BIOS 1107 Module 2: Macromolecules and Metabolism

non polar covalent bonds

equal sharing of electrons in a bond

hydrophilic

molecules with polar groups that interact with water molecules

the rest of us heterotrophs depend on the

organic carbon molecules made by primary producers

all living organisms are made of

organic molecules (large molecules that are constructed from simple organic compounds)

organic molecules must have

carbon and hydrogen but may also include oxygen, nitrogen, phosphorus, or sulfur

organic molecules have must have at least one

covalent bond between C and H or between C and C

inorganic forms of carbon have carbon only bonded to

oxygen

organic molecules can arise naturally from abiotic synthesis, but in the biosphere most organic molecules are

synthesized by living organisms

synthesis of organic carbon molecules from inorganic CO2 requires

energy and chemical reducing power as the carbon atoms in organic molecules are in reduced form

elements react with each other to form molecules held together by

chemical bonds

valence electrons determine

the kinds of reactions and bonds that an element will form

what are the organic molecules that most biomolecules are made up of

C,H,O,N,P,S

polar covalent bonds

unequal sharing of electrons

what is the key element of life

carbon

hydrogen bond

weak electrostatic attraction involving a hydrogen atom with a weak positive charge and an electronegative atom with a weak negative charge; water molecules have a partial negative charge around the oxygen nucleus and partial positives around the hydrogens

ionic bond

electrostatic attraction between ions of opposite charge

hydrophobic

molecules with only non polar bonds that are insoluble in water

what is the distinction between organic carbon and inorganic carbon?

organic carbon is reduced and inorganic carbon is oxidized

what is the purpose of life in the basis of this module?

hydrogenate carbon which is to say that life depends on reduced forms of carbon

autotrophs (photosynthetic and chemosynthetic organisms) can

reduce inorganic carbon to organic carbon

what are the four types of macromolecules

polysaccharides, nucleic acids, and proteins

dehydration reactions

chemical reactions that involve the loss of water from the reacting molecule; linking two subunits together via a covalent bond that extracts an -OH and a H to create a molecule of water; removal of a molecule of water from the starting molecules in the process of forming a covalent bond between the molecules

hydrolysis reactions

a molecule of water is split to -OH and H used to break the bond linking two subunits; the exact reverse of a dehydration reaction

lipids

water soluble organic molecules; lipids in water can spontaneously aggregate via hydrophobic interactions to form lipid bilayer membranes

how to determine if an organic molecule will be hydrophilic or hydrophobic

high number of polar bonds=hydrophilic

high number of non polar bonds=hydrophobic

Polysaccharides

Carbohydrates that are made up of more than two monosaccharides via glycosdic bonds (starch, celluslose, and chitin)

nucleic acids

polymers made by joining nucleotides (DNA and RNA)

polypeptides (protiens)

polymers of amino acids joined together by peptide bonds (peptide backbone of the polypeptide chain)

living organisms contain lipid bilayer membranes made of

phospholipids that spontaneously self-assemble in water to form bilayer membranes via hydrophobic interactions; boundaries are created that separates the internal aqueous environment from the outside of the cell

what are the purpose of membranes

create and maintain large differences in ion concentrations that drive cellular energy metabolism, to regulate transport of materials and water into and out of the cell, and to receive and sense extracellular signals

primary elemental compositions of lipids

C,H

primary elemental compositions of carbohydrates

C,H,O

primary elemental compositions of proteins

C,H,O,N,S

primary elemental compositions of nucleic acids

C,H,O,N,P

major functions of lipids

membranes, energy storage, and signaling

major functions of carbohydrates

energy storage, static, structures cell, adhesion

major functions of proteins

enzymes, dynamic structures, signaling

major functions of nucleic acids

hereditary information, storage and processing

the function of a protein is determined by

its structure

primary structure

linear sequence of amino acids held together by covalent peptide bonds

secondary structure

either alpha helices and beta sheets; stablized by hydrogen bonds between peptide amino groups and carboxyl groups of amino acids within the same polypeptide chain, but not immediately next to each other

tertiary structure

overall 3-D shape of the folded polypeptide chain, that can be described as the spatial relationships of the secondary structure elements linked by loops. Stabilized by various types of amino acid side chain (R-group) interactions

quaternary structure

assemblage of two or more folded polypeptides into a functional protein unit. Stabilized by inter-chain hydrophobic and van der Waals interactions, hydrogen bonds, ionic bonds, and covalent disulfide bonds between cysteine residues on different polypeptide chains

the cell membrane is composed of a ______________ ________ with the hydrophilic head groups facing the aqueous environment on either side and the hydrophobic tails in the middle

phospholipid bilayer

besides the phospholipid bilayer, what else is included in the cell membrane

integral proteins and carbohydrates

lipids and integral membrane proteins diffuse laterally within the plane of the membrane hence the

term fluid mosaic model (however the proteins do not spontaneously cross the lipid bilayer because of the hydrophobic inner core)

all cells have what kind of lipids in their membranes

phospholipids

what are the phospholipids in bacteria and eukarya

composed of fatty acid chains that are ester linked to D-glycerol

what are the phospholipids in archaea

composed of branched isoprene chains instead of fatty acids that are ether linked to L-glycerol (make them more resistant to heat and pH extremes)

eukaryotes also have membrane lipids that are not found in archaea or bacteria called

sterols and sphingolipids

sterols

cholesterol that reduce membrane fluidity and permeability and increase membrane rigidty and strength

what is a key to the evolution of eukaryotes

the evolution of steroid biosynthesis

bacteria have their own special membrane adaptations in the form of

hopanoids (bacterial equivalent of membrane sterols)

what does the fluidity of the lipid bilayer depend on

temperature

at higher temperatures, the lipid bilayers become

more fluid

at lower temperatures, the lipid bilayers become

more rigid

for cell membranes to function properly, they must maintain a

balance between fluidity to allow movement of proteins and lipids within the membrane without compromising membrane integrity and allowing substance to leak into or out of the cell

________ ______ tails of phospholipids also affect membrane fluidity

fatty acid

saturated fatty acids

no double bonds in the hydrocarbon chain with a maximum number of hydrogens

unsaturated fatty acids

have one or more double bonds and have fewer hydrogens

how do saturated fatty acids affect the membrane

makes membranes more rigid and stronger and less fluid (trans-unsaturated does the same)

how do unsaturated fatty acids affect the membrane

makes the membrane more fluid because it disrupts the close packing of the lipids (cis-unsaturated does the same)

the lipid bilayer is _____-________

semi-permiable

Semi-permeable

membranes that allow some substances through but not others (in general, small uncharged molecules can diffuse across freely, while charged or polar molecules cannot)

osmosis

the diffusion of solvent molecules across a membrane

what does diffusion result in

the net movement of molecules down their concentration gradient, from an area of high concentration to low concentration

in the case of osmosis, water molecules move from the side with low solute concentration to

the side with higher solute concentration

if there is a difference in solute concentrations across the membrane, then solute molecules

will try to diffuse across the membrane to equalize solute concentrations; if the membrane is impermeable to the solute molecules, then water will move to try and equalize the solute concentrations

isotonic environment

The concentration of a solution is the same inside and outside the cell so there is no net movement of water across the cell membrane

hypotonic solution

solute concentration outside of the cell is lower than inside the cell so water will enter the cell to try to reduce the internal solute concentration

hypertonic solution

the solute concentration outside is higher than inside the cell so water will exit the cell and the cell will shrivel up

cells transport molecules across the membrane by

dedicated transport proteins with transmembrane domains

aquaporins

water channel proteins

faciliated diffusion (passive transport)

movement of molecules through protein channels (highly specific to the molecule and result in transport down a concentration gradient)

active transport

movement of molecules against the concentration gradient; Energy-requiring process that moves material across a cell membrane against a concentration difference

simple diffusion

Diffusion that doesn't involve a direct input of energy or assistance by carrier proteins

as the concentration difference across the membrane becomes greater,

the rate of molecules diffusing across the membrane increases for both facilitated and simple (but facilitated will reach a limit where it cannot go any faster)

the first cells arose about 3.5 billion years ago most likely resembled

bacteria or archaea

we infer that LUCA had a

simple cell structure, with cytoplasm bounded by some type of phospholipid bilayer membrane and no nuclei or internal membrane compartments or organelles

bacteria and archaea are classified as

prokaryotes

common structural features of bacteria and archaea

single circular chromosome (a few species have two), a nucleoid region that contains the chromosomal DNA with no surrounding membrane to separate it from the cytoplasm, and small circular DNA molecules called plasmids in the cytoplasm

the first eukaryotic cells appear soon after the

great oxygenation event; the current hypothesis for their evolution was that they evolved from an ancient endosymbiosis or cell fusion event between an archaeon and bacterium

endocytosis

process by which a cell takes material into the cell by infolding of the cell membrane by forming a small vesicle

modern prokaryotes lack

endocytosis or phagocytosis which is essential for taking in and harboring endosymbionts within a membrane enclosure

what can account for the formation of the nucleus enclosed by a nuclear envelope, the endomembrane system and the evolution of mitochondria and chloroplasts from endosymbiosis of aerobic bacteria and cyanobacteria

phagocytosis/endocytosis

cytoplasm

internal region of the cell bounded by the plasma membrane excluding the interior of the nucleus and the interior regions of organelles and the endomembrane system; contains ribosomes, tRNA, mRNA, cytoskeleton, metabolic enzymes, and proteins

what is included in the endomembrane system

Nuclear envelope

Endoplasmic Reticulum

Golgi apparatus

Lysosomes

Vacuoles

Cell membrane

Vesicles that transport materials

endosomes

plasma membranes

what are made in the rough ER by ribosomes docked to the protein channels in the ER membrane

membrane proteins and proteins for secretion

how are the proteins made in the endomembrane system

they are made by proteins docked in the rough ER and pass through the ER lumen; then are moved to the smooth ER where they are partially glycosylated , transport vesicles containing membrane proteins and secreted proteins travel to the golgi,

what is the order of protein synthesis in the endomembrane system

rough ER -> smooth ER -> transport vesicles -> Golgi -> secretory vesicles -> PM

cytoskeleton

It consists of actin microfilaments, several types of intermediate filaments, and microtubules. These are dynamic structures required for cell shape, cell mobility, and organization and movement of materials inside the cell

microfilaments

dynamic structures that are required for cell shape, cell mobility, and organization and movement of materials inside of the cell

mictrotubules

serve as tracks for movement of transport vesicles and secretory vesicles by motor proteins

nucleus

contains the cell's chromosomes. All chromosomal DNA replication and transcription to make RNA occurs in the nucleus, as well as RNA processing; enzymes that perform these tasks, the proteins that bind to DNA to form chromatin, indeed all proteins in the nucleus, are made by ribosomes in the cytoplasm, and then imported into the nucleus through the nuclear envelope pore complexes

first law of thermodynamics

Energy cannot be created or destroyed

second law of thermodynamics

Every energy transfer or transformation increases the entropy of the universe.

by assembling small molecules into polymers and higher order structures, this work releases waste heat that

increases the entropy of the environment

gibbs free energy

the measure of the amount of work that is potentially obtainable; deltaG=deltaH - TdeltaS

enthalphy (ΔH)

change in energy in the form of heat

entropy

a measure of the disorder of a system