant to be rapid)

• hydrophilic

• Two types, always open or gated

Carrier proteins

• binds a substrate and triggers a shape change allowing it to pass

• revolving door

Which is faster, channel or carrier proteins do you think is faster?

Channels are faster, if all carriers are bound increasing the

concentration gradient will not make transport rate increase

Osmosis

movement of H2O across the membrane through aquaporins (channel proteins)

• Always moves high to low concentration, or low solute to high solute

Osmolarity

solutions total solute concentration

concentration gradient

difference in concentration across a space

nature always tries to eliminate these by moving from H to L

tonicity

predicts what will happen to cell volume via osmosis

Hypotonic

outside: low solute, high water

water will move into the cell, cell swells/ lyses

extracellular fluid has lower osmolarity

Hypertonic

outside: high solute, low water

water will out of the cell, cell shrinks

extracellular fluid has higher osmolarity

Isotonic

osmolarity is matched

equal solute concetrations, no net water movement, cell size remians constant

Active Transport

• Transport that does not move with the concentration gradient outside/ inside the cell

• Requires energy- usually ATP (directly or indirectly)

• Can move L to H, typically against the gradient

Electrochemical gradients

• Concentration gradient + electrical gradient that affects an ion

• To move against a concentration or electrochemical gradient, the cell must use energy

• Two types: primary and secondary

Transport proteins: uniporter, symporter, and antiporter

Uniporter: carries 1 specific ion

Symporter: carries 2 diff ions or molecules but in the same direction

Antiporter: carries 2 diff ions or molecules but in different directions

Primary Active Transport

• Uses ATP

• Ex. Sodium potassium pump (Na + K + ATPase)

  • for every cycle 3 Na+ out, 2 k+ in

  • electrogeneic b/c 3 pos in, 2 pos out means a net 1+ leaves → cell becomes more negative

  • pump creates a charge inbalance

  • maintain electrochemical gradient in living cells

membrane potential

the electrical potential difference (voltage) across a cell’s plasma membrane, created by unequal distribution of ions/charges outside and inside of the cell

Secondary Active Transport (co-transport)

• Does not use ATP directly

• Electrochemical gradient created by primary active transport (Sodium potassium pump removes Na from inside of the cell) provides energy to move other substances across

• Transport glucose, amino acids

• Mitochondria use the proton gradient across the mitochondrial membrane to convert ADP into ATP

Essentially: ATP creates a gradient first, gradient stores energy, and that stored energy is what drives another molecule up hill

Why maintain a membrane potential?

• The inside of cells is more negative than the outside

• This takes energy to maintain

Why would this be worth the energy it takes to maintain?

Drives secondary transport

• Enables electrical excitability

(neurons/muscles)

• Helps maintain osmotic stability

• Controls Ca2+ entry

Bulk Transport

Endocytosis = type of active transport that moves particles, large molecules, parts of cells or whole cells from outside to inside of a cell by plasma membrane engulfment

• Phagocytosis = “cell eating”; large particles or bacteria

• Pinocytosis = “cell drinking”; small molecules including water

• Receptor-mediated endocytosis = facilitated by a receptor

• Exocytosis = reverse of endocytosis

Why do cells communicate and what does this look like generally?

• Coordinate growth

• Respond to environment

• Maintain homeostasis

• Receive a message

• Transfer the information across the plasma membrane

• Produce changes in the cell as a response to the message

Cell signaling overview

1. signaling cell releases ligand

2. ligand binds to receptor

3. receptor changes shape

4. signaling cascade begins

5. cell responds

6. signal is eventually turned off

intercellular signaling

communication between cells

hormone travels from one cell to another

intracellular signaling

communication inside cells

signaling cascade after receptor activation

ligand

signaling molecule that binds a receptor to produce a signal

receptor

protein that binds a ligand to produce a signal

signaling cell

the cell secreting the ligand

target cell

the cell expressing the receptor

Types of signaling (not applicable to single celled organisms): paracrine signaling

cell to a nearby cell (not touching)

fast, responsive, short lived

ex. neurotransmitters in synapses

Types of signaling: Endocrine signaling

• cell to a distance cell through the bloodstream

• ex: hormones

• distant targets, slower response, longer-lasting response

• insulin, thyroid hormones

Types of signaling: Autocrine

• cell signaling to itself

• signal producing cell is also target cell

• functions: development, inflammation, apoptosis

Direct signaling (across gap junctions)

• neighboring cells physically connected

• allows: ion + small signaling molecules

• can not pass: proteins and DNA

Types of receptors: intracellular (internal)

Location: cytoplasm, nucleus

• respond to ligands that can travel across the plasma membrane

  • ligand must be small, hydrophobic, lipid-soluble

  • ex. steroids hormones, estrogen, testosterone

• Often act as transcription factors to initiate gene expression

• Example = estrogen receptor alpha, crucial for normal function but also constitutively activated in 70% of breast cancer

• Drives proliferation, survival and growth signaling

Types of receptors: cell-surface receptors

• 3 types

• location: membrane

• ligan stays outside the cell

• usually binds large molecules, water-soluble molecules, charged molecles

• integral proteins (membrane-anchored) that bind to external ligands and transduce an extracellular signal to an intracellular signal

• 3 parts

1. external ligand binding domain (extracellular)

2. hydrophobic membrane-spanning domain

3. Intracellular domain

Cell surface receptor: Ion Channel linked receptors

• Bind a ligand and open a channel through the membrane that allows specific ions to pass through (ex. gated ion channels)

Cell surface receptor: G-protein Linked Receptor (GPCRs)

• Bind a ligand and activate a membrane protein called a G- protein

• G-protein interacts with an ion channel or enzyme in the membrane

• G-protein-linked receptors have 7 transmembrane domains but each receptor has its own specific extracellular domain and G-protein binding site

• Allows for diverse responses to various external signals through small mutations

1. ligand binds to receptor (GPCR)

2. GDP replaced by GTP (G protein heterotirmic: alpha, beta, gamma subunits exchanges GDP for GTP on alpha subunit

3. Alpha subunit with GTP dissociates from betta/gamma subunits

4. Activated Alpha subunit (and/or beta/gamma complex) triggers a cellular response

5. GTP hydrolyzed to GDP and subunits reassemble allowing for cycle to repeat

6. Signal stops

GTP= ON

GDP= Off

Cell surface receptor: Enzyme linked receptors

• Cell surface receptors with intracellular domains that are either (1) associated with or (2) are themselves an enzyme

• Ligand binding to the extracellular domain activates the enzyme

• Example = HER2 a receptor tyrosine kinase activated in 30% of breast cancers

1. Ligand binds

2. receptors dimerize (two receptors join each other)

3. Tyrosines become phosphorylated

4. Cellular response starts

Ligands to know

Steroid hormones

• testosterone

• estrogen

• hydrophobic, cross membrane, use internal receptors

Water-Soluble

• cannot cross membrane

• require surface receptors

Nitric Oxide (NO)

• gas

• diffuses through membrane

• short lived

• causes blood vessel relaxation

Signaling cascades

• Ligand binding to a cell surface receptor sets off a chain reaction of events

• Ultimately leads to a change in the cell behavior

Signal integration

Cells receive multiple signals simultaneously. Signaling cascades allow for the integration of these diverse inputs, as different receptors and downstream pathways interact, influencing the same set of cellular outputs. This enables complex and coordinates cellular responses

Signal transfuction process

a signal is sent, received, and translated into a cellular response

• phosphorylation, second messengers, and cellular responses to signaling

phosphorylation

addition of a phosphate group to serine, threonine, and tyrosine residues of proteins

kinase

enzyme that facilitates addition of the phosphate group

Phosphatase

enzyme that removes the phosphate group

Phosphorylation

• Major response for propagating signaling events.

• Addition of a phosphate group to serine, threonine, and tyrosine residues (due to presence of hydroxide groups).

• Kinases: Enzymes that add phosphate groups.

• Phosphatases: Enzymes that remove phosphate groups.

• Evolutionary Origin: Energy use of phosphorylation likely preceded its role in signaling, as it's a simpler process.

Second Messengers: Calcium Ions

• Small molecules that propagate a signal throughout the cell.

• Free calcium ion concentration is very low in cells due to ion pumps (using ATP).

• Ligand-gated calcium ion channels: Open when a signaling molecule (ligand) binds, allowing rapid influx of calcium due to a large concentration gradient.

• Rapid Response: Ions are small, charged, and cannot easily cross the membrane, allowing for a quick, sensitive response with a high signal-to-noise ratio (e.g., muscle contraction).

Cellular Responses to signaling

• Changes in gene expression (transcription) and protein synthesis (translation).

• Alterations in metabolism.

• Regulation of cell growth, cell death, and cell migration.

• Impact on reproduction.

What types of changes in the cell can signaling cause?

• Gene expression / protein synthesis

• Metabolism changes

• Cell growth

• Cell death

• Cell migration

multicellular organization

• Organisms are hierarchically organized: cell → tissue → organ → organ system → organism.

• Tissue Types: Epithelial, nervous, connective, muscular.

• Organization within tissues is determined by the ECM.

• ECM = protein + carbohydrates

If all cells in your body share the same genome, what differentiates a neuron from a gut cell?

Cell differentiation + gene expression

• All cells in an organism share the same genome but differ in gene expression.

• Transcription factors: Determine which genes are expressed by binding to promoters and recruiting RNA polymerase.

• Epigenetic marks: Lock gene profiles during differentiation.

• Cues for Gene Expression: Largely come from outside the cell (ECM, neighboring cells, soluble signals).

Different tissues/organs/organ systems are defined by

• Cell types

• Gene/protein expression of individual cells

• Extracellular matrix content/structure/organization

How cells are organized and interact with each other and the ECM

• Different tissues have wildly different ECM/cell content

• Connective tissue = 90% ECM by volume

• Epithelial tissue = <10% ECM by volume

• Cells don’t exist in a void, ECM determines their biochemical and mechanical environment controlling cell

• Shape

• Migration

• Differentiation

• Communication

ECM

1. Holds cells together to form a tissue (structure)

2. Allows cells to communicate with each other (signaling)

ECM as a scaffold

• Composed of proteins and carbohydrates outside cells.

• Provides structural support, dictates cell behavior, ensures correct cell placement, and controls cell-type interactions.

• Decellularization Failure: Removing cells from an organ's ECM and attempting to re-cellularize it fails because cells do not re-organize correctly without the original cellular cues and pathways.

Tissue-Specific ECM

• ECM content, structure, and organization vary significantly between tissues and even within different compartments of the same organ.

• Connective Tissue: ~90% ECM by volume (e.g., bone, cartilage).

• Epithelial Tissue: <10% ECM by volume, often organized as a basal layer maintaining cell polarity.

• Mechanical Properties: ECM dictates tissue stiffness (e.g., brain is soft, bone is stiff).

ECM Composition and function

• Fibrous Proteins:

  • Collagen: Provides tensile strength (like a molecular rope).

  • Elastin: Provides elasticity, allowing deformation and recoil without breaking (like a rubber band).

  • Relevance to Skincare: Loss of collagen and elastin contributes to wrinkles and loss of skin elasticity.

• Glycoproteins:

  • Fibronectin, Laminin: Facilitate cell attachment and patterning (e.g., integrins bind fibronectin).

• Proteoglycans & Glycosaminoglycans:

  • Hyaluronin (Hyaluronic Acid): Provides hydration.

  • Chondroitin Sulfate: Important for hydration and compression strength.

  • Relevance to Joints: Water in joints (facilitated by proteoglycans) is incompressible, providing cushioning and resisting compression forces.

ECM influence on stem cells

• Stem cells differentiate based on the mechanical properties of the ECM they are exposed to (e.g., brain ECM leads to brain cells, bone ECM leads to bone cells, stiff plastic leads to cartilage/bone-like cells).

ECM to cell-cell communication

• ECM contributes structure and signaling to tissues

• Cells do not exist in isolation in ECM – they are mechanically and chemically coupled to their neighbors

• Cell junctions = interface between cells

cell junctions

interfaces between cells that weld them together in specialized ways

cell junctions- types and roles: tight junctions

• Found in epithelial cells (e.g., stomach lining) to prevent leakage between cells, maintaining compartmentalization.

• seals neighboring cells together in an epithelial sheet to prevent leakage of extracellular molecules between them; helps polarize cells

cell junctions- types and roles: adherens junctions

• Provide strong cell-cell adhesion.

• joins acitn bundle in one cell to a similar bundle in a neighboring cell

cell junctions- types and roles: desmoseomes

• Provide strong cell-cell adhesion, particularly in tissues subject to mechanical stress.

• joins the intermediate filaments in one cell to those in a neighbor

cell junctions- types and roles: gap junctions

• Crucial for direct cell-to-cell communication, allowing small molecules and ions to pass (e.g., in neurons for rapid signal transmission).

• forms channels that allow small, intracellular molecules, water soluble molecules to pass from cell to cell

cell junctions- types and roles: hemidesmosome

anchors intermediate filaments in a cell to the basal lamiina

How do tissues maintain themselves over time?

Stem cells: a reserve that divides to replace cells lost to wear, injury, or programmed

turnover

• The intestinal lining is replaced every 3–5 days (next slides)

Stem cells: embryonic stem cells (ESCs)

•  Differentiate into all cell types in an organism (pluripotent).

Stem cells: Adult Stem Cells

• Provide continuous supply of differentiated cells to specific tissues and repair damaged cells (multipotent).

Stem cells: Induced Pluripotent Stem Cells (iPSCs)

•  Reprogrammed somatic cells (e.g., skin fibroblasts) back into an embryonic-like pluripotent state using specific transcription factors (Yamanaka factors).

stem cells niches

• Each stem cell resides in a niche (microenvironment) that

  integrates

  • ECM cues

  • Cell-cell contacts

  • Soluble factors

  • Niche = local control system that decides whether a stem cell

  divides, differentiates, or just sits there

pluripotent

can become any cell type

multipotent

can become multiple cell types

cytoskeleton overview

• Definition: A network of protein fibers within the cytoplasm.

• Functions:

  1. Maintains cell shape.

  2. Secures organelles (e.g., nucleus) in specific positions.

  3. Facilitates movement of cytoplasm and vesicles within the cell.

  4. Enables cell movement in multicellular organisms (e.g., immune cells).

cytoskeleton fibers (3) (smallest to largest)

• Microfilaments

• Intermediate filaments

• microtubules

Microfilaments (actin): general

• Size: Smallest, approximately 7 nanometers in diameter.

• Composition: Comprised of two actin strands; also known as actin filaments.

• Function: Crucial for cellular movement.

Microfilaments (actin): Actin treadmilling

• ATP-bound actin monomers are added to the "plus end" of the filament.

• As actin moves towards the "minus end," ATP is hydrolyzed to ADP.

• ADP-bound actin dissociates from the "minus end."

• This continuous addition and removal results in a dynamic, recycling process.

Microfilaments (actin): interaction with myosin

• Actin filaments interact with myosin motor proteins to form contractile units.

• Myosin uses ATP hydrolysis to change conformation and "pull" along actin filaments.

• This mechanism is fundamental to muscle contraction (e.g., sarcomeres).

• Biological Importance: Enables cell division, cell movement (e.g., macrophages engulfing bacteria via phagocytosis), and muscle contraction.

• Clinical Relevance: Impaired immune cell movement (e.g., macrophages) can lead to severe infections like sepsis.

Intermediate filaments: general

• Size: Medium, 8-10 nanometers in diameter.

• Composition: Diverse fibrous proteins, forming rope-like structures.

• Function: Primarily structural support, strong under tension (tensile strength).

  • Maintains cell shape.

  • Anchors the nucleus in the center of the cell, protecting it from damage.

  • make up desmosomes

• Examples: Keratins (found in skin, hair, nails) provide structural integrity- found in cytoplasmic

• nuclear: nuclear lamins

Intermediate filaments: structure

• Monomers (alpha-helical) form coiled-coil dimers.

• Two dimers form staggered anti-parallel tetramers.

• Eight tetramers assemble laterally to form a unit of the filament.

• Highly organized, multi-layered (hierarchical) structure that self-assembles.

• Key Difference from Microfilaments: Lack treadmilling and polarity (no distinct plus or minus ends), indicating they are not involved in dynamic movement.

Microtubules: general + function

• Size: Largest, 25 nanometers in diameter, hollow tubes.

• Composition: Polymerized dimers of alpha-tubulin and beta-tubulin. 13 dimers form a circular cross-section.

• Function:

  • Resist compression (unlike intermediate filaments which resist tension).

  • Provide tracks for intracellular transport of vesicles and organelles.

  • Crucial for pulling replicated chromosomes apart during cell division (via centrosomes/centrioles).

Microtubules: dynamic instability

• Driven by GTP hydrolysis.

• Growth: Growing end – add GTP tubulin -> addition of GTP tubulin faster than GTP hydrolysis by dimers -> GTP cap

• Shrinking: Shrinking occurs when GTP hydrolysis faster than addition of GTP dimers -> GTP cap lost, protofilaments peel away -> GDP tubulin in cytoplasm

• Possess polarity: Plus end for growth/shortening, minus end typically attached to the centrosome.

Microtubules: associated structures

• Centrioles: Barrel-shaped structures within the centrosome (Microtubule Organizing Center - MTOC), involved in cell division.

• Flagella and Cilia: Specialized cellular appendages for movement.