Unit 2: Information Flow, Gene Structure and Transcription Flashcards
1
Q
replication
A
- process of copying DNA so genetic information can be passed from cell to cell or from an organism to its progeny
2
Q
How does the DNA structure suggest a mechanism for replication
A
- the two strands of the parental double helix unwind and separate into single strands
- each parental strand serves as a template, or pattern, for the synthesis of a complementary daughter strand
- when process is complete, there are 2 molecule, each containing a parental strand and a daughter strand, and each of which are identical in sequence to the original molecule, except possibly for rare errors that cause one base pair to be replaced with another
3
Q
mutation
A
- any heritable change in genetic material, usually a change in the nucleotide sequence of a gene
4
Q
ribonucleic acid (RNA)
A
- a molecule chemically related to DNA that is synthesized by proteins from a DNA template
5
Q
central dogma (2)
A
- originally, the idea that information flows from nucleic acids to proteins, but not in the opposite direction
- more generally, the view that information transfer in a cell usually goes from DNA to RNA to protein
6
Q
RNA function
A
- an intermediary molecule that DNA acts through to specify the amino acid sequence of proteins
7
Q
What are most of the active molecules in cells and developmental processes?
A
- proteins, including enzymes that concert energy into usable forms and the proteins that provide structural support for the cell
8
Q
transcription (2)
A
- the synthesis of RNA from a DNA template
- the first step in decoding DNA and of gene expression
9
Q
gene expression
A
- production of a functional gene product
10
Q
translation
A
- synthesis of a polypeptide chain corresponding to the coding sequence present in a molecule of messenger RNA
11
Q
why are the terms “transcription” and “translation” used? (2)
A
- transcription: it emphasizes that the information is being copied from DNA to RNA in the same language of nucleic acids
- translation: indicate a change of languages, from nucleotides that make up nucleic acids to amino acids that make up proteins
12
Q
What are some exceptions to the usual flow from DNA to RNA to protein? (2)
A
- transfer of genetic information from RNA to DNA (as in HIV which causes acquired AIDS) and from RNA to RNA (as in replication of the genetic material of influenza virus)
13
Q
How are the processes of transcription and translation regulated? (2)
A
- they do not occur at all times in all cells, even though all cells in an individual contain the same DNA
- genes are expressed or “turned on” only at certain times and places, and not expressed or “turned off” at other times and places.
14
Q
Where does the transcription and translation occur in prokaryotes?
A
- in the cytoplasm
15
Q
Where does the transcription and translation occur in eukaryotes? (3)
A
- transcription occurs in the nucleus
- translation occurs in the cytoplasm
- separation in time and space allows fro additional levels of gene regulation
16
Q
How does the sequence of a molecule of DNA, made up of many monomers of only four nucleotides, encode the enormous amount of genetic information stored in the chromosomes of living organisms?
A
- just 4 nucleotides can give rise to the vast diversity of genetic information because the nucleotides can occur in any order
- any base on a strand of DNA can be followed by any other base (or the same base) which gives rise to an enormous potential genetic diversity of any given gene
17
Q
ribosomes
A
- complex structure of RNA and protein, bound to the cytosolic face of the rough ER in the in the cytoplasm, on which proteins are synthesized
18
Q
RNA transcript
A
- RNA sequence synthesized from a DNA template
19
Q
RNA polymerase
A
- the enzyme that carries out polymerization of ribonucleoside triphosphates from a DNA template to produce an RNA transcript
20
Q
initiation of transcription
A
- RNA polymerase and other proteins are attracted to double-stranded DNA and the DNA strands are separated so that transcription of the template strand actually begins
21
Q
elongation of transcription
A
- successive nucleotides are added to the 3’ end of the growing RNA transcript as the RNA polymerase proceeds along the template strand
22
Q
termination of transcription
A
- RNA polymerase encounters a sequence in the template strand that causes transcription to stop and the RNA transcript to be released
23
Q
In what direction is the RNA synthesized in?
A
- 5’ to 3’ direction
24
Q
In what direction is the DNA template read in
A
- the 3’ to 5’ direction
25
Q
How is the RNA transcript connected to the DNA template?
A
- it is anti-parallel and complementary (base pairing) to the template strand
26
Q
promoters
A
- regulatory region where RNA polymerase and associated proteins bind to the DNA duplex
- refers to a region in a double-stranded DNA because both strands are needed to recruit these proteins even ho transcription is initiated only on one strand
27
Q
TATA box (2)
A
- DNA sequence present in many promoters in eukaryotes and archaeons that serve as a protein binding site for a key general transcription factor
- 5’-TATA-3’ present on the coding strand
28
Q
teminator
A
- a DNA sequence where transcription stops and the transcript is released
29
Q
sigma factor (2)
A
- a protein that associates with RNA polymerase that facilitates its binding to specific promoters in bacteria
- sigma is transient: once transcription is initiated, the sigma factor dissociates and the RNA polymerase continues transcription on its own
30
Q
What are 2 different types of sigma factors (2)
A
- used for transcription of housekeeping genes and many others
- for genes whose expression is needed under special environmental conditions such as lack of nutrients or excess heat
31
Q
general transcription factors
A
- a set of proteins that bind to the promoter of a gene whose combined action is necessary for transcription
- necessary for transcription in eukaryotes to occur, but not sufficient
32
Q
transcriptional activator protein (2)
A
- a protein that binds to a sequence in DNA to enable transcription to begin in eukaryotes
- help control when and in which cells transcription of a gene will occur
33
Q
enhancer (2)
A
- a specific DNA sequence necessary for transcription in eukaryotes
- transcriptional activator protein bind to this site and this bond is required for transcription to occur for any eukaryotic gene
34
Q
mediator complex of proteins (2)
A
- a complex of proteins that interacts with the Pol II complex and allows transcription to begin in eukaryotes
- once transcriptional activator protein have bound to enhancer DNA sequences, they can attract or recruit a mediator complex which in turn recruits the RNA polymerase complex to the promoter
35
Q
Pol II (2)
A
- RNA polymerase complex responsible for transcription of protein-coding genes
- once the mediator complex and the Pol II are in place, transcription is initiated in eukaryotes
36
Q
What happens after transcriptional initiation takes place
A
- successive ribonucleotides are added to grow the transcript in the process of elongation
37
Q
Where does transcription take place?
A
- in a sort of bubble in which strands of DNA duplex are separated and the growing end of the RNA transcript is paired with the template strand, creating an RNA-DNA duplex
38
Q
What are the details of elongation in transcription
A
- incoming ribonucleoside triphosphate is accepted by the RNA polymerase if it undergoes proper base pairing with the base in the template DNA strand
- RNA polymerase then orients the 3’ end of the growing strand so that the pxygen in the hydroxyl group can attack the innermost phosphate of the triphosphate of the incoming ribonucleoside, competing for the covalent bond
- bond connecting the innermost phosphate to the next is a high-energy phosphate bond which can be cleaved to provide energy to drive the reaction to create the phophodiester bond attaching the incoming nucleotide to the 3’ end of the growing chain
39
Q
What does the polymerization reaction release?
A
- releases a phosphate-phosphate group which also has a high-energy phosphate bond that is cleaved by another enzyme making the polymerization irreversible
- then the next ribonucleoside triphosphate is brought into line
40
Q
- what does transcription need in order for it to occur
A
- requires a template DNA, a supply of ribonucleoside triphosphates, and RNA polymerase
41
Q
How does the RNA polymerase function?
A
- forms the transcription bubble and features in the polymerase separate the DNA strands, allow the RNA-DNA duplex to form, and elongate the transcript nucleotide by nucleotide, release the finished transcript, and restore the original DNA double helix
42
Q
primary transcript (3)
A
- initial RNA transcript that comes off the template DNA strand
- contains the complement of every base that was transcribed from the DNA template
- for protein-coding genes, this means that the primary transcript includes the information needed to direct the ribosomes to produce the protein corresponding to the gene
43
Q
messenger RNA (mRNA)
A
- RNA molecule that combines with a ribosome to direct protein synthesis
- carries the genetic “message” from the RNA to the ribosome
44
Q
In prokaryotes, what is the relation between the primary transcript and mRNA
A
- the primary transcript is the mRNA
- as the 3’ end of the primary transcript is still being synthesized, ribosomes bind with special sequences near its 5’ end and begin the process of protein synthesis
45
Q
how is the connection between transcription and translation intimate in prokaryotes?
A
- prokaryotes have no nuclear envelope to spatially separate transcription from translation so the 2 processes are coupled and are connected in space and time
46
Q
what is a feature of primary transcripts for protein-coding genes that is present in prokaryotes and not eukaryotes
A
- they often contain genetic information for the synthesis of 2 or more different proteins
47
Q
polycistronic mRNA
A
- molecules of mRNA that code for multiple proteins
48
Q
RNA processing
A
- chemical modification that converts the primary transcript into finished mRNA, enabling the RNA molecule to be transported to the cytoplasm and recognized by the translational machinery
49
Q
What are the 3 principal types of chemical modifications?
A
- 5’ capping
- polyadenylation (poly A tail)
- splicing (intron removal, exon joining)
50
Q
5’ cap (3)
A
- modification of the 5’ end of the primary transcript by the addition of a special nucleotide attached in an unusual chemical linkage
- essential for translation because in eukaryotes, the ribosome recognizes an mRNA by its 5’ cap
51
Q
polyadenylation
A
- addition of a long string of consecutive A-bearing ribonucleotides to the 3’ end of the primary transcript
52
Q
poly (A) tail
A
- the nucleotides added to the 3’ end of the primary transcript by polyadenylation
53
Q
What is the importance of the 5’ cap and the poly (A) tail?
A
- 5’ cap and poly(A) tail help to stabilize the RNA transcript and protect the ends of the transcript
54
Q
exons
A
- a sequence that us left intact in RNA after RNA splicing
55
Q
introns
A
- a sequence that is excised from the primary transcript and degraded during RNA splicing
56
Q
RNA splicing
A
- process of intron removal
57
Q
alternative splicing (2)
A
- process where primary transcripts from the same gene can be spliced in different ways to yield different mRNAs and therefore different protein products
- presence of multiple introns allows this process to occur
58
Q
ribosomal RNA (rRNA) (2)
A
- noncoding RNA found in all ribosomes that aid in translation
- make up the bulk of ribosomes and is essential in translation
59
Q
necleolus
A
- distinct, dense, non-membrane-bound spherical structure within the nucleus that contains the genes and transcripts for rRNA and where rRNA is concentrated
60
Q
transfer RNA (tRNA)
A
- noncoding RNA that carries individual amino acids for use in translation
61
Q
What is the most abundant form of RNA found in cells?
A
mammalian cells:
- 80% of RNA is rRNA
- 10% of RNA is tRNA
62
Q
gene
A
- a gene is a transcription unit: it is a sequence of DNA from which an RNA transcript can be made
63
Q
Give the general definitions between mRNA, tRNA, and rRNA
A
- mRNA: this is RNA that is translated into proteins
- tRNA: this is RNA that is not translations but rather used in protein synthesis to transfer amino acids
- rRNA: this is RNA that is not translated but used as a component of ribosomes
64
Q
What direction does polymerase read in?
A
- the 3’ to 5’ direction
65
Q
template strand
A
- the strand that is the template for RNA polymerase
66
Q
coding strand
A
- strand that is anti-parallel to the template strand, called the coding strand because the RNA transcribed has the same base sequences (except all the thymine are replaced with uracil)
67
Q
In what direction does the polymerase move down to the terminator?
A
- downstream
68
Q
Which type of RNA are more stable?
A
- rRNA and tRNA are relatively stable because they form secondary folded structures to protect themselves against degradation
- rRNA also interacts with proteins to form the final ribosome structure, making it quite stable
- mRNA tend to remain as a single strand of RNA in an unfolded state and degrades quickly once it has served its function
69
Q
Why does the cell use mRNA instead of simply making the protein directly from the coding strand
A
- efficiency: faster to make proteins from multiple mRNA templates than a single DNA template
70
Q
What are the 3 basic steps for RNA Polymerase to synthesize RNA?
A
- RNA polymerase binds to (or assembles at) a gene promoter
- transcription stars with the first nucleotide being added at a position downstream from the promoter (called the +1 site or the transcription start site)
- transcription continues downstream, passes through the terminator, and then ends
71
Q
polymerization
A
- used to describe the process of building polymers
72
Q
What form do promoters take in bacteria? (2)
A
- the “-10 box and the -35 box” ( the entire promoter is about 40-50 base pairs in total)
- used to bind the sigma factor, which will recruit the RNA polymerase enzyme
73
Q
What do the -10 and -35 refer to? (2)
A
- the average position upstream of the location +1 site where the first RNA nucleotide is added
- orientation of the promoter elements are critical for determining which strand is the template strand and which direction transcription should move (they define the template strand)
74
Q
What do the general transcription proteins define?
A
- define the template direction, the start site, and the direction for the RNA Polymerase
75
Q
In bacteria, how does transcription stop?
A
- stops after passing through a terminator, the growing strand forms a hairpin that signals the RNA Polymerase to stop and release
76
Q
In bacteria, how does transcription stop?
A
- terminator is transcribed and sends a signal to the RNA polymerase to stop transcribing
77
Q
Proteins such as sigma factors need to bind to specific regions of the DNA? What is true about this process? (3)
A
- bind to the major (and even minor) groove of the DNA
- recognize specific sequences of base pairs
- bind by H-bonds and other non-covalent interactions
78
Q
How is transcription regulated by sigma factors or general transcription factors?
A
- how OFTEN something binds to the promoter (this is a function of how much of the “something” is available)
- how TIGHTLY that something binds and sticks to the DNA (this is a function of the something and the DNA sequence it binds to)
79
Q
how can the promoter sequence in the DNA help control the gene?
A
- different sequences can bund with sigma factors more or less tightly
- not all promoter sequences are equal and there are many variations
80
Q
consensus sequence
A
- those that represent the most common base found at each position
- for promoters, these represent the sequences that bind to their corresponding protein more tightly (for a promoter, being more like the consensus sequences means stronger binding of the sigma factor, which leads to more transcription)
81
Q
converging genes
A
- the RNA polymerase moves towards each other during transcription
82
Q
diverging genes
A
- the RNA polymerase move away from each other during transcription
