WATER

Water is polar: electrons spend more time around the oxygen than the hydrogen. this polarity leads to hydrogen bonding, a form of dipole-dipole bonding. water can form hydrogen bonds with other polar molecules.

Properties of Water

polarity:

• good solvent for other polar compounds

• immiscible with nonpolar compounds→ formation of cell membranes

hydrogen bonding

• high boiling point

• high specific heat

• low density of ice

  • gas (vapor): least dense

  • liquid (water): most dense

  • solid (ice): moderate density→is beneficial to life because ice floats on water, which allows aquatic life to survive when lakes/bodies of water freeze over

• adhesion, cohesion, surface tension

other:

• neutral pH

MACROMOLECULES

CARBOHYDRATES

monomer: monosaccharide (simple sugar)

• broken down to release energy during cellular respiration

• glucose, sucrose, malatose

polymer: disaccharides and polysaccharides

• storage and structural compounds

• disaccharides: sucrose, maltose, lactose

• polysaccharides: can be thousands of monomers long

  • starch: stored in plants; can be digested

  • cellulose: stored in plants; cannot be digested (is fiber)

  • glycogen: storage in humans; in liver (sugar stores→ why we carbo-load)

  • chitin: animal polysaccharide; in the exoskeleton of anthropods (used as surgical thread)

bond: glycosidic linkage

chemical composition: CHO→ (CH₂O)n

LIPIDS

monomer: fatty acid

polymer: a combo of multiple fatty acids and glycerol units

• triglyceride: 3 fatty acids + glycerol (fat)

  • saturated fats ( >—— )

    • condensed, with layers of fat like a crepe cake

    • bitter; very saturated

  • unsaturated fats ( >——-\ )

    • not condensed, like wet papers dried with a hairdryer and then stacked on top of each other

    • oils; not dense

• phospholipid

  • head (hydrophilic)

    • VERY POLAR

  • tails (hydrophobic)

    • fatty acid tails

    • NOT POLAR

  • aggregate spontaneously in water

  • form bilayers/micelles with nonpolar tails inside

• steroids

  • lipids with 4 fused rings

  • cholesterol

    • helps membranes stay fluid- is a regulator in different temperatures

  • estrogen

  • testosterone

  • other hormones

bond: covalent-ester linkage

chemical composition: CHO

PROTEINS

monomer: amino acid (peptide)

polymer: polypeptide chains

bond: peptide bond (covalent)

chemical composition: CHON, and

• carboxyl group

• amino acid group

• R side chain

  • there are 20 amino acid side groups necessary for life!

    • nonpolar, aliphatic

    • polar, uncharged

    • polar, charged

    • positively charged

    • negatively charged

structures:

• primary structure:

  • chain of amino acids

  • automatically becomes like this after coming out of the rough ER

  • held together by peptide bonds (r-side group attractions)

• secondary structure:

  • amino acid chains folded onto itself

  • alpha helix

  • beta-sheets

  • held together by hydrogen bonds

• tertiary structures:

  • 3D structure

  • held together by disulfide, ionic, hydrogen, van der waals, LDF bonds

• quarternary structures:

  • not all structures get to this stage

  • assembly of multiple tertiary subunits

  • held together by COVALENT, disulfide, hydrogen, van der waals, LDF

    • no ionic bonds in this stage?

denaturing

• losing 3D shapes/unravelling because of:

  • pH

  • temperature

  • saltinity levels

• sometimes denaturing is reversible…most of the times not.

  • think of eggs cooking and trying to reverse that process..

• STRUCTURE=FUNCTION

  • if a protein denatures, it loses its function.

NUCLEIC ACIDS

monomer: nucleotide

polymer: DNA and RNA chains?

chemical compositions: sugar, nitrogenous base, phosphate group (ACTG)

MEMBRANE STRUCTURE & FUNCTION

membrane characteristics:

• semipermeable

  • lets pass:

    • hydrophobic molecules

    • small uncharged polar molecules

  • doesn’t let pass: (these need a channel to pass)

    • large uncharged polar molecules

    • ions (charged molecules)

• phosphoipids in a fluid mosaic bilayer

  • hydrophobic interactions

  • lateral movement

  • fluidity decreases as temperature decreases

membrane components

• integral proteins

  • transmembrane (pass all the way through)

    • acts as a channel

      • channel proteins

        • selective

        • used in facilitated diffusion

  • embedded (passes halfway through the membrane)

    • acts as an anchor

      • glycoproteins

        • identifies proteins for cell to cell recognition

      • receptors

        • recieves chemical signals

      • cholesterol:

        • keps membranes fluid

          • decreases fluidity at high temperatures

          • prevents solidification at low temperatures

          • “a regulator”

• peripheral proteins

  • bound to the surface of the membrane; often to integral proteins

  • usually inside the cell

    • relays signals

    • acts as attachment points

• phospholipids

  • containment

  • transports O2, CO2, H2O, glucose, ions

STANDARD ERROR OF MEAN

• large standard deviation= large standard error

• large sample size = decreases standard error

  • sample size: # of trials/ # of data points collected

CELL COMPONENTS

cell wall: only plants have this. provide structural support, shape, protection. location: outside cell membrane.

cell membrane: all cells have this. a barrier between outside and inside the cell. semipermeable, and is a fluid mosaic. maintains the inner cell environment. surrounds cytoplasm.

centriole/centrosome: aids in cell division. organizes microtubules (the cell’s skeletal system). within cytoplasm.

chloroplast: only plants have this. take sunlight and convert it into glucose. in the cytoplasm—mesophyll cells.

rough ER: in the cytoplasm, near the nucleus (but is throughout the cell). makes proteins, is the location where they come out and perform post-translation modification folding and sorting. has ribosomes attached to its interior.

smooth ER: in the cell periphery; in cytoplasm. makes lipids (phospholipids, steroids), metabolizes carbs, detoxifies harmful stuff, and stores calcium ions (crucial in muscle contraction).

flagella: little tails at the outside of the cell membrane. provide mobility and act as propellors. only some cells have this.

golgi apparatus: “factory”→ receives proteins and lipid, then processes them, packages them, and transports/directs them to the right location. near the nucleus and rough ER.

lysosome: waste disposal. has digestive enzymes. helps with apoptosis

mitochondria: powerhouse of the cell. produces energy from glucose (ATP). located in the cytoplasm

nuclear envelope (membrane): surrounds the nucleus and protects DNA (separates the nucleus from the cytoplasm.

nuclear pore (NPC): holes in the nuclear envelope that allow small molecules and ions to pass in and out of the nuclear membrane.

nucleolus: produces and assembles ribosomes. located inside the nucleus.

peroxisome: detoxes cells→ oxidation reactions break down toxins.

plasmodesmata: helps in movement of molecules between cells (micro channels). located in the cell wall—only in plants.

ribosome: makes proteins. translates codes from mRNA into amino acid sequences. located in the cytoplasm or in the rough ER.

central vacuole: only in plant cells. is very large, and maintains turgor pressure for the cell. holds onto materials and waste. located at the center of the cell and is the largest organelle.

food vacuole: ingest and digest food particles; phagocytosis. helps provide nutrients to the cell.

vesicle: transports molecules around the cell. secretes substances, digest materials, and regulate pressure. located mainly near the ER and golgi apparatus to transport proteins.

protein production process:

• ribosomes

  • initiate process

  • translates mRNA into amino acid sequences

• rough ER

  • as the proteins are synthesized, they’re threaded into the “ER lumen” where further modifications are made.

• vesicle transport

  • protein is complete→vesicle departs from ER, surrounding the protein

  • moves to golgi apparatus

• golgi apparatus

  • processes and packages the protein

  • modifies by adding sugars or phosphate groups (glycosylation)

  • final function is determined here

• vesicle action again!

  • based on the modifications made by the golgi apparatus, proteins are sorted and packaged into new vesicles and transported to their final destination

SURFACE AREA/VOLUME

• viruses:

  • are not alive.

    • because they can’t reproduce by themselves!

    • have an envelope, protein coat, nucleic acid (DNA or RNA) and spikes (to attach to specific cell surfaces)

• surface area: r²

  • large SA: more materials can enter/exit the cell per unit of time

• volume: r³

  • cell volume determines its energy needs and waste production

• SA/V RATIO

  • if a cell grows too large, it can’t continue to grow, because:

    • diffusion can’t support the necessary exchange of materials

      • nutrients can’t come in fast enough

      • waste can’t be sent out fast enough

    • diffusion is a passive, constant force. the rates of exchange are always the same: its the ratio of sa/v that matters

      • the smaller the ratio, the faster the rate of exchange

MEMBRANE TRANSPORT

PASSIVE TRANSPORT

• requires no energy (spontaneous)

• molecules move down a concentration gradient (high→low)

• decreases free energy (entropy increases)

• diffusion: the tendency for molecules to spread out into available space due to their thermal energy.

  • each substance diffuses down its own concentration gradient.

    • is unaffected by other molecules in the system!

    • molecules move down the concentration gradient until they’re evenly dispersed

• osmosis: the diffusion of water down its concentration gradient across a semipermeable membrane

  • moves from high water concentration to low water concentration

    • or, low solute areas to high solute areas

TYPES OF SOLUTIONS

these are relative terms. (here, it’s the solution in relation to the cell)

• isotonic solution:

  • equal concentration of solute particles inside and outside the cell

  • net movement of water is zero

  • cell stays the same size

• hypertonic solution:

  • more solute particles in the solution than in the cell

    • hyper = more

  • water moves from the hypotonic cell into the hypertonic solution

    • water moves from low solute→high solute

  • cell shrivels

• hypotonic solution:

  • less solute particles in the solution than in the cell

    • hypo = less

  • water moves from the hypotonic solution into the hypertonic cell

  • cell expands

• osmoregulation: cells must maintain balance in different aquatic environments

  • especially for animal cells, who have no cell walls

FACILITATED DIFFUSION

• passive (no energy used)

  • high concentration of molecules→low areas of concentration

  • literally is diffusion with a channel

• requires a specific channel (which are often gated)

• used for polar molecules and ions

ACTIVE TRANSPORT

• requires ATP

• pumps molecules against their concentration gradient

  • from low concentration → high concentration

• uses proteins and channels

EXAMPLES

• sodium-potassium pump

• above:

  • pump out 3 sodium ions and pump in 2 potassium ions

  • uses 1 ATP

  • establishes and maintains an electrochemical gradient with sodium outside and potassium inside

    • this is important because nerves need this electrochemical gradient to function

      • cell’s inside is negatively charged compared to outside

        • this is membrane potential

• proton pumps

  • maintain a hydrogen ion gradient (hydrogen ion is outside the cell)

  • concentration of protons can be used for cellular work

  • uses ATP

• cotransport

  • uses ATP to pump a molecules out of the cell

  • molecules need to do work as it passively diffuses back in

    • examples:

      • sucrose cotransporter

        • plant cells pump out hydrogen ions, which diffuse back in and bring a sucrose along with it!

        • plants use this mechanism to load sucrose into special cells

      • lipid cotransporter

        • lipid molecules are pumped out of the cell, and bring in other molecules with it

          • they passively diffuse back in

      • chloroplasts and mitochondria

        • function as “cotransporters” between themselves by exchanging ATP and NAD(P)H

        • think of just them collaborating to make energy for the cell!

CALCULATING WATER POTENTIAL (PSI)

water potential (Ѱw): the tendency of water to move out of a solution because of the combined forces of solute potential and pressure potential

• high water concentration = high water potential

solute potential (Ѱs): the tendency of water to move (by osmosis) in response to differences in solute concentration

• as molarity increases, Ѱs decreases (due to negative in equation)

• high solute potential → likely that water will leave

  • (high water concentration)

• low solute potential → likely that water will come

  • (low water concentration)

pressure potential (Ѱp): a component of Ѱw that comes from the physical pressure exerted on water within a cell

• Ѱp = 0 in open containers

• Ѱw = 0 if pure water is in an open container

  • Ѱp = 0 because of the open container

  • Ѱw = 0 because its pure water (no molarity)

CALCULATING SOLUTE POTENTIAL (Ѱs) EQUATION

• the greater the concentration, the more negative the product

• higher solute potential = a number that’s closer to zero

CALCULATING WATER POTENTIAL (Ѱw) EQUATION

TRANSPORT PROCESSES IN CELLS

• all membranes are made of the same thing _{the receptor-mediated membranes are a tiny bit different…but they’re still recycled}

  • cell membranes are recycled between the golgi, ER, vesicles, vacuoles, peroxisomes, and outer membrane

  • cell membranes are all the same, except for their embedded proteins

    • proteins are also recycled back to their correct membrane source

  • membranes have a “sidedness” that’s maintained during recycling

vehicles of transportation:

• vacuoles: hold water, occasionally nutrients (pinocytosis)

• peroxisomes: hold detoxifying enzymes (peroxicretion—fuse with the membrane and release their waste extracellularly)

• lysosomes: hold digestive enzymes (release their waste extracellularly)

• secretory vesicles: excrete things from the cell

EXOCYTOSIS:

• removal of materials from the cell

• vesicles can bud from the golgi apparatus/ER, then fuse with the cell membrane and discharge their contents

  • peroxisomes

  • lysosomes

  • secretory vesicles

• food vacuoles might merge with the outer cell membrane and dump debris outside the cell

ENDOCYTOSIS:

• allows intake of large quantities

• a small area of the membrane pinches in (like a divot, then becomes a hole with a small opening)

• becomes a pocked, which seals into a vacuole

• cells with cell walls cannot do this!!

  • phagocytosis: ingestion of large particles into a food vacuole

    • then merges with a lysosome

    • non-specific

    • EX: amoebas, macrophages (white blood cells: engulf viruses, anti-bacteria, and other foreign pathogens)

    • pinocytosis: taking in liquids

      • non-specific

    • receptor-mediated endocytosis

      • highly specific; targets things to take in

      • uses receptors that bind to specific substances

        • receptors are in concentrated regions

          • “coated pits”

      • substances bind to the receptor → cell membrane forms a pocket, then a vesicle, enclosing the substance → brings it to the cell

      • receptor proteins are recycled back to the coated pit area of the membrane