Exam 2 Review

What is the difference between Light and Electron microscopes?

Light microscopes use magnification (visible light) to get a closer look at specimens BUT Electron microscopes use a beam of electrons on or through a surface to study cell surfaces or internal cell structures

• LM uses would use this for animal and plant cells

What is an SEM (Scanning electron microscope)

Focuses a beam of electrons onto the surface to study the detailed 3D architecture of cell surfaces.

• If you need a detailed outside surface of cells to view structures such as cilia

What is an TEM (Transmission electron microscope)

Focuses a beam of electrons through a specimen to study the details of internal cell structure.

• if you needed to look at the detailed internal subcellular structure of cells, such as the ribosomes

Cell Theory

• Cells are the fundamental unit of life

• All organisms are made up of cells

• Cells come from preexisting cells

Differences between prokaryotes and eukaryotes

Eukaryotes are more large & complex, all other life forms excluding bacteria and archaea, membrane-bound organelles, nucleus

Parts and functions of the bacterial cell

• Cell wall outside the plasma membrane

• Flagella: Movement

• Fimbriae & pili: For attachment to other bacteria or cell surfaces

• Capsule: Jelly-like external to the cell wall to provide extra protection

• Plasmids: circular pieces of DNA with additional genes

What structures are unique to plant cells

• Cell Wall: A rigid outer layer made of cellulose that provides structural support and protection

• Chloroplasts: The sites of photosynthesis, containing chlorophyll to convert sunlight into chemical energy.

• Large Central Vacuole: A single, massive membrane-bound organelle that stores water and maintains turgor pressure to keep the plant upright.

• Plasmodesmata: Microscopic channels through the cell wall that allow transport and communication between individual plant cells.

What structures are unique to animal cells

• Centrioles / Centrosomes: Microtubule-organizing structures crucial for organizing the mitotic spindle during animal cell division (absent in higher plants).

• Lysosomes: Organelles containing digestive enzymes to break down waste, foreign debris, and worn-out cell parts.

Plasma Membrane

flexible physical barrier that separates the inside of a cell from its outside environment while controlling what goes in and out.

• Selective Permeable

Nucleus

Nucleus: acts as the cell's "information center.

• Houses Genetic Material: It contains most of the cell's DNA, which is organized into chromatin and chromosomes.

• Directs Protein Synthesis: It holds genes, which are the discrete units of DNA carrying instructions to make proteins.

• Produces Ribosomal RNA (rRNA): It contains the nucleolus, the specific site where rRNA is manufactured.

• Controls Cellular Traffic: It uses nuclear pores to regulate the movement of molecules entering and exiting the nucleus.

Nucleolus

• rRNA Synthesis: It serves as the specific site inside the nucleus where ribosomal RNA is made.

• Ribosome Assembly: Though not fully detailed on this slide, it is the region where rRNA combines with proteins to begin assembling ribosomes, which are essential for making proteins.

Ribosomes

• Protein synthesis

• cell's protein factories by translating genetic instructions into functional proteins.

• All cells have it

• 
  

Endomembrane System

Regulates protein traffic and performs metabolic functions in the cell

Nuclear Envelope

Separates the nucleus from the cytoplasm, protecting the genetic material of eukaryotic cells

• Double membrane each consisting of a lipid bilayer

Endoplasmic reticulum

serves as the cell's biosynthetic factory, dividing its duties between the ribosome-studded Rough ER and the ribosome-free Smooth ER

What is an Rough ER

Rough because its bounded by ribosomes 

Recreates proteins 

Make membranes

Smooth ER

• No bound ribosomes

• Synthesizes lipids

• Metabolizes carbohydrates

•  Stores calcium

• Detoxifies poison

Golgi Apparatus

• Receives proteins & carbohydrates from the rough ER

• Modifies these products

• Sorts and packages these finished products into transport vesicles for delivering to other parts of the cell

• Polysaccharide synthesis

• Gives rise to lysosomes

• Composed of flattened stacks of membranous sacs. Has a receiving “cis” side and a transferring “trans” side

What are lysosomes

Membrane-enclosed organelles containing hydrolytic enzymes in an acidic environment

Can fuse with other vesicles that contain material that needs to be broken down

What ph do lysosomes maintain? pH of the cell

• Maintain a pH of about 4.5-5 while the cell is 7.2

Why is it important that lysosomal digestive enzymes are enclosed by a membrane and not floating around in the cytoplasm?

• Prevents self-digestion: Isolates destructive enzymes from eating the cell's own vital structures

• Maintains optimal environment: Keeps the local pH low so acid hydrolases can function properly.

• Protects against leaks: If a single lysosome breaks, the enzymes become inactive in the neutral cytoplasm anyway

What are vaculoes

Large vesicles derived from the endoplasmic reticulum and Golgi apparatus

Food Vacoules

Store food to be breakdown lysosomes with the help of phagocytosis in the cytoplasm

What is phagocytosis and an example

A process where a cell engulfs large particles or whole cells by wrapping its plasma membrane around them ("cellular eating").

An amoeba engulfing a bacterial cell for nutrition.

Contractile vacuoles location and function

Located in the Cytoplasm; accumulates and pumps out excess water to prevent cell bursting.

Central vacuoles

Help support plant cell shape, hold reserves of water, organic compounds and waste

Center of plant cells

What is the mitochondria

• Are the sites of cellular respiration 

• Generate ATP from sugars, fats, etc.

• Found in plants and animals

What are chloroplasts

• Found in plants

  • Are the sites of photosynthesis

  • Convert solar energy into the chemical energy of food

What are peroxisomes and its 2 main enzymes (with function)

Small organelles bound by a single membrane that are responsible for  Lipid Metabolism & Detoxification

• Catalase: Converts toxic hydrogen peroxide into water and oxygen. This protects the cell from oxidative damage.

• Oxidases: Break down long-chain fatty acids, amino acids, and uric acid.

What are Centrosome/centrioles + function

They are microtubule organizing centers

Help form mitotic spindle that separate chromosomes during cell division 

What is the Endosymbiont theory? 

An early eukaryotic ancestor engulfed a non photosynthetic prokaryote, forming an endosymbiotic relationship that evolved into the mitochondrion. A lineage of these cells later engulfed a photosynthetic prokaryote, which evolved into the chloroplast.

What is the function of the cytoskeleton?

A network of fibers that is involved in cellular support and motility 

What three protein fibers make up the cytoskeleton

Microtubules, Microfilaments,  Intermediate filaments

What is the functions of microtubules

1. Separate chromosomes during cell division 

2. Cell motility-cilia & flagella

3. Movement of organelles and vesicles

4. Shape and support the cell

These are hollow rods of tubulin

What is the functions of Microfilaments

1. Structural support: Bundles of microfilaments make up the core of microvilli of intestinal cells 

2. Cellular motility: interact with the motor protein myosin to cause

   1. ➢ Muscle contraction 

   2. ➢ Movement of white blood cells 

   3. ➢ Cytoplasmic streaming in plant cells

thin solid rods, built from actin protein

What is the functions of Intermediate Filaments

1. Support cell shape and fix organelles in place

 built from several proteins (dependent on the cell type) including keratin protein.

Motor protein are associated with microtubules and microfilaments and help produce movement in the cell. These proteins bind ______ and use the energy from its breakdown to change their shape and power movement.

ATP

• In plants, the extracellular matrix is found in the _____

• The polysaccharide _____ is the main structural component of the plant cell wall.

• cell wall 

• cellulose

Function of plant cell walls

Protects the plant cell, maintains its shape, and prevents excessive uptake of water 

• However, animal cells synthesize and secrete an____ (ECM or sometimes just called the matrix) that helps hold cells together in tissues and protects and supports the plasma membrane.

• This "space" outside the cells is _____ (living/ non-living).

• A common protein found in the matrix in animal cells is ________ (very abundant in the dermis of our skin and in our bones).

extracellular matrix (ECM) , non-living , collagen

- What is the function of integrins?

They connect the ECM to the cytoskeleton (microfilaments) and help cells attach to and communicate with their surroundings.

What junction is find in plants and the function?

Plasmodesmata, Connect plant cell walls 

1. Water, small solutes (and sometimes proteins and RNA) can pass from cell to cell through plasmodesmata 

Tight junctions, def and function and its nickname

“Zipper” Junctions - Membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid between cells

Desmosomes junctions, def and function and its nickname

“Glue” junctions - fasten cells together into strong sheets - Anchor cells to an underlying basement membrane

Gap junctions, def and function and its nickname

- “communicating” junctions - provide cytoplasmic channels between adjacent cells Ions, sugars, amino acids, and other small molecules can pass

What is structure of the plasma membrane

The plasma membrane is primarily a phospholipid bilayer containing lipids, proteins, cholesterol, and carbohydrates.

What is the Fluid mosaic model

Its when the membrane is…

• Fluid: molecules can move laterally within the membrane.

• Mosaic: composed of many different proteins, lipids, and carbohydrates.

How do phospholipids, cholesterol, proteins and carbohydrates contribute to the plasma membrane?

Phospholipids

• Create the membrane's basic barrier.

Proteins

• Transport

• Enzymatic activity

• Cell-cell recognition & Intercellular joining:

• Signal transduction

• Cell Attachment

Cholesterol

• Helps stabilize membrane fluidity.

Carbohydrates

• Important in cell recognition and communication.

Peripheral and Integral proteins and which would have more polar amino acids near there surface

• Integral proteins: span the membrane and are called transmembrane proteins. 

  • Amphitatic

• Peripheral proteins: bound to the surface of the membrane 

  • More likely to contain hydrophilic (polar) amino acids over their entire surface

  • Mostly hydrophobic

How does temp. regulate the fluidity of the membrane

• Higher temperature → membrane becomes more fluid.

• Lower temperature → membrane becomes less fluid

How does saturated/unsaturated fatty acids regulate the fluidity of the membrane

• Unsaturated fatty acids

  • More unsaturated fatty acids → more fluid.

• Saturated fatty acids

  • More saturated fatty acids → less fluid/more viscous.

How does cholesterol regulate the fluidity of the membrane

• Prevents excessive movement at high temperatures.

• Prevents phospholipids from packing too tightly at low temperatures.

Explain the selective Permeability of the membrane

• The plasma membrane is selectively permeable, meaning some substances cross easily while others cannot.

• Hydrophobic (nonpolar) molecules can pass through the membrane easily.

• Hydrophilic (charged or polar) molecules such as sugars and ions do not cross the membrane easily

  •  Transport proteins allow passage of hydrophilic substances across the membrane

Diffusion

• Movement of molecules from high concentration → low concentration.

• Doesn't require ATP.

Osmosis

• Diffusion of water across a selectively permeable membrane.

• Lower solute concentration to higher solute concentration

  • More free water -> lower free water

What is Facilitated Diffusion

• Movement down a concentration gradient through a transport protein.

• High to low

What is active transport

Moves substances against their concentration gradient.

Low to high

• Requires:

• Energy

• Transport proteins

What is Cotransport

This happens when two different substances are transported across a membrane simultaneously

- What is the sodium potassium pump used for in cells? Does it transfer ions by active or passive transport?

• The Na⁺/K⁺ pump is an example of active transport.

• It uses ATP to move ions against their concentration gradients and helps maintain ion gradients across the plasma membrane.

Know which of these three processes would be used to move the following substances down their concentratiion gradient across a membrane: O2, CO2, polar molecules, ions, non-polar molecules, hydrophobic molecules.

• O₂: Simple diffusion

• CO₂: Simple diffusion

• Nonpolar/hydrophobic molecules: Simple diffusion

• Polar molecules: Facilitated diffusion

• Ions: Facilitated diffusion

____is the ability of a solutiion to cause a cell to gain or lose water.

Tonicity

What is an isotonic solution and what occurs in plant and animal cells

• Same solute concentration inside and outside the cell

  • Animal Cell: Normal  

  • Plant Cell: Flaccid

What is an hypertonic solution and what occurs in plant and animal cells

• Higher solute concentration outside the cell.

  • Cell loses water

  • Animal: Crenation/shrinking/shrivel

  •  Plant: Plasmolysis

What is an hypotonic solution and what occurs in plant and animal cells

• Lower solute concentration outside the cell.

  • Cell gains water

  • Animal: May swell and lyse, burst

  •  Plant: Becomes turgid

Which osmosis condition is prefered by plants? animals?

Hypotonic, isotonic

What is Osmoregulation

the control of solute concentrations and water balance

What is Exocytosis?

Vesicles fuse with the plasma membrane and release materials outside the cell.

What is endocytosis?

The plasma membrane folds inward to bring material into the cell.

What is Pinocytosis:

Cellular drinking: Takes in extracellular fluid and dissolved solutes into vesicles

What is Receptor-mediated endocytosis:

cells acquire specific molecules with the help of receptors 

• Uses clathrin-coated pits.

• Cholesterol uptake: Receptor-mediated endocytosis.

Catabolism

Breakdown of molecules to release energy in the form of ATP 

• Usually exergonic

• Usually ΔG < 0

• Examples: Hydrolysis, cellular respiration

Anabolism

Builds molecules and requires an input of energy in the form of ATP 

• Usually endergonic

• Usually ΔG > 0

• Example: protein synthesis

Kinetic energy

the energy associated with motion

Potential energy

stored energy

• 1st law of thermodynamics

• Energy can be transferred or transformed, but it cannot be created or destroyed

2nd law of thermodynamics

When energy is converted from one form to another, some of the energy is lost as hea;, henc,e the entropy of the universe increases

What is Gibbs free energy

Energy that can do work in a cell 

What is ΔG ? What can ΔG tell us whether or not the reaction occurs spontaneously or require an input of energy?

• G is the change in free energy (final state - initial state)

  • ΔG < 0: Exergonic; releases free energy; spontaneous

    • Spontaneous processes can be harnessed to perform work in the cell 

  • ΔG > 0: Endergonic; requires energy input; nonspontaneous

Catabolic Reactions (advanced)

1. Breaks down molecules

2. Releases energy

3. Negative ΔG

4. Spontaneous

5. Exergonic

6. Products have less free energy

Anabolic Reactions (advanced)

1. Builds molecules

2. Requires energy

3. Positive ΔG

4. Nonspontaneous

5. Endergonic

6. Products have more free energy

ATP couples ….

exergonic reactions to endergonic reactions.

ATP is made of

ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups 

ATP powers.

• Chemical work: Making molecules such as proteins

• Transport work: Active transport

• Mechanical work: Muscle contraction/cilia movement

Energy is stored in the ________ of ATP.  

high-energy phosphate bonds

What is activation energy?

This initial energy needed to start a chemical reaction is called the free energy of activation

Why are enzymes biological catalysts

• speed up chemical reactions, lowering EA

What type of macromolecule are they usually? enzymes

• They are usually proteins

• Enzymes bind to a ____ and become ____

substrate, products

• After a reaction for an enzyme ->

• It is not consumed and can be reused.

Substrate bind and catalysis occurs at the

Active SIte

• Enzyme specificity

results from the complementary fit between the shape of the substrate and the enzyme’s active site

How do enzymes lower EA

They provide an alternative reaction pathway that requires less activation energy, often by properly positioning substrates and stabilizing the transition state

Does proteins affect delta G

• Don't affect the change in free energy

• AKA NO

Enzyme Activity can be altered by:

• Substrate Concentration

•  pH  

• Temperature  

• Salt  

• Cofactors  

• Inhibitors

• Enzyme names commonly end in:

-ase

Competitive inhibition

• Inhibitor competes with substrate for the active site.

• Can often be overcome by increasing substrate concentration.

• Noncompetitive inhibition

• Inhibitor binds somewhere other than the active site.

• Changes enzyme shape/function.

• Substrate may still bind, but catalysis is reduced.

• Makes the active site less effective at binding its substrate 

Allosteric Regulation

• Can bind to activators or inhibitors other than the active site and affects the enzyme’s function 

• Binding of an activator stabilizes the active form of the enzyme 

• Binding of an inhibitor stabilizes the inactive form of the enzyme

• Feedback inhibition

• Feedback inhibition is where the end product of a metabolic pathway shuts down the pathway 

• Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

•  Uses an allosteric enzyme

• Cofactors

• 
  

  • Nonprotein helpers required by some enzymes.

  • They help enzymes perform catalysis.