BIOL1502: Macromolecules, Organelles, Plasma membrane, Metabolism, Cell Communication

for first midterm

Organic Molecules

molecules based on carbon

4 major classes of organic molecules

lipids, nucleic acids, proteins, carbohydrates

hydrocarbons

moelcules consisting of carbons only linked to hydrogen

functional groups

small reactive groups of atoms that give the molecule its specific properties, participating in biological reactions, linked by covalent bonds to other atoms in the molecule

examples of functional groups

amino (-NH2), phosphate (-OPO3²-), hydroxyl (-OH), carbonyl (>C=O), carboxyl(-COOH)

isomers

2+ molecules w/ same chemical formula that have different structures

stereoisomers

molecules that are mirror images of each other

asymmetric carbon

1+ carbon atom linking to 4 different atoms/functional groups

L+D isomers

one form typically enters into cellular reactions more readily, as enzymes best fit one

structural isomers

2 molecules w/ same chemical formula but atoms are connected differently

polymer

a molecule assemble from subunit molecules (monomers) into a chain by covalen bondsp

polymerization

dehydration synthesis reaction that form polymers

hydrolysis

where water molecules break down chemical compounds into smaller molecules by adding a hydrogen ion H+ and a hydroxyl group OH-

dehydration synthesis

a chemical reaction that involves the loss of an H₂O from the reacting molecule or ion

monomer

a molecule that can react together with other ______ molecules to form a larger polymer chain

energy providing carbs

starch (plants) glycogen (animals)

carbohydrate monomer

monosaccharides (3-7 carbon atoms)

disaccharide

2 monosaccharides - linked by dehydration synthesis

glycosidic bonds/linkage

bonds between 1’ and 4’ carbon w/ oxygen as a bridge

carbohydrate polymers

polysaccharides: can be a continuous chain, can be branched, can be bonded in different configurations (many different polysaccharide types)

trioses

3 carbons

5 carbons

pentoses

6 carbons

hexoses

monosaccharide form

can occur in the linear or ring form

linear: each carbon in the chain (except 1) will have an -H and -OH attached

ring form: possible with monosaccharides with 4+ carbons, occurs through a reaction between 2 functional groups in the same monosaccharide

• favored for stability, allows for switching betwen alpha and beta configuration

• ring form occurs with attraction between hydroxyl and carboxyl in linear form, twists around

alpha configuration for monosaccharides

-OH group is pointing below the plane of ring, assembled into starches —> biologically reactive polysaccharides easily digested by animals

beta configuration in monosaccharides

-OH group is pointing above the plane of the ring, makes up cellulose, relatively unreaction and indigestible to animals

Lipids

water insoluble, primarily non-polar, composed mainly out of hydrocarbons, can be stored in cells as an energy source

Neutral lipids

found in cells as energy storage molecules (meaning insoluble, non-polar with no charged groups)

oils and fats

oils are liquid when fats are semisolid at biological temperatures

triglyceride

glycerol + 3 fatty acids (glycerol backbone)

synthesized by carboxyl of fatty acid + 1 hydroxyl group of glycerol

amphipathic

molecule having both hydrophobic and hydrophillic parts

glycerol

3 carbon alcohol w/ an -OH attached to each carbon, would be a polar sweet-tasting water soluble molecule

fatty acid

contains a singles hydrocarbon chain with -COOH (carboxyl) at the end

ester linkage

covalent bond between carboxyl (COOH) + hydroxyl (-OH) in lipids, essential for energy storage

• formed by dehydration synthesis

saturated fat

hydrocarbon chain of fatty acid bonds to max # of hydrogen atoms (only single bonds link to carbon atoms)

• ethane

• can compact closely together at room temperature

unsaturated fat

1+ double bonds link the carbons (reducing # of hydrogen atoms bonded) —> will have a kink in the chain, cis double bond, will be more liquidy at room temperature

• ethylene

monounsaturated fat

1 double bond linking the carbons

polyunsaturated fat

1+ double bond linking the carbons (can’t pack as tightly at room temp)

phospholipids

glycerol + 2 fatty acids, 3rd binding site to a polar phosphate group instead of a 3rd fatty acid (bonded to another polar unit)

• fatty acid side is non-polar (hydrophobic)

  • phosphate end is polar (hydrophillic)

steroids

group of lipids w/ structures based on 4 carbon rings

sterols

most abundant steroids, single-OH (polar at one end of a framework, non-polar hydrocarbon cain on the other end (ex. cholesterol)

• in the phospholipid bilayer will fit in between phospholipids (another example of why it is so important that the tails are unsaturated —> tails are fluid and won’t pack together

Protein

macromolecule made out of amino acids

ex: enzymes, antibodies (protection against diseases), transport of substances, hormonal proteins, movement, cellular communication through signaling proteins and receptors, regulation of cell processes

protein monomer

amino acids, charged amino acids can form ionic bonds

peptide bond

formed by dehydration synthesis reaction between amino group of one amino acids + carboxyl group of a second one (protein covalent bonds)

n-terminal end of amino acid

ends of acid w/ NH3+

c-terminal end of amino acid

end of acid with COO-

primary structure protein

sequence in which amino acids are linked

secondary structure of a protein

regions of an alpha helix and beta sheets in a polypeptide sheets formed between hydrogen bonding interactions (alpha helix are rigid coils, beta sheet zigzags on a flat plane)

tertiary structure of a protein

overall 3D folding of a polypeptide chain —> attraction between ± and polar/non-polar side groups

• stablized through hydrophobi interactions, van der waals interactions, ionic bonds, hydrogen bonds, and disulfide bridges

quaternary structure of a protein (optional)

arrangement of a polypetide chains in a protein that contains more than one chain in order to be functional

• ex hemoglobin, sickle-cell disease: beta subunit of quaternary structure is messed up

conformational change

the alteration of a protein’s or macromolecule's three-dimensional shape, often involving shifts in its tertiary or quaternary structure

protein denaturation

the structural modification, or unfolding, of a ____ 3D shape (2nd, 3rd, 4th) while the primary amino acid chain remains intact (temperature, pH changes0

protein renaturation

the process by which a denatured ___ refolds into its functional, native 3D structure, regaining biological activity

Nucleotide

(monomer of nucleic acids) consist of a nitrogenous base, a 5-carbon sugar, and 1+ phosphate groups (typically 1-3)

nitrogenous base

nitrogen-containing molecule that accepts protons

pyrimidines

uracil (U), thymine (T), cytosine (C)

purines

adenine (A), guanine (G)

nucleoside

contains only a nitrogenous based and sugar

deoxyribose sugar

a 5-carbon sugar with a -H at the 2’ carbon

ribose sugar

a 5-carbon sugar with a -OH at the 2’ carbon (what nitrogenous bases will covalently link to)

phosphodiester bond

strong covalent linkages between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another in nucleic acids forming the structural backbone of them, connected by a phosphate group

DNA bases (and pairs)

A-T, G-C

RNA bases (and pairs)

A-U, G-C

Thymine vs. Uracil

different only by functional group, thymine uses methyl, and uracil uses -H

DNA double helix structure

a twisted-ladder structure composed of two antiparallel polynucleotide strands

2nd Law of Themodynamics

from intiial —> final state, the disorder of a system (cell) and its surroundings increases

entropy

a fundamental scientific concept measuring the unavailability of a system's energy to do useful work

• measure of molecular disorder (releasing energy into surroundings even when moving towards organization —> takes a lot of energy to overcome disorder)

spontaneous reactions

a chemical/physical reaction that occurs without the input of energy, delta G will be negative, reactants have higher energy that products do

free energy

portion of a system’s energy that is available to do work

equation for free energy

delta G - delta H -TdeltaS

• delta g: free energy

• delta h: change in enthalpy

• delta s: change in entropy

exergonic reactions

releases free energy (delta g is negative)

endergonic reactions

products contain more energy than reactants (delta g is positive)

metabolic pathway types

catabolic and anabolic pathways

catabolic pathway

energy is released by breakdown of complex molecules (overall delta G is negative- —> individual reactions can have negative or positive delta G)

• breaking down polymers

anabolic pathway

energy used to build complex molecules from smaller ones (overall delta G is positive —> individual reactions can have negative or positive delta G)

• can also be called a biosynthetic reaction, building up polymers

ATP hydrolysis

ATP+H2O→ADP+Pi+free energy, delta G = -7.3 kcal/mol, this Pi can couple reactions

energy coupling

(cell usually breaks things down into smaller processes) using an exergonic reaction (ex. ATP hydrolysis) to drive an endergonic one

• ex. ATP is hydrolysed and phosphate group is transferred to the reactant molecule of an endergonic reaction —> typically the only way that an endergonic/energetically unfavorable reaction can occur (exergonic reaction has to be of a high enough magnitude so the total delta G is negative)

phosphorylation

addition of a phosphate group to a molecule, makes molecules less stable

ATP synthesis

an endergonic reaction, that requires energy from glutamine synthesis

• glutamic acid gets phosphorylated (is unstable), ammonia replaces the Pi to produce glutamine

• can happen in the opposite direction as well, formation of glutamic acid catalyzed by ATP hydrolysis

ATP Hydrolysis + Sodium-Potassium pump

(endergonic reactions) The sodium-potassium pump is an essential transmembrane enzyme that uses energy from ATP hydrolysis to actively move 3 Na+ ions out of the cell and 2 K+ ions in

catalysis

the acceleration of a chemical reaction rate by adding a substance, known as a catalyst, which is not consumed in the process

• at high concentrations of substrate (excess) the rate of catalysis is proportional to the amount of enzyme, rate of reaction is limited by enzyme

saturation

when enzymes are already cycling as quickly as possible —> additional substrate won’t affect reaction rate

purpose of enzyme

• meant to lower activation energy,

• catalyzing a reaction,

• does not get used up over the course of reaction

activation energy

barrier in the movement of reaction progression

plasma membrane

what all cells are bounded by, phospholipid bilayer w/embedded protein molecules

• some water-soluble substances can penetrate the membrane through transport proteins

Role: enclose the organelles, provide cellular structure (being defined by extracellular matrix), receive and transfer signals from the extracellular environment to intracellular pathways, barrier between outside and inside of the cell, regulates which molecules enter and exit the cell

Genes

DNA sections that code for individual proteins

cytoplasm

all parts of the cell between the plasma membrane and central DNA-containing region

organelles

found in cytoplasm - specialized, membrane-bound structures within eukaryotic cells that perform essential, organ-like functions

cytosol

aqueous solution containing ions and various organic molecules

cytoskeleton

protein-based framework of filamentous structures that maintain cell shape + mitosis

• interacts with motor proteins to produce cell motility, other organelles use motor protein “feet” to move around, top can attach to a vesicle and move w/ ATP

prokaryotes

(ex. bacteria + archaea) unicellular organisms

• some bacteria have 2 cell membranes

nucleoid

DNA-containing region in prokaryotes (has no boundary separating it from the cytoplasm) —> no internal memberane

eukaryotes

(eukarya) multicellular organisms

Cell wall

(plant cells, prokaryotes): surrounds plasma membrane, rigid external layer of material

• helps protect cell from physical damage

• in many prokaryotic cells, cell wall is coated with an external layer of polysaccharides called glycocalyx —> slime layer forms when glycocalyx is loosely associated with the cells, forms a capsule when the glycocalyx is gelatinous and attached more firmly to cells

flagella/bacterial flagellum

• threadlike fibers which extend from cell surface,

• helically shaped rotates in a socket to push the cell through a liquid medium

pili

hairlike shafts of protein attaching the cell to surfaces of other cells

nuclear envelope

consists of 2 lipid bilayer membranes, one just outside the other and separated by a narrow space

• nuclear pore complex: large octagonally shaped symmetric complex in the cell, formed of many types of proteins called nucleoporins

• nuclear pore: a channel through nuclear pore complex is the path for assisted exchange moleucles (proteins, RNA)

exocytosis

a form of active, bulk transport where cells export materials—such as neurotransmitters, hormones, and waste—by fusing intracellular vesicles with the plasma membrane

endocytosis

an active transport mechanism where cells internalize external materials—fluids, nutrients, or pathogens—by engulfing them within a plasma membrane-derived vesicle

peroxisomes

small, single-membrane-bound, metabolic organelles found in almost all eukaryotic cells, crucial for breaking down fatty acids and neutralizing toxic materials.