Glossary of Bio 13 Tufts general bio chem

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What is a Non polar bond?
Molecules share electrons evenly making them more stable
what are characteristics of a Polar bond
1. One molecule has a greater affinity for electrons (like oxygen)
2. Tend to be soluble in H2O
What is an ionic bond
Fully charged molecules attract each other
(salt is formed by NA+ and Cl-)
what is Chemical Equilibrium?
When the forward and reverse reactions proceed at the same rate, the quantities of reactants and products remain constant, although not necessarily equal.
When there is more (*quanity) of one reactants than the other this means that one of the two chemicals has a higher free energy
What is free energy. Give 4 basic ideas associated with free energy
Every chemical has a certain free energy
1. The less chemical free energy a molecule has, the more stable it is.
2. Chemical processes tend to proceed to the lowest energy state (the lowest G)
3. Activation Energy still need to be put into the reaction.
4. All life pushes against equilibrium
What is the pH scale?
pH = -log[H+] or 1/log[H+]
What are three properties of acids
1. substances that give up protons (H+) during chemical reactions
2. pH < 7
3. [H+]>>[OH]
What are three properties of bases?
1. molecules or ions that acquire protons (H+) during a chemical reaction
2. pH>7
3. [H+]<<[OH]
What is an acid base reaction?
1. a reaction that involves a transfer of atoms
2. in a solution the tenancy for acid-base reactions to occur depends largely on the number of protons present
1. R-CH3
2. unreactive and hydrophobic
1. Found in alcohols, carbohydrates, and amino acids, etc…
2. polar but not acidic
3. H can take part in H bonds
1. Found in sugars
2. More reactive than alcohols
3. the O can act as an H- bond acceptor
1. The C bonded to the OH is already electron deficient (because of the dbl bonded O) the O of the OH group can only pull e- from the H.
2. As a result, the proton of the H is dissociable
Acetic acid (a weak acid)
CH3COOH <===> CH3COO- + H+
Acetic acid (a weak acid)
in the carboxyl family
1. basic
lone pair of electrons take up a proton at a neutral pH
because N is electronegative the H groups can participate in H bonds
1. found in the amino acid cystein
2. in proteins can for sulfhydry bridges (also called thiol bridges) which link together distant parts of the polyamino acid chain
common constituents of membrane bilayers
what are formed by acids and alcohols?
highly charges and are found in a wide variety of biological molecules
phosphate esters
Alternative forms of molecules that have the same molecular formula
Structural Isomers
Built from the same atoms, but with different arrangements
Geometric Isomers
refers to the arrangement of atoms in space in molecules in which rotation around a bond is not allowed
(molecules with dbl bonds or ring structures)
Optical Isomers
1. Occur whenever a carbon atom has four different atoms or groups attached to it.
a. this carbon is called a chiral carbon or a chiral center or an optical carbon or an optically active carbon or an asymmetrical carbon
2. There will be two different ways to order groups around the carbon (one is a mirror image of the other)
To determine the number of Optical Isomers of any molecule
count the number of chiral centers (n) and it will be 2ⁿ
What functional groups does an amino acid consist of?
amino and carboxy groups
Why is an amino acid reactive?
in water at a pH of 7 the concentration od protons causes the amino group to act as a base and attract a proton [H+] to form NH₃+. The carboxy group looses a proton to form COO-.
Are nonpolar side chaind hydrophobic or hydrophillic? why?
Hydrophobic because they do not have charged or electronegative molecules capable of forming hydrogen bonds with water.
Are polar and/or charged amino acid side chains hydrophobic or hydrophilic? why?
They are both hydrophilic because the charged or polar side chains can form hydrogen bonds with water and can easily disolve. (Think of salt dissolving)
What is a peptide bond?
When two amino acids join. The carboxyl group loses the OH and joins with an N of the amino group (which loses an H as well)
It may seem that a molecule of water is formed however this in not the case. ATP is needed to drive the reaction so there is actually no H2O biproduct.
What properties does the C-N peptide bond have?
it is planer, it acts like a double bond
Which side and group is an amino acid's C-terminus?
Right hand (carboxyl group)
Which side and group is an amino acid's N-terminus?
left hand end (amino group)
What does the interior of a protein gen. consist of?
usually hydrophobic amino acid R groups
What does the exterior of a protein gen. consist of?
there can be a concentration of charged and polar groups on the surface of the protein
What are molecules that help proteins fold?
Chaperone molecules/proteins
What is a protein's Primary structure
Order (sequence) of amino acids
What is a protein's Secondary Structure
1. interaction between amino acids close together
(usually with hydrogen bonds)
2. α-helix
3. β-pleated sheet.
What is a protein's Tertiary structure?
1. interaction with far apart amino acids (the majority of the folding of the protein)
1. disulfide bridges (covalent bonds can form between sulpfer atoms)
2. van der Waals interactions
What are van der Waals interactions?
a. weak attraction until get to radii
b. when too close strong repulsion
What makes a protein's Quaternary structure?
relationships between separate proteins
(Non covalent forces)
1. a.k.a. Ionic forces, hydrophobic, H-bonds
what is the transition state?
the combination of new and old bonds
what is the activation energy?
the amount of free energy needed to reach transition state
How does a protein lower the activation energy needed for a reaction?
A protein orients molecules in a precise way so that the electrons in the transition state molecule can be stabilized when they interact with another ion, atom or molecule
when this occurs, the activation energy required for the reaction drops and the reaction rate increases
How do we know which amino acids are involved in the active site of a protein? (sup p 28)
a. use chemicals that react with specific amino acids in the presence of/not in the presence of substrates
b. test to see which amino acids were modified
c. the ones that were modified w/o substrate but are not present w/ substrate are involved in active site
What are Cofactors?(vitamins)
They help stabilize transition state
1. metal ions
2. coenzymes
What is the formula for a saturation curve?
rate = v = ¯Km¯+¯[S]¯
a. Vmax is max rate of reaction
b. Km is =1/2Vmax (a constant)
c. Km is also a measure of the affinity between substrate and enzyme
d. The LOWER the Km the GREATER the affinity of enzyme for substrate
What are the three types of enzyme inhibition?
1. Irreversible enzyme Inhibitors (poisons)
2. Competitive inhibition (reversible)
3. Allosteric regulation (inhibitors and activators) (reversible)
How do Irreversible enzyme Inhibitors (poisons) work?
react with certain specific amino acids at active site
How does Competitive inhibition (reversible) work?
1. molecule competes with substrate for active site
2. if you add enough substrate you can overcome competitive inhibition because inhibitor is constantly being re-released.
3. cause Km to rise but have no effect on Vmax
How does Allosteric regulation (inhibitors and activators) (reversible) work?
1. binds at different site (regulatory site)
2. causes a conformational change in enzyme that makes it have less affinity for substrate
3. in a long process (such as glycolysis) often slowest step is regulated (see ch 9)
What is the difference between a ribose sugar and a deoxyrobose sugar?
Ribose: OH group attached to 2’ (5 o'clock)carbon

Deoxyribose: H attached to the 2’ carbon
Where is the phospate group of a nuclotide attach to a sugar
At the 5'carbon (the one that hangs off of the ring at the 10:00 position)
Where does the nitrogen base of a nucleotide attach to a sugar?
1' (3:00 position)
What are the Pyrimidines (single ring)(the small ones)
a. Cytosine
b. Uracil
c. Thymine
What are the purines? (dbl ring/the big ones)
a. Guanine
b. Adenine
What is a Phosphodiester linkage or bond
Bond between phosphate group of one nucleotide and hydroxyl group of sugar (at the 3')of second
What is the structure of starch?
1. polymer of α-glucose (6 carbon sugar)molecules (the OH coming of the 1' carbon is on the bottomn)
a.α-1 (3:00),4 (9:00)linkage
2. forms a helix
3. Actually a mixture of two polysaccharides (branched and unbranched)
a. amylose- unbranched helix
b. amylopectin- branched
What is amylose? What is its structure?
an unbranched helix component of starch.
What is amylopectin? What is its structure?
a branched helix component of starch.
What is glycogen? What is its structure?
glycogen is used for storage in animals. It is a polysacheride of alpha-glucose. It is helical and HIGHLY branched
What is cellulose? What is its structure?
structural function in plants (cell wall)
1. polymer of a β-glucose
2. joind by 1, 4 linkages
3. glucose momomer is flipped
a. therefore parallel strands form H bonds making cellulose very rigid
4. indigestible by almost everything but microscopic organisms
What are Glycoprotein molecules?
molecules that project outward from cell and act as an ID strip
a protein that is covalently bonded to a carb—usually a short chain of sugars
each cell type has a specific ID
What is a lipid?
catch all term for carbon containing compounds that are found in organisms and are largely nonpolar and hydrophobic
What are hydrocarbons?
1. molecules containing only carbons and hydrogens
2. they are nonpolar and therefore hydrophobic
3. lipids have significant hydrocarbon compounds and therefore are hydrophibic and do not dissolve in water
What are fatty acids?
1. Hydrocarbon chain (hydrophobic)connected to a carboxyl (COOH) [carboxylic acid] (Hydrophilic)
2. When placed in water fatty acids associate in droplets called micelles
What are micells?
droplets of fatty acids that form in water
1. in micells hydrophobic chains point inward (to avoid the water)
a. these hydrophobic molecules can be “dissolved” in the interior of the micelle (not in water)
2. charged acid ends face outward (towards the water solution)
what are saturated fatty acids?
1. no C=C dbl bonds
2. linear molecules
What are unsaturated fatty acids?
1. C=C dbl bonds
2. kinked because the C=C bonds are rigid
what is Isoprene?
key building block of lipids
What are Neutral Fats?
molecule of glycerol ( three carbon tri-alcohol) esterfied (acids and alcohols react to form esters) to three fatty acid molecules
Not found in membranes but rather in fat
Very energy rich
What are Phospolipids?
a phosphate group linked to a glycerol and either 2 fatty acid chains or two isoprene chains
-major component of cell membranes
-the molecule is highly charged at one end and very hydrophobic at the other.
-it can form bilayers in which the fatty acids face each other in the interior of the bilayer and the phosphate ends project out
What are streoids? why are they classified as lipids?
they are 4 ring structure made of Isoprene subunits
they are NOT made of fatty acids but are considered lipids because of their insolubility in water

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