Metabolism: Energy and Enzymes
• Cells and Energy Flow
• Metabolic Reac?ons and
Energy Transforma?on
• Metabolic Pathways
• Enzymes
• Oxida?on and Reduc?on

Energy
Capacity to do work or bring about change
• All organisms have a constant need for energy
• KINETIC ENERGY
– Energy of Mo?on
– Mechanical energy
• POTENTIAL ENERGY
– Stored energy
– Food = Chemical energy
• Poten?al energy can be converted into kine?c energy


Flow of Energy
1st law of thermodynamics:
Energy cannot be created or
destroyed, but only change form

2nd Law of Thermodynamics
• Energy cannot be changed from one form to another
without a loss of usable energy
• OUen, this loss is in the form of heat

One Way Flow of Energy:
Sun loses E to Earth’s environment
E gained by organisms from environment
E lost by organisms back to environment

The sun is the original source of
energy for the food chain. Sun light
allows plants to grow.
(100,000 Units of Energy)
Plants capture approximately 1%
of the light energy from the sun.
This is done by photosynthesis.
(1,000 Units of Energy)
In a typical foodchain, Herbivores
(Vegetarians) eat approximately
10% of the plants produced.
(100 Units of Energy)
Carnivores (meat eaters) eat the
herbivores. They use around 10%
of the energy stored by the
herbivores.
(10 Units of Energy)

2nd Law of Thermodynamics
• Every energy transforma>on makes the universe
less organized
• Entropy – amount of disorganiza?on
• Randomness of the universe will only increase.

Metabolism
The sum of all of the chemical reac?ons that
occur in a cell
• Anabolic reac?ons: building/synthesis; requires
energy
– Transcrip?on, transla?on, DNA replica?on,
photosynthesis, synthesis of lipids, glycogen, etc.
• Catabolic reac?ons: breaking down; releases
energy
– Cellular respira?on, glycolysis, diges?on


Energy Use
• Chemical Work
– Energy for synthesis/anabolism
• Transport Work
– Energy to pump molecules across membranes
• Mechanical Work
– Energy for movement of cell or within cell
• Muscle contrac?on, cilia movement, chromosome movement

Enzymes
• Proteins that catalyze/speed up biochemical reac?ons
– Enzyme is not changed and is recycled.
– Some enzymes are RNA (rRNA).
• Characteris?c 3D shape determines func?on
– Substrate: reactant for an enzyme
• Specificity: Enzyme only binds to one substrate/set of substrates
– Ac>ve site: region of enzyme that interacts with substrate


1. Substrate binds to ac?ve site of enzyme
2. Enzyme‐substrate (temporary) complex is formed.
3. Substrate is transformed.
4. Products are released. Enzyme is unchanged.
5. Enzyme reacts with another substrate molecule.

How Do Enzymes Work?
• Molecules are in a state of mo?on
• Molecules must come collide with enough energy for a
reac?on to occur (Ac>va>on Energy)
• Temperature or pressure increase the energy of
molecules
– Cells can’t handle changes in these factors
• Enzymes:
– Help bring substrates together
– Posi?on/orient substrates to facilitate interac?on
– Lower the Ac>va>on Energy of a chemical reac?on


Enzyme Names
• End in –ase
• Substrate or type of reac?on catalyzed
Sucrase‐ sucrose  glucose + fructose + H2O
Transferase‐ transfers func?onal groups
Dehydrogenase‐ removes H
– Ex. Lactate dehydrogenase
Oxidase‐ adds O

fuck my life

Eukaryotes Notes

Cell theory- not proved but well supported not the final answer
Took a long time to develop the origin/evolution of cells

• Eukaryotes reproduce by mitosis or meiosis
• Prokaryotes reproduce by asexual and binary fission
• Eukaryotes/Prokaryotes both have: plasma membrane (phospolipids-bilary), nucleus/nucleoid, cytoplasm (stuff floating inside the cell).
  
• Nucleus is very centralized (major difference) a true nucleus, membrane bound!
• Domain Eukarya has 4 kingdoms: Protista, Fungi, Plantae, and Animalia
  
• Membrane bound nucleus& organelles (compartments specialized to perform special functions) Very specialized/centralized.
• Endosymbiotic theory(unifies) how eukaryotes evolved from prokaryotes
• Mitochondria and Chloroplast got engulfed by the early eukaryote and stayed their permanently, not sure how it happened. When reproduced, it made cells with all these things basically incorporated/join the DNA coding making new eukaryote cell.

Plasma membrane

• Similiar to prokaryotes
• Different proteins
• Regulates passage of molecules in/out of cell
• Organelle membranes are similar

Cell wall

• No peptidoglycan
• Plants (cellulose) Protists (variety of types, some more) Fungi (chitin) Animals (most none)
• Support and protection.
  
• Diatom cell wall are protists, cell walls made of glass and very intricate: diatom shouldn't throw stones. They live in a glass house, ohoho.

Nucleus

• Chromatin-unwound chromosomes and they recoil into chromosomes.
• Divide cell cycles, chromatin floating inside.

Ribosomes

• Made of rRNA and protein, 3 locations: free in cytoplasm, attached to ER (attached to the nucleus) , inside mitochondria/chloroplast (have their own ribosomes)
• Ribosomes important to growth/reproduction.
• In the nucleus there are ribosomes, nucleus sends (transcribe) mRNA and reads it; transported to single strand RNA.
  

Biology notes: Viruses

RNA

• RNA- Different type: mRNA and rRNA
• RNA is a molecule (transcriptase) enzyme
  
• Ribonucelic acid, generic translator
• DNA is double stranded, make new cells, makes protein
• RNA comes from DNA (transcribed into)
• mRNA (messenger) carries information somewhere to be used
• Ribosomes: proteins/rRNA--> main function make protein
• rRNA is like a translator, it reads the mRNA and tells the ribosomes how to make proteins

Retroviruses

• RNA virsuses that have a DNA stage
• Converts RNA -> DNA and DNA integrates into a host genome.
• Usually DNA-> RNA but viral RNA-> viral DNA
• Which makes ribosomes new viruses. Examples such as HIV.

1. Attachment
2. Entry
3. Reverse transcription
4. Biosynthesis
5. Maturation
6. Release
   

Viral evolution

• Believed that viruses evolved early& parasites of all 3 domains
• More closely related to host, viruses evolved from the host cell
  
• Viruses have small genomes, 4-100 genes 25%
• Mutatation: treatments needed to be changed, ex: influenza virus
• Antibiotics have no effect, treatments must target virus specific proteins/processes
• Many associated with cancer (promote cancer) human ppv
• integrate into host genome and disrupts host cell function
• Emerging viruses: viruses that have only recently caused disease
• Examples: HIV, SARS, west nile encephalitis, hantavirus
• Viral mutation, becomes more nasty or jump hosts such as avian flu

Viroids

• Similiar to a virus but has no capsid (protein jacket) just a naked RNA
• Infected plants-- extensive damage & millions of money/crops lost

Prions

• Wrongly shaped protein, infectious misfolded protein
• Shape is function, wrong function = death
  
• Deposites in brain causes degenerative brain diseases (spongiform encephalopathies)
  
• Mad Cow Disease
  
• Creutzfeld-Jakob disease
• Kuru (eating brains of their elders, eating prions now going to be in your brain, causing it to misfold, basically enters your body by eating it)

Italian Early Renaissance

Florence Cathedral (Duomo), Arnolfo di Cambio

1. Construction begun in 1296 by Arnolfo di Cambio, scultptors and painters rather than masons were used for the design. More concerned by design than with engineering.
   
2. Long square-bayed nave ends in an octagonal domed crossing, as wide as the nave and side aisles. Three polygonal apses, each with five radiating chapels, surround the central space.
   

Dome of Florence, Brunelleschi

1. Goldsmith studied Roman sculpture, constructed a tall octagonal drum, as a base. The dome is a double shell of masonry 138 feet across. The Octagonal outer shell is supported on eight large and sixteen lighter ribs.
   
2. An oculus, round opening in the center of the dome was surmounted by a lantern, final touch was a gilt bronze ball.
   

Palazzo Medici-Riccardi, Bartolomeo, Florence

1. Style like the "arch of titus" divided arch, diminishing height, "rusticated" Large over hanging protection from the sun, dress masonry.
2. The palazzo symbolized the family place in society, commissioned by the Cosimo de'Medici family. Cartouche-family name/crest, Medici-balls, round circles.
   

Palazzo Medici Riccardi Courtyard, Bartolomeo, Florence

1. Square in plan with rooms, round arches on slender cloumns form a continuous arcade (repetition of arches) and supported an enclosed second story.
   
2. Decorated with sgraffito ( tinted and engraved plaster) Loggia- open courtyard.
   

Sant Andrea Plan, Alberti, Mantua

1. Gonzaga comissioned Alberti to enlarge the church of sant andrea which housed a sacred relic believed to be the actual blood of christ.
   
2. Masonary-support chapel spaces covered with barrel valut. Follows the latin cross plan, which the transept intersects the nave high above the midpoint of the church.
   

Sant Andrea, Facade, Alberti, Mantua

1. Allows light to enter, follows two classical forms- a temple front and a triumphal arch with two sets of colossal Corinthian pilasters.
   
2. Facade now has a clear volume of its own, which sets it off visually from the building behind. Barrel-vaulted triumphal-arch entrance.
   

Sant Andrea, Nave, Alberti, Mantua

1. Immense barrel vaulted nave, extended on each side by tall chapels, inspired by the Basilica of Maxentius and Constantine. Vault width 60'
   
2. The arch has lateral barrel vaulted spaces opening through two story arches on the left and right. Alberti created such colossal scale, spatial unity.
   

Studiolo of Montelfeltro in Ducal Palace Urbino, Italy

1. Intarsia- small pieces of wood to get color like a puzzle gluing down wood to create illusionist painting.
   
2. Tromp l'oeil effects more convincing with development of liearn perspective, studiolo-study or a room for private conversation.
   

Four Crowned Martyrs, Nanni di Banco ( stone mason guild)

1. Commissioned by both the stone mason and wood workers guild, these martyrs were executed for refusing to make an image of pagan roman gods.
   
2. Figures- solid bodies, heavy form revealing togas, stylized hair and beards, very naturalistic features. Drapery falls naturally, gesture with weight shifted contrapposto, how the body looks in reality: knee pressing the fabric.
   

Gates of Paradise, Ghiberti (Baptistry of San Giovanni, Florence)

1. Bronze relief panels for a new set of doors for the east and most important side of the Baptistry of San Giovanni. Commissioned by the Wool Manufacturer Guild, he produced a set of ten old testament scenes from the creation to the reign of Solomon.
2. Organized space in linear perspective, guilded with gold.
   

Jacob and Esau, Ghiberti

1. One point perspective in the setting, Rebecca stands listening to god who warns of her unborn sons future conflict. Adult Esau sells his rights as oldest son to Jacob.
   
2. Jacob receives Isac's blessing while Esau faces his father, Esau symbolized the Jews and Jacob the Christians. Explains the conflict of religion.
   

David, Donatello

1. Bronze sculpture, life size male nude David, heroic nudity, sensuous adolescent boy, taking Goliath's severed head under his feet. The sculpture is placed in the Medici palace, extolling Florentine heroism and virtue.
2. Nudity-beauty, close to god. Circe perdu, bronze casting method. Free standing nude, creates a scene, young/woman-like figure, sleek and shiny surface.
   

Erasmo da Narni (Gattamelata), Donatello, Padua

1. Equestrian statu commemorating the Paduan general of the Ventian army, Gattamelata, honeyed Cat. Example of condottieri-brilliant generals who organized the armies and fought for any city state willing to pay.
   
2. Horse had a symbol for brute strength, mind over matter.
   

Trinity, Masaccio, (Santa Maria Novella, Florence)

1. The trinity was meant to give the illusion of a stone funerary, set below a deep aedicula (framed niche) in the wall.
   
2. Momente mori: reminder of death, dove, holy spirit. Taken view point to look up to look at 3-D space, placed outside chapel to think/reminder of death.
   
3. Coffers sunken panels of the ceiling, skeleton represents Adam on whose tomb the cross was though to have been set.

Brancacci Chapel, Masaccio, Church of Santa MAria del Carmine, Florence

1. Fresco decoration of the Brancacci chapel in the church of Santa Maria del Carmine in Florence. The chapel was dedicated to Saint Peter.
2. Patron Felice Brancacci was exiled, never finished.

Tribute Money, Brancacci Chapel, Masaccio

1. Aerial/atmospheric perspective, modeling hightlights, spacing, shifting weight of the contraposto, individuality expression, contineous narration, telling a story about the first tax levy in florence for war called "catasto"
2. Natural light bathed with light for realism, jewlish tax collector asking for money. angled halos, natural florence landscape, trees/nature less distinctive.
3. Linear perspective, center of the space: jesus overlapping, creating depth shadows.

Camera Picta, Mantegna, Ducal Palace ( Mantua)

1. Ludovico Gonzaga, patron a tower chamber in his palace which Mantegna decorated. The family receives its returning cardinal in scenes set in landscapes and loggias.
2. Organized wall to one single point completely unified illusionist ceiling art, feet hanging form ledge. Foreshorten babies/putti illusion of space, short, proportions, tromple l'oeil to to fool the eye, stimulated oculus with a big opening.
   

The birth of Venus, Botticelli

1. Contraposto hip/knee bended, elongated anatomy for visual effect, personification of spring, her hair is highlighted with gold.
   

Late 15/Early 16 Century

Italian High Renaissance

The Last Supper, Leonardo da Vinci, Milan

1. Leonardo worked directly on dry intonaco- thin layer of smooth plaster with oil and tempera paint. Painting begun to deteriorate.
   
2. Idealized painting, trying to put people in a setting in better what they are, everyone is mirroring each other.
   
3. Last supper is symbolic evocation of Jesus's sacrifice for the salvation of man. Traitor Judas is in the first triad left to Jesus holding a pouch of money.
   
4. Arranging the disciples and architectural elements into four groups of three, numerical symbolism.
   
5. Substituted natural light from triple window framing Jesus's head instead of halos.
   

Virgin and St Anne with Christ Child and Young John the Baptist, da Vinci

1. Cartoon (to scale in size of intended painting) Composition element is a triangle. Done in a sfumato (smoky) manner. Charcoal on brown paper.
2. Mary sits on the knee of her mother, Anne and turns to the right to hold the Christ Child who strains away from her to reach towards the young John the Baptist.
3. Illusion of high relief b modeling the figures with strong contrast light and shadow chiaroscuro ( light/dark)
   
4. Tender expression of Anne and Mary with complex interaction.
   

Mona Lisa, da Vinci

1. Portrait of Lisa Gherardini del Giocondo, the wife of a merchant in Florence.
   
2. No jewelry, receding landscape, with a triangle/pyramidal form.
3. Gentle smile isn't followed by warm eyes: plucked eyebrows and shaved hairline. Leonardo unified his compositions by covering them with a slightly tinted varnish which resulted in a smoky overall haze (sfumato)
   

Vitruvian Man, da Vinci

1. Ideal man with both circle and square, precise details of anatomy and geometric basis.
   

The Small Cowper Madonna, Raphael

1. Named for owner, precise and delicate tilt of the figures' head and peaceful mood. Similar pyramidal form by the spiral movement of he child and figure enhancing draperies of the Virgin.
2. Model forms are soften by the clear even light of the outdoor setting.
   

Stanza della Segnature, Raphael, Vatican Rome

1. Papal library, Pope Julius II put him to work decorate the papal apartments.
   

School of Athens, Raphael, Stanza della Segnature, Vatican Rome

1. Summarize the ideals of the renaisance papacy, viewed through a trompe l'oeil arch, greek philosophers Plato and Aristole placed to the right and left of the vanishing point.
2. Plato suggest ideal immposible world
3. Aristotle palm down, emphasize the importation of gther knowledge from observing the material world.
4. Apollo, Minerva surround the philosphers, a mixture of gods, naturalist, astronomers, geographers debating. A mixture of physical and intellectual presence.
   
5. We also see the figures: architect bramante, Michelangelo working on the Sistine Chapel sketching.
   

Pieta, Michelangelo

1. Saint Peter's Vatican Michelangelo worked on the marble sculpture commisioned by french cardinal.
   
2. Pieta, a young virgin Mary mourning the death of Jesus holding him in her arms. Inconsistent between age and size. Very sweet mourning.
   

David, Michelangelo

1. Commission for a statue of one of the symbols of Florence.
   
2. Athletic and muscular nudity, emotional power of a new expression. Slingshot over his shoulder and a rock in right hand, David frowns and stares into space. Represents right over wrong.
   

Interior Sistine Chapel, Michelangelo, Vatican Rome

1. Pope Julius II, was well paid for the work but preferred scuplting to painting. Frescoes established a new powerful style,simple: trompe l'oeil and 12 apostles seated on thrones.
   
2. Final composition llusionistic marble with decorated putti, siblys (female prophets) and heroic figures of nude young men (ignudi) holding sashes.
3. Divded into scenes of creation, temptation, the fall, expulsion, and eventual desstruction of al people except Noah.
   

Sistine Ceiling, Michelangelo/Sistine Ceiling Diagram


Creation of Adam, Sistine Chapel Ceiling, Michelangelo

1. Adam's heroic body poses mirror those of God in whose image he has been created. God's form symbolizes the brain?
2. Below Adam, an ignudo holds a bundle of oak leaves and acorns which refers to Pope julius's family name.
   

Moses, Michelangelo

1. Muscular figure, swahed in great sheets of drapery seated in a restle contrapposto. His beard is curling.
   
2. Created for the tomb of Julius II
   

Tempietto, Donato Bramante, San Pietro, Rome.

1. Spanish rulers Queen Isabella and King Ferdinand commissioned a small shrine over the spot in Rome where Peter was crucified.
   
2. From the stepped base to the Doric columns and frieze, centralized plan and a tall drum. Circular cloister around the church.
   

The Tempest, Giorgione

1. Poesie (painted poems) a woman seated on the ground, nude while nursing her baby. A german mercenary soldier turns his head to her.
2. A vivid landscape, spring gushes from a lake with a storm in the background. Where you see lighting escaping from the clouds. Main focus is the landscape of the unruly element of nature.
   

Venus of Urbino, Titian

1. For the Duke of Urbino of a venetian courtesan, very provocative streches on her couch in a palace.
   
2. A spaniel symbolic of fidelity, sleeping at her feet, glowing skin from the incandescent light.
3. His work began with a charcoal drawing on the prime coat of lead white that was used to seal the pores and smooth the surface of the coarse venetian canvas. Built up fine glazes of different colors.

15th century notes

Northern Early Renaissance 15th Century

January Page, Tres Riches Heures Limbourg Brothers, Cha (Duke of Berry)

1. -International Gothic Style with spatial recession, detail to nature: flowers, birds, mountains. Noble men and women with delicte features with curling hair and complex headdresses. Wearing elaborate jewelry, landscape of knights.
   
2. Shows of an aristocratic household with many tables of food and rich tableware.
   
3. Zodiac: Capricorn, Pisces, and Apollo. Colors: blue and gold shows dominance and wealth.
   

Februray Page, Tres Riches Heures (Hour of Prayer)

1. Farm people relaxing in a blazing fire, rich color, great attention to detail and nature in a winter setting. Lower or working class people.
   
2. Shows aerial or atmospheric perspective: color getting lighter.
3. X-ray vision-cutaway view of the house showing interior and exterior.
4. High rising horizon line not accurate; people out of proportion to their setting.
5. International gothic style, a lot of detail: you even see someone's genitalia. You see animals such as sheep, donkey, birds, the breath of a very cold person.
   

Well of Moses, Claus Sluter, Chartreuse de Champol France (Philip the Bold)

1. Philip demanded prayers from the monks for his family.
   
2. A prier rose from the water and supported the large figures of Moses, David, and the prophets (Jeremiah, Zachariah, Daniel, and Isaiah)
   
3. Physically distinctive: Mose's sad eyes, curling hair and beard with horns due to mistranslation. King David: dressed in medieval robes and nobility.
   
4. Voluminous drapery, surface realism and naturalism.
   

Merode Atlarpiece, Robert Campin (Netherlandish/Flemish)

1. Triptych of Annunciation- International Gothic Style: disproportionate relationship between figures and nature. X-Ray detail, raising perspective.
   
2. Hidden symbolism: lilies in the majolica (glazed earthenware) pitchter on the table symbolize Mary's virginity. White towel hanging, Mary's purity. Wind snuffs the candle as a tiny figure of Christ descends on ray of light.
   

Man in a Red Turban, Jan van Eyck

1. "As I can" projects a strong sense of personality and humanist spirit of the age and the confident expression. (oil on wood)
   
2. You see every wrinkle and scar, the stubble of bread, tiny relfections of the ligh from a studio window in the eyes.
   

Portrait of Giovanni Arnolfini and his Wife, Giovanna Cenami; Jan van Eyck

1. Represents wedding or betrothal of Giovanni Arnolfini (wealthy merchant) holds the hand of a woman. There is also a pet dog: wealth and fidelity.
   
2. The man is external, into the masculine world outdoors where as woman is on the right, domestic interior. Surrounded by wealth, pietry, and married life. Presence of god, shoes taken off and the candles are snuffed out.
   
3. Convex mirror reflecting the entire room, luxury object, symbolize the all seeing eye of god. Woman wears fur lined overdress with long train.
   
4. Robe held n the front giving appearance of pregnancy, ideal of feminine beauty by potential fertility.
   

Deposition, Weyden (Louvain Crossbowmen's Guild)

1. Act of removing Jesus's body from the cross; fainting virgin mother increases emotional identification. Paints sensibility of John the Evangelist who supports the Virgin and Jesus's friend Mary Magdalen wrings her hand in anguish.
   
2. Great detail to individualize expression of emotion, united by sorrow.
3. Subtle muted colors of red and blue allows viewer's attention to focus on ashen white skin of Jesus, who's skin is almost the same color of the white turban and face of Mary.
   

Portrait of a Lady, Weyden

1. Young lady with pious modest beauty, her hands are clasped in a praying manner showing self control. Almond shape eyes, translucent skin and high waistline, balanced with humility and wealth. (Oil and tempera on wood)
   

Portinari Altarpiece, Hugo van der Goes (Tommaso Portinari- head of Medici Bank)

1. Installed in the Portinari family chapel in Florence. Theme: Nativity with the central panel on the Adoration of the newborn Christ child.
   
2. On the left wing we see: Tommaso and his sons praying and on the right: we see his wife and his daughter kneeling in prayer presented with saints Mary Magdalen and Margret.
3. Central panel: Atmospheric perspective: baby Jesus on the ground, rays of light emanate from his body. Mary is kneeling adoring him.
   
4. Disguised symbolism: ceramic pharmacy jar (albarello) glass, flowers, and wheat. Event at Bethlehem, house of bread to host. Majolica albarello dcorated with vines and grapes, alluding to the wine of Communion.
5. Three irises: trinity of Father, white for purity and purple for royalty. Glass vessel represents Mary and her womb, glass holds violets of future sorrow of the future, symbolizing humility.