Unit 1 Chapters 1-3 BIOL 304

Define macromolecules

Large biological molecules

Define metabolites

Smaller molecules involved in bchem rxns

Define a cell

Smallest unit of life, can reproduce, genetic material holds code for all proteins, capanle of response to environment, and metabolism

Define plasma membrane (eukaryotic organelles)

encloses cell body, limits transport of molecules

Define nucleus (eukaryotic organelles)

contains genetic info

Define mitochondria (eukaryotic organelles)

aspects of metabolism, production of ATP

Define endoplasmic reticulum (eukaryotic organelles)

synthesis and storage, modify protein

Define golgi apparatus (eukaryotic organelles)

processing and sorting, attach lipid + other group

Define lysosomes (eukaryotic organelles)

removal of old organelles, processing of ingested material, garbage disposal

Define peroxisomes (eukaryotic organelles)

breakdown of catabolites, breakdown proteins

What does the phylogenetic tree of life look like?

Define covalent bonds

Formed by electron sharing between atoms

Define resonance

Shifting of bonds/e-s which adds stability

• Multiple covalent structures

Define ionic interactions

Noncovalent interactions (don’t share e-s) that occur between fully charged atoms/molecules

• Charge, distance, and surrounding solvent matter (water weakens electrostatic attractions)

What are electric dipoles, how do they form? Can they interact?

Molecules with no overall charge can have regions where electron distribution is uneven

Electrons may be distributed unevenly, resulting in dipole charge

• Dipoles CAN interact with ions and other dipoles

Define hydrogen bond

When H attached to EN atom interacts with another EN atom

Define hydrogen bond donor

Group that includes atom that the H atom is covalently attached to and the H atom itself (includes both EN bonded atom and H atom)

Define hydrogen bond acceptor

Lone pair of e-s that is on the atom less tightly linked to the H atom

Define van deer Waals interactions

Interaction between neighboring atoms, temporary uneven e- distribution → temporary partial charges → nearby attraction

• E’s constantly moving → may become unevenly distributed in atom → temporary imbalance impacts neighboring atom → creates attraction

For VDW forces, what does it mean if they are too far, proper distance, and too close?

Too far apart → little interaction

Proper distance → attractive interaction

Too close → strong repulsion

What are the forces ranked from strongest to weakest

Covalent > ionic > H-bonding > VDW

What are the properties of water?

Polar molecule (unequal e- sharing), highly cohesive

Max # of H-bonding formed in crystalline ice (large # in liquid water)

What is the hydrophobic effect/Why do hydrophobic interactions take palce?

Hydrophobic: water avoiding

Nonpolar (share e- equally) molecules doesn’t interact favorably with water → NP molecules in water can be driven together by hydrophobic effect (powered by the increase in entropy of water) → associated interactions are called hydrophobic interactions

• Water prefers interacting with itself, NP molecules cluster together, reducing their contact with water and increase the freedom of water molecules

What do hydrophobic interactions lead to?

NP molecules are not water soluble → water interacts with itself and excludes the NPM →

PHOSPHOLIPIDS FORM BIOLOGICAL MEMBRANES IN WATER BECAUSE OF HYDROPHOBICITY OF FATTY ACIDS

Draw out the organic molecules (alkane, alkene, alkynes, alcohol, ketone, aldehyde, carboxylic acid, amine)

Define reduction & oxidation

Basis for most metabolic rxns and pathways

Reduction: gain of e-

Oxidation: loss of e-

• In biological systems, enzymes often perform redox rxns with a coenzyme to donate/accept e- pair to/from a carbon skeleton

Define acyl links and how they are formed

A chemical bond that connects an acyl group (R-C=O) to another atom or molecule

Condensation of carboxylic acids with other EN functional group form acyl linages

Define condensation

Builds acyl linage, WATER AS P

Define hydrolysis

Breaks acyl linkage, WATER AS R

What is the 1st law of thermodynamics

Total E of a system and its surroundings is constant

What is the 2nd law of thermodynamics

Total entropy (disorder) of a system plus that of its surroundings ALWAYS INCREASES

• Entropy can decrease locally in system if there is a corresponding increase in entropy in surroundings

What is the thermodynamics equation for change in entropy of surroundings?

Overall change in entropy equation?

Define gibbs free energy (and its equation)

Describes the energetics of biochemical reactions

What does positive versus negative G indicate, when will entropy increase?

Entropy will increase when G is negative

Define reaction coupling (in terms of G)

Energetically unfavorable rxn with positive G gets driven by pairing it with favorable negative G

Define acid base reactions

Involve addition/removal of a hydrogen (H+ atom)

Define pH and its equation

Measure of H+ concentration

pH = -log[H+]

What does more H+ ions mean for pH, less?

Increase H+ → lower pH, acidic

Decrease H+ → higher pH, basic

How do you find proton/hydroxide ion concentration?

What does it mean for protonation/deprotonation when pH is above, below, and equal to pKa?

pH below pKa = group tends to stay protonated

pH above pKa = group tends to become deprotonated

pH = pKA = equal amounts of protonated and deprotonated forms

pKa = tells you how strong an acid is and how easily it gives away a proton

Define buffer (what does it do)? When are they most effective?

Resist changes in the pH of a solution, regulate pH

• Most effective at pH near its pKa

What is the Henderson-Hasselbalch Equation?

Weak As are most effective as buffers at pH near pKa value of its acid component

• the buffer has its maximum capacity to resist changes in pH because the concentrations of the weak acid and its conjugate base are equal (or nearly equal) in the solution

Why is phosphoric acid an important buffer in biological systems?

pH typically near 7.4

Inorganic phosphate exists as a nearly equal mixture of H2PO4- and H2PO4 2-

Define polymers

Large molecules built from repeating smaller units (monomers)

Define proteins

Linear polymers composed of monomers (amino acods)

What are characteristics of proteins

1. Contain wide range of functional groups → reactive properties are essential to function of the protein (PROPERTIES INFLUENCE HOW THE PROTEIN BEHAVES)

2. Can interact with one another and other macromolecules to form complex assemblies

3. Can be rigid (underlying tissue) or flexible (enzymes, to change shape) [depends on structure]

4. Responsible for physical structures within cells as well as catalysts for rxns

What does amino acid composition dictate?

Amino acid composition → protein structure → protein function

Proteins are built from 20 amino acids, what is the structure of a amino acid? What are the two resulting isomers?

Chiral protein:

• Amino group, CA group, H atom, specific R (amino) group

L Isomer & D isomer

• Living organisms use L-amino acids almost exclusively to build proteins and peptides

7/20 AAs have readily ionizable side chains

Dont have to memorize

What is a peptide bond? What does a peptide bond formation involve?

Peptide bond = a type of covalent chemical linkage where a carbonyl carbon (C=O) binds directly to a nitrogen atom (N)

Involves:

• Linking of alpha-carboxyl group (COO-) of one amino acid to the alpha-amino group (R) of another AA through acyl linkage

  • Loss of water molecule (reacting AAs lose H and OH as they form peptide bond)

Define residue, how many are present in polypeptide chains

Single amino acid unit in a polypeptide

• 50 - 2000 AAs residues

How do you read polypeptide chains?

Read from the N terminus (amino group) to the C terminus (Carboxyl group)

• Polypeptide chain: string of amino acids linked together

Define oligopeptides

Polypeptide chains made of small number of amino acids (short chain)

Define lipids and its characteristics (in terms of solubility)

Water-insoluble biomolecules, highly soluble in organic solvents (most lipids come from fatty acids)

• Hydrophobic due to fatty acids

Define fatty acids and its characteristics

Long hydrocarbon chains that terminate with CA groups

• Vary in length and degree of saturation (= affect physical properties)

• Hydrocarbon chain = largely hydrophobic

• CA group: ionizable (can act as an acid and shed a hydrogen ion into the surrounding liquid) → leads to be shown in COO- form

How do unsaturated and saturated fatty acids differ?

Unsaturated: double bond

Saturated: no double bond

How to name fatty acids?

Based on their parent hydrocarbons

1. First # = carbons

2. Second # = double bonds

   1. 18:1 = 18-C chain, 1 double bond

What are the two different ways of naming a fatty acid cuain

1. Carbons can be numbered starting at carboxyl (COO-) terminal carbon atom

   1. Position of double bond represented by Δ following subscript number

2. Start at last methyl carbon atom (omega (w) carbon)

   1. Position of double bond represented by counting from end

Characteristics of fatty acids in biological systems

1. Even # of C atoms (16/18 most common)

2. Animal fatty acid usually have unbranched chains

3. Unsaturated fatty acids generally have cis double bonds

How does chain length and saturation of fatty acids impact fluidity?

Shorter chain + More unsaturated = More fluid

• Because more double bonds creates more bends → poorer packing → greater fluidity

Longer chain + More saturated = Less fluid

What are the functions of lipids

1. Fuel molecules → more ATP

2. Highly concentrated E stores → stores fat

3. Signal molecules and messengers in signal-transduction pathways → signals body, tells how to respond

4. Essential component of biological membrane

What are the 3 principal lipids (in eukaryotic membranes)

1. Phospholipids

2. Glycolipids

3. Cholesterol

Characteristics of membranes

1. Sheetlike structures, 2 molecules thick, form closed boundaries

2. Contains many lipids and proteins w/ linked carbohydrates

3. Lipids that form lipid bilayers

4. Proteins embedded in lipid bilayers with distinct functions

5. Asymmetric

6. Fluid structures → must STAY IN MOTION

7. Tend to be electrically polarized → # charges on either side of membrane is different

What are phospholipids made of? Draw the structure

1+ fatty acids, platform (glycerol, Sphingosine) which fatty acids are attached, phosphate, OH attached to phosphate

Define phosphoglyceride

phospholipids derived from glycerol (glycerol as backbone)

• Phosphatidate is the simplest phosphoglyceride

Where are the 3 C position on phosphatidate (3C backbone)

1. OH group on C1

2. C2 attach to FA through ester linkages

3. C3 carries phosphate groups

Phosphoglycerides have a 3C glycerol backbone and are also derived from phosphatidate. What is the structure of a phosphoglycerides?

The presence of alcohol in a phosphoglyceride is important why?

Dif alcohol groups produce different phosphoglycerides

Define sphingosine

An amino alcohol that contains a long, unsaturated hydrocarbon chain

Define sphingomyelin

Common membrane phospholipid with sphingosine backbone

Define cholesterol

Component of membrane, steroid built from 4 linked hydrocarbon rings

Characteristics of cholesterol (w phospholipid bilayer)

1. Contains linked hydrocarbon tail at one end and an -OH group at the other end

2. Orientated parallel to FA chains of phospholipids in membranes (→ fits into membrane bc interaction near hydrophilic region, most of molecule sits in hydrophobic interior)

3. OH group interacts with phospholipid head group

   1. Cholesterol fits between phospholipids and helps control membrane fluidity, stability, and permeability

Define amphipathic

One molecule contains both hydrophilic and hydrophobic region

• → so membrane lipids = AMPHIPATHIC MOLECULES

Define moiety

Part or portion

Which part of the membrane lipid is hydrophobic moiety, hydrophilic moiety?

Hydrophobic moiety: fatty acid tails

Hydrophilic moiety: phosphorycholine (phosphate-containing head)

Define micelle

globular structure with the polar head groups on the outside surface and hydrocarbon tails sequestered inside

• Membrane formation is a consequence of the amphipathic nature of the molecules

How are micelles formed?

Formed by many single taniled FA molecules

Describe the lipid bilayer

1. Hydrophobic tails of each sheet interact → forms permeability barrier

2. Hydrophilic head group interact with aqueous medium

Lipid bilayer formation is spontaneous (meaning the arrangement is energetically favorable), how is it stablized?

1. Hydrophobic interactions

2. VDW interactions b/w hydrocarbon tails

3. Electrostatic + H-bonding interactions b/w polar ends and water

What are consequences of hydrophobic interactions between lipid bilayers?

Tend to close on themselves so that there are no edges with exposed hydrocarbon chains

→ forms compartments where organelles are stored

Why are exposed hydrophobic tails bad?

Unfavorable → bilayer self-seals and repairs gaps

What type of molecules have high vs. low permeability?

LOW PERMEABILITY

1. Ions

2. Polar molecules (because they interact well with water)

   1. But water is an exception → has low MW, high [], lack of charge so it crosses better than expected

• Charged / strongly polar (unequal e- sharing) → lower permeability

HIGH PERMEABILITY

1. Hydrophobic

2. Non polar molecules (equal e- share)

Define membrane proteins

Allow transport of molecules and information across a membrane, can open and close channels

• Vary in protein content (<20% - 75%)

What do membrane proteins in a cell reflect?

Reflection of biochem occurring inside cell

Define integral membrane proteins, where are they bound?

Interact with hydrophobic hydrocarbon region of membrane

• Most completely span bilayer

What happens to integral membrane proteins when a chemical that interacts with the hydrophobic region competes?

Held in membrane partly bc their NP regions interact with NP fatty acid → when chemical that also interacts with hydrophobic region competes w/ tail for interaction w/ protein THEY GET RELEASED

Define peripheral membrane proteins, where are they bound?

Loosely bound to membranes primarily by electrostatic and H-bonding interactions with head groups of lipids

• Often bound to surface of INTEGRAL proteins

What happens with tiny changes (pH, pKa, etc.) to peripheral membrane proteins?

Fall off membranes

What would these two proteins look like on the bilayer

Define lateral diffusion

process by which lipids and many membrane proteins are constantly in lateral motion

Are membranes rigid? Define membranes

NO! They are organized, fluid structures

→ lipids + many membrane proteins diffuse rapidly in plane of the membrane

What is the purpose of FRAP and how is it done?

FRAP demonstrates that the membrane is fluid-like amd moves laterally

Membrane glowing everywhere → one area gets bleached → if membrane components move laterally, unbleached fluorescent molecules from surrounding area move into dark area

What does the rate of recovery for FRAP depend on?

Depends on lateral mobility and temp of labeled component

→ Process resulting in an increase in fluorescence intensity in the area previously bleached, recovery occurs if component is mobile

Define fluid mosaic model

Describes biological membrane organization as two dimensional solutions of oriented lipids and globular proteins

What are characteristics of the lipid bilayer (in terms of movement and permeability)

1. Solvent and permeability barrier

2. Lipids rapidly diffuse laterally in membranes

3. Transverse diffusion (flip-flopping) = very slow and unlikely to happen

What is the difference between lateral diffusion and transverse diffusion

Lateral diffusion: moves laterally, rapid

Transverse diffusion: flip flops, slow, preserves membrane asymmetry

What do many membrane processes depend on?

Fluidity of the membrane

What does fluidity of the membrane depend on?

1. Properties of fatty acid chains

2. Temperature

   1. Below transition T = more rigid

   2. Above transition T = more fluid

How does saturation impact the melting temperature of a fluid membrane?

Saturated fatty acid (no double bond) → interact favorably with one another

• Favors rigid state, tighter packing → stronger interactions

• → HIGHER MELTING TEMP

Unsaturated fatty acid (double bond produces bend in hydrocarbon)

• Interferes with highly ordered packing of fatty acid chains

• → LOWER MELTING TEMP