week 1 Flashcards
1
Q
define nucleotide
A
base + sugar + phosphate; monomeric units of nucleic acids
2
Q
define nucleoside
A
sugar + base; essentially a nucleotide w/o inorganic phosphate
3
Q
nucleotide naming identifies…
A
1) base
2) sugar
3) # of phosphates
4
Q
name the purines
A
adenine
guanine
5
Q
name the pyrimidines
A
cytosine
thymine
uracil
6
Q
deoxyribose has ___ attached to 2’ carbon
A
-H
7
Q
ribose has ___ attached to 2’ carbon
A
-OH
8
Q
DNA backbone is composed of…
A
sugars + phosphates
9
Q
what type of bond holds the backbone together
A
phosphodiester bonds
10
Q
what type of bond connects a pyrimidine with a purine to form the “rungs of the ladder?”
A
H-bonds
11
Q
What is the order in which a primary transcript is modified?
A
1) 5’ capping 2) poly A tail added 3) splicing
12
Q
guanine pairs with…
A
cytosine
13
Q
adenine pairs with…
A
thymine (or uracil)
14
Q
advantage of twisted, stacked spiral staircase
A
adds strength
15
Q
phosphate backbone’s charge
A
negative
16
Q
orientation of complementary DNA strands
A
anti-parallel
17
Q
most common conformation of DNA
A
B-DNA; right-handed
18
Q
define genome
A
all of an organism’s DNA (nuclear + mitochondrial)
19
Q
how many chromosomes does the genome of a haploid cell contain?
A
23
20
Q
how many chromosomes does the genome of a diploid cell contain?
A
46
21
Q
define karyotype
A
the display of the 46 human chromosomes
22
Q
ways to distinguish chromosomes
A
size
staining patterns
FISH color
23
Q
each DNA molecule that forms a linear chromosome must contain…
A
1) a centromere
2) two telomeres (ends)
3) replication origin
24
Q
in a karyotype, chromosomes are number in order of…
A
size
25
which amino acids would bind well in the groove of a double helix
arginine
lysine
histidine (in acidic environments; neutral in blood)
26
define locus
a specific location on a chromosome
27
define allele
alternate gene versions
28
define heterozygous
a cell containing two alleles that are functionally different
29
define homozygous
a cell containing two alleles that are NOT functionally different
30
does total number of chromosomes correspond with species complexity?
NO
31
define hemizygous
having only one allele for a given gene
32
introns make up what percentage of genes?
99%
33
DNA in prokaryotes exists as...
a single circular chromosome; double-stranded
34
how much are DNA molecules condensed?
10,000 fold
35
what issue does condensation of eukaryotic DNA pose?
it must be decondensed for replication to occur
36
Where does DNA replication begin in prokaryotes and what does the DNA bind?
single point of origin known as OriC and the DNA coils around the protein DnaA (major initiator protein) at the OriC
37
What is the primosome composed of in prokaryotes?
DnaB (DNA helicase) and DnaG (DNA primase)
38
What is the activity of helicases?
separate the DNA strands and unwind parental duplex
39
What effect does inhibition of HATs and HDACs have?
Inhibition of HATs-->can't acetylate tails, chromatin stuck in heterochromatin
Inhibition of HDACs-->can't deacetylate tails, chromatin stuck in euchromatin
40
What is the function of topoisomerases?
enzymes that break phosphodiester bonds and rejoin them to relieve supercoiling tension
41
What is the major topoisomerase in bacteria?
DNA gyrase
42
What direction does DNA pol move on the template strand?
3'-5'
43
define heterochromatin
highly condensed chromatin that is closed to transcription or replication; associated with de-acetylation
44
What is the function of primase?
lays down RNA primers for both lagging strand and leading strand synthesis
45
What is the function of ligase?
it joins DNA fragments together, typically in lagging strand DNA synthesis
46
What is the function of RNAse H?
removes RNA primers from Okazaki fragments working together with Pol I
47
What is the function of Pol I in prokaryotic DNA synthesis?
Pol I fills in the gaps left by the removal of the primers
48
What prevents DNA polymerase from falling off the template strand during DNA synthesis?
clamp proteins
49
Nonpolar Amino Acids
Glycine, Alanine, Valine, Leucine, Isoleucine, Proline
50
What effect do HATs have on chromatin?
Histone Acetyltransferase:
| Add acetyl groups to histone tail lysines. Acetylation decondenses chromatin->euchromatin expressed
51
What effect do HDACs have on chromatin?
Histone De-acyteltransferase:
De-acytelation of histone tail lysines. De-acytelation allows chromatin recondensation->forms heterochromatin (not expressed)
52
What effect does inhibition of HATs and HDACs have?
Inhibition of HATs-->can't acetylate tails, chromatin stuck in heterochromatin
Inhibition of HDACs-->can't deacetylate tails, chromatin stuck in euchromatin
53
eukaryotic DNA packaging involves wrapping of DNA around ___
histone proteins
54
the histone-DNA complex is called...
chromatin
55
define microRNA (mRNA)
non-coding RNAs with key functions in development, cell differentiation, regulation of cell cycle& apoptosis; regulates mRNA degradation, translation, chromatin condensation
56
define solenoid
helical, tubular coils that allow for further compaction of chromatin
57
core histones are rich in which amino acids?
arginine & lysine (positive charge neutralizes negatively charged DNA backbone)
58
acetylation of histone tails leads to...
destabilization/loosening of the chromatin due to neutralization of the histone's original positive charge --> more difficult to neutralize the negative charge of the DNA as it is compacted
59
define euchromatin
loose chromatin that is open for transcription and replication; associated with acetylation
60
define heterochromatin
highly condensed chromatin that is closed to transcription or replication; associated with de-acetylation
61
What is an example of an HDAC?
Sirtuins (SIR) protein
62
Explain how HDAC inhibitors are used as anti-cancer drugs
HDACs often upregulated in cancer cells to silence tumor suppressor genes by locking them in heterochromatin. Inhibitors allow expression of the silenced tumor suppressor genes.
63
What are the DNA polymerases that are found in E. coli?
Pol I, Pol II, Pol III - Pol III is primarily responsible for replication
64
What phase in eukaryotic cell cycle allows for DNA replication?
S phase
65
How many origins of replication due prokaryotes and eukaryotes have for DNA synthesis?
prokaryotes - 1
| eukaryotes - many
66
What removes RNA primers from Okazaki fragments in eukaryotic cells?
Flap endonuclease I (FEN I) and RNAse H
67
How do eukaryotic cells solve the "winding problem" that occurs in DNA replication?
topoisomerases
68
How does topoisomerase 1 work?
nicks DNA and reforms it to relieve tension through a reversible nicking rxn
69
How does topoisomerase 2 work?
it prevents DNA from getting tangled by breaking dsDNA to allow DNA to be pulled apart
70
Why is topoisomerase 2 a good target for cancer treatment?
topo II is usually confined to proliferating cells in eukaryotes
71
what is the role of HAT?
"histone acetyltransferase" --> acetylates a histone
72
what is the role of HDAC?
"histone de-acetyltransferase" deacetylates a histone
73
HDACs are often unregulated in which type of cells?
cancer cells, leading to silencing of tumor suppressor genes; HDAC inhibitors are used as anticancer drugs
74
how does RNA form base pairs?
it is single stranded, but it may loop back on itself
75
RNAs can also act as...
enzymes (ribozymes)
76
function of mRNA
code for proteins
77
mRNA processing involves...
1) 5' cap
2) poly-A tail
3) splicing out of non-protein coding sequences
78
tRNA function
carry amino acids to ribosomes so they may be incorporated into the polypeptide chain
79
accuracy of amino acid incorporation into proteins occurs via...
anti-codon of tRNA pairing with codon of mRNA
80
all tRNAs form which type of structure?
cloverleaf
81
retrovirus process
1) releases RNA genome into cell cytoplasm
2) reverse transcription into DNA
3) carries with it proteins that get integrated into host genome
4) reproduces within host genome
82
define microRNA (mRNA)
non-coding RNAs with key functions in development, cell differentiation, regulation of cell cycle& apoptosis
83
In DNA synthesis, which DNA strand is close to the product strand?
The coding strand is close to the product strand (same sequence). The template strand is read and the opposite bases are put into the product strand.
84
Define protein primary structure
Amino Acid Sequence
85
Define protein secondary structure
H-bond interactions of adjacent aa's to form alpha helices or beta sheets
86
Define protein tertiary structure
Interactions of alpha helices or beta sheets and R groups
87
Define protein quaternary structure
Interaction of multiple polypeptides
88
Aromatic Amino Acids
Polar: Tryptophan, Tyrosine
Nonpolar: Phenylalanine
89
Sulfur-Containing Amino Acids
Methionine, Cysteine
90
Polar, Uncharged Amino Acids
Serine, Threonine, Asparagine, Glutamine
91
Charged Amino Acids
Negative/Acidic: Aspartate, Glutamate
| Positive/Basic: Arginine, Lysine, Histidine
92
Which amino acids would be found on the interior of a protein?
Nonpolars (glycine, alanine, valine, leucine, isoleucine, proline), Aromatics (tryptophan, tyrosine, phenylalanine)
93
What amino acid can form disulfide bonds?
Cysteine
94
What amino acids can form H-bonds?
Polar, Uncharged Group (Serine, Threonine, Asparagine, Glutamine)
Tyrosine and Cysteine
95
What amino acids can form electrostatic interactions?
Charged Amino Acids
96
Which stereoisomer of alanine is found in bacterial cell walls?
D-alanine (bacDeria)
| L-alanine is in human proteins and cells
97
What is the name of a covalent bond between carboxyl and amino groups of amino acids?
Peptide bond
98
Exposed hydrophobic protein patches form:
Aggregates
99
Denaturation of proteins is caused by:
Heat, oxidative damage, solvents, changes in pH
100
Anti-cancer drugs target chaperone protein inhibition because:
Cancer cells have many misfolded proteins, so chaperones help them survive. Inhibiting chaperones causes excessive protein aggregation and cancer cells die.
101
Hemoglobin has a sigmoid curve because of:
Cooperativity between subunits in ligand binding. This means low affinity at low oxygen pressures (in tissues).
102
What does 2,3-BGP do?
Promotes the T-state (tense/anti-oxygen state) of Hb, making it release oxygen to cells better.
103
Increased 2,3-BPG levels shift the Hb affinity curve:
Right (lower affinity)
104
Which level of protein structure is most important for function?
Tertiary. Primary sequences may vary between 2 proteins but as long as their aa properties are conserved, they form the same tertiary interactions and have similar functions.
105
Sickle Cell anemia caused by pos. 6 beta chain glutamate change to:
valine
106
T/F: Maternal Hb has higher affinity for oxygen than fetal Hb.
False! Fetal Hb has higher affinity (curve is shifted left) so it can take oxygen from the mother's Hb
107
T/F: Hb contains 2 alpha chains throughout life.
True!
Fetal Hb has 2 alpha/2 gamma.
Adult Hb has 2 alpha/2 beta
108
Why don't sickle cell symptoms show until 4 months?
The mutation is in the beta chains, which are not in fetal Hb, only adult Hb.
109
T/F: Fetal Hb has a low affinity for 2,3-BPG
True. It would be bad to bind 2,3-BPG because then it would be stuck in T-state and harder to get oxygen from the maternal Hb.
110
2,3-BPG is what type of molecule?
Allosteric inhibitor
111
Which factors would shift the hemoglobin affinity curve to the right? (lower affinity)
1. Drop in pH
2. Increase in 2,3-BPG
3. Increase in temp.
