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Biochem 2EE3 > Mod 3 > Flashcards

Mod 3 Flashcards

(66 cards)

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1
Q

Pyrimidines vs purines

A

Pyrimidines
Thymine and cytosine
Single ring

Purines
Adenine and guanine
Double rings

Pure as gold

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2
Q

DNA double helix structure

A
  • 10 base pairs / turn
  • Pi-pi interactions as aromatic rings stack next to each other and share electron probabilities
  • Major (bp specific) and minor (bp nonspecific) grooves formed
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3
Q

What are nucleic acids composed of?

A
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4
Q

What does the phosphate do in DNA?

A

Strong acid
pKa around 1

Makes DNA and RNA acidic molecules negatively charged

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5
Q

Cytosine

A
  • Pyrimidine
  • Heterocyclic aromatic ring with 2 substituents attached
    1. Amine group (-NH2) at 4’
    2. Keto group (=O) at 2’
  • Forms 3 hydrogen bonds with guanine
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6
Q

Adenine

A
  • Purine
  • Heterocyclic aromatic ring with pyrimidine ring fused to imidazole ring
  • Forms 2 hydrogen bonds with thymine or uracil
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7
Q

Uracil

A
  • Only in RNA
  • Pyrimidine
  • Heterocyclic aromatic ring
  • Forms 2 hydrogen bonds with adenine
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8
Q

Thymine

A
  • Only in DNA
  • Pyrimidine
  • Heterocyclic aromatic ring
  • Forms 2 hydrogen bonds with adenine
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9
Q

Guanine

A
  • Purine
  • Heterocyclic aromatic ring with pyrimidine ring fused to imidazole ring
  • Forms 3 hydrogen bonds with cytosine
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10
Q

What process allows for the degradation of the covalent backbone of RNA and DNA through hydrolysis?

A

Hydrolysis
- Slow, non-enzymatic hydrolysis of phosphodiester bonds.

Faster in RNA due to the 2’ OH group, which makes RNA more reactive than DNA.

Cyclic 2’,3’ monophosphate nucleotides are produced first and are further hydrolyzed into 2’- and 3’- nucleoside monophosphates.

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11
Q

How is condensation related to DNA synthesis?

A
  • 3’ OH of growing chain + 5’ OH of deoxynucleoside monophosphate
  • Thermodynamically unfavorable
  • Coupled with favorable reaction to proceed (using dNTP)
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12
Q

Role of dNTP in DNA synthesis?

A
  • High-energy triphosphate at 5’ end
  • Hydrolysis to dNMP + pyrophosphate drives condensation
  • Net negative ΔG when coupled
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13
Q

DNA structure?

A
  • Double helix, 2 antiparallel strands
  • H-bonds between complementary bases
  • Phosphate-deoxyribose backbone (hydrophilic)
  • Bases stacked inside, regular major/minor grooves
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14
Q

What did Erwin Chargaff discover?

A
  • Mole percent A = T
  • Mole percent C = G
  • Due to complementary base pairing
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15
Q

Who discovered DNA structure?

A

Dr. James Watson & Francis Crick

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16
Q

Difference between nucleoside and nucleotide?

A

Nucleoside: no phosphate

Nucleotide: with phosphate

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17
Q

Primary structure of protein?

A
  • Linear amino acid sequence
  • Peptide bonds link amino group and carboxyl group
  • Sequence determines protein shape and properties
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18
Q

Secondary structure of protein?

A
  • Alpha helices or beta sheets
  • Stabilized by hydrogen bonding patterns
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19
Q

Tertiary structure of protein?

A
  • Globular shape
  • Hydrophobic residues inside, away from water
  • Essential for protein function (e.g., hemoglobin holding heme)
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20
Q

Quaternary structure of protein?

A

2+ polypeptide chains form one molecule

Example: Hemoglobin has 4 subunits working together

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21
Q

Examples of proteins and their functions?

A

Antibodies: defense, bind foreign molecules

Collagen: structure, triple helix

Calcium pump: transport, ion movement for muscle contraction

Insulin: communication, regulates blood sugar

Alpha amylase: catalysis, breaks down carbs

Ferritin: storage, stores iron

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22
Q

What is chirality in molecules?

A
  • Molecule’s reflection can’t be superimposed on the original
  • Central carbon attached to 4 different groups
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23
Q

Difference between L and D chirality?

A
  • L chirality (levo): rotates light left, typical in cells
  • D chirality (dextro): rotates light right
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24
Q

Which amino acid is achiral?

A

Glycine

R group is hydrogen and there is already a hydrogen

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25
What is a peptide bond?
- Covalent bond between carboxyl and amino groups - Formed through condensation - Rigid, planar due to resonance
26
Ends of a polypeptide chain?
Amino (N) terminal: beginning Carboxyl (C) terminal: end
27
Nonpolar, aliphatic amino acids?
Met, Pro, Gly, Ala, Val, Leu, Ile - Hydrophobic - Cluster in proteins (hydrophobic effect) Pro: rigid ring, found at protein surface
28
Polar, uncharged amino acids?
Ser, Thr, Cys, Asn, Gln - Can form H-bonds - Often on protein surface (interact with water)
29
Aromatic R group amino acids?
Phe, Tyr, Trp - Hydrophobic, absorb UV light at ~280 nm - Used to measure protein concentration Phe: most hydrophobic Tyr: can form H-bonds Trp: bulky, aromatic
30
Negatively charged R group amino acids?
Asp, Glu - Negative charge at pH 7 - Hydrophilic - Found on protein surface, in contact with water
31
Positively charged R group amino acids?
Lys, Arg, His - Basic, polar - Found on exterior or enzyme active sites Histidine: least basic (imidazole ring)
32
Peptide bond formation
1. Nucleophilic attack from electron pair on the amino group on one aa to the carbonyl of the other aa (nuc addition) 2. Release of a water molecule (elimination)
33
What is the purpose of SDS gel electrophoresis?
Resolves proteins according to their molecular weight.
34
How does SDS denature proteins in SDS gel electrophoresis?
- Anionic SDS detergent is added to denature the sample. - SDS binds to proteins, causing unfolding
35
What effect does SDS have on proteins during electrophoresis?
- SDS molecules uniformly coat proteins with a negative charge. - Results in similar shape and mass-to-charge ratio.
36
How does SDS gel electrophoresis separate protein subunits?
SDS disassociates protein subunits into individual polypeptide chains.
37
What happens after the protein sample is prepared in SDS gel electrophoresis?
- Mix transferred into a well at the top of a polyacrylamide gel. - Negatively charged polypeptides move toward the positive end.
38
Why do smaller polypeptides move faster in SDS gel electrophoresis?
- Smaller proteins face less resistance in the gel. - Speed depends on molecular weight, as mass-to-charge ratio is similar for all.
39
What is the first and last amino acid found in the body?
Asparagine Threonine
40
How are amino acids classified?
- 20 common alpha amino acids - Chiral center - Optically active (L and D enantiomers) - Differ based on R groups (side chains)
41
Who devised the one-letter code for amino acids?
* Margaret Oakley Dayhoff * For space efficiency in bioinformatics
42
What is the significance of the letters CHIMSV in the amino acid code?
First letter unique for each amino acid.
43
What is the Greek letter naming convention in amino acids?
* Alpha carbon is the center * Beta (β), Gamma (γ), Delta (∆), Epsilon (ε)
44
What is the number naming convention in amino acids?
C1 is the carbon with the highest atomic number substituent Usually carbon in COO- Then numbers continue to the other end
45
What is the absolute configuration of amino acids based on?
* L-glyceraldehyde * L = levorotatory (left) * L and D refer to absolute configuration, not optical properties
46
Why are most amino acid residues L?
Bc active sites of enzymes are asymmetric and therefore reactions are stereospecific Rare D-configuration ones are introduced via enzyme-catalysed reactions that occur after ribosome synthesis
47
How are amino acids grouped based on polarity? (5)
1. Nonpolar, aliphatic 2. Aromatic 3. Positively charged 4. Negatively charged 5. Polar, uncharged
48
What does the Lambert-Beer Law relate to?
- Absorption of light by biomolecules at characteristic wavelengths - Determines concentration using a spectrophotometer
49
What are some examples of other amino acids formed postsynthetically?
4-hydroxyproline (protein derivative in collagen) γ-carboxyglutamate (in prothrombin, Ca2+ binding) Desmosine (in elastin, derivative of 4 lys residues) Selenocysteine (derived from serine) Pyrrolysine (in methanogenic archaea) Ornithine, Citrulline (precursors for arginine)
50
How can protein activity be modified?
Addition of phosphoryl, methyl, acetyl, adenylyl, ADP-ribosyl, etc.
51
What ionization behavior is seen in amino acids? 3 things
* Ionizable R groups, amino, and carboxyl groups * Amphoteric: can act as acid or base * Zwitterion: dipolar ion
52
What happens during the titration of glycine with NaOH?
First stage: COOH loses H Midpoint: equal concentrations of proton donor (COOH) and proton acceptor (COO-) Point of inflection: pKa = pH of protonated group Second stage: NH3+ group loses proton
53
What is the isoelectric point (pI) of glycine?
pI is the mean of two pKa values No net charge when at pI, glycine is fully ionized and dipolar
54
What determines the titration curve of amino acids with ionizable R groups?
* More complex with 3 stages * Isoelectric point depends on the R groups present * Two carboxyl groups lower the pI, two positively charged groups raise the pI
55
Which aa provides significant buffering power near neutral pH?
Histidine (due to its ionizable R group)
56
What is a peptide bond?
Amide linkage formed between two amino acids Dehydration reaction: OH from one carboxyl and H from another amino group
57
What is the reverse of peptide bond formation?
Hydrolysis (hydrolytic cleavage) Favored under biological conditions
58
What is the difference between a dipeptide, tripeptide, and polypeptide?
Dipeptide: 2 amino acids Tripeptide: 3 amino acids Polypeptide: long chain of amino acids
59
What is a protein versus a polypeptide vs an oligopeptide?
Polypeptide: molecular weight < 10,000 Protein: molecular weight > 10,000 Oligopeptide: a short polymer of amino acids joined by peptide bonds
60
How does the ionization of amino acids change when they become peptide residues?
Chemical environment of the residue alters pKa values Ionizable R groups may have different pKa values
61
3 example of small biologically active peptides?
Oxytocin: 9 residues, stimulates uterine contractions Thyrotropin-releasing factor: 3 residues, stimulates release of thyrotropin Amanitin
62
What are multisubunit proteins?
Proteins with 2+ polypeptides, can be identical (oligomeric)
63
What are protomers
Identical subunits Hemoglobin: 4 subunits, 2 alpha, 2 beta dimer of ab protomers
64
How to estimate # of aas
Can estimate the # of residues by dividing its molecular weight by 110 - Assuming no other chemical constituents - Considers the higher frequency of smaller residues and the impact of water’s weight
65
What is a prosthetic group?
* A metal ion or organic compound bound to a protein * Essential for its activity * Found in conjugated proteins
66
What are conjugated proteins?
- Proteins with one or more prosthetic groups - Classified by the chemical nature of the prosthetic group

Biochem 2EE3 (10 decks)

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