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Cell Biology > Ch 7: From DNA to Protein > Flashcards

Ch 7: From DNA to Protein Flashcards

1
Q

What is true of eukaryotic mRNAs?

A

They are translated after they are exported from the nucleus

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2
Q

An RNA chain is synthesized in what direction?

A

5’-to-3’ only

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3
Q

In eukaryotes, which parts of a gene are transcribed into RNA?

A

Introns and exons: introns are later spliced out by the activity of the spliceosome, leaving only exons in the mature RNA

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4
Q

How many different aminoacyl-tRNA synthetases do most organisms have?

A

One for each amino acid, so 20 total.

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5
Q

What is false regarding codons in mRNA molecules?

A

Some codons code for more than one amino acid

Things that are true:
- some codons do not code of amino acids
- In some cases, several different codons code of the same amino acid
- all codons contain 3 nucleotides

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6
Q

It is thought that, in the early history of life, RNAs not only stored information, but acted as catalysts in the cells. Which reaction is catalyzed by a ribosome in present-day cells?

A

Peptide bond formation during protein synthesis

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7
Q

Gene expression

A

The conversion of DNA into RNAs and proteins

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8
Q

What is the flow of genetic information in all living cells?

A

DNA to RNA to protein

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9
Q

Overview of transcription

A

Transcription is catalyzed by the enzyme RNA polymerase, which uses nucleotide sequences in the DNA molecule to determine which strand to use as a template, and where to start and stop transcribing.

To begin transcription, RNA polymerase binds to specific DNA sites called promoters that lie immediately upstream of genes. Eukaryotic RNA polymerases require the assembly of a complex of general transcription factors at the promoter, whereas bacterial RNA polymerase requires only one additional subunit called sigma factor.

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10
Q

List the main types of functional RNAs

A

mRNAs: messenger RNAs, carry the instructions for making proteins

rRNAs: ribosomal RNAs, form the core of ribosomes

tRNAs: transfer RNAs, act as adaptor molecules in protein synthesis

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11
Q

What are the protein-coding genes in eukaryotic DNA comprised of?

A

Exons: the short, coding regions of the RNA
Introns: non-coding regions.
Both are transcribed into RNA, but the introns are removed from the RNA while it is still in the nucleus, during RNA splicing

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12
Q

Overview of RNA splicing

A

The process where introns are removed from RNA transcripts, and the exons are joined back together. This is catalyzed by RNAs that are part of small ribonucleoprotein complexes called snRNPs.

The splicing can be done a number of different ways on the same gene, allowing multiple different proteins to be produced from the same gene

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13
Q

What processing steps does mRNA go through before it becomes mature mRNA?

A

5’ RNA capping

3’ polyadenylation

splicing

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14
Q

Where does translation take place?

A

The cytoplasm, on large ribonucleoprotein assemblies called ribosomes. As the RNA moves through the ribosome, its message is translated into protein

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15
Q

Codons

A

sequences of 3 consecutive nucleotides that each correspond to one amino acid.

Most amino acids can be specified by more than one codon.

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16
Q

tRNAs

A

adaptor molecules in protein synthesis

Each tRNA contains a sequence of three nucleotides, the anticodon, which recognizes a codon in an mRNA through complementary base-pairing, and serves as the source of the amino acid added to the growing polypeptide chain

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17
Q

What starts protein synthesis?

A

the a ribosome assembles at an initiation codon (AUG) in an mRNA molecule. An RNA in the large ribosomal subunit catalyzes the stepwise linking of amino acids to form the polypeptide chain. A completed chain is released from the ribosome when a stop codon (UAA, UAG, or UGA) is reached

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18
Q

What does the protein concentration in a cell depend on?

A

The rate at which the mRNA and proteins are synthesized and degraded

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19
Q

Where does protein degradation occur?

A

in both the cytosol in nucleus, it occurs inside large protein complexes called proteasomes

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20
Q

What is the likely origin of life on earth?

A

It probably started with self-replicating ribozymes: RNA molecules that can catalyze their own synthesis.

RNA can act both as a catalyst for reactions, and as a carrier of genetic information, so the first cells likely used RNA before DNA replaced it as a more stable structure.

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21
Q

Alternative splicing

A

the production of different mRNAs (and thus proteins) from the same gene by splicing its RNA transcripts in different ways.

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22
Q

aminoacyl-tRNA synthesis

A

during protein syntehsis, an enzyme that attaches the correct amino acid to a tRNA molecule to form “charged” aminoacyl-tRNA. This is a high-energy bond, and the energy is used to covalently link the amino acid to the growing polypeptide chain

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23
Q

anticodon

A

set of 3 consecutive nucleotides in a transfer RNA molecule that recognizes, through base-pairing, the three-nucleotide codon on a messenger RNA molecule. This interaction helps to deliver the correct amino acid to a growing polypeptide chain

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24
Q

general transcription factor

A

proteins that assemble on the promoters of eukaryotic genes near the start dite of transcription and load the RNA polymerase in the correct position

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25
Q

initiator tRNA

A

Special tRNA that initiates the translation of an mRNA on a ribosome. It always carries the amino acid methionine (codon AUG)

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26
Q

mRNA

A

messenger RNA, the RNA molecule that specifies the amino acid sequence of a protein

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27
Q

noncoding RNA

A

an RNA molecule that is the final product of a gene and does not code for protein. These RNAs serve as enzymatic, structural, and regulatory components for a wide variety of processes in the cell

28
Q

polyadenylation

A

the addition of multiple adenine nucleotides to the 3’ end of a newly synthesized mRNA molecule

29
Q

promoter

A

the DNA sequence that initiates gene transcription; includes sequences recognized by RNA polymerase and its accessory proteins

Bacteria use sigma factor as an accessory protein, and eukaryotes have a large conglomeration of different transcription factors

30
Q

protease

A

enzyme that degrades proteins by hydrolyzing their peptide bonds

31
Q

proteasome

A

large protein machine that degrades proteins that are damaged, misfolded, or no longer needed by the cell. Its primary targets are marked for destruction primarily by the attachment of a short chain of ubiquitin

32
Q

reading frame

A

one of three possible ways in which a set of successive nucleotide triplets can be translated into protein, depending on which nucleotide serves as the starting point

33
Q

rRNA

A

ribosomal RNA: forms the structural and catalytic core of the ribosome

34
Q

ribosome

A

large macromolecular complex, composed of RNAs and proteins, that translates a messenger RNA into a polypeptide chain

35
Q

ribozyme

A

an RNA molecule with catalytic activity

36
Q

RNA capping

A

the modification of the 5’ end of a maturing RNA transcript by the addition of an atypical nucleotide

37
Q

RNA processing

A

broad term for the modifications that a precursor mRNA undergoes as it matures into an mRNA. It includes 5’ capping, RNA splicing, and 3’ polyadenylation

38
Q

RNA transcript

A

RNA molecule produced by transcription that is complementary to one strand of DNA

39
Q

snRNA

A

small nuclear RNA: RNA molecules containing on the order of 200 nucleotides that participate in RNA splicing

40
Q

spliceosome

A

large assembly of RNA and protein molecules that spices introns out of pre-mRNA in the nucleus of eukaryotic cells

41
Q

translation initiation factor

A

protein that promotes the proper association of ribosomes with mRNA and is required for the initiation of protein synthesis

42
Q

ubiquitin

A

small proteins that can be covalently attached to the other proteins. A major role is to mark target proteins for degradation by the proteasome

43
Q

Describe, in detail, the process of transcription and translation

A

directionality
proteins involved
mRNA processing
types of RNA involved in both processes

44
Q

Describe the similarities and differences in transcription between eukaryotes and prokaryotes

A

Eukaryotes are mostly similar to prokaryotes, but rely on a larger set of proteins to initiate transcription, have more elaborate mechanisms to control initiation of transcrption, and have to deal with DNA being packed into nucleosomes and chromatin structure

45
Q

Be able to determine the mRNA transcript and protein sequence given a template strand of DNA

A
46
Q

What are the steps of DNA transcription and translation in eukaryotes

A

1) initiation of transcription
2) capping, elongation, and splicing all occur while the transcription is in progress
3) cleavage, polyadenylation, and termination happen before export
4) export from the nucleus to the cytosol
5) some mRNA gets degraded
6) some initiates protein synthesis (translation)
7) protein synthesis is completed and the protein is folded
8) some protein is degraded

47
Q

coding strand vs template strand

A

the coding strand is the one that the RNA is a copy of. The template strand is used to make the copy of the coding strand.

48
Q

What are the key differences between DNA and RNA?

A

1) sugar differences: Ribose, with two -OH groups, is used in RNA. Deoxyribose, with one -OH and one -H group is used in DNA. The two -OH groups means RNA is much more reactive

2) Base differences: Uracil (U) is used in RNA, Thymine (T) is used in DNA.

49
Q

7 types of messenger RNAs produced in cells

A

1) mRNA
2) rRNA
3) miRNA
4) tRNA
5) siRNA (drug design aside: design an siRNA to degrade a certain problematic protein
6) lncRNA
7) other non-coding RNA

50
Q

What signals in DNA tell the RNA polymerase to start and stop?

A

the promoter region is where the RNA polymerase attaches (in bacteria, it has the -35 and -10 regions for RNA polymerase to bind to.) The start site (+1) is where the transcription starts.

the terminator region is where transcription ends

51
Q

What are the two mechanisms for transcription termination?

A

1) Rho independent termination: terminating hairpin (the mRNA makes a shape that recruits a protein that disconnects the polymerase)

2) Rho dependent termination: the termination sequence is transcribed, which recruits a factor called Rho, which will knock the RNA polymerase out of the DNA

52
Q

Can genes be encoded on both strands of a genome?

A

Yes, they can. RNA polymerase can only make RNA in the 5’ to 3’ direction, but it can attach to either side and proceed either way. This can cause crowding an interference problems in cells.

53
Q

Why are there multiple factors (ie proteins) that control transcription? What would happen if all genes are regulated only by a very small set of factors?

A

each gene has multiple regulatory factors, which gives the cell more flexibility about what it can do in what circumstances. This becomes more important as cells become more complex

54
Q

operon

A

in prokaryotes, a cluster of genes that are transcribed together onto on mRNA, so that one mRNA can code multiple proteins

55
Q

What are the main differences between eukaryote and prokaryote mRNA

A

prokaryotic mRNA can code for multiple proteins (an operon). This means that all the genes on the mRNA sequence are regulated by the same factors

eukaryotic mRNA only codes for one protein, and is modified by splicing, adding a 5’ cap, and the poly-A tail.

56
Q

You want to make a mutation in the genome such that a gene is no longer expressed. Where would you choose to make the mutation (aside from the promoter region)

A

You would want to mutate the exon as early as possible in the gene sequence. This would shift the frame, and cause completely different amino acids to be added.

In insertion or deletion of a base pair is called an indel

57
Q

Why are introns important?

A

alternative splicing can produce different versions of mRNA from the same gene. The introns are never kept, but some exons can be cut out during splicing.

58
Q

What is one of the implications of eukaryotic mRNAs being processed?

A

Because they are processed before they are exported from the nucleus to the cytoplasm, they can be selectively transported. This also works as a checkpoint mechanism to make sure that RNA is properly processed.

59
Q

What are the key differences between eukaryotes and prokaryote processing mechanisms?

A

In addition to image: prokaryotes can start translation before transcription even finishes

60
Q

What is the structure of tRNA?

A

it forms a cloverleaf pattern (with the anticodons as leaves) that folds in on itself

61
Q

RNAs often fold into many complex strutures, while DNAs do not. Why?

A

single-stranded DNA can fold into a structure and perform reactions, although this is very rare. The double-strand form of DNA blocks the folding forces

62
Q

What is the process by which RNA is decoded in ribosomes?

A
63
Q

What are some differences between RNA polymerase and DNA polymerase?

A

They are essentially the same chemical reactions, but RNA polymerase can starts and RNA chain without a primer, and does not accurately proofread its work

64
Q

What are the main differences between prokaryotes and eukaryotes after RNA transcription?

A

bacteria don’t have a nucleus, so the RNA is immediately loose in the cytosol.

Eukaryote mRNA needs to go through processing before it is exported into the cytosol

65
Q

Are the transcription start sites the same as translation start sites?

A

No, the ribosome has to have room to bind to the RNA

66
Q
A

Cell Biology (24 decks)

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