BCH 4024 UCF Exam 1

Albert Lehninger

- discovered mechanism for oxidative phosphorylation

- mitochondrial structure and function

Guillain-Barre syndrome

- autoimmune disorder, body makes antibodies against its own gangliosides

- results in inflammation, damaging peripheral nervous system, causing paralysis.

Living matter is characterized by:

- degree of complexity and organization

- extraction, transformation, use of energy

- defined functions of individual components and interactions

- ability to sense and respond to changes in environment by adapting internal chemistry

- self replication capacity

Cell

- 1-2 micrometers long

- limited by diffusion, based on SA to V ratio

3 Domains of Life

Monera (archaea and bacteria)

Protista (unicellular eukaryotes)

Fungi (uni and multi eukaryotes)

Plantar (multi eukaryotes)

Animalia (multi eukaryotes)

Bacteria Cell Structure

Eukaryotes Cell Structure

Nucleus (protect DNA, metabolism, a nuclear cells, selective import and export)

Membrane Enclosed Organelles (golgi complex packages/targets proteins to organelles, chloroplasts, lysosomes/digests unneeded molecules)

Mitochondria have oxidative enzymes, chloroplasts have photosynthetic pigments, light reactions

Differences between bacteria, animal, and plant cells

Cytoplasm/Cytoskeleton

Cytoplasm = solution where reactions take place, dense with proteins

Cytoskeleton = structure, made from protein filaments that crisscross to create network.

- consists of microtubules, actin filaments, intermediate filaments

- bovine pulmonary artery

Chemotrophs vs. Phototrophs

- Chemotrophs get chemical fuel to create energy

- Phototrophs use light fuel to create energy

Biochemistry studies the chemistry about...

Accelerating reactions in cells

Organization of metabolism ,regulation, and signaling in cells

Storage/Transfer of information in cells

Elements Needed for Life

CHONPS (95% dry weight of E.Coli)

Metal ions = K, Na, Ca, Mg, Zn, Fe

Functional Groups in Biomolecules (KNOW STRUCTURE)

acetyl-CoA contents

Thioester, Amido, amido, hydroxyl, phosphanhydride, phosphorylation, imidazole-like, amino, phosphoryl

Building Blocks of Biochem

Sugar, fatty acids/glycerol, amino acids, nucleotides

Models

Structural Formula (solid/dashed wedge)

Ball and Stick (bond angles and length)

Space Filling (van der walls radii)

Chirality

R/S (priority by R group)

D/L (rotation of light`

Structural Isomers

Same atoms, different bonding, different properties

Stereoisomers

Molecules with same bonds,

different configuration,

different properties

Entantiomers (mirror images)

Identical physical properties

Identical reaction to achiral reagents

Diasteromers (not mirror images)

Geometric Isomers (cis/trans)

Different physical properties

Different chemical properties

Isomerase

Converts between racemase, epimerase, cis/trans isomerase

Geometric Isomers

Cis and Trans

No freedom of rotation bc of C=C double bond in Malevich and fumaric acid

Enantiomers and Diastereomers

Hexokinase (interaction w biomolecules)

Glucose fits into the pocket on the surface of enzyme

Interacts with noncovalent interactions

Enzyme specific for d-glucose

Olfactory and taste receptors contain

Chiral groups (R-Carvone = spearmint, S-Carvone = caraway)

Drug Enantiomers (Lexapro)

Enantiopure drug, antidepressant, selective serotonin reuptake inhibitor

Drug Enantiomers (Citalopram)

racemic miture of the levo isomer (active) and the inactive mirror image of dextro isomer

90% of recent drugs are racemic mixtures

Drugs with Single Active Isomers

Beta blockers, ACE inhibitors, calcium channel agonists, beta agonist bronchodilators

Why use eutomer (active isomer) over the racemic mix with distomer (inactive isomer)

Cheaper, not guaranteed better therapeutic benefit

Ex: Eutomer Esomeprozaole (Neixum) wasn't better than the generic omeprazole (Prilosec)

1 Enantiomers for Single Active Isomer

L-thyroxine (levothyroine, synthroid) = thyroid hormone

D-thyroxine (dextrothyroxine, choloxin) = lowers cholesterol with cardiac side effects

Thermodynamics (Law I)

1st Law = energy cannot be created or destroyed, so the energy needed to break a bond is equal to the amount released upon formation

Thermodynamics (Law II)

A chemical/physical process goes spontaneous in the direction of disorder (entropy)

Work Equation

E (Ssystem + Ssurroundings) is positive as the order of surroundings is greater than order made in the system. Then the S is positive.

Free Energy

Energy Available to Do Work

G = H - TS

Moves towards equilibrium concentrations, where G = 0

Ex: NaCl dissolving in solution is favorable (negative G), as heat is absorbed (Positive H) and entropy increases

Look over slides 32-34, 36, 39, 44

Endergonic

Requires energy to complete reactions

thermodynamically unfavorable (Go > 0)

Anabolic

Exergonic

Release of energy (ex: breakdown of metabolites)

Ex: ATP, NADH, NADPH can be made from sunlight/fuel

The cell concentration is higher than equilibrium, from making ATP from oxidation of compound like glucose to make ATP.

Catabolic

Thermodynamically Favorable

Adenosine Triphosphate

Endergonic Reactions (positive G) coupled with exergonic reactions (negative G)

ATP gives energy through hydrolysis

ATP Phosphoanhydride Bonds

ATP hydrolysis has a negative G, promoting hydrolysis.

Competing resonance

Hydrolysis consumers water, where repulsion of oxygen is relieved

ADP has _______ entropy than ATP

Greater

Enzymatic Catalysis offers:

Acceleration under mild conditions

High specificity

Possibility for Regulation

Coupling Reactions to ATP hydrolysis

Avoid side reactions

Substrate channeling

Enzymatically Catalyzed Pathway

Thousands of enzyme reactions in cells are organized into pathways

Metabolic Pathway (make energy or valuable materials, exergonic, endergonic, amphibolic)

Signal Transduction Pathway (information)

Pathway Regulation for enzyme synthesis/degradation

Change net rate of synthesis or degradation (in turn, changing enzyme concentration)

More effective in bacteria than eukaryotes bc they grow rapidly and half concentration per division

Pathway Regulation of enzyme activity

Protein activation/inactivation through covalent modification (phosphorylation)

Protein activity modification through ligand or modulators

Almost Eric feedback inhibition causes conformational changes in the enzyme, binding it to a different active site.

RNA World Hypothesis

RNA self replicated itself, and variants were able to be made into amino acids and proteins.

DNA being complementary, overtook RNA's ability to conserve genetic information.

Evidence: RNA molecules (ribozymes) catalyze formation of peptide bond and can do so without the protein component of ribosomes

Central Dogma

DNA—> RNA —> Protein

Natural Selection and mutations

Mutations occur randomly at a low rate (sufficient to give raw materials for natural selection)

Favors environmentally advantageous mutations

Endosymbiosis

A bacterial genome was consumed by an anaerobic eukaryote. It turns into an aerobic eukaryote bc of the bacterial genome. Light energy, made from endosymbiont, was used to make biomolecules from CO2, and multiplies. The endosymbiont becomes chloroplasts.

Structure of Water

- 4 electron pairs aorund the oxygen atom in sp3.

-2 pairs linked via hydrogen bonds

- 2 pairs nonbonding (lone pairs)

Chemoautotroph

Chemical energy source

CO2 carbon source

Chemoheteortroph

Chemical Energy Source

Organic compound carbon sourc

Relationship between G and Keq

Inverse