Chapters 5-9 COPY Flashcards
Four Classes of Biological Molecules (Macromolecules)
- Carbohydrates
- Lipids
- Proteins
- Nucleic acids
- All considered polymers except lipids
Macromolecules
- Large molecules, complex
- Unique properties that arise from the orderly arrangement of their atoms
- Polymers=macromolecules
Polymer
- A long molecule consisting of many similar building blocks
- Building blocks= monomers
Enzymes
-Specialized molecules that speed up chemical reactions
Dehydration reaction (condensation)
- When two monomers bond together through the loss of a water molecule
- Catalytic reaction
Hydrolysis
- How polymers break apart
- Reverse of dehydration reaction (adds water)
- Metabolic reaction
Carbohydrates
- Fuel, building material, Carbon source, information (blood ABO)
- 25% of dry cell mass
- Sugars and polymers of sugars
- Simplest= monosaccharides (simple sugars)
- Polysaccharides= many sugars
Lactose Intolerance
- Lactase= enzyme
- W/o enzyme or lack of, lactose (sugar) cannot be broken down, ferments in large intestine
Chitin
-Creates exoskeleton of arthropods
Lipids
- 5% of dry cell mass
- Not a true polymer
- Required for membrane, energy, signaling, insulation
- Hydrophonic
- Types: fat, phospholipid, steroid
Fats
- Constructed from glycerol and fatty acids
- Fatty acid= carboxyl group attached to carbon skeleton
- Glycerol= three carbon alcohol w/ hydroxyl group attached to each carbon
- Glycerol connects to chain of fatty acids
- Triacylglycerol: 3 fatty acids joined by glycerol
Saturated Fats
- Solid at room temperature (high melting point)
- No double bond
- Bad for health
Unsaturated Fats
- Liquid at room temp (low melting point)
- Double bond
- Cis: packed poorly, low melting point (better for u)
- Trans: packed tightly, high melting point (bad for u)
Lipid Bilayer
- Makes cell membranes
- One end of phospholipid is polar, other non-polar
- Hydrophilic head, hydrophobic tail
Steroids
- Ring structure: four fused ring
- Percusor= cholesterol, essential for membrane signaling
- Too much= bad (atherosclerosis, build up in arteries)
- Vitamin D and hormone
Nucleic Acid
- 10% dry cell mass
- Store, transmit, and help express hereditary info
- Multiple NA= gene–> multiple gene= DNA
- Polynucleotide made of monomers called nucleotides
Pyrimidines
-Cytosine, Thymine, Uracil
Purines
-Adenine and Guanine
DNA Structure
- Nucleotides linked by phosphodiester linkage
- Phosphate group that links two sugars
- Sequence of bases along a DNA or mRNA= unique to each gene
- Double helix
- A w/ T, G w/ C
- gene–> dna–> chromosome
RNA
-Single-stranded
Thymine is replaced by Uracil, so U and A pair
-More variable in form
Proteins
- 50% of dry mass of most cells
- Speed up chemical reactions, defense, storage, transport, cellular communication, movement, and structural support
Enzymatic Proteins
-Accelerate chem reactions
Defensive proteins
-Protection against disease
Storage proteins
-Store amino acids
Transport Proteins
-Transport of substances
Hormonal Proteins
-Ex: insulin
Receptor proteins
-Response of cell to chemical stimuli
Contractile and motor proteins
-Movement
Structural proteins
-Support
Polypeptides
- Polymers built from amino acids
- Make up proteins
Amino acids
- Organic molecules w/ amino and carboxyl groups
- R groups/ side chains make them differ in properties
- Linked by covalent peptide bonds
- Carboxyl end (C-terminus) and Amino end (N-terminus)
Four levels of Protein Structure
- Primary
- Secondary
- Tertiary
- Quaternary
Primary
- Unique sequence of amino acids
- Like order of letters in long word (order matters)
- Determined by inherited genetic info
Secondary
- Consists of coils and folds in polypeptide chain
- Result from hydrogen bonds between repeating parts of the polypeptide backbone
- A helix (coil) and B pleated sheet
Tertiary
- Determined by interactions among various side chains ( R groups)
- Interactions: hydrogen bonds, ionic bonds, hydrophobic interactions, and van der waals
- Disulfide bridges= strong covalent bonds that reinforce structure
Quaternary
- Protein consists of multiple polypeptide chains
- Ex: collagen, hemoglobin
What determines protein structure?
- Primary structure, pH, salt concentration, temp, environment
- Loss of native structure= denaturation
- Biologically inactive
Cells
- Fundamental units of life
- Simplest collection of matter that can be alive
- Studied using microscopes
Light Microscope (LM)
-Visible light passed through a specimen and glass lens
Magnification
-The ratio of an object’s image size to its real size (due to lens)
Resolution
-The measure of the clarity of the image, or the minimum distance between two distinguishable points
Contrast
-Visible differences in brightness between parts of the sample (between colors)
Electron microscopes
- Used to study subcellular structures
- Types: scanning electron microscopes (SEMs) and Transmission electron microscopes (TEMs)
- SEMs: Focus beam of electrons onto surface of specimen 3D
- TEMs: focus beam of electrons through specimen, internal structure
Cell fractionation
- Take cell apart and separate into organelles
- Uses centrifuge and diff speeds
- Heaviest is separating using low speed and vice versa
- Heaviest: Nuclei and cell debris
- Lightest: Ribosomes
Eukaryotic Cells
- Cells that have a nucleus (DNA) and membrane-enclosed organelles
- Membranes= lipid bilayer
- plants of chloroplasts, animals do not
- Ex: protists, fungi, animals, plants
Prokaryotic Cells
- Cell that does not have membrane-enclosed organelles, only a cell membrane and DNA
- Ex: Bacteria and Archaea
Nucleus
- Contains the cell’s genes
- Enclosed by the nuclear envelope (lipid bilayer), separates it from cytoplasm
- Lined w/ pores (regulate entry and exit of molecules from the nucleus)
- Nuclear Lamina: maintain its shape
Chromatin
- One DNA molecule in a chromosome
- Condenses to form chromosomes
Nucleolus
- Located within the nucleus
- Site of ribosomal RNA (rRNA) synthesis
Ribosomes
- Made of rRNA (ribosomal RNA) and protein
- Carry out protein synthesis in:
- Cytosol (free ribosomes)
- Outside ER or nuclear envelope (bound ribosomes)
Endoplasmic Reticulum
- Biosynthetic factory
- Continuous w/ nuclear envelope
- Regions: Smooth ER (no ribosomes) and Rough ER (studded w/ ribosomes)
Smooth ER
- Synthesizes lipids
- Metabolizes carbohydrates
- Detoxifies drugs and poisons
- Stores calcium ions
Rough ER
- Bound ribosomes that secrete glycoproteins
- Distributes transport vesicles, secretory proteins surrounded by membranes
- Membrane factory for the cell
Golgi Apparatus
- Shipping and receiving
- Consists of flattened sacs called cisternae
- Modifies products of ER
- Manufactures macromolecules
- Sorts and packages materials into transport vesicles
Lysosomes
- Digestive compartments
- Membraneous sac of hydrolytic enzymes that digest macromolecules
- Made by rough ER and transferred to the Golgi for processing
- clean cell up if messy or broken
Vacuoles
- Diverse maintenance compartments
- Larger version of a vesicle, maintain cell shape and pressure
- Derived from ER and golgi
- Types: food, contractile (pump out water from cell), and central (hold organic compounds and water)
Mitochondria
- Cellular respiration, metabolic process that uses oxygen and glucose–> ATP
- Cristae: inner folds, create large surface area for enzymes that synthesize ATP
- Mitochondrial matrix does some of the steps of cellular respiration
- Animal cells
Chloroplasts
- Plants, leaves, algae
- Green pigment= chlorophyll, function for photosynthesis
- Tylakoid–> granum
Peroxisomes
- Oxidative organelles
- Produce hydrogen peroxide and convert to water
Endosymbiont Theory
- Early ancestor of eukaryotes engulfed an oxygen-using nonphotosynthetic prokaryote\
- Engulfed cell formed relationship w/ host cell (endosymbiont)–>mitochondria
- Same thing happened w/ photosynthetic prokaryote–> chloroplast
- Plausible due to similarities in mitochondria and chloroplasts
Cytoskeleton
- Network of fibers extending throughout the cytoplasm
- Organizes cell’s structure and activities
- Composed of microtubules, microfilaments, and intermediate filaments
- Vesicles travel along it
- Interacts w/ motor proteins to produce cell mobility
Microtubules
- Thickest fiber
- Constructed w/ tubulin
- Function: Shaping the cell, guiding movement of organelles, separating chromosomes during cell division
- Attach to chromosomes and separate them
- Grow out from centrosome near nucleus
Microfilaments
- Thinnest fiber (actin filament)
- Support cell’s shape– cortex
- Cytoplasmic streaming, flow of cytoplasm in cell, is driven by microfilaments
Intermediate filaments
- Middle in width of all 3 fibers
- More permanent cytoskeleton fixtures
- Fix organelle in place
Cilia and Flagella
- Controlled by microtubules
- Share common structure
Plant Cell wall
- Protects plant cell
- Maintains its shape
- Prevents excess uptake of water
- Primary: relatively thin and flexible
- Middle lamella: Thin layer btwn adjacent cells
- Secondary: Added btwn plasma and primary cell wall
Extracellular components
- Help coordinate cellular activities
- Cells synthesize and secrete material that are external to the plasma membrane
Extracellular Matrix of Animal Cells
- Animal cells= no cell wall
- Covered by EM
- Made of collagen, proteoglycans, and fibronectin
- Binds to receptor proteins in plasma membrane called integrins
- Communication btwn cells* (mechanical signaling and chemical signaling
- Influences activity of gene in nucleus
Cell Junctions
- Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through physical contact
- Types: tight, desmosomes, gap
Tight cell junction
-Membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid
Desmosomes
- Anchored junctions
- Fasten cells together into strong sheets
Gap cell junctions
- Communicating junctions
- Provide cytoplasmic channels between adjacent cells
Selective Permeability
- Exhibited by the plasma membrane
- Some substances cross it more easily than others
- Controlled by transport proteins
Amphipathic
- Exhibited by phospholipids in the plasma membrane
- Hydrophobic and hydrophilic regions
- Hpho: tails. sheltered from water
- Hphil: heads, exposed to water
Fluid Mosaic Model
- The plasma membrane is made of protein molecules bobbing in a fluid bilayer of phospholipids
- Not randomly distributed
- Fluid due to weak hydrophobic interactions
- as temp cools, becomes more solid
- Membranes rich in unsaturated fatty acids= more fluid than those of saturated
- decrease hydrophobic interactions–> increase fluidity
Membrane Proteins
- Made up of diff proteins, clustered in groups, embedded in a fluid matrix of lipid bilayer
- Phospholipids form main fabric of membrane
- Proteins determine the membrane’s function
- Peripheral: surface of membrane
- Integral: penetrate hydrophobic core
Cell-Surface Membrane Functions
- Transport
- Enzymatic activity
- Signal transduction
- Cell-cell recognition
- Intercellular joining
- Attachment to the cytoskeleton and ECM
Transportation
-Cell must exchange materials with its surroundings
Permeability of Lipid Bilayer
- Hydrophobic molecules can dissolve in the lipid bilayer and pass through the membrane
- Hydrophilic molecules cannot pass easily
Facilitated Diffusion
- Does not require energy
- Transport proteins speed up the passive movement of molecules across plasma membrane
- Allow passage of hydrophilic substances across membrane
- Channel proteins
- Carrier proteins
- Example= water movement through aquaporin
- Solute moves down its concentration gradient, no energy= passive*
Channel Proteins
- Provide corridors that allow specific molecules or ions to cross membrane
- Ex: aquaporin
- Ion channels: transport of ions
- Gated channels: open or close in response to stimulus
Carrier Proteins
- Subtle change of shape to bind and transport across membrane
- Change triggered by binding and releasing of transport molecule
Passive Diffusion
- A substance across a membrane w/ no energy used
- Diffusion= the spreading out evenly in space
Osmosis
- Osmosis= passive diffusion of water
- Substances diffuse down their concentration gradient (spread evenly)
Tonicity
- Ability of a surrounding solution to cause a cell to gain or lose water
- T of solution depends on its concentration of solutes that cannot cross the membrane
Isotonic Solution
- Solute concentration is the same as inside the cell
- No net water movement
Hypertonic Solution
- Solute concentration is greater than that inside the cell
- Cell loses water
Hypotonic Solution
- Solute concentration is less than inside the cell
- Cell gains water
Cells w/o cell walls
- Shrivel in hypertonic solution
- Lyse (Burst) in a hypotonic solution
Osmoregulation
- Control of solute concentrations and water balance in cells that do not have rigid walls
- Ex: contractile vacuole as water pump in paramecium
Water balance of cells w/ cell walls
- Help maintain water balance
- Hypotonic solution and plant cell: turgid/firm, swells until can’t take any more water
- Isotonic: no net movement, flaccid/limp
- Hypertonic: plant cell loses water
- Plasma membrane pulls away from cell wall, plant wilts= plasmolysis
Active Transport
- Requires energy (ATP) to move substances against concentration gradient
- Uses carrier proteins
- Allows cell to maintain concentration gradients that differ from surroundings
- Ex: sodium-potassium pump
Membrane Potential
- Voltage across membrane
- Created by difference in distribution of charges across membrane
Electrochemical Gradient
- Two combined forces
- Chemical force
- Electrical force
- Drive the diffusion of ions across a membrane
Electrogenic Pump
- Transport protein the generates voltage across a membrane
- Ex: sodium-potassium pump, proton pump
- Helps store energy used for cell work
Cotransport
- When active transport of a solute indirectly drives transport of other substances
- Diffusion of an actively transported solute down its gradient w/ transport of a second substance against its concentration gradient
Bulk Transportation
- Occurs by exocytosis and endocytosis
- Small molecules and water enter or leave the cell through the lipid bilayer or via transport proteins
- Large molecules cross in bulk via vesicles
- Requires energy
Endocytosis
- The cell takes in macromolecule by forming vesicles from plasma membrane
- Types:
- Phagocytosis
- Pinocytosis
- Receptor-mediated endocytosis
Phagocytosis
- Cell engulfs particle in a vacuole (extends plasma membrane)
- Vacuole fuses w/ lysosome to digest particle
Pinocytosis
-Molecules dissolved in water droplets are taken up when extracellular fluid is “gulped” into tiny vesicles
Receptor-Mediated Endocytosis
- Binding of specific solutes to receptors triggers vesicle formation
- Emptied receptors are recycled into plasma membrane
Exocytosis
- Transport vesicles migrate to the membrane, fuse w/ it, and release their contents outside the cell
- Used by secretory cells
Hypercholesterolemia
- R-M endocytosis used to take in cholesterol, carried by particles called low-density lipoproteins (LDLs)
- Missing receptors= cholesterol build up
Catabolic vs. Anabolic
- C: creates energy
- A: uses energy
- Metabolism= balance of the two
Metabolism
- Totality of an organism’s chemical reactions
- Emergent property of life that arises from interaction between molecules
- Pathway begins w/ specific molecule and ends w/ product
Catabolic Pathways
- Release energy by breaking down complex molecules into simpler compounds
- Ex: breaking down of glucose in cellular respiration
Anabolic Pathways
- Consume energy to build complex molecules from simpler ones
- Ex: synthesis of protein from amino acids
Bioenergetics
-Study of how energy flows through living organisms
Energy
- Capacity to cause change
- Can be converted from one form to another
- Exists in various forms, some of which can perform work
Kinetic Energy
-Energy associated with motion
Thermal Energy
- Kinetic energy associated w/ random movement of atoms or molecules
- Heat= thermal energy transfer btwn objects
Potential Energy
-Energy matter possesses because of its location or structure
Chemical Energy
-Potential energy available for release in a chemical reaction
Thermodynamics
- The study of energy transformations
- Open system: energy and matter transfers
- Ex: organisms
First Law of Thermodynamics
- Conservation of energy
- Constant, cannot be created or destroyed
- Transformed and transferred
Second Law of Thermodynamics
-During energy transfer or transformation, unstable energy is lost as heat
Energy Transformation
- Living cells convert energy to heat, more disordered form of energy
- Spontaneous processes occur w/o energy input (quick or slow)
- Can only occur if it increases entropy of the universe
- If decrease entropy, not spontaneous, energy needs to be provided
Free Energy Change
- Energy that can do work when temperature and pressure are uniform, as in a living cell
- Delta G= deltaH -TdeltaS
- G= change in free energy
- H= change in enthalpy/ total energy
- T= temp in Kelvin
- S=Entropy (disorder/ randomness)
Exergonic Reaction
- Net release of free energy, spontaneous
- Ex: continuous energy source of the sun
Endergonic Reaction
-Absorbs free energy from its surrounds, nonspontaneous
Closed system vs. Open
- Reactions in closed system eventually react equilibrium and do not work
- Cells are never in equilibrium, open systems w/ constant flow of materials
- Life is never in equilibrium
Types of work a cell does
- Chemical work: pushing endergonic reactions
- Transport work: pumping substances against the direction of spontaneous movement
- Mechanical work: contraction of muscle cells
- Do work by energy coupling: using exergonic to drive endergonic, mediated by ATP
Hydrolysis of ATP
- ATP tails are broken by hydrolysis, releases energy (exergonic), drives endergonic reactions
- Coupled reactions are exergonic*
Catalyst
- Chemical agent that speeds up a reaction w/o being consumed by the reaction
- Ex: enzyme
Activation Energy Barrier
- Initial energy needed to start a chemical reaction (activation energy)
- The more energy needed, the harder it is to start the reaction (vice versa)
Catalysis
-Enzymes or other catalysts speed up reactions by lowering the activation energy barrier
Substrates
- The reactant that an enzyme acts on
- When enzyme binds w/ in, forms enzyme-substrate complex
- Converts substrate to product
Cofactors and Coenzymes
- Cofactor: Nonprotein enzyme helpers, Inorganic
- Coenzyme= same but organic (vitamins)
Competitive Inhibitors
-Bind to the active site of an enzyme, compete w/ substrate
Noncompetitive Inhibitors
-Bind to another part of enzyme, causing it to change shape and make active site less effective
Regulation of Enzyme Activity
- Chemical chaos if metabolic pathway is not tightly regulated (products would go to waste)
- Switch off enzymes or regulate activity so this doesn’t happen
- Allosteric Regulation
- Feedback Inhibition
Allosteric Regulation
- Inhibit or stimulate enzyme’s activity
- Occurs when regulatory molecule binds to a receptor protein at one site and affects the function of protein function at another site
- Activator: makes reaction happen
- Inhibitor: Enzymes cannot use substrate, no reaction
Cooperativity
- Form of allosteric regulation
- Applifies enzyme activity
- One substrate molecule primes and enzyme to act on additional substrate molecules more readily
Feedback Inhibition
- The end product of a metabolic pathway shuts down the pathway
- End product binds to enzyme, substrate cannot bind and make more product
