A&P Organic chemistry Flashcards
organic chemistry
Molecules and compounds that are much larger and complex chemically and structurally than inorganics
info on carbon
carbon allows for building on for bigger molecules
Located in the IV (4th group) of elements on the periodic table of elements (therefore shares common reactive properties with Silicon, Germanium, Tin, and Lead- contains 4 electrons in the valence (outer) shell.
Found on the 2nd row (period) of the periodic table of elements and thus has 2 electron shells around the nucleus of the atom.
Atomic # of 6 – therefore 6 protons & about 6 neutrons in the nucleus; atomic mass of 12.011
Constitutes about 18.5% of overall body mass
(carbon is also 1 of the major 4 elements found in the body)
Forms the backbone chains and rings of all organic molecules called carbon skeleton.
The 4 major categories of organics are
- Carbohydrates (CHOs) – “carbs” or sugars
- Lipids (e.g. fats)
- Proteins (made up of amino acids)
- Nucleic acids: RNA & DNA
Adenosine triphosphate (ATP) (Considered a minor category of organic molecules but traditionally is grouped with nucleic acids due to the adenine group)
covalent bonds
Organic molecules & compounds ALWAYS contain CARBON (C) and almost all the time HYDROGEN (H), and most of the time, oxygen & nitrogen (“CHON”).
Sulphur & phosphorus are also present sometimes.
Organic compounds are held together by COVALENT BONDS
hydrocarbons
the carbons in a carbon skeleton, that are bound to hydrogen atoms.
Functional groups – there are 7 common functional groups that can combine with carbon and confer unique chemical characteristics. R = variable group functional group is attached to.
You need to recognize the different functional groups!!!
7 major functional groups
- *Hydroxyl – contains OH, polar and hydrophilic – alcohols
- Sulfhydryl – contain SH group – some amino acids – thiols creates polarity in a molecule
- Carbonyl – ketones and aldehydes – ketones are breakdown products of fats & proteins
- **Carboxyl – contains COOH – a component of amino acids – can act as an acid
- Ester – compounds found in fats, oils, and triglycerides
- *Phosphate – contains PO4 – key component of ATP
- *Amino – contains NH2 – a component of amino acids – can act as a base => NH3
Hydroxyl
contains OH, polar and hydrophilic –
Phosphate
contains PO4 – key component of ATP
Amino
contains NH2 – a component of amino acids – can act as a base => NH3 building blocks of proteins
a base is a
proton acceptor
the more polar a molecule are, the more they
dissolve in water
OH is base H is acidic
oxygen is an electron hog
polar molecules
dissolve more easily in water
fats are non soluble non polar
fats and oils are hydrophobic
structure of carbon compounds
MONOMER– Smallest unit of an organic molecule
one of the beads.. like an amino acid
POLYMER – Larger organic molecule consisting of monomers (usually created by dehydration synthesis reactions where an H2O is formed and results in a hydroxyl group and a hydrogen being removed)
-would be the protein itself
-imagine a beaded necklace is like a polymer
the monomer is a part of the larger structure of the polymer
ISOMERS – Molecules with the same chemical formula but different chemical structure allowing it different reactive properties. E.g. C6H12O6 = glucose and fructose. Both are considered monomers, both have pentose ring shaped configurations but functional groups are located on different # carbon. (Because of this, fructose yields a higher ATP energy content) [“iso” means “the same”.]
same amount of atoms but configured in different shapes its all about specificity and so they have different functions
dehydration synthesis
removal of water to form peptide bonds:
A + B A-B + H2O
hydrolysis
Hydrolysis – addition of water to break peptide bonds:
A-B + H2O A + B
carbohydrates
Includes sugars, glycogen, starches, and cellulose.
carbohydrates most rapid and readily form of energy in the body
Consists of (C)arbon, (H)ydrogen, and (O)xygen – (polar covalent bonds, polar=disolvable)
Thus carbohydrates are molecules of carbon saturated with hydrogen & oxygen i.e.“watered or hydrated carbon”.
Most will have an “-ose” suffix, e.g.: glucose, fructose, mannose, galactose, hexose, etc….
Usually accounts for < 3% of total body mass. (WHY? B/c vast majority of CHOs are utilized for ATP/energy production. However, if you have less of a need for energy, CHOs are easily converted into lipids and are deposited into love handles.
classifications of carbohydrates
A) MONOSACCHARIDES – Simplest of the 3 (this is the monomer of carbohydrates) and includes:
Glucose (blood sugar), fructose (found in fruits), galactose (milk and milk products), deoxyribose (DNA), and ribose (RNA)
B) DISACCHARIDES – Product of a combination of 2 monosaccharides by dehydration synthesis (removal of H2O)
E.g. glucose + fructose = sucrose + H2O
glucose + galactose = lactose + H2O
Note: the addition of water (hydrolysis reactions) will reverse this.
Sucrose + H2O = glucose + fructose
C) POLYSACCHARIDES – Up to thousands of monosaccharides in combination.
GLYCOGEN – The human body’s main polysaccharide stored in muscles and the liver (this compound will be broken down during catabolic reactions when energy is needed).
Starches – Polysaccharide found in plants (e.g. potatoes and wheat).
Cellulose – Stored in plants, indigestible in humans, but helps with bowel movements, and cleansing of the colon (people who consume large amounts of green leafy vegetables have a lower incidence of colon cancer).
when exercising ATP comes from
When we first begin exercising, our muscles require energy in the form of ATP (adenosine triphosphate)
ATP comes from 3 sources:
#1 – Creatine phosphate (CP) – compound is always present in our muscles, generates enough ATP for max contraction for <15 secs
# 2 – Anaerobic metabolism – kicks in after CP, no O2 needed, generates enough ATP for max contraction for 30-40 secs (utilizes glucose as part steps 1 & 2 of cellular respiration)
# 3 – Aerobic metabolism – generates ATP for >40 secs to hours, requires O2 (utilizes glucose as part of steps 3 & 4 of cellular respiration but also taps into lipid sources!!!)
lipids
not many oxygens which makes them less disolvable in water
These comprise up to 25% of body mass.
Tend to have less hydrogen to oxygen ratio and therefore are not as polar. That means they are more HYDROPHOBIC and NON-POLAR, and thus DO NOT dissolve easily in water (recall our discussion about them floating on surfaces of water).
Only very small lipids or lipids that are attached to proteins may dissolve in water. For example:
Glyco-lipids (“sugar-fats”)
Lipo-proteins (“fat-proteins”)
a) FATTY ACIDS
A) Fatty Acids (FA’s) – Simplest of lipids
Used to make PHOSPHOLIPIDS and TRIGLYCERIDES & also ATP when needed.
Consists of a CARBOXYL group and a hydrocarbon chain.
If the hydrocarbon chain has only SINGLE COVALENT bonds, it’s termed SATURATED (i.e. it’s completely saturated with hydrogen).
If there is 1 or more DOUBLE COVALENT bond (a kink), it’s called UNSATURATED (i.e. it’s only partially saturated with hydrogen).
MONOUNSATURATED – 1 db-covalent bond = 1 kink
POLYUNSATURATED – More than 1 db-covalent bond = 2 or more kinks
b) TRIGLYCERIDES
Triglycerides (fats and oils) – AKA triglycerols
Unlimited capacity to store adipose tissue in various locations throughout the body (breasts, abdomen, bottom, thighs, face….etc.).
Contains 1 GLYCEROL molecule and 3 FA (fatty acids) chains. (Again they’re formed by dehydration synthesis.)
3 main types:
1. SATURATED FATS – Contains FAs of SINGLE covalent bond only.
Found in meats, dairy products (milk, cheese, butter) but also in some plants (coconut & palm oil)
- MONOUNSATURATED FATS fats – Contains 1 DOUBLE covalent bond.
Found in olive, peanut, canola, and most other nut oils. - POLYUNSATURATED FATS – Contains MORE than 1 DOUBLE covalent bond.
Found in corn, soybean, sunflower, and some fish oils.
The more double covalent bonds present in the chain, the less hydrogen, and the easier it is for the body to metabolize and Incorporate into our tissues (the better it is for us)
OILS = triglycerides that are liquid @ room temp tends to be more UNSATURATED (the more kinky it is)
FATS = triglycerides that are solid @ room temp tends to be more SATURATED
essential & non essential fatty acids
Excess proteins, CHOs, fats & oils (more than the body requires for energy) all have the same fate. They are converted to triglycerides and stored in adipose tissue!!!!!
*Essential fatty acids (EFAs) – Must be derived from our diets b/c our bodies can’t make them. Examples are:
Omega 3s (ALA, EPA, & DHA) - Found in flaxseed, canola, soybean, & most fishes. Omega 6s (LA) - Found in sunflower, soybean, pumpkin, grapeseed, olives, hempseed.
*Non Essential fatty acids – Our bodies can make these compounds.
Example Omega 9’s (Oleic acid) – found in olive oil, almonds, peanuts, pecans, pistachios, cashews…
These FAs have all been discovered to protect against heart disease by lowering LDLs and raising HDLs. May play key roles in inflammation, wound healing, skin disorders, and mental functioning.
trans is refering to the opposite side artificially produced to elongate shelf life hydrogynation and last forever. bad
cis refers to same side
When -cis- fatty acids (the good kind) are heated, pressurized, and/or treated (chemically or physically) they become hydrogenated and take on a trans form (this process is called hydrogenation). This is for the sole benefit of longer shelf life of products. But we all now know that the trans fatty acids have been linked to increases of LDLs and decreased HDLs and therefore, a plethora of cardiovascular disease (baked, fried, BBQd, & deep fried foods).
Lipoproteins
Low Density Lipoprotein (LDL) – “BAAAAD cholesterol” – responsible for adding cholesterol to our circulation (clogging our arteries).
High Density Lipoprotein (HDL) – “Good cholesterol” – responsible for taking cholesterols out of our circulation.
Both HDLs & LDLs are produced in the liver & released into the blood stream. (We will examine Lipoproteins in much more detail in Chp 25 & 26 in AP400.)
c) phospholipids
Contains PHOSPHOROUS in its structure, hence the name.
Major component of cellular membranes and
Is AMPHIPATHIC – a molecule that has both POLAR and NON-POLAR ends. This is due to the fact that the phosphate head is polar (HYDROPHILIC) and the fatty acid tails are non-polar (HYDROPHOBIC).
The heads are exposed to water environments (ICF intracellur fluid & ECF extracellular fluid), whereas the tails are hidden away from water environments
NOTE: Molecules that are NON POLAR, such as fats, may pass through the membrane EASILY, others that are POLAR/hydrophilic may NOT pass through very easily.
d) steroids
Consists of 4 rings of carbon.
CHOLESTEROL – Precursor to hormones & vit D – can create low density (bad) and high density (good) lipoproteins & also a part of cell membrane structure.
HORMONES – estrogens & testosterone
BILE-SALT – produced by the liver, stored in the gall bladder, - “emulsifies” (digests) fats
VITAMIN D – Req’d for normal bone growth.
e) eicosanoids
Eicosanoids – 20-carbon FA chains
Prostaglandins (PGs) – Inflammatory responses, bronchiole dilation, body temperature, blood clots.
Leukotrienes (LTs) – Allergic & inflammatory responses.
f) other lipids
Carotenes – Precursor to vit A (pigments of rods and cones in the eyes), and also for antioxidant properties. Found in beets, carrots, & tomatoes.
Vitamin E – Tissue healing and powerful antioxidant (neutralizes free radicals).
Vitamin K – Helps in the formation of blood clots (more on this in AP200 or Chp. 19).
PROTEINS
acronym: STRICCt
Makes up 12-18% of body mass.
Many varying types of proteins found in the body:
- Structural – Plays a key role in the formation and framework of different cells and tissues. E.g. keratin in skin, hair and nails.
- Regulatory – Function as key parts of the structure of hormones (e.g. insulin & glucagon).
- Contractile – Forms filaments in muscles and cellular components (i.e. myosin and actin).
- Immunological – Forms key parts of immunological cells like white blood cells and antibodies.
- Transport – Forms key components of red blood cells and membrane structures of certain cells.
- Catalytic – Forms majority of enzymes produced in the body (recall enzymes contribute to all biochemical reactions in the body).
MONOMERS of PROTEINS are
- AMINO ACIDS which includes a
1. CARBOXYL group (acid),
2. an AMINE group (base), and a
3. SIDE CHAIN (hence the term amino acid).
- AMINO ACIDS which includes a
*There are about 20 total amino acids altogether. The human body can synthesize 12 of these needed to make protein. These are called NON-ESSENTIAL amino acids
The other ones that are also required but not found in the body are called ESSENTIAL amino acids (we need to get these 8 from our diet).*
PEPTIDE BONDS= PROTEINS
ALL PROTEINS HAVE A AMINO GROUP AND A CARBOXYL GROUP
Amino acids when combined together to make proteins are joined by PEPTIDE bonds (a type of covalent bond formed by dehydration synthesis reactions).
the creation of these proteins is called:… “PROTEIN SYNTHESIS”
- PRIMARY STRUCTURE
know the four structures and what they are
Primary structure – Unique sequence of amino-acids of a polypeptide chain (genetically determined).
- SECONDARY STRUCTURE
Secondary structure – The repeated twisting of neighboring amino acids in the polypeptide chains – can be either or both of beta pleated sheets or alpha helices.
- TERTIARY STRUCTURE
Tertiary structure – 3-D shape of the polypeptide chain. Secondary structures folding upon themselves.
- QUATERNARY
Quaternary structure - Arrangement of 2 or more poly peptide chains
DENATURATION
Denaturation – Term used to describe the altering or DESTRUCTION of the protein structure, usually in pathological conditions. E.g. Frying an egg, stomach enzymes during digestion.
ENZYMES – Protein molecules that act as catalysts in biochemical reactions.
Consist of:
*Apoenzyme – protein portion
*Cofactor – non protein portion
NUCLEIC ACIDS
nucleotides are the monomers
NUCLEIC ACIDS** (Originally found in the nucleus of cells) Contain :
carbon, oxygen, nitrogen, hydrogen &
phosphorus contributing to 3 parts of a nucleic acid:
**
1. Nitrogen base, there are 5 types -
(Adenine, Guanine, Cytosine, Thymine, & Uracil)
- Pentose sugar (5-carbon sugar)
- Phosphate group – PO43-
2 main types of nucleic acids: DNA & RNA
DNA
A) DeoxyRIBOnucleic acid (DNA) – “the blue print” – forms the genetic material (chromosomes).
form of nucleic acid and makes us*
Present in all our cells. Consists of “genes” which are
segments of the DNA molecule that consists of
specific nucleotides which encode for various
combinations of amino acids, which in turn will
produce proteins. These proteins, when grouped with
many other proteins, become functional and are
expressed as traits that we pass on from 1
generation to the next. E.g. Eye color, height, body
shape & size, etc.
DOUBLE STRANDED
**Double stranded structure
- The sugar is de-oxyribose
Nitrogenous bases are
Adenine, Thymine, Cytosine, & Guanine
DNA is represented via the Double Helix model discovered by Watson & Crick in 1953 (they won the Nobel peace prize in physics that year).
Similar to the rungs of a ladder, the
phosphate & sugar alternate forming the sides,
purines & pyrimidines alternate forming the rungs.
The bases are held together by hydrogen bonds.
4 NUCLEOTIDES
PHOSPHATE group SUGAR AND nitrogonous BASES
There are 4 nitrogenous bases:
PURINES:
Adenine – (A)
Guanine – (G)
PYRIMIDINES:
Thymine – (T) —–(Replaced by URACIL (U) in RNA.)
Cytosine – (C)
adenine loves thymine A&T
guanine loves cytosine G&C
adenine loves uracilU (in RNA)
RNA
Ribonucleic acid (RNA) – Relays instructions from the genes to guide the cell’s protein synthesis. Single stranded structure The sugar is ribose NITROGENOUS BASES are Adenine, Uracil, Cytosine, & Guanine
For RNA, there are 3 different types in the cell:
MESSENGER (mRNA) – Plays a role in TRANSCRIBING the original DNA.
TRANSFER (t-RNA) – Plays a role in amino acid TRANSLATION
RIBOSOMAL (r-RNA) – Forms a TEMPLATE for amino acid translation.
ATP**
Adenine + 1 ribose and a group of phosphates
Adenosine Tri Phosphate (ATP):
The energy currency of the body. ATP is required to drive all reactions in the body.
ATP comes from many sources (lipids, sugars, proteins…)
Consists of 1 adenine (same as the purine in RNA & DNA), 1 ribose sugar, & a group of phosphates.
ATP is converted to ADP (Adenosine-Di –Phosphate) by the enzyme ATPase to liberate or release 1 phosphate group during exergonic reactions).
hydrolisis (exergonic)
when you add h2o to ATP
when you add water and break a bond
dehydration synthesis (endergonic)
adds energy breaks bond releases water
Carbon compounds may be 1 of 3 shapes or combinations of:
Straight – carbons are arranged in a linear sequence – e.g. ethane
Branched – carbons are arranged in branching sequences – e.g glycogen
Ringed – carbons are arranged in a closed ringed pattern e.g. glucose
peptide bonds
peptide bonds (a type of covalent bond formed by dehydration synthesis reactions)
activation energy
activation energy is the amount of energy required for a chemical reaction to occur
an uncatalyzed reaction requires a higher activation energy than does a catalyzed
enzymes
ENZYMES – Protein molecules that act as catalysts in biochemical reactions.
Consist of:
*Apoenzyme – protein portion
*Cofactor – non protein portion
Highly SPECIFIC
Highly SPECIFIC – its active site (portion on the enzyme) will bind only to certain substrates of reactant molecules.
efficient
EFFECIENT – acts as catalysts to speed up reactions by lowering the activation energy required to initiate reactions.
Subject to cellular control – efficiency & activity of the enzyme is controlled by the cellular environment. The cell controls the activities of its enzymes. E.g. Pepsinogen pepsin only in the presence of HCl.
