Unit 5 Flashcards
1
Q
What is gene expression?
A
converting DNA sequence to RNA sequence through transcription
2
Q
What is RNA translated into? (sometimes)
A
proteins
3
Q
What are RNA molecules responsible for?
A
phenotypes/traits
4
Q
What is transcription?
A
synthesis of RNA from a DNA template
5
Q
What is DNA transcribed into?
A
RNA
6
Q
What do all nucleotides consist of?
A
5-carbon sugar, a nitrogenous base, and a phosphate group
7
Q
What is the difference in between RNA and DNA?
A
the sugar
8
Q
What sugar does DNA have?
A
deoxyribose
H on the 2’ carbon
9
Q
What sugar does RNA have?
A
ribose
OH on the 2’ carbon
10
Q
Why do organisms use DNA as genetic material instead of RNA?
A
because RNA is more reactive and less stable and more susceptible to forming covalent bonds
11
Q
When is RNA not single-stranded?
A
some viruses have a double-stranded genome
12
Q
What are the types of RNA found in prokaryotes and eukaryotes?
A
tRNA, rRNA, mRNA
13
Q
What is mRNA?
A
messenger RNA; template for protein synthesis
14
Q
What do all types of RNA need to be produced through?
A
transcription from DNA
15
Q
What does a transcription unit (a gene) consist of?
A
a promoter, RNA coding region, and a terminator
16
Q
What is a gene promoter?
A
sequence in DNA where transcription machinery assembles to start transcription at the +1 transcriptional start site
17
Q
Is the gene promoter transcribed?
A
no
18
Q
Is the gene promoter in RNA?
A
no, only DNA
19
Q
What is the RNA coding region?
A
sequence in DNA that is transcribed into RNA
20
Q
What is the terminator?
A
a sequence in DNA that signals where transcription ends
Tells RNA polymerase where to stop
21
Q
How many DNA stands get transcribed into RNA?
A
1 of the 2 strands
22
Q
What are molecular mechanisms of transcription?
A
initiation, elongation, termination
23
Q
What is translation initiation?
A
transitional complex forms, and tRNA brings first amino acid in polypeptide chain to bind to start codon on mRNA
24
Q
What is translation elongation?
A
tRNAs bring amino acids one by one to add to polypeptide chain
25
What is translation termination?
release factor recognizes stop codon, translational complex dissociates, and completed polypeptide is released
26
What is RNA polymerase?
synthesizes RNA from a DNA template
27
What are the subunits of prokaryotic RNA polymerase?
sigma and beta
28
What is each individual subunit of prokaryotic RNA?
an individual protein that is synthesized and assembled to make a functional RNA polymerase
29
1) What is the sigma factor?
2) What shape is it?
3) Why is this shape important?
4) What does it bind to?
5) What do these numbers represent and what do they allow?
1) binds to the DNA sequences in the promoter
2) bean shape
3) Shape is important because it recognizes these specific DNA sequences in the promoter and binds to them
4) Always binds the same two DNA sequences
Minus 10 and minus 35 sequences
5) Numbers represent their position relative to that +1 start space, Allows the beta subunit to be positioned at the +1 start site
30
What is the beta?
part of the polymerase molecule forming phsophodiester bonds in between individual nucleotides
31
Does transcription elongation need a helicase?
because RNA polymerase already has the activity needed to unwind short stretches of the DNA template and transcribe simultaneously
32
How many base pairs are in the unwound region?
18
33
What bond does RNA bind to the DNA template with during transcription?
hydrogen bond
34
What do rNTPs bind onto?
5’ end and to temporarily form a hydrogen bond with the DNA template
35
What is the synthesis of the new RNA molecule made through?
formation of phosphodiester bonds
36
What do rNTPs come in with to form a phosphodiester bond?
3 phosphate groups, 2 of them are cleaved, and the leftover one joins a hydroxyl group to form a phosphodiester bond
37
Do RNA polymerases have a proofreading capability?
no, so the error rate is much higher than DNA polymerase
38
What binds to RNA in transcription termination and what does it follow?
a protein called rho that binds to RNA and follows behind polymerase
39
What does rho need to function?
ATP
40
How does rho catch up to RNA polymerase?
when RNA polymerase pauses at the terminator
41
What happens when rho catches up to RNA polymerase?
Causes polymerase to fall off of the DNA and causes RNA strand to break off of the DNA strand
DNA rewinds
RNA is now free and folds into whatever structure it needs to be
42
What is RNA in relation to the DNA template?
RNA is antiparallel and complementary
43
When is RNA able to be translated into a protein?
when it is mRNA
44
What ratio of nucleic acids are translated into amino acids?
3:1
45
What is the 1' carbon bound to?
nitrogenous base
46
What does the 3' carbon bind to?
5' phosphate on the next nucleotide coming in to make a chain (sugar phosphate backbone)
47
When are nitrogenous bases capable of hydrogen bonding?
During transcription DNA and RNA are forming temporary hydrogen bonds
48
What is primary sequence?
order of base pairs
49
How do complementary bases fold over?
by forming a hydrogen bond with the other base on the other strand
50
What is the transcription start site?
+1
51
What value do all nucleotides to the right of +1 have?
positive (downstream of gene)
52
What value do all nucleotides to the left of +1 have?
negative (upstream of the gene)
53
What orientation does DNA have to be copied in?
5' to 3'
54
Which strand is the template and nontemplate?
bottom strand is 5' template strand
Top strand is 3’ nontemplate strand
55
What is the name of the coding strand?
nontemplate
56
What is the name of the noncoding strand?
template strand
57
What is translation?
synthesis of amino acid sequence from an mRNA template to form proteins
58
What does mRNA go on to be translated by?
a ribosome into the amino acid sequence
59
What are proteins built from?
amino acid
60
What is the structure of amino acids?
central alphacarbon covalently bound to an amino group, carboxyl group, hydrogen atom, and an R group
61
What are R groups categorized as?
basic, acidic, polar, and nonpolar
62
1) What do peptide bonds join together?
2) What is this called?
1) Joins carboxyl group of first amino acid to the second amino acid
2) dehydration synthesis reaction
63
What is a dehydration synthesis reaction?
Losing a molecule of water and forming a bond between the carbon in the carboxyl group and the nitrogen in the amino group
64
What is a codon?
sequence of 3 nucleotides that specify one amino acid
65
What is the start codon?
where translation starts and Ribosome keeps reading sequence of 3 nucleotides to specify one amino acid until it reaches a stop codon
66
What direction is mRNA synthesized from?
5' to 3'
67
What does the ribosome bind to on mRNA?
to five prime end and scan down the RNA to translate it into protein
68
1) What are the termini of proteins?
2) What does protein synthesis start at?
3) What way does synthesis go?
1) amino terminus and carboxyl terminus
2) amino terminus
3) n-terminus to c-terminus
69
1) What is genetic code?
2) What does it tell us?
3) How many codons, amino acids, and stop codon?
4) What is always the start codon?
1) how mRNA gets translated into amino acid
2) which amino acid is specified by a codon
3) 64 codons specify 20 amino acids and 3 stop codons
4) Methionine is always the start codon and is AUG
70
What is tRNA?
transfer RNA carries amino acids to the ribosome for incorporation into a growing protein chain
71
What is tRNA synthesized as and what does it form?
tRNA is synthesized as a single-stranded RNA but due to internal complementary base pairing, tRNA molecule forms a complex of 3-dimensional structure
72
Where is the amino acid attachment site located at?
3' end of RNA
73
What is the amino acid attachment site?
Where amino acid is added onto tRNA
74
What is an anticodon?
sequence complementarity to the codon in the mRNA, Allows specific tRNA molecules to recognize specific codons in the mRNA
Each tRNA is attached to a different amino acid
75
What is rRNA?
ribosomal RNA is a major structural and enzymatic component of the ribosome
76
What do all ribosomes have and what is it made up of?
All ribosomes have a large subunit and a small subunit made up of ribosomal RNA and protein
77
What synthesizes proteins and how does it do that?
Ribosomes and Converts RNA sequence into an amino acid sequence
78
What is the sigma factor?
bound to RNA polymerase and brings it to the promoter by binding it to -10 and -35 sequence in promoter
Positions RNA polymerase at +1 nucleotide so transcription starts at that position
79
Is the top DNA strand the coding or noncoding strand?
coding
80
Is the bottom DNA strand coding or noncoding?
noncoding
81
Explain the entirety of transcription
the sigma protein binds to RNA polymerase and binds to -35 and -10 so it can be positioned at the +1 start site in the promoter, and RNA polymerase moves down the DNA molecule, transcribing DNA into RNA (5' to 3'), RNA polymerase synthesizes RNA and forms phosphodiester bonds between rNTPs as well as hydrogen bonds being formed between template strand and newly synthesized RNA. Rho protein attaches to the 5' end of the newly synthesized strand of RNA and follows polymerase until it reaches the terminator sequence, rho catches up and bumps RNA polymerase off of the DNA molecule so it forms new kinds of RNA
82
What is the coding strand?
same sequence of nucleotides but Ts are changed to U and same orientation as RNA molecule
Bottom is coding strand (nontemplate strand)
83
What is the noncoding strand?
complementary sequence of nucleotides and will be antiparallel to RNA molecule
Top on noncoding (template strand)
84
What does it mean when a codon is degenerate?
more than 1 codon will specify the same amino acid
85
What does the cell sacrifice in transcription?
accuracy for speed
86
What is the starting sequence of the start codon?
AUG
87
How do the large and small subunits attach around mRNA?
they are broken apart
88
What does the anticodon loop bind to?
codon
89
How is a full polypeptide chain formed?
Ribosome shifts down mRNA one codon at a time, and each time tRNA brings in a new amino acid to form a peptide bond, linking amino acids together
90
1) What is translation initiation?
2) What does the ribosome consist of?
3) What does the small subunit bind to?
4) What does initiator tRNA bind to?
5) How does the ribosome find the start codon?
6) What happens after tRNA is bound?
7) What is the last step of initiation?
1) assembly of translation machinery (ribosome) on mRNA
2) large and small subunit
3) mRNA
4) mRNA
5) Sequences in the mRNAs that have complementarity to the rRNA found in the small subunit tells the ribosome where the start codon is
6) large subunit binds to small subunit
7) Ribosome starts to synthesize peptide bonds between incoming amino acids to create a chain of proteins
91
1) What starts translation elongation?
2) What has sequence complementarity to mRNA, and what does this tell us?
3) What does the ribosome do?
4) What does ribosomal translation require?
5) Where does the amino acid on the tRNA P site get transferred to?
6) What does this form?
7) Where does the tRNA exit the ribosome?
8) What does this mean for the A site?
9) When does the process stop?
1) tRNA entering the A site and carrying the next amino acid to be incorporated on the chain
2) tRNAs, tells us which amino acid will be inserted next
3) shifts down the mRNA by one position (1 codon)
4) an input of GTP
5) transferred to the next amino acid that came in when ribosome shifts
6) forms a peptide bond in between 2 amino acids
7) through the E site
8) open to the next amino acid to come in
9) stops when the ribosome reaches a stop codon
92
What are the 3 positions on the inside of the ribosome?
E, P, A
93
What is the E site?
exit, where used tRNAs get kicked out of the ribosome
94
What is the P site?
peptidyl, always bound to tRNA carrying growing protein chain
95
What is the A site?
aminoacyl, new tRNAs enter the ribosome
96
1) What is translation termination?
2) What proteins are there and what do they do?
3) What happens to the large ribosomal subunit?
4) What does this do to the protein?
5) What happens to the tRNAs?
6) What happens to the mRNA?
1) when a ribosome reaches a stop codon
2) release factors that recognize stop codons and bind in the A site, causing the process to stop
3) dissociates from the small subunit
4) gets released and folds into its 3d confirmation
5) gets recycled for another round of translation
6) gets recycled for another round of translation
97
What is transcription initiation?
The transcription apparatus is assembled on the promoter and begins RNA synthesis
98
What is transcription elongation?
RNA polymerase moves along DNA, unwinding it and adding new nucleotides to the 3’ end of the growing strand
99
What is transcription termination?
recognition of the termination site and separation of the RNA molecule from the DNA template
100
What is the Shine Delgarno sequence in translation initiation?
ribosome binding site on the mRNA, finds the start codon, Small subunit has an rRNA that has a sequence complementary to the Shine-Dalgarno sequence in the mRNA, and forms hydrogen bonds between rRNA and mRNA to find the start codon
