✅ Unit 2 - Exchange of materials

Properties of carbon

1. ability to form covalent bonds (strong)

2. ability to bond with same or different atoms and form chains of any length

3. ability to form single + double covalent bonds (single allow rotation)

macromolecule

A giant molecule created by atoms covalently bonded to one another (monomer + monomer)

4 main classes of macromolecules

1. carbohydrates

2. lipids

3. proteins

4. nucleic acids

types of monosaccharides

pentose

• ribose

• deoxyribose

• fructose

hexose

• galactose

• alpha glucose

subcategories of carbohydrates

1. monosaccharides

2. disaccharides

3. polysaccharides

subcategories of lipids

1. triglyceride

2. steroids

3. phospholipids

subcategories of proteins

1. polypeptides

   1. structural

   2. enzymes

   3. transport

   4. antibodies

2. animo acids

   1. essential

   2. nonessential

subcategories of nucleic acids

1. DNA

   1. genes

   2. chromosomes

2. RNA

   1. mRNA

   2. tRNA

   3. rRNA

draw the ring form of alpha glucose

draw the ring form of beta glucose

properties of glucose

• Soluble: due to multiple hydroxyl groups that form h-bonds with water = easily transportable in bloodstream

• transportability: effectively transportable so it’s an energy carrier

• chemical stability: relatively stable and doesn’t degrade easily over time (=good to store energy)

• energy yield: oxidation of glucose during cellular resporation yields ATP

hydrolysis reactions

catabolic reactions where H20 molecules break covalent bonds between monomers from polymers

glycosidic bond

between monosaccharide units creating a disaccharide

______ and _____ are reversible

hydrolysis and condensation are reversible

condensation reactions

anabolic polymerisation reactions where 2 molecules join together where one molecule loses a hydroxyl (-OH) group and the other losing (-H) to create H_²O as a byproduct

draw produce of alpha glucose + alpha glucose

numbering carbons in a-glucose

1. carbon 1 has no attachments, adjacent to O

2. carbon 5 has a branch of c connected

   1. alpha = OH on C-1 facing downwards

   2. beta = OH on C-1 facing upwards

which polysaccharides are used as energy storage

1. glycogen

2. starch

   1. amylase

   2. amylopectin

glycogen as energy storage in animals

Highly branched (α-1,4 & more frequent α-1,6 than amylopectin) → very compact + rapid mobilization. Stored mainly in liver & muscles. Insoluble, doesn’t disturb osmotic balance.

starch as energy storage in plants

Made of amylose (α-1,4) and amylopectin (α-1,4 and α-1,6). Compact due to coiling (amylose) and branching (amylopectin). Insoluble, so doesn’t affect osmosis. Glucose units easily added/removed for energy use.

Amylose vs. Amylopectin

• Amylose: Unbranched, α-1,4 bonds → coils into helix → compact but slower to hydrolyze.

• Amylopectin: Branched (α-1,4 + α-1,6) → more ends → faster glucose release.
  Both make starch efficient for storage in plants.

cellulose + function as a structural polysaccharide in plants

• made up of beta-glucose monomers linked by 1,4-glycosidic bonds.

• alternating orientation of beta-glucose = straight chains.

  • bundled together in microfibrils, + cross-linked with h-bonds

    • prevent the cellulose from bursting and help regulate osmotic pressure

• High tensile strength is due to covalent bonds within the microfibrils

glycoproteins are a _____ of a _______ and a ______ , fundamental in cell ______ acting as ______ as well as for cell ______

glycoproteins are a combination of a carbohydrate and a protein, fundamental in cell recognition acting as receptors (identify + destroy foreign cells) as well as for cell adhesion

structure of glycoprotein

conjugated proteins with carbohydrate as the prosthetic group, embedded in the plasma membrane projecting out into the exterior environment

How do ABO antigens affect blood transfusions?

Red blood cells have glycoproteins with different oligosaccharides:

• Type A and B have unique 5th monosaccharides

  → AB can't donate universally

• Type O lacks this 5th sugar = base structure shared by all
  → universal donor (no “foreign” sugar triggers immune response)

examples of carbohydrates

1. glucose

2. sucrose (plants)

3. cellulose

4. glycoproteins

5. starch

6. glycogen

glycolipids

molecules with carbohydrates linked to lipids

glycolipids’ role in cell recognition

helps immune systems distinguish between self vs. non-self cells to destroy pathogens

lipids

organic molecules that insoluble in water and are found in the structure of cell membranes + used as energy stores

common examples of lipids

• oil

• fats

• waxes

• steroids

• phospholipids

roles of lipids

1. long-term energy storage/chemical energy

2. structural integrity (phospholipid bilayer)

3. communication (hormones to start/stop protein production)

4. thermal insulation

lipids as energy storage

1. Triglycerides = long-term storage as more dense

2. Carbohydrates = short term

3. ATP = immediate

properties of triglycerides

• chemically stable: energy isn’t lost over time

• immiscible: naturally forms droplets in cytoplasm and doesn’t affect osmotic balance

• energy dense: 2x j/g than carbs and is useful for animals that move (more energy, less space)

• liquid at body temp: acts as a shock absorber

• poor heat conductors: thermal insulators for animals to conserve heat

triglycerides as energy storage in adipose tissue

specialised group of cells (adipose tissue) is located beneath the skin and around some organs (kidneys)

How are triglycerides formed?

through condensation reaction with h2o as byrpoduct where glycerol and 3 fatty acids form glycosidic bonds to become a triglyceride

Phospholipid structure

Condensation reaction with ester bonds

• Hydrophillic Head = 1 glycerol + 1 phosphate group

• Hydrophobic Tails = 2 fatty acids

  • Saturated → single bonds (straight)

  • Unsaturated → double bond

    • trans-fat: straight chain

    • cis-fat: kinks (lower MP due to easy separation)

unsaturated fatty (__-fat) are _____ to stack on top of each other due to their ____ and thus reduce ___ in blood vessels, decreasing chances of ____

unsaturated fatty (cis-fat) are harder to stack on top of each other due to their kinks and thus reduce clogs in blood vessels, decreasing chances of stroke

amphipathic molecules

part of the molecule is hydrophillic, the other part is hydrophobic

The ______ phosphate heads are _____ to the water and face ______, while the _______ tails are packed together ____ from the water, creating a _____ layer

The hydrophilic (water-loving) phosphate heads are attracted to the water and face outward, while the hydrophobic (water-fearing) tails are packed together away from the water, creating a double layer

non-polar steroids

• 4 rings of carbon atoms (17 C total)

  • 1 cyclohexane

  • 1 cyclopentane

• Low carbon to oxygen proportion (lipid)

• mostly hydrocarbon and thus hydrophobic

• can pass through bilayers

ex. oestradiol, testosterone

general structure of an amino acid (AA)

amine group (basic) bonded to the central carbon bonded to the r’ group and carboxyl group (acidic)

r groups in amino acids

• differs from one AA to the next

• determines the properties of the AA

  • polarity (acidic or basic)

  • h-h bonds

structure of alanine

structure of glycine

amino acids are bonded together by _____ bonds through _____ reactions (H_²O ______)

amino acids are bonded together by peptide bonds through condensation reactions (H_²O byproduct)

polypeptides

A chain of amino acids that is linked together by peptide bonds

disulfide bridges

covalent bonds that form between pairs of cysteine amino acid residues → S-S bond which affects the function of the AA)

____ containing R-groups are ___-_____

sulfur containing R-groups are non-polar

adding ___ group increases _____ charge

adding amine group increases positive charge

adding ___ group increases _____ charge

adding carboxyl group increases negative charge

formula to calculate # of bonds in polypeptide

20ⁿ, n = amino acid #

Denaturation definition

the process where a protein loses its 3D structure due to the breaking of non-covalent bonds like hydrogen bonds and hydrophobic interactions

Primary protein structure

polypeptide chain with no definite 3D structure, can de depicted with letters

Secondary protein structure

polypeptide chain folding and coiling into regions of alpha helices and beta-pleated cheets due to H bonds (C from carbonyl and H from peptide bond)

Tertiary protein structure

1 Polypeptide chain folded into 3D structure stabilised by R-group interactions;

1. Ionic bonds

2. Hydrogen bonds

3. (Covalent) Disulfide bridges: between pairs of cysteines

4. Hydrophobic interactions

Ionic bonds in tertiary protein structure

Occur when + and - R groups interact where the amine takes a P ion from carboxyl to become more + while making the carboxyl more -

Differentiate between Fibrous vs. Globular Proteins

Feature	Fibrous Proteins	Globular Proteins
Shape	Elongated polypepties (long, strandish)	Folded polypeptides stabilised by R group bonds (round, spherical)
Solubility	Insoluble in water	Soluble in water
Function	Structural/support (ex. strength, rigidity)	Functional/metabolic/catalytic (ex. enzymes, hormones)
Examples	Collagen, Keratin, Fibrin	Hemoglobin, Insulin, Enzymes
R-Groups	Hydrophobis AA in center to stabilise tertiary structure	Hydrophillic AA on surface to allow solubility
Stability	More stable	Less stable

Collagen as a fibrous protein

• Made of 3 polypeptides wound into a triple helix (P-G-X repeating sequence)

• Rope-like structure → high tensile strength

• R-groups face outward → allows functional variation

• Found in tendons, ligaments, skin, and bones

Insulin as a globular protein

• Small, compact globular hormone

• Soluble in blood → easy transport to target cells

• Binds to insulin receptors (specific conformation only bindable to its receptor) → regulates blood glucose

• Functional role in metabolism, not structural

Role of R-groups in Integral proteins

• Hydrophobic AA R-groups face outward towards membrane’s non-polar core = anchors protein

• Hydrophilic R-groups face cytoplasm = interaction with water or solutes

Role of R-groups in Transmembrane proteins

• Hydrophobic R-groups face out in membrane-spanning regions = interact with phospholipid tails

• Hydrophilic R-groups face inward (channel) or on exterior ends = interact with aqueous environments + stability + function in transport/signaling

Role of R-groups in Channel proteins

Tunnel lined with hydrophilic AA = allows hydrophilic solutes to diffuse across hydrophobic core

Quaternary protein structure

2 or more polypeptide chains combined, can be conjugated or non-conjugated

Conjugated proteins

contain prosthetic groups, ex. haemoglobin with 4 polypeptides and haem groups that increases chemical and functional diversity

• haem binds to oxygen allowing its transport

Non-conjugated proteins

purely made of AA with same linkage as tertiary structure

ex. insulin with 2 polypeptides linked by disulfide bridges or collagen with 3 polypeptides wound together

Simple diffusion

PASSIVE movement down a concentration gradient across the phospholipid bilayer for;

• Small nonpolar/hydrophobic molecules (e.g., O₂, CO₂)

• Small uncharged polar molecules (e.g., H₂O, ethanol) — limited permeability

Dynamic equilibrium

No net change in concentration with particles continuously moving to maintain equilibrium

Semi-permeable membrane allows certain ____ solutes and is freely permeable to _____ (ex. artificial membrane used in kidney dialysis)

Semi-permeable membrane allows certain small solutes and is freely permeable to solvent (ex. artificial membrane used in kidney dialysis)

Selectively permeable membrane allows passage of ____ particles through _____ diffusion and _____ transport (ex. chloride channel)

Selectively permeable membrane allows passage of specific particles through facilitated diffusion and active transport (ex. chloride channel)

Types of membrane proteins

1. Integral Proteins

   1. Channel proteins

      1. Transmembrane

   2. Pump proteins

2. Peripheral Proteins

characteristics of channel proteins

• diameter of pore is tailored so only one type of particle passes

• bidirectional but normally higher to lower conc

• facilitated diffusion

characteristics of pump proteins

• use energy to carry out active transport

• one directional

• against the concentration gradient

• interconvertible: atp switches between more → less stable configurations

characteristics of peripheral proteins

• hydrophilic on the non-embedded surface

• attached to the surface of integral proteins

• 1 hydrocarbon chain is inserted into membrane = anchor

osmosis

net movement of particles moving in and out of a cell due to differences in concentrations

aquaporins

integral water channels increasing membrane permeability to water

(ex. kidney cells to reabsorb water, root hair cells to absorb water from soil)

high membrane fluidity

lower density of phospholipids making the membrane more permeable, mix of saturated and unsaturated fatty acids.

low membrane fluidity

high density of phospholipid decreasing permeability, freezes easily

cholesterol’s role in membrane fluidity

High temperatures: holds together the phospholipids to stabilise and minimise permeability

Low temperatures: acts as a buffer to prevent solidifying

types/examples of endocytosis

1. pinocytosis (drinking)

2. phagocytosis (eating) (ex. macrophages engulf large particles, including bacteria, for digestion)

3. receptor-mediated endocytosis

example of exocytosis

cells release hormones like insulin (pancreatic beta cells) and other signaling molecules into the bloodstream

3 types of channels

1. voltage-gated channels

2. ligand-gated channels

3. mechanically-gated channels

example of a voltage gated channel

Sodium potassium pump (direct active transport)

Outline the processes of the sodium potassium pump / Describe an example of direct active transport

1. 3 Na+ and 1 ATP bind to the pump

2. ATP dephosporylates becoming ADP and induces a conformational change opening the pump side facing the cytoplasm

3. 3 Na+ ions are released outside the membrane and 2 K+ ions bind to the pump

4. K+ is released inside the membrane with releasing the Phosphate

Against the concentration gradient, inside is relative more - charged than outside (3+ go out, 2+ come in) creating an electrochemical gradient that creates an action potential

Describe an example of indirect active transport

Sodium-dependent glucose co-transporters

• Indirect as ATP isn’t directly involved but it was in previous processes (sodium potassium pump)

• Glucose ‘grabs onto’ the excess Na+ from the pump and goes back into the cell against it’s concentration gradient allowing glucose reabsorption (ex. small intestine)

Describe an example of a ligand-gated channel

Nicotinic acetylcholine receptor

1. Acetylcholine (exitatory neurotransmitter) binds to the receptor present at skeletal neuromuscular joints

2. Induces a conformational change opening the ion channel

3. Na+ ions diffuse down the concentration gradient

   1. Inner cell becomes more positive and creates action potential through depolarisation

Cell Adhesion Molecules

type of cell surface protein that bind cells with other cells or with the extracellular matrix (containing supporting structures like collagen proteins)

• in tumors they prevent cells from seperating and mitigate metastasis

Types of intracellular junctions (CAMs)

• Tight junctions

• Adherens junctions

• Desmosomes

• Gap junctions

Water potential

a measure (kPa) of the (potential energy of water / per unit of volume water).

highest is 0 so normally - values, (ex. -200kPa cell inside a -300kPa solution, water moves from inside the cell to outside)

formula for total water potential

total water potential = solute potential + pressure potential

Hypertonic effect on animal cells

Shrivelled / Crenated

Hypertonic effect on plant cells

Plasmolysed

Isotonic effect on animal cells

Normal

Isotonic effect on plant cells

Flaccid

Hypotonic effect on animal cells

Lysed

Isotonic effect on plant cells

Turgid

Hypertonic

A solution with a higher solute concentration than the cell, causing water to move out of the cell

Hypotonic

A solution with a lower solute concentration than the cell, causing water to move into the cell

Isotonic

A solution with the same solute concentration as the cell, resulting in no net movement of water