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Bio 540 - Biochem > Exam 1 > Flashcards

Exam 1 Flashcards

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Biology 101 flashcards
1
Q

What are the 2 things that electronegativity depend on?

A
  1. Number of protons in the nicleus (atomic number)
  2. Distance between the outer electrons and the nucleus
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2
Q

Why are hydrogen bonds stronger than Van Der waals?

A
  • Since Hydrogen only has 1 atom, its atom is able to get closer to the core of the Oxygen atom it is bound to.
    • Therefore resulting in a stronger bond/molecule.
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3
Q

Acid + base = ??

A

Salt + Water

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4
Q

Keq, or the dissociation constant, can be described as a ratio of….

A

Ratio of products to substrates

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5
Q

Keq of water = ?

Molarity of water = ?

A
  1. 1.8 x 10-16
  2. 55.5 M
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6
Q

What type of acids are organic acids?

A
  1. Weak Acids
    1. partially dissociate forming an equilibrium between the H+ of the organic acid and the anion
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7
Q

What is the most important thing to drive hydrophobic interactions?

A

Entropy

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8
Q

What are the 2 “main” characteristics of enzymes?

A
  1. will not change the reaction’s thermodynamics
  2. Not part of the reaction and will not be consumed. Just makes the reaction go faster
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9
Q

When energy is used, it is given off as [] and []?

A
  1. Heat (Q)
  2. Work (W)
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10
Q

Is NADH or NADPH catabolic?

A
  • NADH - Catabolic
  • NADPH - Anabolic
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11
Q

What are the 3 “ways” to move energy around in the cell?

A
  1. Redox Reactions
  2. Chemical bonds
  3. High Energy Transfer groups
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12
Q

What are the 3 energy reactions?

A
  1. Redox
  2. Nucleophilic Substitution
  3. Hydrolysis
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13
Q

Acid + Alcohol = ?

A

Anhydride

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14
Q

An ether linkage is another way to say [] linkage?

A

Glycosidic

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15
Q

O2 - [] agent

H2O - [] agent

A
  1. O2 - oxidizing agent
  2. H2O - reducing agent
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16
Q

Does the proteome = phenotype?

A
  • No
  • Chemicals in the cell kind of equal the phenotype
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17
Q

What are the 3 functions of DNA?

A
  1. Reposit of genetic informatino that is you
  2. Has to be template fo replication
  3. Controls metabolic output for everything
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18
Q

What is the difference between Nucleoside and Nucleotide?

A
  • Nucleoside
    • These are our purines and pyramidines
  • Nucleotide is the nucleoside + phosphate designation
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19
Q

What letters give us purines and pyramidines?

A
  • Purine - A,G,
  • Pyramidine - C, T, U
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20
Q

Whys is DNA more stable than RNA?

A

DNA does not have the 2’ OH, so it can survive alkaline condition whereas RNA cannot.

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21
Q

In what directions are nucleotides added to the growing chain?

What direction is the template strand read?

A

5’ –> 3’

3’ –> 5’

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22
Q

What type of linkage connects a chain of nucleosides?

A
  • phospho-diester linkage
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23
Q

Elucidation of DNA structure require 3 observations:

A
  1. Crystalline Structure
  2. Chargoff Base pair ratio (A-T and G-C)
  3. Bases in tautormeric Form
24
Q

What are 3 characteristics of DNA dependent RNA Polymerase (RNAP)??

A
  1. Requires template
  2. Requires proteins to bind to promoter
  3. Reads template 3’–>5’ but creates polymer in 5’ –>3’
25
Q

Which strand of DNA is the template strand?

Coding or Non-coding?

A

Non-coding strand of DNA is the template

26
Q

Is rRNA ever used as a template?

A

No

27
Q

Does transcription require a primer?

A
  • No
  • Transcription uses protein-protein interactions to begin initiation
    • Transcription factors help guide RNAP to promoter region on DNA
28
Q

What are the 2 types of promoter elements? And where can they be found on a gene?

A
  1. Binding sites for transcription factors
    1. Basal - 0-3 bp away
    2. Proximal - 0- 200 bp away
    3. Distal - 1000 - 2000 bp away
  2. Enhancer Regions
    1. Can be found anywhere in the gene
29
Q

What is the basic/simple definition of a gene?

A
  • Segment of DNA that encodes a protein
30
Q

Is proofreading a characteristic of Eukaryotic Transcription?

A

No

31
Q

What are the main “classifications” of protein function?

A
  1. Transport
  2. Structure
  3. Catalytic
  4. Motor
  5. Protection
  6. Metabolic regulation
32
Q

What is the distinction between protein and peptide?

A
  • Protein - amino acid polymer composed of more than 50 amino acids
  • Peptide - amino acid polymer composed of less than 50 amino acids
33
Q

What “5 things” do all amino acids basically have…

A
  1. Amine
  2. Alpha Carbon
  3. Carboxylic Acid
  4. Hydrogen
  5. R-group
34
Q

What 5 amino acids are considered “Polar-Charged side groups”?

Where are these residues found on proteins and why?

A
  1. Aspartic Acid (L- Aspartate)
  2. GLutamic Acid (L-Glutamate)
  3. Lysine
  4. Arginine
  5. Histidine
  • These residues are generally found at the core of proteins because water can easily disrupt their structure.
35
Q

Which AA disrupts higher order structures and forms kinks?

A
  1. Proline
  2. Glycine
36
Q

What mechanism forms a peptide bonds?

A

Nucleophilic Substitution

37
Q

On a peptide polymer, the phi bond connects to [] and the psi bond connects to []?

A
  • phi - Nitrogen
  • Psi - Carbon of carboxylic acid portion
38
Q

A difference in pH-pKa equals a [] [] change in the ratio of base to acid…

A

10-fold

39
Q

What types of linkages define a protein’s primary structure?

A

Covalent linkages

40
Q

What 3 things does a protein’s secondary structure depend on?

A
  1. Bond angles of Phi and Psi
  2. Inability of amide to rotate
  3. H-bonding
41
Q

What two types of side groups influence protein reactivity with water?

A
  1. Polar (non-charged) - hydrophilic
  2. Nonpolar - hydrophobic
42
Q

What type of R-group make-ups can destabilize secondary structure/structure in general?

A
  • Branched R-Groups
  • Ionic runs of residues (due to steric hindrance)
  • Proline/Glycine - causes kinks
  • 1st and 4th residue are + and -
  • Nonpolar aromatics
43
Q

Super secondary structures of proteins depend on what type of interactions?

A

R-group interactions

44
Q

What type of molecular interactions are involved in tertiary protein structure?

A
  • Mainly R group interactions
    • Hydrophobic interactions - core
    • Ionic interactions - Core +peripherary
    • Hydrogen Bonding - periphery
    • Van der Waals and London - periphery
45
Q

What determines protein’s tertiary structure?

A
  • Geometric relationship between segments
  • Position of side groups to one another
46
Q

Quaternary Protein Structure

  • Greater than [] kDA
  • Association must be []
A
  • 100 kilo Daltons
    • 1 amino acid weights about 110 daltons
  • Noncovalent associations
47
Q

What is “gene expression”?

A

Everything from DNA in its compact from –> Proteins doing shit

48
Q

Which enzyme catalyzes the activation of tRNA?

Does this enzyme have proofreading capability?

A

aminoacyl-tRNA synthetase

Yes

49
Q

What steps in translation initiation hydrolyze a GTP?

A
  1. eIF5-GTp is hydrolyzed and beings looking for the start site on the mRNA
  2. eIF2-GTP being hydrolyzed and dropping active tRNA off
    1. releasing eIF1A leaving A site and eIF3 leaving as well
50
Q

What are the 3 stop codons?

A

UGA, UAG, UAA

51
Q

What is the name of the enzymatic function of the ribosome?

A

peptidyltransferase

52
Q

What does glcosylation provide to the protein?

A
  • Stability
  • Signaling for localization
53
Q

This class of enzymes transfers a sugar to a protein…

A

glycosyltransferase

54
Q

N-Linked Glycosylation

  • beings in []. and completed in the [] apparatus
  • Requires the sequence [] /[]
  • Co-[]. process
  • Two types are recognized - High - [] type and [] type
A
  • ER and finished in Golgi
  • Asn-X-Thr/Ser
  • Co-translational
  • High Mannose type and Complex
55
Q

O-linked Glycosylation

  • Only happens in [] apparatus, on [] folded proteins
  • []- [] process
  • No defined [] sequence
A
  • Golgi, fully folded
  • Post-translational
  • consensus sequence
56
Q

What types of modifications are found on the following amino acids?

  1. Asparagine
  2. Histidine
  3. Lysine
  4. Serine
  5. Threonine
  6. Tyrosine
A
  1. Asparagine - glycosylation, Methylation
  2. Histidine - methylation
  3. Lysine - Acetylation, methylation
  4. Serine - Phosphorylation
  5. Threonine - Phosphorylation
  6. Tyrosine - Phosphorylation
57
Q

At equal molar concentrartions - pH = []?

A

pH = pK

Bio 540 - Biochem (14 decks)

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