How do you determine the number of possible stereoisomers exist for a compound?
2^n
n = the number of chiral carbons
Important Monosaccharides:
D-fructose
D-glucose
D-galactose
D-mannose
D-Fructose
Important Monosaccharide
D-glucose
Important Monosaccharide
D-galactose
Important Monosaccharide
D-mannose
Important Monosaccharide
Hemiacetal
Hemiacetals react with alcohols to form acetals
Hemiketal
Mutarotation
When a hemiacetal ring spontaneously cycle from open to closed form.
Epimers
A special subtype of diastereomer that differ in configuration by exactly one chiral center.
Anomeric Carbon
When the carbonyl carbon becomes chiral during the process of turning into a hemiacetal or hemiketal.
Monosaccharides
Contain alcohols and aldehydes or ketones.
These functional groups undergo the similar reactions: oxidation, reduction, esterification, and nucleophilic attack.
Tautomerization
The rearrangement of bond in a compound, usually by moving a hydrogen and forming a double bond.
Enol
A compound with a double bond and an alcohol group.
Explain the difference between esterification and glycoside formation.
Esterfication is the reaction of a carboxylic acid with a hydroxyl group. Glycoside formation is the reaction of alcohol and a hemiacetal on a sugar to make an alkoxy group.
From a metabolic standpoint, does it make sense for carbohydrates to get oxidized or reduced? What is the purpose of this process?
It makes sense for carbs to be oxidized while reducing other groups. This is because aerobic metabolism required reduced electron carriers to facilitate processes like oxidative phosphorylation.
Disaccharides
Two monosaccharides joined by a glycosidic bond
Sucrose, Lactose, Maltose
Polysaccharides
(three kinds)
long chains of monosaccharides linked together by glycosidic bonds.
Cellulose--the main structural component of plants, beta-D-glucose molecules that humans cannot digest
Starch--stored in plants, more easily digestible to humans because they are alpha-D-
Which of the two forms of starch is more soluble in solution. Why?
Amylopectin is more soluble than amylose because it is more branched.
Regarding glycogen and amylopectin, which of these two polymers should experience a higher rate of enzyme activity from enzymes that cleave side branches? Why?
Glycogen, because it has more branching.
What are the four groups attached to the alpha carbon of a proteinogenic amino acid?
1. -COOH
2. -NH2
3. -H
4. R-Chain
What is the stereochemistry of the amino acids that appear in eukaryotic proteins?
L or D?
(R) or (S)? One Exception: _____?
L
(S)
Cysteine is (R).
Where do hydrophobic amino acids tend to reside within the protein?
What about hydrophilic?
Hydrophobic--in the interior of the protein
Hydrophilic--on the surface of the protein
Amphoteric Species
Capable of accepting OR donating a proton, depending on the environment (pH)
Amino Acids are amphoteric because they have an acidic carboxylic acid group and a basic amino group.
pKa and percent protonation
The pKa of a group is the pH at which 50% of the molecules of that species are deprotonated.
[HA-] = [A-]
pH < pKa, the majority of the species will be protonated.
pH > pKa, the majority of the species will be deprotonated
Amino Acid Charge and pH
At highly acidic pH values, amino acids tend to be positively charged. At highly alkaline (basic) values, they tend to be negatively charged.
When the pKa of a solution is approximately equal to the pKa of the solute, the solution acts as a ________
Buffer
The second proton from an amino acid with a charged side chain is lost from what part of the molecule?
The
side chain
not the amino group.
Three equations for calculating pI for an amino acid.
1. neutral amino acid
2. acidic amino acid
3. basic amino acid
1. (pka_NH3 + pKa_COOH) / 2
2. (pKa_R group + pKa_COOH) / 2
3. (pKa_NH3 + pKa_R group) / 2
For generic amino acid -- NH2CRCOOH -- what would be the predominant form at the following pH's?
pH 1
pH 7
pH 11
pH 1 = (NH3+)CRCOOH (+) net charge
pH 7 = (NH3+)CR(COO-) 0 net charge
pH 11 = NH2CR(COO-) (-) net charge
What molecule is released during the formation of a peptide?
H2O
What stabilizes the alpha helix?
Intramolecular H bonds between a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain.
What stabilizes Beta pleated sheets? What conformations may they have?
Parallel or antiparallel
Held together by H bonds forming between carbonyl oxygen on one chain and amide hydrogen on the adjacent chain.
What are the definitions of primary and secondary structure, and how do they differ in subtypes and the bonds that stabilize them?
Primary: Linear sequence of Amino Acids, no subtypes, stabilized by peptide bonds
Secondary: Local structure determined by nearby amino acids, subtypes: alpha helix and beta pleated sheets, stabilized by hydrogen bonds.
What role does proline serve in secondary structure?
Proline's structure causes it to introduce kinks into alpha helices, and create turns in Beta pleated sheets.
Tertiary structure is primarily the result of moving ________________________ into the interior of the protein.
hydrophobic amino acid side chains
What are the definitions of tertiary and Quaternary structure, and how do they differ in subtypes and the bonds that stabilize them?
Tertiary: three-dimensional shape of protein, subtypes--hydrophobic interactions, acid-base salt bridges, disulfide linkages -- Stabilizing Bonds-van der Waals, H bonds, Ionic Bonds, Covalent Bonds
Quaternary Structure: Interaction between separate subuni
What is the primary motivation for hydrophobic residues in a poly peptide to move to the interior of the protein?
Entropy
Why are proteins denatured by heat and solutes, respectively?
Heat -- heat increases the average KE of proteins, disrupting hydrophobic interactions.
Solutes -- disrupt elements of secondary, tertiary, and quaternary structure.
Nucleoside
Composed of a five-carbon sugar (pentose) bound to a nitrogenous base and formed by linking the base to C-1' of the sugar.
Nucleotide
Formed when one or more phosphate groups are attached to C-5' of a nucleoside
CUT
the
PY
e
PUR
e
A
s
G
old
Mnemonics to remember the types and structures of nitrogenous bases.
CUT the PYe
C, U, & T are PYrimidines
A pie has only one crust (ring)
PURe
A
s
G
old
A & G are PURines
There are two rings at a wedding (two rings)
Huckel's Rule
(for aromatic compounds)
4n + 2 = the number of pi electrons in the compound
Watson & Crick Model of DNA Structure
1. The two strands of DNA are antiparallel
2. The sugar-phosphate backbone is on the outside of the helix with nitrogenous bases on the inside.
3. Complementary Base Pairing: A - T & C - G
C - G pairing is strongest
4. Chargaff's Rules -- The amount of A
What are the 3 major structural differences between DNA & RNA?
1. DNA contains deoxyribose, while RNA contains ribose.
2. DNA contains Thymine while RNA contains Uracil.
3. DNA is double stranded while RNA is single stranded (usually).
How does the aromaticity of purines and pyrimidines underscore their genetic function?
The aromaticity makes the compounds very stable and unreactive, which is ideal for storing genetic information and avoiding mutations.
What are the five histone proteins in eukaryotic cells? Which one is not part of the histone core around which DNA wraps to form chromatin?
H1 is not in the histone core.
The five histones are: H1, H2A, H2B, H3, and H4
Compare and contrast heterochromatin and euchromatin.
Heterochromatin is: dense, dark, and silent (transcriptionally silent)
Euchromatin is: Not dense, Light, and Active
What property of telomeres and centromeres allow them to stay tightly raveled, even when the rest of DNA is uncondensed?
High C-G content increases the hydrogen bonding, making the association between DNA strands very strong at telomeres and centromeres.
For each of the enzymes listed, list the function of the enzyme and if they are found in prokaryotes, eukaryotes, or both:
Helicase
Single-Stranded DNA Binding Protein
Primase
DNA Polymerase III
DNA Polymerase Alpha
DNA Polymerase I
RNase H
DNA Ligase
DNA
Helicase -- both -- Unwinds DNA double helix
Single-Stranded DNA Binding Protein -- both -- Prevents reannealing of DNA double helix during replication
Primase -- both -- Places RNA primer to begin DNA replication
DNA Polymerase III -- prokaryotes -- adds
Between the leading and lagging strand, which is more likely to have mutations?
Why?
The lagging strand is more prone to mutations because it is constantly starting and stopping the process of DNA replication. Additionally, it contains many more RNA primers, all of which must be removed and filled with DNA.
DNA ligase, which closes the ga
What is the function of a telomere?
Telomeres are the ends of the eukaryotic chromosomes and contain repetitive sequences of noncoding DNA. These protect the chromosome from losing important genes from incomplete replication of the 5' end of the DNA strand.
What is the difference between an oncogene and a mutated tumor suppressor gene?
Oncogene (a mutated proto-oncogene) code for cell cycle-promoting proteins, leading to rapid cell cycling. (Stepping on gas pedal)
A mutated tumor suppressor gene would allow cell cycling to proceed unchecked. (Cutting brake lines)
How does DNA polymerase recognize which strand is the template strand once the daughter strand is synthesized?
The parent strand is more heavily methylated, whereas the daughter strand is barely methylated at all. This allows DNA Polymerase to distinguish between the two when proofreading.
For each of the repair mechanisms below, in which phase of the cell cycle does the repair mechanism function? What are the key enzymes or genes specifically associated with each mechanism?
DNA Polymerase (proofreading)
Mismatch Repair
Nucleotide Excision
DNA Polymerase (proofreading)
Stage: S
Enzyme: DNA Polymerase
Mismatch Repair
Stage: G2
Enzyme: MSH2, MLH1 (MutS and MutL in prokaryotes)
Nucleotide Excision Repair
Stage: G1, G2
Enzyme: Excision endonuclease
Base Excision Repair
Stage: G1, G2
Enzyme: Gly
What is the key structural difference in the types of lesions corrected by nucleotide excision repair vs. those corrected by base excision repair?
Nucleotide excision repair corrects lesions that are large enough to distort the double helix.
Base Excision Repair corrects lesions that are small enough not to distort the double helix.
What are the roles of the three main types of RNA?
mRNA -- carries information from DNA by traveling from the nucleus (where transcribed) to the cytoplasm (where translated).
tRNA -- translates nucleic acids to amino acids by pairing its anticodon with mRNA codons; it is charged with an amino acid, which
The three-base sequences listed below are DNA sequences. Which amino acid is encoded by each of these sequences, after transcription?
GAT
ATT
CGC
CCA
GAT: mRNA codon = AUC; Isoleucine
ATT: mRNA codon = AAU; Asparagine
CGC: mRNA codon = GCG; Alanine
CCA: mRNA codon = UGG; Tryptophan
Which mRNA codon is the start codon? What amino acid does it code for?
Which mRNA codons are the stop codons?
Start codon: AUG -- methionine
Stop codons: UAA, UGA, UAG
What is a wobble, and what role does it serve?
The wobble refers to the third base codon that often plays no role in determining the amino acid made. This is protective against mutations because the wobble will not have any effect on the protein.
For each of the mutations listed, what changes in DNA sequence are observed? What effect do they have on the encoded peptide?
Silent (degenerate)
Missense
Nonsense
Frameshift
Silent (degenerate) -- Substitutions in the wobble position, introns, or noncoding DNA; No change observed
Missense -- Substitution of one base, creating an mRNA codon that matches a different amino acid; One amino acid is changed in the protein, variable
Stop Codons Mnemonic
U Are Annoying -- UAA
U Go Away -- UGA
U Are Gone -- UAG
What is the role of each eukaryotic polymerase?
RNA polymerase I
RNA polymerase II
RNA polymerase III
RNA polymerase I -- synthesizes most rRNA
RNA polymerase II -- synthesizes most mRNA (hnRNA) and snRNA
RNA polymerase III -- synthesizes tRNA and some rRNA
When starting transcription, where does RNA polymerase bind?
RNA polymerase II binds to the TATA box, which is located within the promoter region of a relevant gene, at about -25.
What are the 3 major post-transcriptional modifications that turn hnRNA into mature mRNA?
1. Splicing -- removal of introns, joining of exons. Uses snRNA and snRNP in the splicesosome to create a lariat, which is then degraded. Exons are ligated together.
2. 5' cap -- addition of a 7 methylguanylate triphosphate cap to the 5' end of the transc
What is alternative splicing? What does it accomplish?
The ability of some genes to use various combinations of exons to create multiple proteins from hnRNA transcript. This increases protein diversity and allows a species to maximize the number of proteins it can create from a limited number of genes.
Terminology & 5' --> 3'
Replication
Transcription
Translation
Replication = DNA --> DNA
New DNA synthesized in 5' --> 3' Direction
Transcription = DNA --> RNA
RNA synthesized in 5' --> 3' direction (template is read 3' --> 5')
Translation = RNA --> protein; mRNA read in 5' --> 3' direction
Compare GLUT2 & GLUT4
1. Important Tissues?
2. Relative Km?
3. Saturated at normal glucose levels?
4.Responsive to insulin?
GLUT2
1. Important Tissues: Liver, Pancreas
2. Relative Km: High
3. Saturated at normal glucose levels: No
4.Responsive to insulin: No
GLUT4
1. Important Tissues: Adipose Tissue, Muscle
2. Relative Km: low
3. Saturated at normal glucose levels: yes
4. Res
How does insulin promote glucose entry into the cells?
It increases the umber of transporters. Insulin promotes vesicles of GLUT4 to fuse to the cell membrane, making them available for transport.
Name the rate-limiting enzyme for:
Glycolysis
Phosphofructokinase-1
Name the rate-limiting enzyme for:
Fermentation
Lactate Dehydrogenase
Name the rate-limiting enzyme for:
Glycogenesis
Glycogen Synthase
Name the rate-limiting enzyme for:
Glycogenolysis
Glycogen phosphorylase
Name the rate-limiting enzyme for:
Gluconeogenesis
Fructose-1,6-biphosphatase
Name the rate-limiting enzyme for:
Pentose Phosphate Pathway
Glucose-6-phosphate dehydrogenase
Mnemonic to remember Irreversible steps of glycolysis.
H
ow
G
lycolysis *P*ushes *F*orward the
P
F
ow *G*lycolysis *P*ushes *F*orward the
P
rocess:
K
inases
H
exokinase
G
lucokinase
P
FK-1
P
yruvate
K
inase
Types of Pyruvate
1. Pyruvate Dehydrogenase (PDH)
^^Its two regulators:
a. PDH Kinase
b. PDH Phosphatase
2. Pyruvate Carboxylase--enzyme involved in gluconeogenesis
What is the overall reaction of the pyruvate dehydrogenase complex?
Pyruvate + CoA-SH + (NAD+) --> acetyl CoA + CO2 + NADH + (H+)
What other molecules can be used to make acetyl-CoA? What are the processes?
1. Fatty Acids -- shuttle acyl group from cytosolic CoA-SH to mitochondrial CoA-SH via carnitine; then undergo Beta-oxidation
2. Amino Acids -- Transaminate to lose Nitrogen; convert carbon skeleton into ketone body, which can be converted into acetyl-CoA
The TCA Cycle
Mnemonic for Substrates and Order of the TCA
Please, Can I Keep Selling Smack for Money, Officer?
P
yruvate
C
itrate
I
socitrate
alpha -
K*etoglutarate
S
uccinyl-CoA
S
uccinate
F
umerate
M
alate
O
xaloacetate
Steps of the TCA Cycle
1. Citrate Formation
2. Citrate Isomererized to Isocitrate
3. alpha-Ketoglutarate and CO2 Formation
4. Succinyl-CoA and CO2 Formation
5. Succinate Formation
6. Fumarate Formation
7. Malate Formation
8. Oxaloacetate Formed Anew
Steps of the TCA Cycle:
1. Citrate Formation
Acetyl-CoA and oxaloacetate undergo a condensation reaction to yield citrate and CoA-SH
Steps of the TCA Cycle:
2. Citrate Isomererized to Isocitrate
...
Steps of the TCA Cycle:
3. alpha-Ketoglutarate
...
Steps of the TCA Cycle:
4. Succinyl-CoA and CO2 Formation
...
Steps of the TCA Cycle:
5. Succinate Formation
...
Steps of the TCA Cycle:
6. Fumarate Formation
...
Steps of the TCA Cycle:
7. Malate Formation
...
Steps of the TCA Cycle:
8. Oxaloacetate Formed Anew
...
Common Carbohydrates
Holoenzyme
A complete enzyme which has all need cofactors and coenzymes
Apoenzyme
An incomplete enzyme (missing cofactors or coenzymes)