Exam 1 Flashcards
1
Q
What are the 2 things that electronegativity depend on?
A
- Number of protons in the nicleus (atomic number)
- Distance between the outer electrons and the nucleus
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.
3
Q
Acid + base = ??
A
Salt + Water
4
Q
Keq, or the dissociation constant, can be described as a ratio of….
A
Ratio of products to substrates
5
Q
Keq of water = ?
Molarity of water = ?
A
- 1.8 x 10-16
- 55.5 M
6
Q
What type of acids are organic acids?
A
- Weak Acids
- partially dissociate forming an equilibrium between the H+ of the organic acid and the anion
7
Q
What is the most important thing to drive hydrophobic interactions?
A
Entropy
8
Q
What are the 2 “main” characteristics of enzymes?
A
- will not change the reaction’s thermodynamics
- Not part of the reaction and will not be consumed. Just makes the reaction go faster
9
Q
When energy is used, it is given off as [] and []?
A
- Heat (Q)
- Work (W)
10
Q
Is NADH or NADPH catabolic?
A
- NADH - Catabolic
- NADPH - Anabolic
11
Q
What are the 3 “ways” to move energy around in the cell?
A
- Redox Reactions
- Chemical bonds
- High Energy Transfer groups
12
Q
What are the 3 energy reactions?
A
- Redox
- Nucleophilic Substitution
- Hydrolysis
13
Q
Acid + Alcohol = ?
A
Anhydride
14
Q
An ether linkage is another way to say [] linkage?
A
Glycosidic
15
Q
O2 - [] agent
H2O - [] agent
A
- O2 - oxidizing agent
- H2O - reducing agent
16
Q
Does the proteome = phenotype?
A
- No
- Chemicals in the cell kind of equal the phenotype
17
Q
What are the 3 functions of DNA?
A
- Reposit of genetic informatino that is you
- Has to be template fo replication
- Controls metabolic output for everything
18
Q
What is the difference between Nucleoside and Nucleotide?
A
- Nucleoside
- These are our purines and pyramidines
- Nucleotide is the nucleoside + phosphate designation
19
Q
What letters give us purines and pyramidines?
A
- Purine - A,G,
- Pyramidine - C, T, U
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.
21
Q
In what directions are nucleotides added to the growing chain?
What direction is the template strand read?
A
5’ –> 3’
3’ –> 5’
22
Q
What type of linkage connects a chain of nucleosides?
A
- phospho-diester linkage
23
Q
Elucidation of DNA structure require 3 observations:
A
- Crystalline Structure
- Chargoff Base pair ratio (A-T and G-C)
- Bases in tautormeric Form
24
Q
What are 3 characteristics of DNA dependent RNA Polymerase (RNAP)??
A
- Requires template
- Requires proteins to bind to promoter
- Reads template 3’–>5’ but creates polymer in 5’ –>3’
25
Which strand of DNA is the template strand?
Coding or Non-coding?
Non-coding strand of DNA is the template
26
Is rRNA ever used as a template?
No
27
Does transcription require a primer?
* No
* Transcription uses protein-protein interactions to begin initiation
* Transcription factors help guide RNAP to promoter region on DNA
28
What are the 2 types of promoter elements? And where can they be found on a gene?
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
What is the basic/simple definition of a gene?
* Segment of DNA that encodes a protein
30
Is proofreading a characteristic of Eukaryotic Transcription?
No
31
What are the main "classifications" of protein function?
1. Transport
2. Structure
3. Catalytic
4. Motor
5. Protection
6. Metabolic regulation
32
What is the distinction between protein and peptide?
* Protein - amino acid polymer composed of **more** than 50 amino acids
* Peptide - amino acid polymer composed of **less** than 50 amino acids
33
What "5 things" do all amino acids basically have...
1. Amine
2. Alpha Carbon
3. Carboxylic Acid
4. Hydrogen
5. R-group
34
What 5 amino acids are considered "Polar-Charged side groups"?
Where are these residues found on proteins and why?
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
Which AA disrupts higher order structures and forms kinks?
1. Proline
2. Glycine
36
What mechanism forms a peptide bonds?
Nucleophilic Substitution
37
On a peptide polymer, the phi bond connects to [] and the psi bond connects to []?
* phi - Nitrogen
* Psi - Carbon of carboxylic acid portion
38
A difference in pH-pKa equals a [] [] change in the ratio of base to acid...
10-fold
39
What types of linkages define a protein's primary structure?
Covalent linkages
40
What 3 things does a protein's secondary structure depend on?
1. Bond angles of Phi and Psi
2. Inability of amide to rotate
3. H-bonding
41
What two types of side groups influence protein reactivity with water?
1. Polar (non-charged) - hydrophilic
2. Nonpolar - hydrophobic
42
What type of R-group make-ups can destabilize secondary structure/structure in general?
* Branched R-Groups
* Ionic runs of residues (due to steric hindrance)
* Proline/Glycine - causes kinks
* 1st and 4th residue are + and -
* Nonpolar aromatics
43
Super secondary structures of proteins depend on what type of interactions?
R-group interactions
44
What type of molecular interactions are involved in tertiary protein structure?
* Mainly R group interactions
* Hydrophobic interactions - core
* Ionic interactions - Core +peripherary
* Hydrogen Bonding - periphery
* Van der Waals and London - periphery
45
What determines protein's tertiary structure?
* Geometric relationship between segments
* Position of side groups to one another
46
Quaternary Protein Structure
* Greater than [] kDA
* Association must be []
* 100 kilo Daltons
* 1 amino acid weights about 110 daltons
* Noncovalent associations
47
What is "gene expression"?
Everything from DNA in its compact from --\> Proteins doing shit
48
Which enzyme catalyzes the activation of tRNA?
Does this enzyme have proofreading capability?
aminoacyl-tRNA synthetase
Yes
49
What steps in translation initiation hydrolyze a GTP?
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
What are the 3 stop codons?
UGA, UAG, UAA
51
What is the name of the enzymatic function of the ribosome?
peptidyltransferase
52
What does glcosylation provide to the protein?
* Stability
* Signaling for localization
53
This class of enzymes transfers a sugar to a protein...
glycosyltransferase
54
N-Linked Glycosylation
* beings in []. and completed in the [] apparatus
* Requires the sequence [] /[]
* Co-[]. process
* Two types are recognized - High - [] type and [] type
* ER and finished in Golgi
* Asn-X-Thr/Ser
* Co-translational
* High Mannose type and Complex
55
O-linked Glycosylation
* Only happens in [] apparatus, on [] folded proteins
* []- [] process
* No defined [] sequence
* Golgi, fully folded
* Post-translational
* consensus sequence
56
What types of modifications are found on the following amino acids?
1. Asparagine
2. Histidine
3. Lysine
4. Serine
5. Threonine
6. Tyrosine
1. Asparagine - glycosylation, Methylation
2. Histidine - methylation
3. Lysine - Acetylation, methylation
4. Serine - Phosphorylation
5. Threonine - Phosphorylation
6. Tyrosine - Phosphorylation
57
At equal molar concentrartions - pH = []?
pH = pK
