1
Q
4 ways that carbon skeletons can vary
A
length, branching, double bond positions, presence of rings
2
Q
fat
A
- molecules w/ long hydrocarbon tails attached to a nonhydrocarbon component.
- constructed from 2 kinds of smaller molecules: glycerol and fatty acids
- triacylglycerol (or triglyceride): 3 fatty acid molecules are each joined to glycerol by an ester linkage
3
Q
enantiomers
A
- mirror isomers
- differ in shape b/c of an asymmetric carbon, one that is attached to 4 diff atoms / groups of atoms
- only 1 isomer is biologically active b/c only that from can bind to specific molecules in an organism
4
Q
functional groups
A
chemical groups that affect molecular function by being directly involved in chemical reactions. each functional group participates in chem rxns in a characteristic way from 1 orgnanic molecule to another
5
Q
disaccharide
A
- 2 monosaccharides joined by a glycosidic linkage, a covalent bond formed btwn 2 monosaccharides by a dehydration rxn.
6
Q
storage polysaccharides: plants
A
- plants store STARCH, a polymer of glucose monomers, as granules within cellular structures known as plastids, which include chloroplasts. most of the glucose monomers are joined by 1-4 linkages.
- the simplest form of starch, AMYLOSE, is unbranched. AMYLOPECTIN, a more complex form, is branched w/ 1-6 linkages at the branch points
7
Q
storage polysaccharides: animals
A
- animals store GLYCOGEN, a polymer of glucose that is like amylopectin but more extensively branched. stored as dense clusters of granules within liver and muscle cells
- hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases
- glycogen can’t sustain an animal for long – depleted in a day if not replenished
8
Q
cellulose
A
- major component of cell walls.
- polymer of glucose.
- animals can’t digest cellulose; it’s eliminated w/ feces. along the way, cellulose abrades the wall of the digestive tract and stimulates the lining to secrete mucus, which aids in the smooth passage of food thru the tract. “insoluble fiber” (but microorganisms living in cows and termites’ gut can)
9
Q
starch vs cellulose
A
- shape: starch molecules are helical; cellulose molecules are straight, never branched
- starch: gluclose monomers in alpha configuration
- cellulose: beta (each monomer is “upside down” w/ respect to its neighbors)
10
Q
microfibrils
A
- some hydroxyl groups on the glucose monomers of cellulose are free to hydrogen-bond w/ the hydroxyls of other cellulose molecules lying parallel to it. parallel cellulose molecules held together in this way are grouped into units called microfibrils.
- cable-like; strong building material for plants
- 80 cellulose molecules long
11
Q
chitin
A
- the carb used by arthropods (insects, spiders, crustaceans, etc) to build their exoskeletons
- pure chitin is leathery and flexible, but becomes hardened when encrusted w/ calcium carbonate, a salt
- found in many fungi, which use it as the building material of their cell walls
- beta linkages, but the glucose monomer has a nitrogen-containing appendage
12
Q
glycerol
A
an alcohol. each of its 3 carbons bears a hydroxyl group.
13
Q
why do fats separate from water?
A
nonpolar C-H bonds in the hydrocarbon chains of fatty acids make fats hydrophobic. the water molecules hydrogen-bond to one another and exclude the fats.
14
Q
ester linkage
A
a bond btwn a hydroxyl and a carboxyl group.
15
Q
fatty acid
A
- has a long carbon skeleton, usually 16 or 18
- the carbon at 1 end of the skeleton is part of a carboxyl group, which gives it the name ‘acid’
16
Q
saturated fatty acid
A
- there are no double bonds btwn carbon atoms composing a chain. as many H atoms as possible are bonded to the C skeleton. (saturated w/ hydrogen)
- no double bonds –> flexibility allows the fat molecules to pack together tightly
17
Q
unsaturated fatty acid
A
- 1 or more double bonds btwn the carbon atoms composing a chain, w/ 1 fewer H atom on each double-bonded C.
- nearly all double bonds in naturally occurring fatty acids are cis double bonds, which cause a kink in the hydrocarbon chain wherever they occur.
18
Q
saturated vs unsaturated fats
A
- most animal fats are saturated. ex: lard and butter. solid at room temp
- most plant and fish fats are unsaturated. liquid at room temp.
19
Q
why are unsaturated fats liquid at room temp?
A
the kinks where the cis double bonds are located prevent the molecules from packing together closely enough to solidify at room temp.
20
Q
trans fat
A
the process of hydrogenating vegetable oils produces not only saturated fats but also unsaturated fats w/ trans double bonds
21
Q
atherosclerosis
A
- cardiovascular disease
- deposits called plaques develop w/in the walls of blood vessels, causing inward bulges that impede blood flow and reduce the resilience of the vessels
22
Q
omega-3 fatty acids
A
- required for normal growth in children
- protect against cardiovascular disease in adults
- so named b/c they have a double bond at the 3rd carbon-carbon bond from the end of the hydrocarbon chain
23
Q
phospholipid
A
- hydrophilic (polar) head + 2 hydrophobic (nonpolar) tails
- similar to a fat molecule but has only 2 fatty acids attached to glycerol rather than 3
- the 3rd hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell
24
Q
phospholipid diversity
A
based on differences in the 2 fatty acids and in the groups attached to the phosphate group of the head.
25
steroids
- lipids characterized by a carbon skeleton consisting of 4 fused rings
- diff steroids are distinguished by the particular chemical groups attached to these rings
26
cholesterol
- crucial steroid molecule
- common component of animal cell membranes and also the precursor from which other steroids are synthesized
- in vertebrates, synthesized in liver and obtained from diet
27
cholesterol and health
- high cholesterol level may contribute to atherosclerosis
| - both saturated and trans fats exert their negative impact on health by affecting cholesterol levels
28
amino acid
- organic molecule possessing both an amino group and a carboxyl group
- at the center is an asymmetric carbon atom called the alpha carbon
- its 4 partners are: amino group, carboxyl group, H atom, and R group
29
peptide bond
- when 2 amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration rxn
- the resulting covalent bond is a peptide bond
30
polypeptide chain ends
- one end has a free amino group; opposite end has a free carboxyl group
- amino end: N-terminus
- carboxyl end: C-terminus
31
transthyretin
- globular blood protein that transports vitamin A and one of the thyroid hormones throughout the body
- made up of 4 identical polypeptide chains, each composed of 127 amino acids
32
secondary structure
- most proteins have segments of their polypeptide chains repeatedly coiled or folded in patterns
- these coils and folds are the result of H bonds btwn the repeating constituents of the polypeptide backbone (NOT R GROUPS)
- within the backbone, the O atoms have a partial negative charge, and the H atoms attached to the nitrogens have a partial positive charge; therefore, H bonds can form btwn these atoms
33
alpha helix
| discuss structure for transthyretin, hemoglobin, keratin
- type of 2ndary structure
- a delicate coil held together by H bonding btwn every 4th amino acid
- transthyretin: only 1 alpha helix region
- hemoglobin and other globular proteins: multiple stretches of alpha helix separated by nonhelical regions
- alpha-keratin (structural protein of hair) and other fibrous proteins: have alpha helix formation over most of their length
34
beta pleated sheet
- 2 or more strands of the polypeptide chain lying side by side (called beta strands) are connected by H bonds btwn parts of the 2 parallel polypeptide backbones
- make up the core of many globular proteins, such as transthyretin
- dominate some fibrous proteins, including the silk protein of a spider's web
35
tertiary structure
overall shape of polypeptide resulting from interactions btwn R groups
36
hydrophobic interaction
- 1 type of interaction that contributes to tertiary structure
- as a polypeptide folds into its functional shape, amino acids w/ hydrophobic (nonpolar) side chains usually end up in clusters at the core of the protein, out of contact w/ water
- once nonpolar amino acid side chains are close together, van der Waals interactions help hold them together
37
disulfide bridges
- form where 2 cysteine monomers, which has sulfhydryl groups (-SH) on their side chains, are brought close together by the folding of the protein
- the sulfur of one cysteine bonds to the sulfur of the second
38
quaternary structure + 3 ex
- the overall protein structure that results from the aggregation of polypeptide subunits
- ex: transthyretin (4 polypeptide subunits)
- ex: collagen -- fibrous protein w/ 3 identical helical polypeptides intertwined into a larger triple helix
- ex: hemoglobin -- 4 polypeptide subunits (2 alpha, 2 beta)
39
heme
each subunit of hemoglobin has a nonpolypeptide component called heme, w/ an iron atom that binds oxygen
40
normal vs sickle cell hemoglobin: primary structure
amino acid #6: Glu (glutamic acid) replaced by Val
41
normal vs sickle cell hemoglobin: secondary/tertiary structure
beta subunit has an exposed hydrophobic region
42
normal vs sickle cell hemoglobin: function
normal: molecules don't associate w/ e/o. each carries oxygen || sickle: molecules interact w/ one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced.
43
denaturation
- when protein unravels and loses its native shape if pH, salt concentration, temperature, or other aspects of environment are altered --> the weak chemical bonds and interactions within a protein are destroyed
- biologically inactive b/c misshapen
44
why does excessive heat cause denaturation? + example
- heat agitates the polypeptide chain enough to overpower the weak interactions that stabilize the structure
- egg white becomes opaque during cooking b/c the denatured proteins are insoluble and solidify
45
most proteins become denature if?
they're transferred from an aqueous environment to a nonpolar solvent; the polypeptide chain refolds so that its hydrophobic regions face outward toward the solvent
46
4 diseases caused by misfolding of polypeptides
- alzheimer's, parkinson's, mad cow disease
- misfolded versions of the transthyretin protein have been implicated in several diseases, including one form of senile dementia
47
X-ray crystallography
A technique used to study the three-dimensional structure of molecules. It depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule.
48
3 methods for analyzing protein structure
- x-ray crystallography
- NMR (nuclear magnetic resonance) spectroscopy, which doesn't require protein crystallization
- bioinformatics: predicts 3-D structure from amino acid sequence
49
nucleotide
- nitrogenous base + pentose (5-C sugar) + 1 or more phosphate groups
- in a polynucleotide, each monomer has only 1 phosphate group
50
nucleoside
the portion of a nucleotide w/o any phosphate groups.
51
nitrogenous base
- has 1 or 2 rings that include N atoms
| - called bases b/c the N atoms tend to take up H+ from solution, thus acting as bases
52
pyrimidine
- 1 6-membered ring of C and N atoms
| - C, T, U
53
purines
- larger than pyrimidines
- 6-membered ring fused to 5-membered ring
- A and G
54
phosphodiester linkage
- join adjacent nucleotides
- The phosphodiester bonds that join one DNA nucleotide to another always link the 5’ carbon of the first nucleotide to the 3’ carbon of the second nucleotide.
55
rna vs dna molecules
- RNA molecules usually exist as single polynucleotide chains
- RNA: A pairs w/ U
56
casein
- the protein of milk
| - major source of amino acids for baby mammals
57
ovalbumin
- protein of egg white
| - used as an amino acid source for the developing embryo
