Module 2 Bio 1107

Organic Molecules

Molecules with a least one C-H bond

(can also have P, N, O, S)

What are lipids made up of? What are they called?

C+H → Hydrocarbons

What are carbohydrates made of? What are they called?

C+H+O → Sugars

What are DNA/RNA made of? What are they called?

C+H+N+O+P → NucleotidesWh

What are proteins made of? What are they called?

C+H+O+N+S → Amino acids

Other names for carbohydrates? Examples?

Polysaccharides or glycans or sugars
Starch, glycogen, cellulose

What are DNA/RNA called?

Nucleic AcidsW

Another name for Proteins?

PolypeptidesHo

How do we classify most of the macromolecules? What is not the same?

Polymers (shared chemical structure), but LIPIDS are NOT polymers

Lipids are classified by shared physical properties

Monomer, function, and bonds of Glycans/Polysaccharides/Carbohydrates/Sugar

monosaccharide

energy storage & cell recognition/signaling

glycosidic

Monomer, function, and bonds of Nucleic Acids

Nucleotides (5 carbon sugar, phosphate group, nutrogenous base)

genetic information, info storage, and retrieval

phosphodiester

Monomer, function, and bonds of Proteins

amino acids

structure, enzymatic activities, signaling

peptide

Monomer, function, and structure of Lipids

hydrocarbons

lipid bilayaer membrane structure, storage, signaling

NO BONDS → structure is determined by hydrophobic interactions

Which macromolecule is the most complex?

proteins

Both lipids and carbs function as energy storage. What is the difference?

Lipids: Better for long-term energy storage because they have more C–H bonds, which release more energy when broken down. They store more energy per gram. Higher PE

Carbohydrates: Better for short-term energy because they are easier for cells to break down quickly. They store less energy per gram because they contain more oxygen. Lower PE

Difference between DNA and RNA

DNA: Double-stranded, with complementary, antiparallel strands that form a double helix → RNA: Usually single-stranded, but can fold into complex 3D shapes.

DNA: More stable → RNA: Less stable and more reactive because ribose has an extra OH group at the 2′ carbon instead of just a H.

DNA: Contains deoxyribose sugar → RNA: Contains ribose sugar.

What are the four levels of structure in proteins and their definitions?

Primary: Order/sequence of amino acids

Secondary: Alpha helices & beta sheets

Tertiary: 3D shape of protein

Quaternary: Multiple proteins forming one unit

What are the bonds/forces in each of the protein structure levels?

Primary: peptide bonds

Secondary: hydrogen bonding between peptide backbones

Tertiary: hydrogen bonds, hydrophobic interactions, van der walls, covalent, and ionic bonds

Quaternary: hydrogen bonds, hydrophobic interactions, van der walls, covalent, and ionic bonds

Where is the location of the interaction in each of the protein structure levels?

Primary: between amino acids

Secondary: between parts of the backbone → R-groups not involved

Tertiary: between R groups and peptide bonds

Quaternary: between multiple polypeptides

What does a change in the primary structure of a protein mean?

it alters its fundamental amino acid sequence which can completely disrupt how the protein folds at every subsequent level

What are the three categories of amino acid R-groups?

nonpolar, polar, and electrically charged

What is a nonpolar r-group?

hydrocarbon-based side chains that lack electric charges or highly electronegative atoms → hydrophobic

cluster on inside of folded protein, away from water

What is a polar r-group?

partial charges or highly electronegative atoms (oxygen, nitrogen, sulfer) that allow them to readily form hydrogen bonds and dissolve in water and carry no net charge → hydrophilic

What is an electrically charged r-group?

they carry a net positive or negative charge and interact strongly with water and other charged molecules → highly hydrophilic

Why is the type of r-group side chain important in the scheme of things?

Swapping one amino acid for another can change which category the R-group falls into

What is the fluid mosaic model of membranes?

Describes the structure of the cell membrane

What are the two main parts of the fluid mosaic model?

Fluid: the dynamics

Mosaic: the composition

What is the fluid:

the dynamic flexible nature of membrane

• the lateral movement of lipids and proteins within membrane

• fluidity is influenced by temperature

What is the mosaic?

the componenets embedded/associated with bilayer

proteins, carbohydrates, etc

What is the structure of the fluid mosaic model of membranes?

• phospholipid bilayer

  • hydrophilic heads (face outwards)

  • hydrophobic tails (face inwards)

• semi-permeable

What are the types of lipids that can make up the phospholipid bilayer in the mosaic model?

Fats (triglycerides), Phospholipids, Steroids

What is the backbone, hydrophilic head, hydrophobic tail, and linkage/features of fats (triglycerides)?

backbone: glycerol

hydrophilic: none → highly hydrophobic

hydrophobic: 3 fatty acid chains

linkage/features: ester linkages

What is the backbone, hydrophilic head, hydrophobic tail, and linkage/features of phospholipids?

backbone: glycerol

hydrophilic: phosphate + polar head group

hydrophobic: 2 fatty acid chains

linkage/features: amphipathic

What is the backbone, hydrophilic head, hydrophobic tail, and linkage/features of steroids?

backbone: 4-fused rings

hydrophilic: polar “r” group (like -OH)

hydrophobic: steroid rings + isoprene chain

linkage/features: ether linkage (bilky, rigid structure)

What is a fatty acid chain?

a hydrocarbon carbon bonded to carboxyl group

what is the subunit, linkage, tail, and glycerol configuration of archaea membrane lipids?

subunit: monolayer

linkage: ether linkage

tail: isoprene

glycerol configuration: L-glycerol

what is the subunit, linkage, tail, and glycerol configuration of bacteria membrane lipids?

subunit: bilayer

linkage: ester linkage

tail: fatty acid

glycerol configuration: D-glyceron

what is the subunit, linkage, tail, and glycerol configuration of eukarya membrane lipids?

subunit: bilayer

linkage: ester linkage

tail: fatty acid

glycerol configuration: D-glyceron

what is an ether linkage?

• Has an oxygen atom connecting two carbon-containing groups.

• Does not have the carbonyl group (C=O) found in an ester.

• Found in some membrane lipids, including the membrane lipids of archaea.

What is an ester linkage?

• Contains a carbonyl group (C=O) next to an oxygen that connects to another carbon.

• Common in fats and oils, where fatty acids attach to glycerol.

• Found in many triglycerides and phospholipids.

Can the tails of phospholipids affect membrane fluidity?

Yes

How can the tails of phospholipids affect membrane fluidity?

Fatty acids can very in length

Fatty acids can vary in number of double bonds in hydrocarbon chain

Cis-unsaturated are kinked → prevent close packing → increase fluidity

Longer fatty acid → more rigid → reduce fluidity

What does no double bonds in a hydrocarbon chain mean?

Saturated

• has the maximum amount of hydrogens (saturated with hydrogens)

What does one or more double bonds mean?

Unsaturated

• each C that is part of the double bond will be able to dorm one less bond to H

• Bent tail

• Cis-unsaturated (H on same side) or trans-unsaturated (H on opposite sides)

What are sterols, where are they, and what do they do?

they are a type of lipid with a structure made of four connected carbon rings

they are in phospholipid tails between the fatty acids

they stabilize membranes and buffer membrane permeability by increasing the riigidnes/packness of the tail

(they’re called cholesterol in mammals)

How do unsaturated tails affect membrane fluidity?

rigid kinks on the tail that prevent tight packing increase fluidity

How do saturated fatty acid tails affect membrane fluidity?

the tight rigid packing means less space for things to go through so it decreased fluidity

how do shorter hydrocarbon tail lengths affect membrane fluidity?

fewer hydrophobic interactions with neighboring tails allows lipids to move freely so it increased fluidity

How do longer hydrocarbon tail lengths affect membrane fluidity?

they have more surface area which increases hydrophobic behavior with other tails so they decrease membrane fluidity

how does the temperature of the sterol affect membrane fluidity?

at low temp, the cis-unsaturated tails increase fluidity to prevent membrane from freezing

at high temp, the rigid structure prevents over permeability

so what increases rigidity and strenth of the membrane?

low temperatures, longer fatty acids, sterols (cholesterol buffers membrane fluidity → limits phospholipid at high temps and prevents tight packing at low temps), trans-unsaturated

so what increases fluidity and permeability in a membrane?

high temps, cis-unsaturated fatty acids, shorter fatty acids

are membrnes permeable

they are semi-permeable

how do hydrophobic molecules move through the semi-permeable membrane?

Small and nonpolar molecules cross most easily. They can slip through the hydrophobic core, and their small size helps. Examples would be oxygen, carbon dioxide, and lipids themselves.h

how do small, uncharged, polar molecules move through the membrane?

Polar molecules are hydrophilic and unfavorable in the hydrophobic core and need help

What are the types of membrane transport?

simple diffusion, facilitated diffusion, active transport

What is simple diffusion?

Moves a molecule down its concentration gradient

• no transport proteins needed, just moves SMALL & NONPOLAR molecules → passive transport

What is facilitated diffusion?

moves a molecule down its concentration gradent

• moed LARGE, POLAR, & CHARGED molecules → passive transport

  • ex: osmosis, water moves through aquaporin channel protein

What is active transport?

moves molecule against its concentration gradient

• requires ATP/energy and moves one or more molecule simultaneously with transport molecules

what are the options for the kinetics of a membrane?

simple (no saturation), facilitated (saturation), and active (saturation)

what does the simple kinetics look like?

straight line from origin

what does facilitated kinetics look like?

concave from origin

what does active kinetics look like?

concave from before the origin

what is osmosis?

diffusion of solvent/water across a membrane

which direction does the solvent move in osmosis?

moves from lower solute concentration toward higher solute concentration across a selectively permeable membrane

what are the cytoplasm solute concentrations?

hypertonic, isotonic, and hypotonic

what is hypertonic:

The outside solution has a higher solute concentration than the cytoplasm, so water flows out of the cell and the cell shrinks.

what is isotonic?

The solute concentrations are equal on both sides, so there's no net water movement. The cell stays the same size.

What is hypotonic?

The outside solution has a lower solute concentration than the cytoplasm, so water flows into the cell and the cell swells, and in extreme cases can burst (lyse).

compare prokaryote and eukaryote cells: size, cellularity, chromosome structure, placement of dna, cell walls, cell division, organelles

size: P small E large

cellularity: P unicellular E uni and multicellular

chromosome structure: P circular E linear

placement of dna: P nucleoid region E nucleus

cell walls: P most have them E plants/fungi

cell division: P binary fission E mitosis

organelles: P not bound E membrane bound

what is the endosymbiotic theory?

mitochondria and chloroplasts originated from prokaryotes that became incorporated into an ancestral eukaryotic cell.​

what is the evidence for the endosymbiotic theory?

1.Have their own DNA

2. Have circular DNA (similar to bacterial chromosomes)

3. Are approximately the size of prok cells

4. Have ribosomes more similar to prok ribosomes

5. Reproduce by binary fission like prok

What is the endomembrane system?

Network of organelles in eukaryotic cells that work together to modify,

package, and transport lipids and proteins

what are the different organelles?

nuclear evelope, rough ER, smooth ER, transport vesicle, golgi, secretory vesicle

What does the nuclear envelope do?

separates nucleus from cytoplasm and allows transport through nuclear pores

what does the rough ER do?

the ribosomes synthesize proteins

what does the smooth ER do?

lipid synthesis and someee proteins

what does the transport vesicle do?

moves lipids from the ER to the golgi

what does the golgi do?

modifies and sorts proteins and lipids

what does the secretory vesicle do?

carries secreted proteins to the plasma membrane for release outside the cell

how did the endomembrane system originate?

hypothesized to have originated through endocytosis—a process where the outer cell membrane folds inward

what is the process of endocytosis

This formed vesicles inside the cell, which eventually evolved into specialized, membrane-bound compartments (organelles).

believed to have directly contributed to the formation of:

• Nuclear envelope

• Endomembrane system (which includes structures like the ER & Golgi)

• Other internal membrane-bound structures

→ development of internal membranes → cell’s specialized compartments

what is the difference between free ribosomes and the rough ER?

Proteins made by free cytoplasmic ribosomes are undocked to any membrane and are released directly into the cytoplasm. They are destined for: Mitochondria, Chloroplasts, Nucleus interior, Cytoplasm (cytosol)

Proteins made on the ER enter the endomembrane pathway during translation. They are destined for: Secretion (outside the cell), Plasma membrane (surface of the cell), Lysosomes (or other endomembrane organelles)

What is the route of proteins through the different organelles of the endomembrane system?

1. rough ER: proteins are synthesized by ribosomes and injected into the rough ER lumen or membrane where initial folding takes place

2. transport vesicle: the proteins package into transport vesicles that go out in the ER. the vesicles are pulled by motor proteins along microtubule tracks

3. golgi apparatus: as proteins undergo further modifications (sorting and trimming)

4. secretory vesicles: modified proteins are packaged into these vesicles at the trans-golgi network

5. plasma membrane: vesicles move along microtubules toward the cell surface

What do microfilaments do?

Microfilaments manage anchoring and fusion with the membrane for either permanent insertion (transmembrane proteins) or exocytosis (secretory proteins)

what is the second law of thermodynamics:

entropy (disorder) of any isolated or closed system always increases

what is the biological loophole for the 2nd law of thermodynamics?

Living organisms are not closed systems. To build and maintain highly ordered complex structures (anabolism), organisms must perform thermodynamic work.

what does the work powered by metabolic processes relase?

heat energy and molecular waste producs like CO2

The increase in disorder (entropy) of the surrounding environment heavily outweighs the localized decrease in entropy inside the organism. Therefore, the total entropy of the universe still net increases

what do we use gibbs free energy for?

direction and spontaneity of a chemical reaction are determined using the Gibbs Free Energy equation

equation for gibbs free energy

ΔG = ΔH – TΔS; H=enthalpy, T=temperature(K), S=entropy

different options for gibbs free energy

ΔG < 0 -> exergonic, releases free energy, spontaneous

ΔG > 0 -> endergonic, requires energy input

ΔG = 0 -> reaction is in equilibrium

difference between chemical equilibrium and steady state?

Chemical Equilibrium:

• For a specific reaction in equilibrium, ΔG = 0

• The rates of forward and reverse reactions are equal, so there is no net change

Steady-State (homeostasis):

• Describes the complex, interconnected internal environment of a living biological system.

• Biological systems are open systems that remain far from equilibrium to stay alive.

• Individual reactions inside the system continuously proceed spontaneously toward equilibrium, but a constant influx of energy keeps the overall system in a stable, dynamic steady-state.

How do catalysts affect reaction pathways?

lower activation energy (for both the forward and reverse reactions

Do catalysts change thermodynamics?

No they increase the reaction speed but it does not alter the overall energy change

What are the different components of enzyme kinetics?

Vmax, Km, and reaction optimization

What is Vmax?

the maximum velocity: the max rate enzymes can catalyze a reaction. occurs when all available enzyme molecyles are completely saturated with substrate

what is Km?

the michaelis contant: the substrate concentation at which the reaction rate reaches exactly half of Vmax

what is reaction optimization?

an ideal enzymatic reation with a high Vmax (fast processing speed) and a low Km (high affinity) → the enzyme works efficiently even at low substate levels

HIGH VMAX & LOW KM

What are the two ways to regulate enzymes?

competitive inhibition and non-competitive inhibition

what is competitive inhibition?

• Competitive inhibitors compete with the substrate for binding to the active site

• Inhibitor physically blocks the substrate from binding the active site