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FOM > week 1 > Flashcards

week 1 Flashcards

1
Q

define nucleotide

A

base + sugar + phosphate; monomeric units of nucleic acids

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2
Q

define nucleoside

A

sugar + base; essentially a nucleotide w/o inorganic phosphate

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3
Q

nucleotide naming identifies…

A

1) base
2) sugar
3) # of phosphates

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4
Q

name the purines

A

adenine

guanine

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5
Q

name the pyrimidines

A

cytosine
thymine
uracil

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6
Q

deoxyribose has ___ attached to 2’ carbon

A

-H

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7
Q

ribose has ___ attached to 2’ carbon

A

-OH

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8
Q

DNA backbone is composed of…

A

sugars + phosphates

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9
Q

what type of bond holds the backbone together

A

phosphodiester bonds

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10
Q

what type of bond connects a pyrimidine with a purine to form the “rungs of the ladder?”

A

H-bonds

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11
Q

What is the order in which a primary transcript is modified?

A

1) 5’ capping 2) poly A tail added 3) splicing

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12
Q

guanine pairs with…

A

cytosine

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13
Q

adenine pairs with…

A

thymine (or uracil)

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14
Q

advantage of twisted, stacked spiral staircase

A

adds strength

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15
Q

phosphate backbone’s charge

A

negative

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16
Q

orientation of complementary DNA strands

A

anti-parallel

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17
Q

most common conformation of DNA

A

B-DNA; right-handed

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18
Q

define genome

A

all of an organism’s DNA (nuclear + mitochondrial)

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19
Q

how many chromosomes does the genome of a haploid cell contain?

A

23

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20
Q

how many chromosomes does the genome of a diploid cell contain?

A

46

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21
Q

define karyotype

A

the display of the 46 human chromosomes

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22
Q

ways to distinguish chromosomes

A

size
staining patterns
FISH color

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23
Q

each DNA molecule that forms a linear chromosome must contain…

A

1) a centromere
2) two telomeres (ends)
3) replication origin

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24
Q

in a karyotype, chromosomes are number in order of…

A

size

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25
Q

which amino acids would bind well in the groove of a double helix

A

arginine
lysine
histidine (in acidic environments; neutral in blood)

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26
Q

define locus

A

a specific location on a chromosome

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27
Q

define allele

A

alternate gene versions

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28
Q

define heterozygous

A

a cell containing two alleles that are functionally different

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29
Q

define homozygous

A

a cell containing two alleles that are NOT functionally different

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30
Q

does total number of chromosomes correspond with species complexity?

A

NO

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31
Q

define hemizygous

A

having only one allele for a given gene

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32
Q

introns make up what percentage of genes?

A

99%

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33
Q

DNA in prokaryotes exists as…

A

a single circular chromosome; double-stranded

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34
Q

how much are DNA molecules condensed?

A

10,000 fold

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35
Q

what issue does condensation of eukaryotic DNA pose?

A

it must be decondensed for replication to occur

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36
Q

Where does DNA replication begin in prokaryotes and what does the DNA bind?

A

single point of origin known as OriC and the DNA coils around the protein DnaA (major initiator protein) at the OriC

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37
Q

What is the primosome composed of in prokaryotes?

A

DnaB (DNA helicase) and DnaG (DNA primase)

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38
Q

What is the activity of helicases?

A

separate the DNA strands and unwind parental duplex

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39
Q

What effect does inhibition of HATs and HDACs have?

A

Inhibition of HATs–>can’t acetylate tails, chromatin stuck in heterochromatin
Inhibition of HDACs–>can’t deacetylate tails, chromatin stuck in euchromatin

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40
Q

What is the function of topoisomerases?

A

enzymes that break phosphodiester bonds and rejoin them to relieve supercoiling tension

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41
Q

What is the major topoisomerase in bacteria?

A

DNA gyrase

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42
Q

What direction does DNA pol move on the template strand?

A

3’-5’

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43
Q

define heterochromatin

A

highly condensed chromatin that is closed to transcription or replication; associated with de-acetylation

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44
Q

What is the function of primase?

A

lays down RNA primers for both lagging strand and leading strand synthesis

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45
Q

What is the function of ligase?

A

it joins DNA fragments together, typically in lagging strand DNA synthesis

46
Q

What is the function of RNAse H?

A

removes RNA primers from Okazaki fragments working together with Pol I

47
Q

What is the function of Pol I in prokaryotic DNA synthesis?

A

Pol I fills in the gaps left by the removal of the primers

48
Q

What prevents DNA polymerase from falling off the template strand during DNA synthesis?

A

clamp proteins

49
Q

Nonpolar Amino Acids

A

Glycine, Alanine, Valine, Leucine, Isoleucine, Proline

50
Q

What effect do HATs have on chromatin?

A

Histone Acetyltransferase:

Add acetyl groups to histone tail lysines. Acetylation decondenses chromatin->euchromatin expressed

51
Q

What effect do HDACs have on chromatin?

A

Histone De-acyteltransferase:
De-acytelation of histone tail lysines. De-acytelation allows chromatin recondensation->forms heterochromatin (not expressed)

52
Q

What effect does inhibition of HATs and HDACs have?

A

Inhibition of HATs–>can’t acetylate tails, chromatin stuck in heterochromatin
Inhibition of HDACs–>can’t deacetylate tails, chromatin stuck in euchromatin

53
Q

eukaryotic DNA packaging involves wrapping of DNA around ___

A

histone proteins

54
Q

the histone-DNA complex is called…

A

chromatin

55
Q

define microRNA (mRNA)

A

non-coding RNAs with key functions in development, cell differentiation, regulation of cell cycle& apoptosis; regulates mRNA degradation, translation, chromatin condensation

56
Q

define solenoid

A

helical, tubular coils that allow for further compaction of chromatin

57
Q

core histones are rich in which amino acids?

A

arginine & lysine (positive charge neutralizes negatively charged DNA backbone)

58
Q

acetylation of histone tails leads to…

A

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
Q

define euchromatin

A

loose chromatin that is open for transcription and replication; associated with acetylation

60
Q

define heterochromatin

A

highly condensed chromatin that is closed to transcription or replication; associated with de-acetylation

61
Q

What is an example of an HDAC?

A

Sirtuins (SIR) protein

62
Q

Explain how HDAC inhibitors are used as anti-cancer drugs

A

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
Q

What are the DNA polymerases that are found in E. coli?

A

Pol I, Pol II, Pol III - Pol III is primarily responsible for replication

64
Q

What phase in eukaryotic cell cycle allows for DNA replication?

A

S phase

65
Q

How many origins of replication due prokaryotes and eukaryotes have for DNA synthesis?

A

prokaryotes - 1

eukaryotes - many

66
Q

What removes RNA primers from Okazaki fragments in eukaryotic cells?

A

Flap endonuclease I (FEN I) and RNAse H

67
Q

How do eukaryotic cells solve the “winding problem” that occurs in DNA replication?

A

topoisomerases

68
Q

How does topoisomerase 1 work?

A

nicks DNA and reforms it to relieve tension through a reversible nicking rxn

69
Q

How does topoisomerase 2 work?

A

it prevents DNA from getting tangled by breaking dsDNA to allow DNA to be pulled apart

70
Q

Why is topoisomerase 2 a good target for cancer treatment?

A

topo II is usually confined to proliferating cells in eukaryotes

71
Q

what is the role of HAT?

A

“histone acetyltransferase” –> acetylates a histone

72
Q

what is the role of HDAC?

A

“histone de-acetyltransferase” deacetylates a histone

73
Q

HDACs are often unregulated in which type of cells?

A

cancer cells, leading to silencing of tumor suppressor genes; HDAC inhibitors are used as anticancer drugs

74
Q

how does RNA form base pairs?

A

it is single stranded, but it may loop back on itself

75
Q

RNAs can also act as…

A

enzymes (ribozymes)

76
Q

function of mRNA

A

code for proteins

77
Q

mRNA processing involves…

A

1) 5’ cap
2) poly-A tail
3) splicing out of non-protein coding sequences

78
Q

tRNA function

A

carry amino acids to ribosomes so they may be incorporated into the polypeptide chain

79
Q

accuracy of amino acid incorporation into proteins occurs via…

A

anti-codon of tRNA pairing with codon of mRNA

80
Q

all tRNAs form which type of structure?

A

cloverleaf

81
Q

retrovirus process

A

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
Q

define microRNA (mRNA)

A

non-coding RNAs with key functions in development, cell differentiation, regulation of cell cycle& apoptosis

83
Q

In DNA synthesis, which DNA strand is close to the product strand?

A

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
Q

Define protein primary structure

A

Amino Acid Sequence

85
Q

Define protein secondary structure

A

H-bond interactions of adjacent aa’s to form alpha helices or beta sheets

86
Q

Define protein tertiary structure

A

Interactions of alpha helices or beta sheets and R groups

87
Q

Define protein quaternary structure

A

Interaction of multiple polypeptides

88
Q

Aromatic Amino Acids

A

Polar: Tryptophan, Tyrosine
Nonpolar: Phenylalanine

89
Q

Sulfur-Containing Amino Acids

A

Methionine, Cysteine

90
Q

Polar, Uncharged Amino Acids

A

Serine, Threonine, Asparagine, Glutamine

91
Q

Charged Amino Acids

A

Negative/Acidic: Aspartate, Glutamate

Positive/Basic: Arginine, Lysine, Histidine

92
Q

Which amino acids would be found on the interior of a protein?

A

Nonpolars (glycine, alanine, valine, leucine, isoleucine, proline), Aromatics (tryptophan, tyrosine, phenylalanine)

93
Q

What amino acid can form disulfide bonds?

A

Cysteine

94
Q

What amino acids can form H-bonds?

A

Polar, Uncharged Group (Serine, Threonine, Asparagine, Glutamine)
Tyrosine and Cysteine

95
Q

What amino acids can form electrostatic interactions?

A

Charged Amino Acids

96
Q

Which stereoisomer of alanine is found in bacterial cell walls?

A

D-alanine (bacDeria)

L-alanine is in human proteins and cells

97
Q

What is the name of a covalent bond between carboxyl and amino groups of amino acids?

A

Peptide bond

98
Q

Exposed hydrophobic protein patches form:

A

Aggregates

99
Q

Denaturation of proteins is caused by:

A

Heat, oxidative damage, solvents, changes in pH

100
Q

Anti-cancer drugs target chaperone protein inhibition because:

A

Cancer cells have many misfolded proteins, so chaperones help them survive. Inhibiting chaperones causes excessive protein aggregation and cancer cells die.

101
Q

Hemoglobin has a sigmoid curve because of:

A

Cooperativity between subunits in ligand binding. This means low affinity at low oxygen pressures (in tissues).

102
Q

What does 2,3-BGP do?

A

Promotes the T-state (tense/anti-oxygen state) of Hb, making it release oxygen to cells better.

103
Q

Increased 2,3-BPG levels shift the Hb affinity curve:

A

Right (lower affinity)

104
Q

Which level of protein structure is most important for function?

A

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
Q

Sickle Cell anemia caused by pos. 6 beta chain glutamate change to:

A

valine

106
Q

T/F: Maternal Hb has higher affinity for oxygen than fetal Hb.

A

False! Fetal Hb has higher affinity (curve is shifted left) so it can take oxygen from the mother’s Hb

107
Q

T/F: Hb contains 2 alpha chains throughout life.

A

True!
Fetal Hb has 2 alpha/2 gamma.
Adult Hb has 2 alpha/2 beta

108
Q

Why don’t sickle cell symptoms show until 4 months?

A

The mutation is in the beta chains, which are not in fetal Hb, only adult Hb.

109
Q

T/F: Fetal Hb has a low affinity for 2,3-BPG

A

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
Q

2,3-BPG is what type of molecule?

A

Allosteric inhibitor

111
Q

Which factors would shift the hemoglobin affinity curve to the right? (lower affinity)

A
  1. Drop in pH
  2. Increase in 2,3-BPG
  3. Increase in temp.

FOM (11 decks)

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