Midterm 1 Flashcards
1
Q
What is the optimal distance for Van der Waals interactions?
A
Occurs at a distance slightly greater than the length of the covalent bond.
2
Q
1 nm = 10-9 m
1 Aº = ?
A
10-10 m
3
Q
Order bond strength from strongest to weakest
A
- Covalent
- Ionic
- Hydrogen Bond
- Van Der Walls
4
Q
Given the Second Law of Thermodynamics, how can reactions that create order (which are entropically unfavorable) occur?
A
- A favorable enthalpy change overcomes entropic penalty.
- The unfavorable reaction is coupled to a favorable one.
5
Q
Plant cell shape is determined by the amount of water stored in the central vacuole. What is directly responsible for maintaining turgor pressure in a leaf?
A
osmotic pressure
6
Q
What are amino acids and how do they differ from one another?
A
Differ by the R group attached to central carbon
7
Q
What 3 components make up a nucleotide?
A
- Nitrogen Base
- Pentose (5-ringed) Sugar
- Phosphate (1-3 groups)
8
Q
Sugars contains what 3 atoms and what is the base molecular formula?
A
C, O, H
CH2O (Glucose is C6H12O6)
9
Q
What does it mean if a molecule is amphipathic and which molecules usually exhibit this feature?
A
Has both hydrophobic and hydophilic parts.
Fatty acids
10
Q
Compare saturated, polyunsaturated, and monounsaturated fats.
A
Saturated - No C=C double bonds
Polyunsaturated - Multiple C=C double bonds
Monounsaturated - One C=C double bond
11
Q
Amino acids are _______ linked through _______ bonds.
A
covalently
peptide
12
Q
Monosaccharides are _______ linked thorough _______ bonds.
A
covalently
glycosidic
13
Q
What is supramolecular assembly?
A
NO covalent bonds involved
ex. membranes, DNA + Histones
14
Q
What is the Organizational Heirarchy in Biochemistry?
A
15
Q
What are the 3 unique properties of water?
A
- Solid water less dense than liquid water
- Liquid over wide range of Earth’s temperature
- Universal Solvent
16
Q
What is a cofactor?
A
Any element required in conjuction with an enzyme to perorm a reaction.
17
Q
When forming a hydrogen bond, there is always a H-bond ______ and H-bond _______.
A
donor
acceptor
18
Q
In liquid, water makes about ____ H-Bonds
In ice, water makes about ____ H-Bonds.
A
3.4
4
19
Q
What happens when a crystal of NaCl is dropped in water?
A
A hyrdation layer forms around the ions, preventing them from rejoining the crystal.
20
Q
What exactly is a hydrogen bond?
A
A noncovalent weak bond that occurs between a hydrogen atom on an electronegative atom (N,O,) and a different electronegative atom.
21
Q
What are Van Der Waals interactions?
A
Occur when temporary dipoles interact
22
Q
What is the Van Der Waals radius?
A
Perfect distance between two atoms in order for Van Der Waals interaction to occur.
*Note: If atoms are too close, they will repel. If they are too far, they will not interact*
23
Q
What are hydrophobic effects?
A
Weak noncovalent interactions between non-polar molecules in which the molecules clump together to reduce the size of the hydration layer.
24
Q
Cell membranes are made of __________ bilayers.
A
phospholipid
25
What is Osmosis?
When solvent (water) moves from an area of **lower** solute concentration to an area of **higher** solute concentration through a **semipermeable** membrane.
Low Concentration ⇒ High Concentration
26
What is the Henderson-Hasselbach equation?
27
What is the central dogma of molecular biology?
DNA → mRNA → Protein
28
What 3 parts do nucleic acids consist of?
1. Nitrogen **base**
2. Pentose **sugar** (Ribose or Deoxyribose)
3. **Phosphate** group
29
What bases are purine and which are pyrimidines?
30
What is the difference between ribose and deoxyribose sugars?
Ribose - **OH** at C-2'
Deoxyribose - **H** at C-2' (more stable)
31
What does a nucleoside consist of?
32
Phosphate group + nucleoside =
nucleotide
33
Nucleotides are linked together via ___________ bonds.
phosphodiester
34
How are the phosphoryl groups labeled on a nucleotide?
35
How many base pairs are in eukaryotic DNA?
6 billion
36
Purines have _______ rings while pyrimidines have ______ ring.
two
one
37
How do you name a nucleoside?
suffix "osine" or "idine"
38
How do you name a nucleotide?
Nucleoside-5' "monophosphate"
or
suffix "ylate"
39
Compare the primary and secondary structure of DNA.
**Primary** - nucleotides in a chain
**Secondary** - two complementary strands of DNA bind together in an antiparallel fashion to form a _double helix_.
40
Compare the minor and major grooves.
**Minor** - backbones _closer_ together
**Major** - backbones _further_ apart
41
Base pairs (A-T, C-G) are bonded via ________ bonds.
hydrogen
42
The nitrogen bases are \_\_\_\_\_\_\_\_\_, therefore, move to the interior of the DNA molecule.
hydrophobic
43
A complete turn of the helix in B-form DNA contains ____ base pairs.
10.5 (36 Aº)
44
Compare the DNA coding strand and DNA template strand.
DNA coding strand runs 5' → 3'
45
What is Chargaff's Rule?
Molar ratio of A = molar ratio of T, C=G
46
A-T has ___ H-Bonds and C-G has ___ H-Bonds.
2
3
47
How does base stacking provides stability for DNA?
**Hydrophobic effects** and **Van Der Waals** interactions create _less_ interaction with water.
48
Compare the 3 types of DNA.
A - Short, wide, right-handed, dehydrated, bases are tilted 20º
**\*B - Right-handed, most stable****/common**
Z - Left handed, narrow
49
What is DNA denaturation and how does it occur?
When a double strand **separates** into single strands.
Occurs under **heat** or addition of **acid/base**.
\*Note: Separation can also occur enzymatically via **helicases**
50
At what temperature (Tm) is half of DNA double-stranded and half single-stranded?
85ºC
51
The absorbance of DNA ________ as it becomes single stranded.
increases
52
What is renaturation of DNA and when does it occur?
2 single strands **reform** to form a double helix.
Occurs when you _decrease temperature_.
53
The phenomenon of UV absorbance increasing as DNA is denatured is known as the \_\_\_\_\_\_\_\_\_\_\_\_.
hyperchromic shift
54
What is the absorbance trend for DNA?
single nucleotides \> single-stranded \> double-stranded
55
Compare the Linking number (Lk), Twist number (Tw), and Writhe number (Wr) and how are they related.
**Lk** - Number of times DNA strand winds in right-hand direction
**Tw** - Number of times one strand completely crosses over the other
**Wr** - Number of times helix crosses over itself
**_Lk = Tw + Wr_**
\*Note: As long as the DNA backbone is not disrupted, Lk is constant.
56
Compare positive, negative, and relaxed supercoils.
**Negative** most common
57
What is a nucleosome?
**DNA +** **histone** proteins.
58
What are topoisomerases?
Enzymes that **relieve positive supercoils** through cleavage and reannealing of DNA.
59
Compare Topoisomerase I and Topoisomerase II.
**Topoisomerase I** - Cleaves 1 strand of DNA and reduces supercoil region by 1 turn
**Topoisomerase II** - Cleaves 2 strands of DNA and reduces supercoil region by 2 turns
60
Why is DNA more stable than RNA.
**Autocleavage** can occur in **RNA** but the absence of the C-2' OH group in DNA keeps autocleavage from happening.
61
What is the deamination of cytosine and what base is produced?
_Loss_ of an _amine_ group.
## Footnote
**Uracil**
62
What are ribozymes and what do they do?
RNA molecules with catalytic activity.
Cleave nucleic acids.
63
What is the function of tRNA?
tRNA - anticodon
mRNA - codon
In the process of translation, a tRNA anticodon must match up with each codon in mRNA to add the correct amino acid to a growing protein chain.
64
What is Inosine?
Inosine is a nucleoside often found in **tRNA** that can base pair with A, C and U. This can be used in translation. **2 H-Bonds**
65
How can you end up with a triple helix?
Triplet interactions can occur between a single stranded region of DNA, or RNA with an RNA, DNA, or RNA-DNA duplex.
Quadraplexes can occur among guanine bases found in particular G-rich DNA sequences.
66
How many genes do humans have?
50,000
67
What is a genome?
The genome is the collection of genes and it remains **constant**, however, expression of that gene can change.
68
What is the importance of telomeres?
Keep chromosomes intact/stable. Every time a cell divides, telomere length decreases and decreased telomere length contributes to cancer.
\*Note: Telomerase increases length of telomere
69
What is the promoter region?
A specific DNA sequence upstream of the coding sequence that is necessary to interact with **transcription factors.**
70
Exons are ________ regions and introns are ________ regions.
coding
non-coding
71
RNA polymerase binds to the __________ \_\_\_\_\_\_\_\_\_\_\_\_ which initiates transcription.
promoter region (TATA)
72
A ____________ gene has one coding-sequence resulting in _one_ protein.
A __________ gene has multiple coding-sequences resulting in _multiple_ proteins.
Monocistronic
Polycistronic
73
What occurs when RNA undergoes processing?
- Remove intron sequences,
- Add a 5′ cap
- Add a 3′ poly(A) tail
74
What are transcription factors?
Proteins that help _initiate transcription_ by recruiting _RNA polymerase_.
75
What is a single nucleotide polymorphism (SNP)?
One nucleotide substituted for another.
76
What are short tandem repeats (STR)?
**Deletion** or **insertion** in genome
77
What are 3 major ways that bacteria transfer DNA?
1. **Transduction** - Bacteriophage brings in DNA
2. **Conjugation** - DNA transferred via direct contact
3. **Transformation** - exogenous DNA introduced
78
What is a restriction endonuclease?
An enzyme that _cleaves DNA._
Type I: Recognize and cleaves at **different** sites (25bp)
Type II: Recognize and cleaves at the **same** site.
Type III: Recognize and cleaves and **different** sites (100bp)
79
A nucleosome particle consists of ______ base pairs double-stranded DNA wrapped around 8 histone proteins H2A, H2B, H3, and H4, with H1 (green) on the outside of the structure.
147
80
Right-handed twists produce a _______ supercoil and left-handed twists produce a ________ supercoil.
negative
positive
81
Many tRNA anticodons contain the nucleoside _________ which is able to base pair with the nucleosides C, U, or A.
inosine
82
Plasmids, Cloning?
White - DNA insertion has occurred (no functional B-enzyme)
Blue - DNA insertion has NOT occurred (functional B-enzyme)
83
For the _________ nitrogenous bases, the heterocyclic ring contains nine atoms and the _________ nitrogenous bases have six atoms within the ring.
purine
pyrimidine
84
The presence of 1.5 M NaCl causes a ________ in the melting temperature of DNA.
**increase**
Curve would _shift right_
85
Why does mp increase when %G-C increases?
3 hydrogen bonds; therefore, when DNA contains greater G-C content, the melting temperature is higher.
86
Supercoiling DNA is a property of what kind of cells?
Both _prokaryotic_ cells and _eukaryotic_ cells
87
What role do Topoisomerases play in DNA replication?
Topoisomerase enzymes alleviate the supercoil that develops during DNA replication_. IF inhibited DNA replication cannot occur_.
88
Compare euchromatin and heterochromatin. Which is more susceptible to DNA cleavage?
**Euchromatin** - open structure
**Heterochromatin** - DNA is compact structure
Euchromatin leaves more DNA exposed and is, therefore, more susceptible to DNA cleavage.
89
Heterochromatin is associated with _________ DNA and the ___________ of a chromosome.
non-coding
centromere
90
Outline the steps that eukaryotic DNA take in the progression toward reducing its size and becoming a chromosome.
1. The initial DNA–histone association produces the **nucleosome**
2. Nucleosomes join to form **looped chromatin**
3. **Chromatin coils**.
4. **Chromosome**
91
What is the formula for the number of DNA molecules generated by PCR?
2n
n is the cycle number
92
When making cDNA from mRNA, what is the appropriate primer to use?
5'-TTTTTTTTTTTTTTT-3'
93
The Sanger method of DNA sequencing requires what being in the reaction tube?
- template DNA
- deoxyribonucleotides
- dideoxyribonucleotides.
94
What are the steps for PCR (Polymerase Chain Reaction)?
1. **Denature DNA** at high temperature
2. **Primers anneal** at lower temperature
3. **Taq DNA polymerase** catalyzes the extension of the primer to produce a sequence complementary to each template strand
95
How do you make cDNA from mRNA?
1. mRNA + primer that is complementary to mRNA tail
2. Treat with reverse transcriptase → 1 strand cDNA
3. Treat with ribonuclease H to degrade mRNA
4. Treat with DNA polymerase → 2nd strand cDNA
96
If you start with 6 DNA molecules and do 25 PCR cycles, how many DNA molecules will you end up with?
6 X 225 molecules
97
What is the chain-termination method used to determine?
The sequence of a region of DNA.
Utilizes ddNTP (dideoxyribonucleoside triphosphate) which has H's at the 2' and 3' Carbons. Terminates elongation of chain.
Random incorporation of a ddNTP in the DNA product terminates synthesis and incorporates a different fluorescent label for each ddNTP.
98
What is the configuration for most amino acids? Which one is the exception?
S (L) - amino on left
\*Exception is **Cysteine** which is **R** (D) configuration
99
What is the abbreviation and formula for Glycine?
**Gly**
**G**
100
What is the abbreviation and formula for Alanine?
**Ala**
**A**
101
What is the abbreviation and formula for Valine?
**Val**
**V**
102
What is the abbreviation and formula for Leucine?
Leu
L
103
What is the abbreviation and formula for Isoleucine?
Ile
I
104
What is the abbreviation and formula for Proline?
**Pro**
**P**
105
What is the abbreviation and formula for Methionine?
Met
M
106
What is the abbreviation and formula for Phenylalanine?
Phe
F
107
What is the abbreviation and formula for Tryptophan?
**Trp**
**W**
108
What is the abbreviation and formula for Tyrosine?
Tyr
Y
109
What is the abbreviation and formula for Serine?
Ser
S
110
What is the abbreviation and formula for Threonine?
Thr
T
111
What is the abbreviation and formula for Cysteine?
Cys
C
112
What is the abbreviation and formula for Aspartic Acid?
Asp
D
113
What is the abbreviation and formula for Glutamic Acid?
Glu
E
114
What is the abbreviation and formula for Asparagine?
Asn
N
115
What is the abbreviation and formula for Glutamine?
Gln
Q
116
What is the abbreviation and formula for Histidine?
His
H
117
What is the abbreviation and formula for Lysine?
Lys
K
118
What is the abbreviation and formula for Arginine?
Arg
R
119
Which amino acid makes a disulfide bridge?
Oxidation of 2 **Cysteine** residues
120
\_\_\_\_\_\_\_\_\_ are enzymes that add a phosphate group to a protein and _________ are enzymes that remove a phosphate group.
Kinases
Phosphatases
121
What is the pKa1 of the C-terminal of amino acids?
2.2
122
What is the pKa2 of the N-terminal for amino acids?
9.4
123
What is the pKa3 of Aspartic Acid (Asp, D)?
3.9
124
What is the pKa3 of Glutamic Acid (Glu, E)?
4.07
125
What is the pKa3 of Histidine (His, H)?
6.04
126
What is the pKa3 of Lysine (Lys, K)?
10.54
127
What is the pKa3 of Arginine (Arg, R)?
12.48
128
What is the pKa3 of Tyrosine (Tyr, Y)?
10.46
129
What is the pKa3 of Cysteine (Cys, C)?
8.37
130
Peptide bonds are formed by _________ between the amine and carboxylic acid groups and catalyzed by \_\_\_\_\_\_\_\_\_.
condensation
ribozymes
131
Why is free rotation restricted around a peptide bond?
It has partial **double bond** character.
132
What are the 3 stop codons in RNA?
UAA
UAG
UGA
133
What is the isoelectric point (pI)?
The pH at which a molecule (amino acid) is neutral.
134
How do you calculate pI for an **acidic** amino acid?
_pKa1 + pKa3_
2
135
How do you calculate pI for a basic amino acid?
_pKa2 + pKa3_
2
136
What is the Buffering Zone?
1 pH above and 1 pH below pI
137
What is the Wobble Hypothesis?
There exists _unconventional base pairing_ for the **3rd** base of the _codon/anticodon_. So we don't need a tRNA for all 61 codons, most cells have around 40 tRNA.
138
What are some characteristics of the alpha-helix?
- Right-handed helix
- H-Bond between residues **n and n+4**
- Favored by MALEK
- Destabilized by GP
-
139
Alpha-helices have a dipole moment toward which terminus?
C-terminus (carbonyl)
140
ß strands form \_\_\_\_\_\_\_\_\_\_\_.
ß-pleated sheets
141
ß-sheets can be _______ or \_\_\_\_\_\_\_\_.
parallel
antiparallel (MORE STABLE due to H-bonds)
142
What are Beta Turns?
Connect **2 ß strands** in an **antiparallel fashion**.
143
What are the two types of ß turns?
**Type 1** - Carbonyl oxygen facing _inward_
**Type 2** - Carbonyl oxygen facing _outward_
144
Compare homodimer and heterodimer.
**homodimer** - 2 _identical_ protein subunits
**heterodimer** - 2 _different_ protein subunits
145
What is the 4 helix bundle?
ALL **alpha-helices**
146
What is the Greek Key fold?
4 or more B-strands to form a **B-sheet**
147
What is the Rossman Fold?
**Alternating alpha-helices and B-strands** (alpha/Beta 50/50)
148
What is the TIM Barrell fold?
Protein fold that has alternating alpha helix and beta strand
(α/βbarrel)
