Dr. Leys Study Guide Flashcards
(138 cards)
1
Q
Cells acquire nucleotides through two processes: .
A
de novo synthesis and salvage pathways
2
Q
De novo synthesis of purines results in the synthesis of inosine that can be converted into
A
adenosine and guanosine.
3
Q
Atoms in a newly synthesized purine are derived from several sources including the amino acids __,__,__ and methyl groups supplied by
A
AA’s = aspartate, glutamine and glycine
CH3 group supplied by folic acid and carbon dioxide.
4
Q
__ and __ regulate de novo synthesis of purines at multiple points in the pathway.
A
adenosine diphosphate (ADP) and guanosine diphosphate (GDP)
5
Q
Hypoxanthine and guanine can be recycled through the ___ pathway with Hypoxanthine guanine phosphoribosyl transferase (HGPRT).
A
salvage
6
Q
Xanthine oxidase catalyzes a hydroxylase type reaction leading to the formation of
A
uric acid that can be excreted.
7
Q
Excess uric acid is the cause of
A
gout
*a kind of arthritis caused by a buildup of uric acid crystals in the joints
8
Q
Gout is most often caused by low levels of secretion of __, but can also be caused by excess production.
A
uric acid
9
Q
Crystallization of ___ in the joints leads to a localized inflammatory response.
A
Sodium urate
10
Q
____, a purine analog, is used to treat gout. It inhibits Xanthine oxidase preventing the formation of uric acid
A
Allopurinol
11
Q
A Hypoxanthine guanine phosphoribosyl transferase (HGPRT) deficiency causes ____ that results in severe retardation, crippling gouty arthritis and self-mutilation
A
Lesch-Nyhan syndrome
12
Q
Lesch-Nyhan occurs in (males/females) only because the HGPRT gene is located on the _chromosome
A
males only
X chromosome
13
Q
The breakdown of purines can replenish TCA cycle intermediates through the production of
A
fumarate
14
Q
The atoms in a pyrimidine ring are derived from __ and __
A
aspartate and carbamoyl phosphate.
15
Q
The first 3 enzymes in the synthesis of pyrimidines are located on the same
A
protein (CAD protein).
16
Q
The pyrimidines _ and _can be interconverted.
A
U and C
17
Q
dUMP is converted to TMP by ___, an enzyme requiring the transfer of a methyl group from tetrahydrofolate.
A
thymidylate synthase
18
Q
Inhibitors of tetrahydrofolate production are used as therapeutic agents for treating
A
cancer and bacterial infections.
19
Q
Fluro substituted pyrimidine analogs that inhibit ___ are used as anticancer agents
A
thymidylate synthase
20
Q
Ribonucleotide reductase converts ribonucleotides to
A
deoxyribonucleotides
21
Q
Base-pairing in DNA is ___?In RNA it’s
A
DNA A-T and G-C
RNA A-U and G-C.
22
Q
Homologous regions of DNA can be compared among different species to determine ___relationships
A
phylogenetic
23
Q
Closely related organisms contain similar __ compliments, however they are often arranged differently on the chromosomes of each species.
A
DNA
24
Q
The living world is made up of 3 divisions, or domains:
A
bacteria, archaea and eukaryotes.
25
There are 4 main processes for generating change in a genome:
intragenic mutation (single base change),
gene duplication,
DNA segment shuffling,
horizontal transfer (from one cell to another).
26
Bacterial genes are usually clustered into groups (___) that are transcribed as a single unit.
operons
27
Eukaryotic genes are often broken up with regions of noncoding DNA or ___ between regions of coding DNA (__).
introns - noncoding
exons - coding
28
In a comparison of the same gene in several closely related species, the ___ will generally be very similar (conserved), while the ___ will vary in size and content.
exons similar
introns vary
29
___ chromosomes are densely packed with genes leaving very little DNA that is non-coding.
Bacterial
30
Most of the DNA in ____ does not code for
proteins. Most of the human genome is made up of repeated sequences. Many of those sequences are mobile elements that can move around in the genome
higher eukaryotes including humans
31
Bacterial chromosomes are ___ and eukaryotic chromosomes are __
circular - bacterial
linear- eukaryotic
32
In addition to the human genome, the entire genomes of a large number organisms have been completed including several bacteria that are found in the
oral cavity
33
It is possible to construct metabolic pathways and compare them with other organisms by examining their
entire genome content.
34
Genes can be grouped into families bases on similar ___ found in different organisms. Homologous sequences can be
found in genes of the same organism that carry out different but similar functions. Genes that have similar functions in very distantly related organisms can have similar
(homologous)
sequences
sequences (homology).
35
The phylogenetic relationships of different organisms can be compared by
comparing ___ in the two organisms
the DNA sequence of similar genes
36
___ is a DNA dependent (uses DNA as a template) DNA synthesizing enzyme
DNA polymerase
37
___ is a DNA dependent RNA synthesizing enzyme.
RNA polymerase
38
___ is an RNA dependent DNA synthesizing enzyme.
Reverse transcriptase
39
___ is a DNA dependent RNA polymerase.
Primase
40
Primase synthesizes a small RNA “primer” that can be used by the DNA polymerase to .
elongate the chain
41
___minimizes the number of mistakes (mis-incorporated
| nuceotides) by using a 3’ to 5’ exonuclease (or proofreading) activity that is part of the same protein
DNA polymerase
42
DNA polymerase as well as all other nucleic acid polymerases synthesize DNA in the
5’ to 3’ direction only
43
During replication, each new nucleotide is added to the __ carbon on the last
nucleotide of the new DNA chain.
3’ carbon
44
The base component of each nucleotide is connected to the sugar at the __ carbon. The adjacent nucleotides in a DNA chain are attached at the _ and _ carbons. And the 2’ carbon differs between __ and __
1’ - connected to sugar
5’ and 3’ carbons
RNA and DNA
45
DNA polymerase is an elongating enzyme; it cannot initiate ___. Therefore a __is required for elongation of a new stand using the DNA polymerase.
synthesis
primer
46
Bacterial chromosomes contain one origin of
replication
47
___ proceeds in both directions away from the origin until the two
replication forks meet at a specific sequence on the other side of the chromosome.
DNA synthesis
48
In __ new rounds of DNA replication can begin before the previous round is completed
bacteria
49
___chromosomes contain many origins of replication that may change during the development of the organism
Eukaryotic
50
In ____, each entire chromosome is replicated only once each cell division and new rounds of replication do not start until after the cell divides
eukaryotes
51
Eukaryotic chromosomes are linear and special structures called ___are placed on each end
telomeres
52
____ are constructed with the enzyme telomerase that uses an RNA template to synthesize a short repeated DNA sequence at the ends of chromosomes.
Telomeres
53
Because the polymerase must synthesize new DNA in the 5’ to 3’ direction,
the two polymerase molecules on opposite strands move
away from each other.
54
___ unwinds (separates) the 2 DNA strands before polymerization of the new strands.
Helicase
55
___ proteins keep the two complementary strands for reforming a double helix.
Single-stranded binding proteins
56
The polymerase on the ___ strand moves toward the replication fork and the polymerase on the __ strand moves away from it.
leading strand moves toward
lagging stand away
57
The ___ strand is synthesized in short (Okizaki) fragments.
lagging
58
Primase initiates synthesis of each Okizaki fragment by making a short
RNA primer.
59
The ___ strand is synthesized by the continuous movement of the DNA polymerase along the template
leading
60
___ of the DNA signals that the DNA is unreplicated and is ready to be used as a template for the next round of synthesis
Methylation
61
New or modified genes can be generated by one or a combination of 4 events:
1) point mutations in the coding region that change the amino acid composition of the protein.
2) duplication of the entire gene.
3) Mixing of segments of one gene with segments of another gene – segment shuffling.
4) Acquisition of new activities by transfer of genes between two organisms –horizontal gene transfer.
62
Mixing of segments of one gene with segments of another gene
segment shuffling
63
Acquisition of new activities by transfer of genes between two organisms
horizontal gene transfer
64
Many genes belong to __ that share homologous regions. These regions usually code for proteins that carry out similar functions.
gene families
65
Breaks in the DNA (especially double stranded breaks) facilitate the initiation of
recombination
66
A defect in ___, affects joining together of adjacent segment of DNA on a chromosome, can cause abnormal amounts of recombination
DNA ligase
67
___ is the reciprocal exchange of genetic information.
Recombination
68
recombination can be the result of
1) reciprocal exchange during cell division.
2) DNA damage, e.g. X-ray damage.
3) Introduction of foreign DNA.
4) Programmed recombination during the development or maturation of a cell type, e.g. antibody producing genes during B-cell maturation.
69
__is the non-reciprocal exchange of genetic information
Gene conversion
70
Recombination between ___ causes the loss of DNA that was between the two repeated segments
direct repeated sequences on the same chromosome
71
Circular DNA can be inserted in a chromosome by recombination between a region on of __ molecule and an __ region on the chromosome
circular molecule and an homologous region
72
X-rays and other agents that cause breaks in DNA induce
recombination
73
___elements are found in all species from bacteria to human.
Transposable
74
Transposable elements move from one location in the DNA to
another location within that cell
75
Transposable elements can cause changes in the DNA at the site of
insertion
76
There are two major types of transposable elements, one type that contains inverted repeated sequences at the ends and causes a short region of the genome to be ____and a second type that is structurally similar to a __ and __ through an RNA intermediate.
duplicated at the site of insertion
and
similar to a retrovirus and transposes through an RNA intermediate
77
____ is recombination that resulted from imprecise pairing of tandemly repeated sequences.
Unequal crossing-over
78
Unequal crossing over results in
the loss or gain of gene copies.
79
There are two types of mutations:
DNA rearrangements and base substitutions
80
There are many mechanisms in each cell for repairing
DNA
81
Damage to a __ (e.g. deamination) can either be repaired or lead to a permanent mutation.
nucleotide
82
___ can be caused by either errors during replication or by injury to the DNA from chemicals or radiation.
Mutations
83
A small fraction of every genome (about 3% in humans) is made up of __ or large regions of DNA that are present in more than one copy.
segmental duplications
84
The duplicated DNA is generated by a process called
gene amplification
85
__ can result in resistance to drugs, transformation into cancerous cells or other changes in the cell phenotype
Gene amplification
86
Several human diseases are due to defects in DNA repair ___.
enzymes
87
difference between fat-soluable and water-soluable vitamins
water-soluable = B vitamins, act as coenzymes, cant be stored in body, excess eliminated via urine, the greater the caloric intake the larger requirement for B vitamin, not toxic
fat-soluable = do not act as coenzymes (except vitamin K), not as readily absorbed from diet, can be stored in tissues, vitamins A and D can be toxic in excess
88
fat soluable vitamins that are toxic in excess levels?
not toxic ?
toxic in excess = A and D
not toxic = E and K
89
Measurements of vitamin levels in the blood relate more to __ than to __
recent intake than to overall body status.
90
__vitamins act as coenzymes in many metabolic pathways
Water-soluble
91
The body has no storage capacity for water-soluble vitamins, except vitamin __
B12
92
Evidence is emerging that suggests an excess of some __vitamins can be toxic
B vitamins or water-soluable vitamins
93
Most vitamins are ___ before they become active
modified
94
B Vitamins are __in different types of reactions
co-enzymes
95
B1 type reaction
carboxylations
96
B2/B3 type rxn
oxidoreductases
97
B6 type rxn
transaminases
98
Biotin(B7) type rxn
carboxylases
99
Folic acid/B12 type rxn
single carbon transfers
100
Lack of __causes angular stomatitis
riboflavin
101
Eating raw egg whites can cause __deficiency
Biotin
102
Folic acid is needed, __, for DNA synthesis
indirectly, for DNA synthesis
103
Inhibitors of __ reduction are used as antibiotics (trimethoprim) and cancer therapy (methotrexate).
folate
104
There is an increased demand for folic acid during
pregnancy
105
__ deficiency is one of the most common vitamin deficiencies
Folic acid (B9)
106
The functions of __ and __are interrelated
B12 and folic acid
107
vitamin __ is concentrated in the liver
B12
108
Vitamin C deficiency causes scurvy resulting in defective
collagen synthesis
109
Lack of vitamin C impairs __ function
immune
110
Fat-soluble vitamins are not as readily absorbed as water-soluble vitamins, but can be stored in
tissues
111
Some __-soluble vitamins (A and D) can be toxic in excess
fat-soluable
112
Vitamin __ is teratogenic and should be avoided during pregnancy
vitamin A
113
__is a signaling molecule that interacts with ligand-activated transcription factors
Retinoic acid
114
Deficiency of vitamin _ causes night blindness
vitamin A
115
Vitamin _ regulates calcium and phosphorous homeostasis
vitamin D
116
The majority of vitamin D is produced by
UV exposure of skin
117
People in northern climates have a difficult time getting sufficient vitamin _in the winter
vitamin D
118
Deficiency of vitamin _ causes demineralization of bones with increased susceptibility to fractures
vitamin D
119
Vitamin _ deficiency is link to early childhood caries
vitamin D
120
Vitamin _ is necessary for blood coagulation
vitamin K
121
Proteins that have crossed a __ are no longer topologically inside the cell. They must re-cross the ___ to get back inside the cell.
membrane
122
___ move from compartment to compartment within a cell by budding off and membrane fusion.
Vesicles
123
Many proteins have signal sequences at their ___that direct the proteins to cross the membrane. Fewer proteins have internal signal sequences
amino terminus
124
The nucleus is surrounded by a double lipid membrane bilayer, however ___ allow molecules, including proteins to pass from the cytosol into the nucleus and back.
nuclear pores
125
Larger proteins pass through nuclear pores by .
an active process
126
Nuclear import receptors bind to __ found on some nuclear bound proteins and facilitate transport into the nucleus.
nuclear transport signals
127
It generally requires ___to transport proteins from the cytosol into the lumen of the mitochondria
multiple signals
128
There are multiple protein translocators in the ___. Each translocator interacts with a specific set of proteins.
mitochondrial membrane
129
Transport of protein into the mitochondria requires
energy
130
Proteins enter peroxisomes using a mechanism similar to __entry
mitochondrial
131
Proteins travel from the endoplasmic reticulum (ER), through the __ to many sites.
golgi
132
A signal recognition protein (SRP) binds to the signal sequence during __ and directs the nascent peptide to the ER membrane
translation
133
Proteins bound for the mitochondria are translated in the __ and than transported through the mitochondrial membrane. A process that requires ATP.
cytosol
134
Proteins that are headed into or through the ___ are transported through the ER membrane during translation. This process does not require any additional energy.
ER
135
Carbohydrate modification of proteins in the ___ helps direct them to their ultimate location
ER
136
The “default pathway” if there are no other signals directing the protein to other locations, is to send the protein to
the cell surface
137
In regulated secretory pathway cells store proteins in ___ until they are signaled to release them from the cell by fusion of the vesicles with the cellular membrane.
secretory vesicles
138
major intracellular compartments of an animal cell
```
cytosol 54%
mitochondria 22%
RER cisternae 9%
smooth ER 6%
nucleus 6%
peroxisomes 1%
lysosomes 1%
endosomes 1%
```
