Biology Unit 1

Primary Structure of Protein

Linear sequence of amino acids joined by peptide bond

Secondary structure of protein

Regular repeated local spatial patterns. Form alpha helices and beta pleated sheets through hydrogen bonding.

Tertiary structure of proteins

Bending path of polypeptide chain in 3D chain in three dimensional space

Quaternary structure of proteins

Spatial arrangement of polypeptide subunits in proteins made up of more than one polypeptide chain

Beta Pleated Sheet

Formed from two or more polypeptide chains that are almost completely extended and aligned side by side. Stabilizes between the N—H groups on one chain and the C=O groups on the other. A β pleated sheet may form between separate polypeptide chains or between different regions of a single polypeptide chain that is bent back on itself. 3.5 Angstroms per amino acid residue

Alpha Helices

Right handed coil. The R groups extend outward from the peptide backbone of the helix. The coiling results from hydrogen bonds that form between the δ+ hydrogen of the N—H of one amino acid an. 3.6 amino acids per turn. 1.5 amino acids per residue, 5.4 amino acids per turn

Alpha Helix Modifiers

Proline: Alpha helix breaker, no h because it loops so cannot form hydrogen bond required

Glycine: Too flexible

Parallel and anti parallel beta strands

Parallel beta strands are when both adjacent strands goes from N terminus to C terminus. Anti parallel beta strands are when proteins go in opposite direction. Parallel=zigzag and antiparallel=straight across

What defines a cell?

Interior of cell is separated from its environment, and the inside of the cell is chemically different from its environment.

Prokaryote

Bacteria and archaebacteria. No nucleus or membrane bound organelles. Genome is one circular molecule. Still need to do DNA replication, transcription, and translation

Micrometer

10^-6 meters

Nanometer

10^-9

Eukaryotic Nuclear Architecture

Has two layers that are contiguous with the endoplasmic reticulum. Encloses DNA and is the site of RNA production

Nucleolus

Site of ribosomal biogenesis (rRNA transcription and assembly)

Nucleoplasm

Filled with chromatin which are uncondensed chromosomes.

Nuclear Lamina

Proteins lining the inside of the nuclear envelope that provide structural support to the nucleus

Nuclear Pore

Regulates movement of ions and molecules between the nucleus and cytoplasm

Endomembrane System

Contains the rough ER, smooth ER, and golgi apparatus

Rough ER

Ribosomes are on the surface of the rough ER. Synthesize proteins that are destined for another cell organelle, the plasma membrane, or outside the cell. Proteins are inserted into the lumen, folded, and modified (ex: adding sugar group).

Smooth ER

Contiguous with the rough ER. Site of steroid and lipid synthesis. Detoxification and calcium ion storage.

Golgi Apparatus

Sorts, modifies, and packages proteins to their final destination. Proteins enter via vesicles on the “cis” side and leave outside the “trans” side. Vesicles are carried by motor proteins on cytoskeletal tracks. Lysosomes come from the golgi apparatus.

Lysosomes

Digestive enzymes that break down waste

Endocytosis

3 Types: Receptor mediated endocytosis, pinocytosis “cell drinking”, and phagocytosis. Matter is taken in via vesicles. The plasma membrane is pinched off and forms a vesicle.

Exocytosis

Vesicles carrying matter fuse with the plasma membrane and leave the cell.

Mitochondria

Site of cellular respiration and energy production. Site of steroid and heme synthesis. Contains ribosomes and circular DNA. Has a double membrane.

Endosymbiont Theory

Mitochondria are ancestral bacteria that got engulfed by an ancient eukaryotic cell. Developed a symbiotic relationship.

Plastids

Site of photosynthesis. Site of biosynthesis of fatty acid and starch synthesis. Have their own circular genome.

Actin Microfilaments

Cytoskeletal elements that help with cell shape and locomotion. Monomer: G-actin

Intermediate Filaments

Cytoskeletal elements that are fibrous proteins which provide support and make up nuclear lamina.

Microtubules

Cytoskeletal elements that are important for chromosome division and vesicle movement.

Motor Proteins

Ex: Kinesin. Drive movement down microtubule tracks

Six most common elements found in tissue

C, H, O, N, P, and S

Elements found at a lower level

Na, Mg, K, Ca, Mn, Fe, Co, Cu, Zn, Si, and Cl

Covalent Bond

Formed by the sharing of a pair of electrons between adjacent atoms. Strength 50-100 kcal/mol

Octet Rule

Tendency for atoms in stable molecules to have 8 electrons in their valence shell

Electronegativity

Attractive force an atomic nucleus exerts on electrons

Non-Covalent Bonds

Ionic interactions, hydrogen bond, van der waals, hydrophobic interactions

Ionic Interaction + Strength

Oppositely charged groups. Simple ions are elemental, such as Na+ or Cl-. Complex ions include R-COO- (carboxyl ion). 3-7 kCal

Salt Bridge

Between a R-COO- (carboxyl) and a R-NH3+ group (alkyl ammonium)

Hydrogen Bond + Strength

Between an electronegative atom and a hydrogen bond covalently bonded to it and another hydrogen atom bonded to another. 1-5 kCal

Van der Waals Interaction + Strength

Transient fluctuation induces a dipole in a neighboring atom. 0.5 to 1 kcal.

Hydrophobic Interaction

Nonpolar molecules group together, energetically favorable

Hydroxyl Group

Aldehyde

Keto

Carboxyl

Amino

Phosphate

Sulfhydryl

Condensation Reaction

Removing a water to form a bond

Hydrolysis

Inserting a water molecule to break a bond

Proteins

Involved in energy production, catalysis, cell structure, and regulation. Not involved in information or energy storage.

Zwitterion

A positive and negative charge on an amino acid

Special case amino acids

Cysteine, glycine, and proline

Disulfide Bridge

The —SH groups of two cysteine chain react to form a covalent bond between two sulfur atoms

Four macromolecules found in living things

Proteins, nucleic acids, carbohydrates, and lipids

Trans Configuration

Alpha Carbon and R groups are on opposite sides of a peptide bond

What types of interactions drive tertiary structures

Hydrophobic interactions, ionic interaction, hydrogen bonding, disulfide bridges

Denaturation

Disrupts the tertiary and secondary structure of a protein and destroys the protein’s biological functions

Chaperonins

A protein that helps other proteins fold correctly. Step 1: Protein binds to the “cage” and enters it. Step 2: Chaperonin “lid” seals the cage

Induced Conformational Change of Protein Examples

Metal binding protein/metal, enzyme/substrate, hormone receptor/hormone, transcription factor/DNA

Prion Diseases

Kuru, Creutzfeldt-Jacob Disease, Mad Cow Disease, Scrapies

What makes the alpha helix rich version convert to the beta version

Normal endogenous PrP^C. PrP^SC converts PrP^C into a mutated version. PrP^SC comes from a random mutation or inoculation to PrP^SC

Sickle Cell Disease

Glutamic Acid to Valine substitution in the Beta hemoglobin protein. Result is the change in the shape of red blood cells

Insulin

Disulfide bridge holds together 2 polypeptides (quatenary structure) and is also within the same polypeptide chain.

Leucine

Held together by hydrophobic interactions. One hydrophobic leucine held together every 7 amino acids (two turns).

B Cell

Contains antigen and antigen receptor. Antigen binds to antigen receptor, activating the B cell. The B cell then proliferates (multiple copies of B cell) and differentiates (becomes unique) and releases antibodies.

Antibody Structure

Made up of 4 chains: two heavy chains and two light chains. Disulfide bonds hold together the heavy and light chains and the hinge regions in the heavy chains

What do both heavy and light chains contain?

Variable region and constant region. The variable region is unique for each B cell and is on the tips of the Y. The hypervariable region is where the cell binds. The constant region is on the Stem of the Y and is the same for antibodies of the same class.

Gel Electrophoresis

Separation by size. Smaller proteins move farther and larger proteins move less. Compare to the molecular weight ladder.

Beta Turn (AKA Hairpin Turn)

A tight turn of ~4 amino acids. An example of this is a sucrose porin, which is made of beta sheets and hairpin turns.

Hyper variable Region

Where antigens bind. Created through beta sheets with loops. Lots of variation within loops which make it hyper variable

Properties of Proteins that can be used to seperate

Solubility, size, charge, hydrophobicity, affinity

Protein Purification

Isolating a protein from a mixture based on charges.

Assay

Controlled experiment used to measure a biological thing or activity

Size Exclusion Chromatography

Separation by size. Smaller molecules become trapped in porous beads while larger molecules bypass the pores and elute from the column first.

Ion Exchange Chromatography

Separation by charge. A positively charged protein will bind to a negatively charged bead while a negatively charged protein will flow through

Affinity Chromatography

Separation by specific affinity. Beads are attached to a specific molecule (ex glucose). Any protein that can bind to that specific molecule will get stuck. Then, you add more of that molecule (ex glucose) so the protien binds to the excess molecule added.

Western Blot (What it is and the process of it)

An optional step after SDS PAGE to identify a specific protein. Used to confirm the protein band is a protein of interest and not just another protein of the same size. Press gel against membrane and the proteins will move from the gel to the membrane. A primary antibody will be mixed with this membrane and bind to the antigen (your protein of interest). Unbound antibodies will be washed away. Then, a secondary antibody will bind to the primary antibody and send a signal. Secondary antibody can bind to the constant regions on the primary antibody.

Differential Centrifugation

Start with intact cells. (1) These intact cells are then broken to produce a whole cell extract, which contains everything that was inside the cells. (2) After a low-speed spin, the heaviest organelles pellet at the bottom of the tube. (3) The supernatant and pellet are separated. (4) The supernatant is then centrifuged at a higher speed and the next largest organelle pellet to the bottom of the tube.

Metabolism

Network of biochemical pathways with each reaction catalyzed by an enzyme

Gibb’s Free Energy

Delta G<0, the reaction proceeds spontaneously. Delta G>0, energy has to be put into the energy to proceed

Kinetics

Rate at which a reaction will occur

Catalysts

Substances that speed up a reaction without being permanently altered by a reaction

Catalysts

Substances that speed up a reaction without being altered by the reaction. Change the kinetics of a reaction, not the thermodynamics

Enzymes

Specific biological catalysts, typically proteins but can be RNA. Lower the activation energy for a biochemical reaction. Facilitate the formation of a transition state

Active Site

3D cleft or crevice where enzyme and substrate interact, and catalysis occurs. Typically a small part of the enzyme. E+S —> ES—> ES* (Transition state) —> EP —? E+P.

Active Site

Unique microenvironments where substrates are bound by multiple weak interactions. 1) Orients substrates 2) Physically strains substrates 3) Adding chemical charges to substrates

Lock and Key Model

Substrate fits exactly into enzyme

Induced Fit Model

When the substrate binds, it induces a shape change in the enzyme, so the active site fits the substrate more precisely during the reaction

Michaelis-Menten Kinetics

V0=Vmax*(S)/(S+Km)

Vmax

Maximum initial velocity of the reaction at high substrate concentrations

Km

How efficiently an enzyme binds to a substrate and converts it to a product. Measure of the substrate concentration required for significant catalysis to take place. Lower Km= maximal catalytic efficiency at low substrate concentration. Unique for each enzyme/substrate pair

Competitive Inhibition

Substrates binds to enzyme at active site. Km increases and Vmax stays the same

Noncompetitive inhibition

Enzyme binds to substrate at an allosteric site and changes the shape of the enzyme, so the substrate can no longer bind to the active site. Km stays the same and Vmax decreases

Lipid

Made up of hydrocarbons, making them hydrophobic. Form macromolecular aggregates in aqueous environments through hydrophobic interactions

Roles of lipids in biology

Major component of the plasma membrane, energy source and energy storage, signaling molecules (ex: steroid hormones), structural/architectural

3 Types of Lipids and Function

Triglycerides (energy storage), phospholipids (membranes), steroids (membranes and signaling)

Triglycerides

Made up of 2 components: 1) Glycerol 2) 3 Fatty Acids

Fatty Acid

Hydrocarbon chains + Carboxylic acid. Typically 16-18 carbons (even numbers)