Bio 43 Unit 1

Radicals

Highly reactive atoms or molecules with unpaired outer-shell electrons

Reactive Oxygen Species (ROS)

Oxygen radicals that are produces as a byproduct of metabolism

Antioxidants

dietary molecules that neutralize oxygen radicals

Ionic Interactions

Weaker, dissolvable, more transient interactions between ions in water

Strong Polar Bonds

N-H, C=O, O-H

Weak Polar Bonds

C-N, N-O, C-O

Non-Polar

C-H

H-Bond acceptor

an electronegative atom/group with a lone pair

Covalent Bonds (in regard to how they compare to H-Bonds)

• Bond via shared electrons

• Bonding only occurs within the same molecule

• Hard to break

• Changes molecule identity when broken

H-Bonds (in regard to how they compare to Covalent Bonds)

• attraction results from opposite polar charges

• Bonding can occur within or between molecules

• Doesn’t change molecule identity when broken

• Easy to break

Amphipathic

Made possible due to the polarity of water

cell membranes are formed this way due to their polar

and non-polar ends

pKa

the pH at which the molecule/group is half protonated and half deprotonated

Amine Group

Any functional group where nitrogen is bonded to hydrogens or carbons

Can be an H-bond acceptor or donor

Carboxylic Acid Groups

A functional group made up of C=O and -OH, which forms -COOH

Provide most negative charges found in proteins

Phosphate group

P-atom bonded to four oxygens

used as a marker for signaling through kinases

Hydroxyl group

an oxygen bonded to a hydrogen

very polar

Can act as H-bond donor and acceptors

Chemical energy

Potential energy in the form of high-energy molecules or unstable bonds

Heat/Temperature

Kinetic energy in the form of molecular movement/vibration

First Law of Thermodynamics: Conservation of Energy

Energy may change location or form, but it cannot be created or destroyed

Corollary of the First law of Thermodynamics

In the absence of external influences, atoms, molecules, etc. will always move towards lower-energy states

Second Law of Thermodynamics

The entropy of the universe must always increase

Maintaining the entropy of a system requires a constant input of energy

Amino Acids

The monomers of proteins

Made up of a protonated amine group + deprotonated carboxylic acid group + variable side chain

The hydrophobic effect

-the segregation of water from nonpolar materials caused by the aggregation of these non-polar substances in aqueous materials

-maximizes entropy of the water molecules and minimizes the area of contact between water and non-polar materials

London dispersion forces

Temporary, weak bonds between electrons based on their random movement which creates temporary charge balances known as dipoles

Are non-polar bonds are…

hydrophobic

Polar bonds are…

Hydrophillic

H-Bond donor

A group that provides the partially positive hydrogen atom

H-bond acceptor

Will always be an electronegative atom with a lone pair

AA Side Chains: Negative Polar

Acidic; lose their protons at neutral pH

AA Side Chains: Positive Polar

Basic; binds protons at neutral pH

Salt Bridge

Interactions formed between oppositely charged side chains in a protein

Peptide Bond

• Covalent chemical bond

• Formed when the carboxyl group of one amino acid is linked with the amine group of another

• Carboxyl group donates OH> amine group donates H> water molecule is created and leaves reaction> peptide bond is formed

Primary Protein Structure

Linear order of amino acids from the N-terminus (NH2) to the C-terminus (COOH) bound by peptide bonds

• sequence determined by genes

Secondary Protein Structure

-formed by the local folding of the polypeptide

-H-bonds between atoms within the polypeptide backbone form either an alpha helix or a beta sheet

Tertiary Protein Structure

The final three-dimensional shape of the polypeptide after it undergoes folding

Forces involved in tertiary structure

H-bonds, Ionic interactions the hydrophobic effect, disulfide bridges

Quartenary Structure

Multiple folded protein come together to form a larger complex

Disulfide Bond

A strong covalent bond between sulfur atoms

contribute to both tertiary and quaternary structures

Enthalpy

H, the total energy of a system

Free Energy Gibbs

G, the amount of available energy that can do work

Entropy

S, A measure of the randomness/disorder of molecules

Passive Transport

the movement of materials in/out of the cell down the concentration gradient without using energy in the form of ATP; includes simple and facilitated diffusion

Simple Diffusion

A type of passive transport where materials flow in and out through the phospholipid bilayer down the concentration gradient

Facilitated Diffusion

A type of passive transport that sends molecules through the plasma membrane through the use of membrane transport proteins

Active transport

membrane transport proteins use energy to move their substances against the concentration gradient

Diffusion

the entropy-driven net movement of particles from areas of higher concentration to areas of lower concentration

isotonic

when the concentration of solutes on both sides of the plasma membrane are equal

hypertonic

when the concentration of solutes outside the cell is higher than inside the cell

hypotonic

When the concentration of solutes outside the cell is lower than inside the cell

Osmosis

The process of water moving down its gradient, across a membrane from a hypertonic compartment to a hypotonic compartment

Primary Active Transport

Uses a pump transporter; this pump uses energy to transport solutes against its concentration gradient

Eukaryotic Cells

• Protists, Fungi, Plants, Animals

• Large

• Many linear chromosomes

Prokaryotic Cells

• include bacteria/archaea

• Smaller

• Nearly all have protective cell walls

• 1 circular chromosome

Nucleotide

Made up of phosphate group, pentose sugar, and base

DNA Bases

Adenine, Guanine, cytosine, thymine

Purine bases

Adenine and Guanine: Have a fused double ring of carbon and nitrogen atoms

Pyrimidine Bases

Cytosine, Thymine, Uracil: Have a single ring structure

Pentose Sugar: Carbon #5

Phosphate

Pentose Sugar: Carbon #3

Hydroxyl group

Pentose Sugar: Carbon #2

Hydrogen

Pentose Sugar: Carbon #1

Base

When in doubt with a nucleotide, the one that’s sticking out is number…

Five

Triglycerides

-When glycerol bonds to three fatty acids

-Bond occurs after a dehydration reaction forms an ester than bonds glycerol to a carboxyl group of a fatty acid

-completely non-polar

Fatty Acid

-a chain of non-polar carbon and hydrogen atoms with a polar carboxylic acid group at one end

-amphipathic

Phospholipids

Third hydroxyl group of the glycerol is bonded to phosphate

Saturated Fats

-All the carbons in a fatty acid are linked through single covalent bonds between hydrogens

-the maximal number of hydrogens able to bond to the carbon has been reached

Unsaturated fats

Contain one or more double bond between carbons

Cytosol

Inside of the cell

Chromosome

Large structure of DNA that carries genetic information of the organism

Plasma Membrane

-a bilayer of phospholipids and embedded that controls movement of molecules into and out of the cell

-the site for cell signaling

Rough Endoplasmic Reticulum (ER)

• Sorts proteins to send them to the Golgi Apparatus,

• Studded with ribosomes, lysosomes, vacuoles, plasma membrane, and extracellular environment

Smooth Endoplasmic Reticulum (ER)

-Detoxifies: Use enzymes to convert harmful hydrophobic toxins into hydrophilic molecules which makes them easy to excrete from the body

-Regulates Calcium release into cytosol

-Modifies lipid cholesterol to produce steroid hormones

Golgi Apparatus

Proteins that are going to be secreted into the Er travel through the Golgi and are carried out through vesicles to the plasma membrane

Cytoskeleton

• a network of microtubules, intermediate filaments, and actin filaments

• primarily found in the cytosol and the inner nucleus membrane

Nucleus

• organelle in eukaryotic cell’s that contains the cell’s genetic information

• wrapped in a double0layer membrane known as the nuclear envelope

Intermediate Filaments

purely structural cytoskeleton material, more stable than other filaments

Microtubules

• long, hollow, cylindrical structures made up of alpha and beta tubulin

• oscillates between growing and shortening phases known as dynamic instability

Actin filament

Long thing fibers that make up the cytoskeleton

• support the membrane and make up the shape of the cell