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Biochemistry and Mollecular Biology > Cell Molecular biology Final Exam prep > Flashcards

Cell Molecular biology Final Exam prep Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Genomic imprinting involves:

A

DNA methylation, long coding RNA’s that can regulate gene expression in a parent specific fashion, histone modification, chromatin remodeling

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2
Q

What transcription regulator recognizes promoter sequence and helps the RNA polymerase to bind to the promoter in eukaryotes?

A

TFIID

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3
Q

What is transcription factor TFIID (for transcription factor polymerase II)?

A

It is a complex of proteins that binds to a TATAA sequence on the DNA some 25–30 nucleotides upstream of the initiation site

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4
Q

Characteristics of Mature eukaryotic mRNA are:

A

they have a 5’ methylguanosine cap, have a polyAtail at 3’ end, the introns are spliced out

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5
Q

What structure in eukaryotes are responsible for aiding ribosome binding?

A

5’ Methylguanosine cap and the Kozak sequence

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6
Q

What role does lactose play in bacterial sugar metabolism?

A

Lactose can be used as an alternative carbon source when glucose is absent

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7
Q

Attenuation:

A

minimizes the transcription of Trp operon when the attenuator sequence 4 base pairs with the attenuator sequence 3 to form a hairpin

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8
Q

Structural parts of the Crispr-CAS9 two component system include:

A

Endonuclease, spacer, single stranded tracer RNA, Hairpin loop and single stranded guide RNA

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9
Q

Adapters that employ the genetic code and allow translation to happen are:

A

tRNA, amino acyl tRNA synthetase

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10
Q

What gene is transcribed by RNA polymerase 1?

A

rRNA

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11
Q

Examples of epigenetic inheritance

A

Random inactivation of X chromosome, inheritance of chromatin condensation pattern, inheritance of chemical modification of histones

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12
Q

The anticodon sequence of a tRNA is 5’AGI3’. What base would be present in the wobble position in the codon recognized by this tRNA?

A

U

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13
Q

Name 3 traits of Antisense RNAs:

A

1) if employed in genetic engineering, does not silence genes in a stable fashion compared to RNAi technology, 2) can form double stranded structures with sense RNAs, 3) silence genes via mRNA degradation

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14
Q

Name 3 traits of Eukaryotic transcription:

A

1) TFIID binds at the TATA box,
2) TFIIH is a kinase,
3) Dephosphoylated RNA polymerase II can initiate transcription

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15
Q

What mechanism is used to regulate gene expression at the translational level without affecting stability to the mRNA?

A

Changing the secondary structure of the 5’UTR according to environmental or cellular conditions, using a proton that binds at the ribosome biding site.

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16
Q

Transit peptides are responsible for the transport of:

A

proteins encoded by a nuclear gene to a particular organelle.

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17
Q

Name two qualities of the Tryptophan operon:

A

1) repressor prevents RNA polymerase from initiating transcription
2) tryptophan operon promoter is stronger than that of the Lac operon

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18
Q

A kinetochore is:

A

1) formed in prophase

2) a protein complex that is deposited on the centromere

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19
Q

A drug that can inhibit translation in prokaryotes has the potential to inhibit translation in animal cells in the:

A

mitochondria

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20
Q

What form of DNA would you expect in a section of DNA strand that is being transcribed by RNA polymerase and is partially Hydrogen bonded to the mRNA?

A

A form

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21
Q

What base, when present in the 5’ end position in the anticodon makes the tRNA recognize maximum number of codons?

A

I

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22
Q

True or false, Riboswitches are not widely used by eukaryotes for post-transcriptional gene regulation

A

True

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23
Q

What are the modifications a pre-mRNA has to go through to become a mature mRNA molecule that can leave the nucleus and be translated?

Can they be regulated during this process?

A

1) splicing
2) capping,
3) addition of a poly-A tail,

*all of which can potentially be regulated – sped up, slowed down, or altered to result in a different product.

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24
Q

What are introns?

A

pre-mRNA molecules have sections that are removed from the molecule

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25
Q

What are exons?

A

sections that are linked or together to make the final mRNA

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26
Q

What are transcription factors?

What is an example?

A

proteins that help turn specific genes “on” or “off” by binding to nearby DNA.
Binding of the growth factor causes the receptor to change shape, triggering a series of chemical events in the cell that activate proteins

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27
Q

What is Transcription?

A

process where a gene’s DNA sequence is copied (transcribed) into an RNA molecule. Transcription is a key step in using information from a gene to make a protein

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28
Q

What is Gene expression?

A

It is when a gene in DNA is “turned on,” that is, used to make the protein it specifies.

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29
Q

What has to happen for a gene to be transcribed?

A

The enzyme RNA polymerase, which makes a new RNA molecule from a DNA template, must attach to the DNA of the gene. It attaches at a spot called the promoter.

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30
Q

In bacteria, Where does the RNA polymerase attach to?

A

RNA polymerase attaches right to the DNA of the promoter.

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31
Q

In eukaryotes, how does the RNA polymerase attach to the promoter?

A

ONLY with the help of proteins called basal (general) transcription factors.

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32
Q

What is one way a repressor can interfere with transcription?

A

a repressor may get in the way of the basal transcription factors or RNA polymerase, making it so they can’t bind to the promoter or begin transcription.

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33
Q

What is combinatorial regulation?

A

When many genes are controlled by several different transcription factors, with a specific combination needed to turn the gene on; this is particularly true in eukaryotes.

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34
Q

How is a cell’s gene expression pattern determined by information from inside the cell?

A

Examples of information from inside the cell: the proteins it inherited from its mother cell, whether its DNA is damaged, and how much ATP it has

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35
Q

How is a cell’s gene expression pattern determined by information from outside the cell?

A

Examples of information from outside the cell: chemical signals from other cells, mechanical signals from the extracellular matrix, and nutrient levels.

36
Q

How is Chromatin regulated?

A

The structure of chromatin (DNA and its organizing proteins) can be regulated. A more open or “relaxed” chromatin makes a gene more available for transcription. and if the chromatin is more tightly bound to the DNA, the less likely it is to be transcribed

37
Q

What happens in RNA processing

A

Splicing, capping, and addition of a poly-A tail to an RNA molecule can be regulated, and so can exit from the nucleus.

38
Q

Different mRNAs may be made from the same pre-mRNA by:

A

alternative splicing

39
Q

How does RNA stability affect transcription?

A

The lifetime of an mRNA molecule in the cytosol affects how many proteins can be made from it.

40
Q

what do the small regulatory RNAs called miRNAs do?

A

bind to target mRNAs and cause them to be chopped up.

41
Q

Translation of an mRNA may be increased or inhibited by regulators, do miRNA’s only chop up?

A

miRNAs sometimes block translation of their target mRNAs (rather than causing them to be chopped up).

42
Q

How can protein modifications regulate and effect the activity or behavior of a protein?

A

Proteins can undergo a variety of modifications, such as being chopped up or tagged with chemical groups.

43
Q

Where does the main gene expression get regulated, transcription or translation?

A

All stages of gene expression can be regulated, the main control point for many genes is transcription

44
Q

What is the regulatory purpose of Antisense RNAs in post transcriptional gene regulation ?

A

Antisense RNAs are single-stranded RNA molecules that specifically target mRNA molecules used for protein synthesis and bind to the complementary strand and prevent them from being translated into a functioning protein.

45
Q

Can Antisense RNAs pair with the mRNA?

A

The antisense RNA can physically pair and bind to the complementary mRNA.

46
Q

How do miRNAs (microRNAs) regulate gene expression post-transcriptionally?

A

MiRNAs are short non-coding RNAs that generally bind to the 3’-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing.

47
Q

How is RNAi used in post transcription?

A

RNAi are small pieces of RNA that can shut down protein translation by binding to the messenger RNAs that code for those proteins

48
Q

What are siRNAs and where are they produced?

A

siRNAs are highly specific and are usually synthesized to reduce the translation of specific messenger RNAs (mRNAs).
They form from double-stranded RNA transcribed and then cut to size in the nucleus before releasing into the cytoplasm.

49
Q

What are miRNA’s?

A

micro RNAs are a more general suppressive tool, formed from single-stranded RNA precursors and characterized by their distinctive hairpin shape.

50
Q

What are some differences between siRNA and miRNA?

A

miRNAs are a more general suppressive tool and formed from single stranded RNA, and have a disctintive hairpin shape.

siRNA are highly specific, formed from double stranded RNA and then cut to size

51
Q

What are the direct products of genes?

A

RNA

52
Q

How can transcription be inhibited pre-transcriptionally?

A

By the silencing mechanism of RNA interference, through which an enzyme complex catalyzes DNA methylation at genomic positions complementary to complexed siRNA or miRNA

53
Q

What are the effects of RNAs directing enzyme complexes to degrade messenger RNA (mRNA) molecules?

A

decreases activity by preventing translation, via post-transcriptional gene silencing.

54
Q

The RNAi pathway is found in many eukaryotes, including animals, but what initiates it?

A

RNAi pathway is initiated by the enzyme

55
Q

What does the enzyme Dicer do?

A

Cleaves long double-stranded RNA (dsRNA) molecules into short double-stranded fragments of ~21 nucleotide siRNAs.

56
Q

How is RNAi linked to RISC?

A

After the Dicer cleaves the double stranded RNA into two siRNA’s,
Each siRNA is unwound into two single-stranded RNAs (ssRNAs) called the passenger strand and the guide strand. The passenger strand is degraded and the guide strand is incorporated into the RNA-induced silencing complex (RISC).

57
Q

In anaphase II of Meiosis

A

Recombinant chromosomes separate to the two poles of the spindle

58
Q

What is phragmoplast?

A

The phragmoplast is a plant cell specific structure that forms during late cytokinesis. It serves as a scaffold for cell plate assembly and subsequent formation of a new cell wall separating the two daughter cells.
Formed from the remnants of interpolar microtubules

59
Q

What drug inhibits transcription in prokaryotes?

A

Rifamycin

60
Q

What does the drug Puromycin (an aminonucleoside antibiotic) do?

A

It inhibits protein synthesis by disrupting peptide transfer on ribosomes causing premature chain termination during translation. Useful in both prokaryotes and Eukaryotes

61
Q

Can Puromycin be used in humans?

A

No, It is toxic to prokaryotic and eukaryotic cells and only used in the lab

62
Q

what is streptomycin prescribed for?

A

Streptomycin (an aminoglycoside antibiotic) is used to treat moderate to severe tuberculosis, pneumonia, E. coli, influenza, plague and other infections caused by certain bacteria.

63
Q

How does streptomycin work?

A

Streptomycin irreversibly binds to the subunits: 16S rRNA and S12 protein within the bacterial 30S ribosomal subunit. As a result, this agent interferes with the assembly of initiation complex between mRNA and the bacterial ribosome, thereby inhibiting the initiation of protein synthesis.It works by blocking the ability of 30S ribosomal subunits to make proteins, which results in bacterial death

64
Q

How does Tetracycline work?

A

Tetracycline interferes with the ability of the bacteria to produce certain vital proteins required for bacterial growth. They target the ribosomal machinery within the bacteria that assembles proteins from amino acids. Due to this mode of action, tetracyclines inhibit bacterial growth rather than killing them

65
Q

What is Tetracycline prescribed for?

A

Tetracycline is used to treat infections caused by bacteria including pneumonia and other respiratory tract infections; ; certain infections of skin, eye, lymphatic, intestinal, genital and urinary systems; and certain other infections that are spread by ticks, lice, mites, and infected animals

66
Q

A strong promoter:

A

1) has a conserved TATA box or -10, and -35 consensus sequences in the promoter.
2) Does not need additional proteins to boost the performance of RNA polymerase.

67
Q

What is the allosteric activator of CRP protein?

A

cAMP

68
Q

The 3 traits of the initiator tRNA in Eukaryotes:

A

1) carries methionine
2) Is different from the tRNA that inserts methionine elsewhere in the protein chain
3) is the tRNA that inserts the first amino acid in the growing protein chain

69
Q

Promoters in bacteria contain two short DNA sequences located at:

A

1) the -10 (10 bp 5’ or upstream) 2) the -35 positions from the transcription start site (TSS). Their equivalent to the eukaryotic TATA box, the Pribnow box (TATAAT) is located at the -10 position and is essential for transcription initiation.

70
Q

What is the transcription start site (TSS)?

A

The bacterial equivalent to the eukaryotic TATA box

71
Q

Where is the the Pribnow box (TATAAT) located and what is its importance?

A

At the -10 position and is essential for transcription initiation.

72
Q

What are the basic features that all tRNA have in common?

A

1) Has 3 loops (cloverleaf structure)
2) 5’ end has a guanine nucleotide
3) Has the sequence 5’CCA3” at the 3’ end (serves as an attachment site for an amino acid)

73
Q

The 5’ cap is added to the first nucleotide in the transcript during transcription. What is the purpose of the 5’ cap?

A

The cap is a modified guanine (G) nucleotide, and it protects the transcript from being broken down.
It also helps the ribosome attach to the mRNA and start reading it to make a protein.

74
Q

what is sgRNA?

A

sgRNA is a single-stranded guided RNA (or guided RNA) is a type of nucleic acid sequence used in gene editing for target-specific cleavage.

75
Q

what is a protospacer?

A

A protospacer adjacent motif is a 2–6-base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system

76
Q

What stage of cell division does actin play a role?

A

Cytokinesis

77
Q 
True or False
Non conventional (non-watson Crick base pairing) is going in  RNA
A

True

78
Q

RISC is associated with:

A

miRNAs and RNA interference

79
Q

What does a ribozyme catalyze?

A

1) splicing of introns

2) Peptidyl chain transfer to aminoacyl tRNA in translation

80
Q

List 4 reasons that prove RNA existed before DNA

A

1) Deoxyribose sugars are only formed from ribose sugars
2) many of activated carriers have ribonucleotide in their chemical structures
3) Splicing of introns and peptide bond formation during translation is mediated by rRNA
4) primitive Earth had abundant formaldehyde which was easily used for synthesis of ribose sugar

81
Q

What DNA/RNA sequences are non-coding?

A

1) Promoter
2) Terminator
3) 5’UTR
4) 3’UTR

82
Q

Anaphase A is characterized by

A

Shortening of kinetochore microtubules

83
Q

What is the first step in translation?

A

Binding of the small subunit of ribosome and amino acyl initiator tRNA to the regulatory sequence in the 5’ UTR

84
Q

What is the Tryptophan operon?

A

The tryptophan operon is responsible for the production of the amino acid tryptophan, whose synthesis occurs in five steps, each requiring a particular enzyme.

85
Q

Characteristics of operation of transcriptional regulators/factors in eukaryotes.

A

1) Combined effects of different transcriptional regulators that bind regulatory sequences of a specific gene determine its expression
2) Interacts with transcription factors and RNA polymerase through DNA looping and mediators
3) activators attract histone modifying enzymes that add acetyl or phosphate groups to histone tails

Biochemistry and Mollecular Biology (6 decks)

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