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Biochemistry - Exam 2 > Dr. Leys Study Guide > Flashcards

Dr. Leys Study Guide Flashcards

1
Q

Cells acquire nucleotides through two processes: .

A

de novo synthesis and salvage pathways

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2
Q

De novo synthesis of purines results in the synthesis of inosine that can be converted into

A

adenosine and guanosine.

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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.

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4
Q

__ and __ regulate de novo synthesis of purines at multiple points in the pathway.

A

adenosine diphosphate (ADP) and guanosine diphosphate (GDP)

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5
Q

Hypoxanthine and guanine can be recycled through the ___ pathway with Hypoxanthine guanine phosphoribosyl transferase (HGPRT).

A

salvage

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6
Q

Xanthine oxidase catalyzes a hydroxylase type reaction leading to the formation of

A

uric acid that can be excreted.

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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

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8
Q

Gout is most often caused by low levels of secretion of __, but can also be caused by excess production.

A

uric acid

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9
Q

Crystallization of ___ in the joints leads to a localized inflammatory response.

A

Sodium urate

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10
Q

____, a purine analog, is used to treat gout. It inhibits Xanthine oxidase preventing the formation of uric acid

A

Allopurinol

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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

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12
Q

Lesch-Nyhan occurs in (males/females) only because the HGPRT gene is located on the _chromosome

A

males only

X chromosome

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13
Q

The breakdown of purines can replenish TCA cycle intermediates through the production of

A

fumarate

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14
Q

The atoms in a pyrimidine ring are derived from __ and __

A

aspartate and carbamoyl phosphate.

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15
Q

The first 3 enzymes in the synthesis of pyrimidines are located on the same

A

protein (CAD protein).

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16
Q

The pyrimidines _ and _can be interconverted.

A

U and C

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17
Q

dUMP is converted to TMP by ___, an enzyme requiring the transfer of a methyl group from tetrahydrofolate.

A

thymidylate synthase

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18
Q

Inhibitors of tetrahydrofolate production are used as therapeutic agents for treating

A

cancer and bacterial infections.

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19
Q

Fluro substituted pyrimidine analogs that inhibit ___ are used as anticancer agents

A

thymidylate synthase

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20
Q

Ribonucleotide reductase converts ribonucleotides to

A

deoxyribonucleotides

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21
Q

Base-pairing in DNA is ___?In RNA it’s

A

DNA A-T and G-C

RNA A-U and G-C.

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22
Q

Homologous regions of DNA can be compared among different species to determine ___relationships

A

phylogenetic

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23
Q

Closely related organisms contain similar __ compliments, however they are often arranged differently on the chromosomes of each species.

A

DNA

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24
Q

The living world is made up of 3 divisions, or domains:

A

bacteria, archaea and eukaryotes.

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25
Q

There are 4 main processes for generating change in a genome:

A

intragenic mutation (single base change),

gene duplication,

DNA segment shuffling,

horizontal transfer (from one cell to another).

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26
Q

Bacterial genes are usually clustered into groups (___) that are transcribed as a single unit.

A

operons

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27
Q

Eukaryotic genes are often broken up with regions of noncoding DNA or ___ between regions of coding DNA (__).

A

introns - noncoding

exons - coding

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28
Q

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.

A

exons similar

introns vary

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29
Q

___ chromosomes are densely packed with genes leaving very little DNA that is non-coding.

A

Bacterial

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30
Q

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

A

higher eukaryotes including humans

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31
Q

Bacterial chromosomes are ___ and eukaryotic chromosomes are __

A

circular - bacterial

linear- eukaryotic

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32
Q

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

A

oral cavity

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33
Q

It is possible to construct metabolic pathways and compare them with other organisms by examining their

A

entire genome content.

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34
Q

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

A

(homologous)
sequences

sequences (homology).

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35
Q

The phylogenetic relationships of different organisms can be compared by
comparing ___ in the two organisms

A

the DNA sequence of similar genes

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36
Q

___ is a DNA dependent (uses DNA as a template) DNA synthesizing enzyme

A

DNA polymerase

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37
Q

___ is a DNA dependent RNA synthesizing enzyme.

A

RNA polymerase

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38
Q

___ is an RNA dependent DNA synthesizing enzyme.

A

Reverse transcriptase

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39
Q

___ is a DNA dependent RNA polymerase.

A

Primase

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40
Q

Primase synthesizes a small RNA “primer” that can be used by the DNA polymerase to .

A

elongate the chain

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41
Q

___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

A

DNA polymerase

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42
Q

DNA polymerase as well as all other nucleic acid polymerases synthesize DNA in the

A

5’ to 3’ direction only

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43
Q

During replication, each new nucleotide is added to the __ carbon on the last
nucleotide of the new DNA chain.

A

3’ carbon

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44
Q

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 __

A

1’ - connected to sugar

5’ and 3’ carbons

RNA and DNA

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45
Q

DNA polymerase is an elongating enzyme; it cannot initiate ___. Therefore a __is required for elongation of a new stand using the DNA polymerase.

A

synthesis

primer

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46
Q

Bacterial chromosomes contain one origin of

A

replication

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47
Q

___ 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.

A

DNA synthesis

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48
Q

In __ new rounds of DNA replication can begin before the previous round is completed

A

bacteria

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49
Q

___chromosomes contain many origins of replication that may change during the development of the organism

A

Eukaryotic

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50
Q

In ____, each entire chromosome is replicated only once each cell division and new rounds of replication do not start until after the cell divides

A

eukaryotes

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51
Q

Eukaryotic chromosomes are linear and special structures called ___are placed on each end

A

telomeres

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52
Q

____ are constructed with the enzyme telomerase that uses an RNA template to synthesize a short repeated DNA sequence at the ends of chromosomes.

A

Telomeres

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53
Q

Because the polymerase must synthesize new DNA in the 5’ to 3’ direction,
the two polymerase molecules on opposite strands move

A

away from each other.

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54
Q

___ unwinds (separates) the 2 DNA strands before polymerization of the new strands.

A

Helicase

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55
Q

___ proteins keep the two complementary strands for reforming a double helix.

A

Single-stranded binding proteins

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56
Q

The polymerase on the ___ strand moves toward the replication fork and the polymerase on the __ strand moves away from it.

A

leading strand moves toward

lagging stand away

57
Q

The ___ strand is synthesized in short (Okizaki) fragments.

A

lagging

58
Q

Primase initiates synthesis of each Okizaki fragment by making a short

A

RNA primer.

59
Q

The ___ strand is synthesized by the continuous movement of the DNA polymerase along the template

A

leading

60
Q

___ of the DNA signals that the DNA is unreplicated and is ready to be used as a template for the next round of synthesis

A

Methylation

61
Q

New or modified genes can be generated by one or a combination of 4 events:

A

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
Q

Mixing of segments of one gene with segments of another gene

A

segment shuffling

63
Q

Acquisition of new activities by transfer of genes between two organisms

A

horizontal gene transfer

64
Q

Many genes belong to __ that share homologous regions. These regions usually code for proteins that carry out similar functions.

A

gene families

65
Q

Breaks in the DNA (especially double stranded breaks) facilitate the initiation of

A

recombination

66
Q

A defect in ___, affects joining together of adjacent segment of DNA on a chromosome, can cause abnormal amounts of recombination

A

DNA ligase

67
Q

___ is the reciprocal exchange of genetic information.

A

Recombination

68
Q

recombination can be the result of

A

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
Q

__is the non-reciprocal exchange of genetic information

A

Gene conversion

70
Q

Recombination between ___ causes the loss of DNA that was between the two repeated segments

A

direct repeated sequences on the same chromosome

71
Q

Circular DNA can be inserted in a chromosome by recombination between a region on of __ molecule and an __ region on the chromosome

A

circular molecule and an homologous region

72
Q

X-rays and other agents that cause breaks in DNA induce

A

recombination

73
Q

___elements are found in all species from bacteria to human.

A

Transposable

74
Q

Transposable elements move from one location in the DNA to

A

another location within that cell

75
Q

Transposable elements can cause changes in the DNA at the site of

A

insertion

76
Q

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.

A

duplicated at the site of insertion

and

similar to a retrovirus and transposes through an RNA intermediate

77
Q

____ is recombination that resulted from imprecise pairing of tandemly repeated sequences.

A

Unequal crossing-over

78
Q

Unequal crossing over results in

A

the loss or gain of gene copies.

79
Q

There are two types of mutations:

A

DNA rearrangements and base substitutions

80
Q

There are many mechanisms in each cell for repairing

A

DNA

81
Q

Damage to a __ (e.g. deamination) can either be repaired or lead to a permanent mutation.

A

nucleotide

82
Q

___ can be caused by either errors during replication or by injury to the DNA from chemicals or radiation.

A

Mutations

83
Q

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.

A

segmental duplications

84
Q

The duplicated DNA is generated by a process called

A

gene amplification

85
Q

__ can result in resistance to drugs, transformation into cancerous cells or other changes in the cell phenotype

A

Gene amplification

86
Q

Several human diseases are due to defects in DNA repair ___.

A

enzymes

87
Q

difference between fat-soluable and water-soluable vitamins

A

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
Q

fat soluable vitamins that are toxic in excess levels?

not toxic ?

A

toxic in excess = A and D

not toxic = E and K

89
Q

Measurements of vitamin levels in the blood relate more to __ than to __

A

recent intake than to overall body status.

90
Q

__vitamins act as coenzymes in many metabolic pathways

A

Water-soluble

91
Q

The body has no storage capacity for water-soluble vitamins, except vitamin __

A

B12

92
Q

Evidence is emerging that suggests an excess of some __vitamins can be toxic

A

B vitamins or water-soluable vitamins

93
Q

Most vitamins are ___ before they become active

A

modified

94
Q

B Vitamins are __in different types of reactions

A

co-enzymes

95
Q

B1 type reaction

A

carboxylations

96
Q

B2/B3 type rxn

A

oxidoreductases

97
Q

B6 type rxn

A

transaminases

98
Q

Biotin(B7) type rxn

A

carboxylases

99
Q

Folic acid/B12 type rxn

A

single carbon transfers

100
Q

Lack of __causes angular stomatitis

A

riboflavin

101
Q

Eating raw egg whites can cause __deficiency

A

Biotin

102
Q

Folic acid is needed, __, for DNA synthesis

A

indirectly, for DNA synthesis

103
Q

Inhibitors of __ reduction are used as antibiotics (trimethoprim) and cancer therapy (methotrexate).

A

folate

104
Q

There is an increased demand for folic acid during

A

pregnancy

105
Q

__ deficiency is one of the most common vitamin deficiencies

A

Folic acid (B9)

106
Q

The functions of __ and __are interrelated

A

B12 and folic acid

107
Q

vitamin __ is concentrated in the liver

A

B12

108
Q

Vitamin C deficiency causes scurvy resulting in defective

A

collagen synthesis

109
Q

Lack of vitamin C impairs __ function

A

immune

110
Q

Fat-soluble vitamins are not as readily absorbed as water-soluble vitamins, but can be stored in

A

tissues

111
Q

Some __-soluble vitamins (A and D) can be toxic in excess

A

fat-soluable

112
Q

Vitamin __ is teratogenic and should be avoided during pregnancy

A

vitamin A

113
Q

__is a signaling molecule that interacts with ligand-activated transcription factors

A

Retinoic acid

114
Q

Deficiency of vitamin _ causes night blindness

A

vitamin A

115
Q

Vitamin _ regulates calcium and phosphorous homeostasis

A

vitamin D

116
Q

The majority of vitamin D is produced by

A

UV exposure of skin

117
Q

People in northern climates have a difficult time getting sufficient vitamin _in the winter

A

vitamin D

118
Q

Deficiency of vitamin _ causes demineralization of bones with increased susceptibility to fractures

A

vitamin D

119
Q

Vitamin _ deficiency is link to early childhood caries

A

vitamin D

120
Q

Vitamin _ is necessary for blood coagulation

A

vitamin K

121
Q

Proteins that have crossed a __ are no longer topologically inside the cell. They must re-cross the ___ to get back inside the cell.

A

membrane

122
Q

___ move from compartment to compartment within a cell by budding off and membrane fusion.

A

Vesicles

123
Q

Many proteins have signal sequences at their ___that direct the proteins to cross the membrane. Fewer proteins have internal signal sequences

A

amino terminus

124
Q

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.

A

nuclear pores

125
Q

Larger proteins pass through nuclear pores by .

A

an active process

126
Q

Nuclear import receptors bind to __ found on some nuclear bound proteins and facilitate transport into the nucleus.

A

nuclear transport signals

127
Q

It generally requires ___to transport proteins from the cytosol into the lumen of the mitochondria

A

multiple signals

128
Q

There are multiple protein translocators in the ___. Each translocator interacts with a specific set of proteins.

A

mitochondrial membrane

129
Q

Transport of protein into the mitochondria requires

A

energy

130
Q

Proteins enter peroxisomes using a mechanism similar to __entry

A

mitochondrial

131
Q

Proteins travel from the endoplasmic reticulum (ER), through the __ to many sites.

A

golgi

132
Q

A signal recognition protein (SRP) binds to the signal sequence during __ and directs the nascent peptide to the ER membrane

A

translation

133
Q

Proteins bound for the mitochondria are translated in the __ and than transported through the mitochondrial membrane. A process that requires ATP.

A

cytosol

134
Q

Proteins that are headed into or through the ___ are transported through the ER membrane during translation. This process does not require any additional energy.

A

ER

135
Q

Carbohydrate modification of proteins in the ___ helps direct them to their ultimate location

A

ER

136
Q

The “default pathway” if there are no other signals directing the protein to other locations, is to send the protein to

A

the cell surface

137
Q

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.

A

secretory vesicles

138
Q

major intracellular compartments of an animal cell

A 
cytosol 54%
mitochondria 22%
RER cisternae 9%
smooth ER 6%
nucleus 6%
peroxisomes 1%
lysosomes 1%
endosomes 1%

Biochemistry - Exam 2 (3 decks)

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