Organic Chemistry

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Organic Chemistry

• Why Do We Eat?

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Carbohydrates

1. Atoms C,H,O in a 121 ratio
2. Monomers Monosaccharides

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Carbs Continued

• Examples
• Monosaccharides glucose, fructose, galactose
• Disaccharides sucrose (glucose fructose)
• lactose (glucose galactose)
• maltose (glucose
  glucose)
• Polysaccharides chains of glucose (starch,
  glycogen, cellulose)
• Functions immediate energy or short term energy
  storage

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Structure/Function Relationships

• Contains a lot of C-H covalent bonds that store
  energy
• We have enzymes that can break these bonds to
  release the energy
• The O-H bonds make carbs very polar so they
  dissolve easily and so can be move in water
  easily to meet up with enzymes and can be easily
  transported to cells and meet up with enzymes
  there

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Struc/Func Continued

• Even if molecules are polar the larger the
  molecule the less water soluble harder to
  transport and harder for enzymes to get to and
  break down (also more bonds to break)
• Polysaccharides are more storable because more
  bonds and bigger
• Starch is made by plants straight chains more
  packable
• Cellulose is made by plants used for structure
  since there are no enzymes that break it down,
  can bind to other cellulose chains making it
  stronger called fiber in our diet important
  for bulking up feces and cleaning intestine
• Glycogen is made by animals branched so can
  break down quicker than starch

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Physiology

• When you eat monosaccharides, you just absorb
  them into the blood
• When you eat disaccharides and polysaccharides,
  you first digest them to monosaccharides so they
  are small enough to absorb
• These go to the cells to be further broken down
  to release the energy in them to run everything
• Any extra should be taken out by the liver,
  chained together into glycogen for longer storage
  then stored in the liver and muscles.
• Any excess carbs beyond what can be stored as
  glycogen get turned into fat for long term
  storage.

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Getting Ready for a Game or Contest? Which would
you choose?
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Good Carbs vs. Bad Carbs

• Good whole fruits, whole vegetables, whole
  grains
• Bad processed carbs white bread, pastas,
  white rice, any white flour product
• What Makes them Good or Bad?
• Its all about the speed of absorption from the
  digestive track
• The speed of absorption is determined by
  packaging.

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Good vs. Bad Carbs Continued

• Whole fruits and vegetables the simple sugars
  are encased in cellulose cell walls hard to
  tear the cell walls open so it slows the
  absorption
• Whole grains and brown rice have capsule so same
  as above

Refined flour remove outside capsule and germ
which has vitamins and important nutrients so its
absorbed quickly and doesnt have a lot of
nutrients almost all powdered starch
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Good vs. Bad carbs

• The amount a carb shoots up the blood sugar is
  called the Glycemic Index (GI). The higher the
  GI, the faster your blood sugar increases and the
  more unhealthy the carb is for you.
• Processed carbs have a high GI because the sugar
  is absorbed so fast, the liver cant take all of
  the extra out for storage. Therefore, your blood
  sugar spikes.
• This causes you to overproduce insulin which
  leads to insulin resistant diabetes and other
  problems.

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Why is the Speed of Absorption Important?

• High GI Sugar High/Sugar Low feel tired,
  hungry, and maybe shaky. Creates insulin
  resistance and diabetes.

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Lipids

• Atoms C,H,O but hardly any O (non-polar)
• Monomers fatty acids (hydrocarbon chains)

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Examples

• Fats saturated and unsaturated
• Cholesterol
• Steroid Hormones
• Wax
• Mucus

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Functions

• Long term energy storage
• Insulation
• Cushioning
• Protection (wax, mucous)

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Structure/Function Relationships

• Has more C-H bonds than carbs so contains a lot
  more energy/gram (compact energy)
• Had little O and is non-polar so doesnt dissolve
  easily hard to transport and hard for enzymes
  to get to it to break it down can be stored for
  a long time

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Proteins

• Atoms C,H,O,N (sometimes S)
• Monomers amino acids

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Examples/Functions

• Globular Proteins
• Work by shape
• Enzymes catalyze chemical reactions
• Carrier Proteins carry oxygen to cells,
  transport things across membranes
• Receptors receive messengers
• Messengers molecules to communicate like
  hormones
• Antibodies proteins that help kill foreign
  invaders
• Protein Channels in the cell membrane let only
  certain things in or out of cells
• Marker Proteins on cell surface ids cell as
  your own

• Fibrous Proteins
• For Structure
• Hair, teeth, nails, skin, muscles, bones,
  tendons, ligaments
• Internal structure of cells

Protein Folding Video
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Fibrous vs. Globular Proteins
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Why is shape so important?
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Protein Structure/Function Relationships

• Fibrous multiple polypeptides wound around each
  other like a rope all of the intermolecular
  forces (bonds) that form between the strands
  makes them super strong which makes them good for
  building the structural parts of animals
• Globular all have very intricate shapes with
  specifically shaped pockets on their surface
  which allow them to match by shape with other
  molecules. This makes them good for

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How Proteins Fold

• Primary Structure straight chain of aa not
  functional hooked together by peptide bonds
  which are covalent
• Secondary Structure starts to fold
• uncharged parts start of collapse together
• the O of the acid groups form H bonds
• with the H from the amino group
• Spirals and curves start to form

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Protein Folding continued

• Tertiary Structure caused by interactions of R
  groups that have now been brought closer together
  by secondary folding Functional!
• Held together by
• Hydrogen bonds - form between two polar R groups
  (most numerous)
• Hydrophobic interactions (water pushing non-polar
  groups to the inside
• Ionic bonds form between a positive and a
  negative R group
• Covalent bonds very few form between R groups
  of 1 amino acid type
• Quarternary Structure when more than one
  polypetide binds together to make the final shape
  of the protein (ex. Hemoglobin) Functional!

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Nucleic Acids DNA

• Structure?
• base pairing (purine/pyrimidine,
• A-T, G-C, covalent bonding of back-
• bone, H bonding between bases
• Function?
• Code for proteins
• Copy itself before cell division
• Structure/function relationships?

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Structure/Function

• Why covalent bonds in backbone?
• In order to code for proteins order of the
  bases is most imp. The order is maintained by
  the backbone which cannot fall apart or DNA is
  useless
• Why H bonds between base pairs?
• Enough to hold the 2 strands together but easy
  enough to sep. for replication and transcription
• Why purine-pyrimidine pairs
• Purines double ringed, pyr single ringed by
  pairing, all along the DNA is the same width so
  the covalent bonds of the backbone arent
  strained
• Why do we need base pairing?
• Ensures exact copying

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Structure/Function

• Why covalent bonds in backbone?
• In order to code for proteins order of the
  bases is most imp. The order is maintained by
  the backbone which cannot fall apart or DNA is
  useless
• Why H bonds between base pairs?
• Enough to hold the 2 strands together but easy
  enough to sep. for replication and transcription
• Why purine-pyrimidine pairs
• Purines double ringed, pyr single ringed by
  pairing, all along the DNA is the same width so
  the covalent bonds of the backbone arent
  strained
• Why do we need base pairing?
• Ensures exact copying

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Structure/Function

• Why covalent bonds in backbone?
• In order to code for proteins order of the
  bases is most imp. The order is maintained by
  the backbone which cannot fall apart or DNA is
  useless
• Why H bonds between base pairs?
• Enough to hold the 2 strands together but easy
  enough to sep. for replication and transcription
• Why purine-pyrimidine pairs
• Purines double ringed, pyr single ringed by
  pairing, all along the DNA is the same width so
  the covalent bonds of the backbone arent
  strained
• Why do we need base pairing?
• Ensures exact copying

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Enzymes

• Chemical reactions will not happen in living
  things without enzymes because we cant produce
  enough energy available to get them to happen!
• Enzymes lower the activation energy of a chemical
  reaction so that it can happen at body
  temperature.
• This makes enzymes catalysts because they speed
  up chemical reactions

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How do Enzymes Work

• Each enzyme is different The each have a
  specially shaped pocket on their surface that
  matches the substrate
• Each enzyme can only catalyze one type of
  chemical reaction
• It works basically
• like a lock and key

Motion model of enzyme action
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Why are enzymes important?

• Because each enzyme can only catalyze one type of
  chemical reaction, reactions can only happen in
  the body where those enzymes are located.
• Enzymes control what chemical reactions happen
  where and how fast in the body so they generally
  run the body.

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Enzymes can either catalyze chemical reactions to
make bonds or to break bonds
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Making Reaction
The substrates go into the active site of the
enzyme it changes shape in such a way as to
smash the two substrates together they are now
so close that it takes less energy to form the
bond The bond now forms at regular body
temperature
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Breaking Reaction
The substrate goes into the active site the
enzyme changes shape in such a way as to twist
the substrate out of shape this strains one of
the bonds (the one that is supposed to break) by
making the atoms bonded together farther
apart Now body heat is enough to finish breaking
the bond
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How do Enzymes and Substrates Meet?

• Both are in motion so random collision
• If they match by shape and the substrate goes
  into the active the reaction will happen

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Things that affect enzyme activity and therefore
all of the chemical reactions in a cell or body

• Enzyme Concentration
• Substrate Concentration
• Temperature
• pH
• Co-enzymes vitamins large organic molecule
  fit into active site and makes the substrate fit
  better
• Co-factors ions fit into active site and make
  the substrate fit better
• Inhibitors
• Competitive fit into active site and block the
  real substrate from getting in no reaction when
  inhibitor is in active site
• Allosteric fits into a site other than active
  site changes shape of active site so it no
  longer works
• Cell signaling signals a shape change in the
  enzyme so that it now becomes the right shape and
  activates

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Role of Coenzymes
Allosteric Inhibitors
Cell signaling and Activation of Enzymes
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The Big Picture

• Body makes chemical reactions optimal by
  maintaining the temperature and pH within the
  body
• It can make reactions happen in certain places by
  having enzymes there or not
• It can make reactions go faster by making more
  enzymes
• It can make reactions happen based on signals by
  signaling to make enyzmes in a certain place or
  to activate enzymes that are already there but
  not the right shape yet.
• If cofactor or coenzymes are needed for a
  reaction, they wont work well without them
• If an inhibitor is present, the reaction will
  slow down or may not work at all