A&P Organic chemistry

Question 1

organic chemistry

Answer 1

Molecules and compounds that are much larger and complex chemically and structurally than inorganics

Question 2

info on carbon

carbon allows for building on for bigger molecules

Answer 2

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.

Question 3

The 4 major categories of organics are

Answer 3

1. Carbohydrates (CHOs) – “carbs” or sugars
2. Lipids (e.g. fats)
3. Proteins (made up of amino acids)
4. 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)

Question 4

covalent bonds

Answer 4

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

Question 5

hydrocarbons

Answer 5

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!!!

Question 6

7 major functional groups

Answer 6

1. *Hydroxyl – contains OH, polar and hydrophilic – alcohols
2. Sulfhydryl – contain SH group – some amino acids – thiols creates polarity in a molecule
3. Carbonyl – ketones and aldehydes – ketones are breakdown products of fats & proteins
4. **Carboxyl – contains COOH – a component of amino acids – can act as an acid
5. Ester – compounds found in fats, oils, and triglycerides
6. *Phosphate – contains PO4 – key component of ATP
7. *Amino – contains NH2 – a component of amino acids – can act as a base => NH3

Question 7

Hydroxyl

Answer 7

contains OH, polar and hydrophilic –

Question 8

Phosphate

Answer 8

contains PO4 – key component of ATP

Question 9

Amino

Answer 9

contains NH2 – a component of amino acids – can act as a base => NH3 building blocks of proteins

Question 10

a base is a

Answer 10

proton acceptor

Question 11

the more polar a molecule are, the more they

Answer 11

dissolve in water

Question 12

OH is base H is acidic

Answer 12

oxygen is an electron hog

Question 13

polar molecules

Answer 13

dissolve more easily in water

Question 14

fats are non soluble non polar

Answer 14

fats and oils are hydrophobic

Question 15

structure of carbon compounds

Answer 15

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

Question 16

dehydration synthesis

Answer 16

removal of water to form peptide bonds:

A + B  A-B + H2O

Question 17

hydrolysis

Answer 17

Hydrolysis – addition of water to break peptide bonds:

A-B + H2O  A + B

Question 18

carbohydrates

Answer 18

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.

Question 19

classifications of carbohydrates

Answer 19

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).

Question 20

when exercising ATP comes from

Answer 20

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!!!)

Question 21

lipids

not many oxygens which makes them less disolvable in water

Answer 21

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”)

Question 22

a) FATTY ACIDS

Answer 22

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

Question 23

b) TRIGLYCERIDES

Answer 23

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)

2. MONOUNSATURATED FATS fats – Contains 1 DOUBLE covalent bond.
   Found in olive, peanut, canola, and most other nut oils.
3. 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

Question 24

essential & non essential fatty acids

Answer 24

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.

Question 25

trans is refering to the opposite side artificially produced to elongate shelf life hydrogynation and last forever. bad
cis refers to same side

Answer 25

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.)

Question 26

c) phospholipids

Answer 26

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.

Question 27

d) steroids

Answer 27

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.

Question 28

e) eicosanoids

Answer 28

Eicosanoids – 20-carbon FA chains
Prostaglandins (PGs) – Inflammatory responses, bronchiole dilation, body temperature, blood clots.
Leukotrienes (LTs) – Allergic & inflammatory responses.

Question 29

f) other lipids

Answer 29

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).

Question 30

PROTEINS

acronym: STRICCt

Answer 30

Makes up 12-18% of body mass.
Many varying types of proteins found in the body:

1. Structural – Plays a key role in the formation and framework of different cells and tissues. E.g. keratin in skin, hair and nails.
2. Regulatory – Function as key parts of the structure of hormones (e.g. insulin & glucagon).
3. Contractile – Forms filaments in muscles and cellular components (i.e. myosin and actin).
4. Immunological – Forms key parts of immunological cells like white blood cells and antibodies.
5. Transport – Forms key components of red blood cells and membrane structures of certain cells.
6. Catalytic – Forms majority of enzymes produced in the body (recall enzymes contribute to all biochemical reactions in the body).

Question 31

MONOMERS of PROTEINS are

Answer 31

• • AMINO ACIDS which includes a
    1. CARBOXYL group (acid),
    2. an AMINE group (base), and a
    3. SIDE CHAIN (hence the term amino acid).

*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).*

Question 32

PEPTIDE BONDS= PROTEINS

ALL PROTEINS HAVE A AMINO GROUP AND A CARBOXYL GROUP

Answer 32

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”

Question 33

1. PRIMARY STRUCTURE

know the four structures and what they are

Answer 33

Primary structure – Unique sequence of amino-acids of a polypeptide chain (genetically determined).

Question 34

2. SECONDARY STRUCTURE

Answer 34

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.

Question 35

3. TERTIARY STRUCTURE

Answer 35

Tertiary structure – 3-D shape of the polypeptide chain. Secondary structures folding upon themselves.

Question 36

4. QUATERNARY

Answer 36

Quaternary structure - Arrangement of 2 or more poly peptide chains

Question 37

DENATURATION

Answer 37

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

Question 38

NUCLEIC ACIDS

nucleotides are the monomers

Answer 38

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)

2. Pentose sugar (5-carbon sugar)
3. Phosphate group – PO43-

2 main types of nucleic acids: DNA & RNA

Question 39

DNA

Answer 39

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.

Question 40

DOUBLE STRANDED

Answer 40

**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.

Question 41

4 NUCLEOTIDES

PHOSPHATE group SUGAR AND nitrogonous BASES

Answer 41

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)

Question 42

RNA

Answer 42

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.

Question 43

ATP**

Adenine + 1 ribose and a group of phosphates

Answer 43

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).

Question 44

hydrolisis (exergonic)

Answer 44

when you add h2o to ATP

when you add water and break a bond

Question 45

dehydration synthesis (endergonic)

Answer 45

adds energy breaks bond releases water

Question 46

Carbon compounds may be 1 of 3 shapes or combinations of:

Answer 46

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

Question 47

peptide bonds

Answer 47

peptide bonds (a type of covalent bond formed by dehydration synthesis reactions)

Question 48

activation energy

Answer 48

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

Question 49

enzymes

Answer 49

ENZYMES – Protein molecules that act as catalysts in biochemical reactions.
Consist of:
*Apoenzyme – protein portion
*Cofactor – non protein portion

Question 50

Highly SPECIFIC

Answer 50

Highly SPECIFIC – its active site (portion on the enzyme) will bind only to certain substrates of reactant molecules.

Question 51

efficient

Answer 51

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.