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54 Cards in this Set

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What are enantiomers?
-2 biomolecules containing 1 or more chiral centers which are nonsuperimposable mirror images of each other
What is definition of conformation?
-the spatial arrangement of substituent groups that are free to assume different positions in space WITHOUT BREAKING BONDS

-elcipse
-staggered
-boat
-chair
How do you spot oxidation?
-molecule gains an O
How do you spot reduction?
-molecule gains H
What does it mean if G is +'ve?
-not spontaneous, needs input of free energy to proceed; endergonic
What does it mean if G is -'ve?
-spontaneous, releases free energy which can be used to do work; exergonic

-continues until equilibrium is reached
What does it mean if H is -'ve?
-exothermic; heat is released
What does it mean if H is +'ve?
-endothermic, heat is absorbed
What does it mean if S is -'ve?
-less random, more structured
What does it mean if S is +'ve?
-more random, less structured
What are enzymes?
-biological catalyests which allow chemical reactions to proceed quickly and efficiently
How is information transfered living organisms?
DNA->transcription->RNA->translation->
PROTEIN->function

**the 3-D shapes of proteins are unique and important. if the shape changes, due to mutations, the function changes**
What are some characteristics of water?
-has high heat of vaporization
-has high heat capacity
-solvent for polar and ionic biomolecules
-contributes to structure and function of biomolecules
-medium for biochemical processes and reactions
-Hydrogen bonding gives water its unusual properties
What is electronegativity?
-the ability of an atom to attract electrons to its nucleus

**the greater the difference in electronegativity between 2 atoms, the greater the polarity of the bond**
What 2 behaviors of water affect the behavior of biological molecules?
1)Polarity: it's cohesive and it likes other polar molecules too

2)Tendency to dissociate into OH and H
How many H-bonds can a single water molecule form?
-4
What is hydration/solvation?
-the insulation of charged particles by water
What does amphipathic mean?
-molecules with a polar group (hydrophilic) and a nonpolar region (hydrophobic)
Consider bilayers and micelles. Which allows water to have more entropy?
-micelles allow water to have more entropy

**just in case, micelles are those globular amphipathic balls**
What are the 4 major types of noncovalent interactions that influence the structure and function of biomolecules?
1)Ionic Interactions: attract and repel

2)Hydrogen Bonds: H bonds

3)Van der Waals forces:
a)Dipole-Dipole
b)Dipole-Induced Dipole
c)Transient dipole-transient dipole

4)Hydrophobic interactions: nonpolar molecules create a 'water shell'. Increase in entropy of surrounding water
How do you calculate pH? or p anything for the matter.
pH = -log[H]
Why is it important to maintain constant pH in living organisms? 2 reasons
1) Maintain catalytic activity of enzymes

2) Maintain homeostasis intracellularly and extracellularly
What does it mean if K is a large number?
-means that the molecule is more likely to ionize

**therefore, if K is large, acid is strong**
What does it mean if pKa is a large number?
-means that the acid strength is decreasing
Whats the difference between Monoprotic, Diprotic and Triprotic acids?
-Monoprotic acids lose 1 H
-Diprotic acids lose 2 H
-Triprotic acds lose 3 H

**Monoprotic is weak, triprotic is strong**
When is a weak acid best able to resist change in pH?
-when pH=pK
-when [HA]=[A]
What are the 3 main types of carbohydrates?
1)Monosaccharides- single sugar

2)Oligosaccharides- 2 to 20 sugars

3)Polysaccarides- more than 20 sugars
What are the 5 main functions of carbohydrates?
1) Primary source of energy metabolism

2) Storage form of energy

3) Biosynthesis

4) Structural components

5) Informational roles
What is an epimer?
-2 monoscaccharides which differ only in the configuration about a SINGLE chiral center

-that chiral center is now called an epimeric carbon
What is a hemiacetal?
-a chiral carbon with an -OH and a -OR

**Acetals have 2 -OR's**
What is alpha bonding?
-occurs when monosaccharides form a ring
-OH group is trans to the CHHOH on the 6 carbon (across the O)

**Remember: When 2 rings join, the bond type of the leftmost ring takes priority and that bond is used in the final name!**
What is Beta bonding?
-occurs when monosaccharides form a ring
-OH group is cis to the CHHOH on the 6 carbon (across the O)

**Remember: When 2 rings join, the bond type of the leftmost ring takes priority and that bond is used in the final name!**
What are reducing sugars?
-sugars which contain a potentially reactive aldehyde group that can be oxidized (ie: has a free OH at the anomeric carbon)

-reducing sugars are the rightmost group of sugar when drawn properly (ie: from left to right)
What's the difference between linear and branched polysaccharide chains?
-linear chains are in a straight, single line

-branched chains branch off from main chains

**sugars are removed from the non-reducing end**
What's the difference between amylose and amylopectin in terms of linkage?
-amylose is a linear polysaccharide, composed of 10->1000 D-flucose residues. Bonds are alpha(C1->C4)

-amylopectin is a branched polysaccaride composed of 300->6000 sugars or more. Bonds are alpha(C1->C4) on linear sugars but are alpha(C1->C6) on branching sugars.
What is glycogen?
-it's like amylopectin but with way more branches (I'm talking about a branch every 8-10 glucoses!!!)
What is cellulose?
-linear polysaccharides
-differs from the rest because it has Beta(C1->C4) bonding
What are the 7 amino acids that belong to the 'nonpolar, aliphatic R groups'?
-glysine
-alanine
-proline
-valine
-leucine
-isoleucine
-methionine
What are the 3 amino acids that belong to the 'aromatic R groups'?
-phenylalanine
-tyrosine
-tryptophan
What are the 5 amino acids that belong to the 'polar, uncharged R groups'?
-serine
-threonine
-cysteine
-asparagine
-glutamine
What are the 3 amino acids that belong to the 'positively charged R groups'?
-lysine
-arginine
-histidine
What are the 2 amino acids that belong to the 'negatively charged R groups'?
-aspartate
-glutamate
What's so special about tyrosine. serine and thereonine?
-there OH group can be phosphorylated
Are amino acids S or R configured?
-they are 'S' configured

-remember: CORN
[1]CO=COO
[2]R=R group
[3]N=NH3
What so special Proline, Glycine and Cysteine?
-Proline has a rigid backbone

-Glycine has a flexible backbone

-Cysteine can form S-S (disulphide bonds)
What are zwitterions?
-result of amino acid being dissolved in water
-a dipolar ion, with spatially separated positive and negative charges
-can act as an acid or a base
What is pI?
-it is the isoelectric point
-the point at which the net electric charge is zero

**so if pH is less then pI, amino acid is more acidic therefor have a relatively larger postive charge. if pH is greater than pI, amino acid is more basic therefor having a relatively larger negative charge**
How does an amino acid titration curve work... or any titration curve for the matter?
-farthest right is where it is most acidic.
-as the titration plateaus (ie hits a pK value), the original amino acid becomes more basic (ie: loses an H) when more base is added

**so... curve rises, plateaus, turns more basic, rises, plateaus, turns more basic, etc.**
How do amino acids form peptide bonds?
-amino acids join head to tail by dehydration. OH of carboxylic head makes off with H of tail.
What is the 'direction' of amino acids?
N---> Residues---> C
What is residue?
-each amino acid in the chain is referred to as residue
-proteins are about 60-800 residues long
-average weight is 110 Daltons
What are some characteristics to peptide bonds?
*Consists of O=C-N-H
-O and H are trans 99% of the time
-rigid and planar
-has partial double bonds (ie:O or N can be double bonded to C at any time)
*N-C[alpha] bonds are called phi
*C-C[alpha] bonds are called psi
-phi and psi bonds are free to rotate
For amino acids, what is the alpha carbon?
-the central, chiral carbon is referred to as the alpha carbon
How do you calculate G?
G = G + RT(lnKeq)

G = H - TS