Term Test 1 Prep Flashcards
1
Q
A-DNA
A
- right handed
- short and broad
- 26 Å in diameter
- 11 base pairs/turn
- 26 Å rise per base pair
- 20° tilt to helix axis
2
Q
B-DNA
A
- right handed
- longer and thinner
- most common in living cells
- has major and minor grooves
- 20 Å in diameter
- 10.5 base pairs/turn
- 34Å rise per base pair
- 6° tilt to helix axis
3
Q
Z-DNA
A
- left handed
- slim and elongated
- unknown function
- distorted
- 18Å in diameter
- 12 base pairs/turn
- 3.7Å rise per base pair
- 7° tilt to helix axis
4
Q
How wide is each base pair?
A
10.85 angstroms (1.085 nm)
5
Q
How many H bonds form between AT and CG?
A
2 H bonds between A and T
3 H bonds between C and G (takes more energy to break apart)
6
Q
How long is each turn in a DNA helix?
A
34 angstroms or 3.4 nm
7
Q
Which C and N are involved in N-glycosidic bonds?
A
pyrimidines: C1’ to N1
purines: C1’ to N9
8
Q
How thick is the whole DNA helix?
A
20 angstroms or 2nm
9
Q
How many nucleotide bases per turn?
A
10
10
Q
Angles of the major and minor grooves of B-DNA
A
major: 257°
minor: 103°
11
Q
What are “zinc fingers”?
A
DNA binding proteins that wrap around DNA and interact specifically within major group
12
Q
Why is DNA an ideal molecule to carry genetic information?
A
- stable, doesn’t carry on promiscuous reactions
- regular structure
- no evidence of catalytic activity
13
Q
What type of bond links nucleotides together?
A
phosphodiester
14
Q
intramolecular base pairing
A
when regions of the same rna molecule complementarily base pair with each other with H bonds
rna folds onto itself forming unique structures
15
Q
T/F: RNA can catalyze reactions.
A
true
16
Q
Which optical isomer form are amino acids usually?
A
L form
17
Q
What type of reaction forms a peptide bond?
A
condensation rxn
18
Q
N-terminus
A
amino end, (+)
19
Q
C-terminus
A
carboxyl end, (-)
20
Q
How are secondary structures formed?
A
by intramolecular hydrogen bonds between small portions of the polypeptide backbone
21
Q
alpha helix
A
- N-H forms H bond with C=O 4 peptide bonds away
- H bonds run parallel to the helix (vertically)
- each turn is 0.54nm in length
- can be amphipathic–one side hydrophobic one side hydrophilic (one side will form towards lipids the other side will form towards water)
22
Q
beta sheet
A
- H bonds between N-H and C=O of different strands, holding the polypeptide chains together (very rigid)
- can be parallel, antiparallel or mixed
- 5 to 10 amino acids per strand
- each sheet contains approx 2-15 strands
23
Q
3° structure
A
folding of 2° structures with respect to each other
24
Q
4° structure
A
overall 3D structure of multiple polypeptide chains; these chains interact with each other to create a stable molecule
25
The -NH3+ and -COO- can come together to form
an ionic/electrostatic bond
26
Disulfide bonds are formed in ____ conditions and broken in ____ conditions
formed in oxidizing condition and broken in reducing conditions
27
molecular chaperons
helps in the folding of proteins (or refolding of misfolded proteins)
28
How many amino acids are there per turn in an alpha helix?
3.6
29
motif
- recurring/repeating 2° structure in different proteins (e.g. helix-turn-helix)
- generally specific functions
- smaller
30
domain
- subunit of 3° structure that folds independently
- larger
- have particular functions
31
What is each level of protein structure stabilized by?
primary: peptide bonds
secondary: H bonding between groups on backbone
tertiary: bonds and interactions involving R groups
quaternary: bonds and interactions involving R groups and peptide backbone of different polypeptide chains
32
dimer
protein with two subunits
33
nucleases
enzymes that cleave phosphodiester bonds between nucleotides
34
difference between exonucleases and endonucleases
exonucleases cleave nucleotides at the end of the chain, endonucleases cleave phosphodiester bonds in the middle of the chain
35
restriction endonucleases/restriction enzymes
- a subset of endonucleases that cut dsDNA at a specific DNA sequence
- came from bacteria; it was a method for them to protect themselves from viruses (viral DNA)
36
type II restriction endonucleases
- more than 90% REs are type II
- recognize and cut symmetric/palindromic sequences 4-8 base pairs in length
- most molecular biology applications use type II endonucleases
37
methylase
methylates bacterial DNA to prevent it from being cleaved by endonucleases; REs target unmethylated
38
RE nomenclature
```
e.g. EcoR1
E-genus
co-species
R-strain
1-order isolated in
```
39
REs can recognize DNA sequences # to # base pairs in length
4 to 8
40
inverted palindrome
same nucleotide sequence in antiparallel directions (sequence is read the same way forward and back)
41
EcoRI, BamHI, HindIII produce __ sticky ends (overhang)
5' sticky ends
42
PstI and KpnI produce __ sticky ends (overhang)
3' sticky ends
43
SmaI and AluI produce ___ ends
blunt ends (no overhang)
44
isoschizomers
REs from different organisms that have the same cut site
45
DNA ligase
the enzyme that joins the ends of two strands of DNA to make one continuous strand; catalyzes formation of 3'-5'-phosphodiester bonds; ATP dependent
46
Which parts of eukaryotic cells contain DNA
Nucleus, mitochondria and chloroplasts (all segregated/separate)
47
promotor
region on DNA where RNA polymerase will bind to begin transcription
48
exon
region of the gene that is transcribed to RNA and encodes part or all of a particular protein
49
UTRs
untranslated regions; regions that are transcribed but not translated; contain control elements; region before and after area to be translated
50
terminator
region of DNA that signals the end of a gene; disengages RNA polymerase
51
introns
- non coding region of a eukaryotic gene that is transcribed but not translated
- gene expression regulation
52
promotor is typically ~__ nucleotides upstream of transcription site
25
53
What does the strength of the promotor have to do with protein production?
strong promotors
= strong enhancers
= rapid engagement of rna polymerase
= more protein produced
54
"equation" for transcription
dsDNA + RNA polymerase + NTPs (nucleotide triphosphates for energy) --> ssRNA + dsDNA + RNA polymerase
55
primary transcript
- the ssRNA initially produced by transcription
- may undergo further processing to become mRNA, tRNA, rRNA
- prokaryotes: primary transcript is mRNA
- eukaryotes: primary transcript is hnRNA (heterogeneous nuclear) or pre-mRNA --> MUST UNDERGO FURTHER PROCESSING TO BECOME mRNA
56
the coding strand is also known as...
non-template, + strand, this is what the sequence of a gene would be
57
the non-coding strand is also known as...
template, - strand
58
RNA is polymerized __ to __, DNA template strand is read __ to ___
RNA polymerized 5' to 3', DNA read 3' to 5'
59
alpha helices are generally __ amino acids long with __ turns, and __ amino acids per turn
11 amino acids long, 3 turns, 3.6 amino acids per turn
60
amino acids that are "helix preference"
ala, leu, met, glu
61
amino acids that are "helix breakers"
pro, gly, ser, thr
62
What bond/interaction does not directly influence tertiary structure of a protein?
peptide bonds (it influences primary structure)
63
consensus sequence
sequence of DNA having similar structure and function in different organisms
64
bacterial culture growth phases
1) lag phase: 30 minutes following inoculation, no cell growth
2) log phase: cell number doubles every 20-25 minutes
3) stationary phase: nutrients depleted, cells stop dividing
4) death phase: waste products accumulate, cells begin to die
65
intragenic mutation
gene can be randomly modified by errors in DNA replication
66
gene duplication
- accidental duplication of a gene in a single cell
| - 2 genes may diverge through evolution
67
DNA segment shuffling
2 or more genes break and rejoin to make a hybrid gene
68
What did the mitochondria originate from?
- a long time ago it existed as a free living organism
- was an aerobic bacteria in a symbiotic relationship with an anaerobic ancestral cell (generated energy from oxygen)
- have their own circular DNA, ribosomes, tRNA
69
hydrophobic force
pushing nonpolar surfaces together to push them out of a hydrogen-bonded water network (reducing their contact with water)
70
nucleoside names of each nitrogenous base
adenosine, guanosine, cytidine, thymidine, uridine
71
nucleotide names of each nitrogenous base
adenylate, guanylate, cytidylate, thymidylate, uridylate
72
nuclear envelope
- made of lipid bilayer membrane
- punctured by large pores that allow molecules to move between nucleus and cytosol
- supported by network of filaments (NUCLEAR LAMINA)
* keeps nuclear and cytosolic enzymes separate
73
domain shuffling
evolutionary process where large proteins evolve by joining domains in new combinations
74
protein modules
domains repeatedly found in diverse proteins; have versatile structures
75
RNA polymerase
- enzymes that perform transcription; catalyze formation of phosphodiester bonds that link ribonucleotides
- substrates are ribonucleoside triphosphates
- hydrolysis of phosphoanhydride bonds release energy to drive this process
76
upstream goes toward the __ end and downstream goes toward the __ end
upstream: 5' end
downstream: 3' end
77
gene expression
process involving the transcription and translation of a discrete DNA sequence
78
core promotor (TATA box)
- TATAAA
| - 25 nucleotides upstream
79
CAAT box
- a proximal control element
- GCCCAATCT
- 80 nucleotides upstream
80
GC box
- a proximal control element
- GGGCGG
- 100 nucleotides upstream
81
What type of interactions contribute to the stability of a DNA molecule along the vertical axis?
hydrophobic interactions along the base pairs of the vertical axis
82
types of covalent bonding that can contribute to protein tertiary structure (5)
1. hydrogen bonding between side chain and carboxyl oxygen
2. hydrogen bonding between two side chains
3. van der Waals interactions between hydrophobic regions
4. disulfide bonds
5. ionic bonds (non covalent)
83
X-ray crystallography is a biophysical technique typically used to determine the 3-D structure of ___.
proteins
84
“Phages” are infectious agents that attack __.
bacteria
