Chapter 3 Flashcards
What are the 2 major biological functions of DNA?
- stores genetic information that is encoded in the sequence of subunits along its length
- transmits genetic information in other molecules and from one generation to the next
What does some of the information in DNA encode?
proteins that provide structure and do much of the work of the cell
What form is genetic information in DNA organized in?
genes
How do genes exist?
in different forms in different individuals, even with a single species
What is gene expression?
turning on of a gene
What is gene regulation?
the molecular process that control whether gene expression occurs at a given time, in a given cell, or at what level
3.1
What are nucleotides composed of?
5-carbon sugar
base
phosphate group(s)
3.1
What are the nucleotide components’ roles in DNA structure?
- 5-carbon sugar and phosphate groups form the backbone of the molecule, with each sugar being linked to the phosphate group of the neighbouring nucleotide
- bases sticking out from the sugar give each nucleotide its chemical identity
3.1
What makes DNA a mild acid?
phosphate group attached to 5’ carbon has negative charges on two of its oxygen atoms because at cellular pH, the free hydroxyl groups attached to the phosphorous atom are ionized by the loss of a proton and therefore are negatively charged
3.1
Where is each base located?
attached to 1’ carbon of the sugar and projects above the sugar ring
3.1
What are nucleosides?
combination of sugar and a base
3.1
What is a nucleotide?
a nucleoside with one or more phosphate groups
3.1
What is a nucleotide with one, two, or three phosphate groups called?
nucleoside monophosphate, diphosphate, triphosphate
3.1
What is nucleoside triphosphate?
- molecules that are used to form DNA and RNA
- carriers of chemical energy in the form of ATP and GTP
3.1
What is a phosphodiester bond?
covalent bond that connects 3’ carbon of one nucleotide to 5’ carbon of the next nucleotide in line through the 5’ phosphate group
3.1
Describe the phosphodiester bond.
in DNA, it is a relatively stable bond that can withstand stresses such as heat and substantial changes in pH that would break weaker bonds
- succession of phosphidester bonds traces the backbone of the DNA strand
3.1
What gives DNA strand polarity?
phosphodiester linkages
3.1
What does polarity in a DNA strand mean?
one end differs from the other - 5’ end (phosphate) and 3’ end (hydroxyl)
3.1
Describe the Watson-Crick structure of DNA.
- space-filling model in which each atom is represented as a colour-coded sphere
- two DNA strands, each wrapped around the other in the form of a helix coiling to the right, with the sugar-phosphate backbones winding around the outside of the molecule and bases pointing inward
3.1
How many base pairs are there per DNA turn?
10 base pairs per complete turn
3.1
What are major and minor grooves?
outside contours of the twisted strands form an uneven pair of grooves
3.1
Why are major and minor grooves important?
because proteins that interact with DNA often recognize a particular sequence of bases by making contact with the bases by the major or minor groove or both
3.1
Describe the ribbon model of DNA.
- sugar-phosphate backbones wind around the outside with the bases paired between the strands
- closely resembles a spiral staircase, with the backbones forming the bannisters and the base pairs the steps
3.1
What is Chargaff’s rule?
- AT and GC base pairing maintains the structure of the double helix
- pairing one purine and on pyrimidine preserves the distance between the backbones along the length of the entire molecule
- pairing two purines would cause the backbone to bulge and pairing two pyrimidines would cause them to narrow, putting excessive strain on the covalent bonds in the sugar-phosphate backbone
3.1
Why is it that A pairs only with T, and G only with C?
- AT forms two hydrogen bonds
- GC forms three hydrogen bonds
3.1
When is a hydrogen bond formed in DNA?
when an electronegative atom (O or N) in one base shares a hydrogen atom with another electronegative atom in the base across the way
3.1
Describe hydrogen bonds in DNA.
- relatively weak, 5-10% of the strength of covalent bonds
- can be disrupted by high pH or heat
- added together, millions of these weak bonds along the molecule contribute to the stability of the DNA double helix
3.1
What is base stacking?
interactions between bases in the same strand
stabilizing force that occurs because the nonpolar, flat surfaces of the bases tend to group together away from water molecules and stack on top of one another as tightly as possible
3.1
What contributes to the stability of the double helix?
- hydrogen bonds
- base stacking
3.2
What does the structure of DNA suggest about its function?
how genetic info is stored in DNA - in the linear order or sequence of the base pairs
3.2
How can DNA carry the genetic info for so many different organisms?
number of possible base sequences of a DNA molecule only 133 nucleotides in length is equal to the estimated number of electrons, protons, and neutrons in the entire universe
3.2
Why can DNA serve as the genetic material?
it is unique among cellular molecules in being able to specify exact copies of itself, a process known as replication
3.2
How does DNA replication occur?
- two parental strands of double helix unwind and separate into two single daughter strands
- each of the parent strands serves as a template for the synthesis of a complimentary daughter strand
- when process is complete, there are two molecules each containing one parental strand and one daughter strand, and each of which is identical in sequence to the original molecule, except possibly for rare errors that cause one base pair to be replaced with another
3.2
Why is reproducing the sequence of nucleotides as precisely as possible important?
mistakes that go unrepaired may be harmful to the cell or organism
3.2
What is a mutation?
a change in genetic info in DNA as a result from an unrepaired error in DNA replication
3.2
How does DNA specify the amino acid sequence of proteins?
DNA acts through an intermediary molecules known as RNA
3.2
What is the central dogma of molecular biology?
the usual flow of genetic info in a cell is from DNA to RNA to protein
3.2
What is the first step in decoding DNA?
transcription
3.2
What is transcription?
FIRST STEP OF GENE EXPRESSION
genetic info in a molecule of DNA is used as a template to generate a molecule of RNA
- base pairing between a strand of DNA and RNA means that the information in DNA is transferred to RNA
3.2
What is gene expression?
production of a functional gene product
3.2
What is translation?
SECOND STEP OF GENE EXPRESSION
molecule of RNA is used as a code for the sequence of amino acids in a protein
3.2
Where does transcription and translation occur in prokaryotes?
in the cytoplasm
3.2
Where does transcription and translation occur in eukaryotes?
transcription: nucleus
translation: cytoplasm
separation of the processes in time and space allows for additional levels of gene regulation that are not possible in prokaryotes
3.3
What is RNA?
a polymer of nucleotides linked by phosphodiester bonds, in which the 5-carbon sugar is ribose
3.3
What is the polarity of RNA?
one end carries 3’ hydroxyl group, one end carries 5’ phosphate group
3.3
What are hydroxyls?
reactive functional groups, so the additional hydroxyl group on ribose in part explains why RNA is a less stable molecule than DNA
3.3
What are the differences between DNA and RNA?
- sugar in RNA is ribose which carries a hydroxyl group on the 2’ carbon, DNA is deoxyribose
- base uracil (U) replaced thymine (T) in DNA
- 5’ end of RNA is triphosphate, DNA is monophosphate
- RNA is shorter
- RNA is single-stranded
3.3
Describe the process of transcription.
as a region of DNA duplex unwinds, one strand is used as a template for synthesis of an RNA transcript that is complementary in sequence to the template according to the base-pairing rules, except that RNA transcript contains U instead of T
3.3
What is the RNA transcript produced by?
polymerization pf ribonucleoside triphosphates
3.3
What is RNA polymerase?
the enzyme that carries out polymerization, which acts by adding successive nucleotides to the 3’ end of the growing transcript
3.3
Which strand of DNA is transcribed?
only the template strand
3.3
What is the first stage of transcription?
initiation: RNA polymerase and other proteins are attracted to double-stranded DNA, the DNA strands are separated, and the transcription of the template strand actually begins
3.3
What is the second stage of transcription?
elongation: successive nucleotides are added to the 3’ end of the growing RNA transcript as the RNA polymerase proceeds along the template strand
3.3
What is the third stage of transcription?
termination: RNA polymerase encounters a sequence in the template strand that causes transcription to stop and the RNA transcript to be released
3.3
In what direction are all nucleic acids synthesized?
they grow in a 5’ to 3’ direction (3’ direction) by addition of nucleotides to the 3’ end
3.3
In what direction is RNA transcript synthesized?
5’ to 3’ direction
3.3
In what direction is DNA template read?
3’ to 5’ direction
opposite of synthesized RNA transcript
3.3
Where does transcription start and end?
starts at promoter, ends at terminator
3.3
What are promoters?
regions of typically a few hundred base pairs where RNA polymerase and associated proteins bind to the DNA duplex
3.3
What is needed to recruit promoters?
although the term refers to a region, both strands of DNA are needed, and transcription is initiated on only one strand
3.3
What is a TATA box?
a DNA sequence present in many promoters in eukaryotes and archaeons that serves as a protein-binding site for a key general transcription factor
5’-TATA-3’
3.3
Where does transcription occur?
uses the opposite strand as the template strand, usually starting about 25 nucleotides from the 3’ end of the complement to the TATA box
3.3
Where does elongation occur?
as the RNA polymerase moves along the template strand in the 3’ to 5’ direction
3.3
When does transcription continue until?
until RNA polymerase encounters sequence known as terminator
3.3
What happens at the terminator?
transcription stops, and the transcript is released
FOR ANY GENE, USUALLY ONLY ONE DNA STRAND IS TRANSCRIBED
HOWEVER, DIFFERENT GENES IN THE SAME DOUBLE-STRANDED DNA MOLECULE CAN BE TRANSCRIBED FROM OPPOSITE ENDS
which strand is transcribed depends on the orientation of the promoter
3.3
When are most genes transcribed?
only at certain times, under certain conditions, or in certain cell types
3.3
What does regulation of transcription often depend on?
whether the RNA polymerase and associated proteins are able to bind with the promoter
3.3
What is a sigma factor?
a protein that associated with RNA polymerase and facilitates its binding to specific promoters
3.3
How is promoter recognition meditated in bacteria?
by sigma factor
3.3
How is sigma binding transient?
once transcription is initiated, sigma factor dissociates and the RNA polymerase continues transcription on its own
3.3
Describe promoter recognition in eukaryotes.
transcription requires combined action of
- at least 6 proteins known as GENERAL TRANSCRIPTION FACTORS that assemble at promoter of gene
- one or more types of transcriptional activator protein, each of which binds to a specific DNA sequence needed for transcription known as an enhancer
3.3
What do transcriptional activator proteins help control?
when and in which cells transcription of a gene will occur
- able to bind with enhancer DNA sequences as well as with proteins that allow transcription to begin
3.3
Where does transcription take place?
in a bubble in which strands of DNA duplex are separated and growing end of RNA transcript is paired with template strand, creating an RNA-DNA duplex
3.3
Describe the details of a polymerization reaction.
- incoming ribonucleoside triphosphate is accepted by RNA polymerase only if it undergoes proper base pairing with base in template DNA strand
- RNA polymerase orients 3’ end of growing strand so oxygen in hydroxyl group can attack innermost phosphate of triphosphate of incoming ribonucleoside, competing for the covalent bond
- bond connecting innermost phosphate to next is a high-energy phosphate bond, which when cleaved provides energy to drive the reaction that creates the phosphodiester bond attaching the incoming nucleotide to 3’ end of growing chain
(“high-energy” refers to amount of energy released when phosphate bond is broken, this energy can be used to drive other reactions)
3.3
What does polymerization reaction release?
phosphate-phosphate group (pyrophosphate), which also has a high-energy phosphate bond that is cleaved by another enzyme
- cleavage of pyrophosphate molecule makes polymerization reaction irreversible, and next ribonucleoside triphosphate that complements the template is brought into line
3.3
What is the RNA polymerase complex?
a molecular machine that opens, transcribes, and closes duplex DNA
3.3
Transcription does not take place spontaneously. What does it require?
requires template DNA, a supply of ribonucleoside triphosphates, and RNA polymerase (large multiprotein complex in which transcription occurs)`
3.3
What features does RNA polymerase contain?
- structural features that separate DNA strands
- allows RNA-DNA duplex to form
- elongate transcript nucleotide by nucleotide
- release finished transcript
- restore original DNA double helix
3.3
Describe the process of transcription.
as a region of DNA duplex unwinds, one strand is used as a template for the synthesis of an RNA transcript that is complementary in sequence to template according to base-pairing rules
3.3
How is the RNA transcript produced?
by polymerization of ribonucleoside triphosphates carried out by RNA POL which adds successive nucleotides to the 3’ end of the growing transcript
3.3
What is the first step of transcription?
initiation
RNA POL and other proteins are attracted to DNA, the DN strands are separated, and transcription of template strand begins
3.3
What is the second step of transcription?
elongation
successive nucleotides are added to the 3’ end of growing RNA transcript as RNA polymerase proceeds along template strand
3.3
What is the third step of transcription?
termination
RNA POL encounters a sequence in template strand that causes transcription to stop and RNA transcript to be released
3.3
What is the direction of the growth of the RNA transcript?
all nucleic acids are synthesized by addition of nucleotides to 3’ end
5’ to 3’ growth direction
3.3
Where does transcription start and end?
starts a promoter, ends at terminator
3.3
What are promoters?
regions of typically a few 100 base pairs where RNA polymerase and associated proteins bind to DNA duplex
refers to a region in double-stranded DNA because both strands are needed to recruit these proteins, BUT transcription is initiated in only one strand
3.3
What is a TATA box?
in eukaryotic promoters, the promoter sequence in NONTEMPLATE strand includes 5’-TATA’3’
- transcription takes place using opposite strand, usually starting about 25 nucleotides from 3’ end of complement TATA box
- elongation occurs as RNA POL moves along template strand in 3’ to 5’ direction
3.3
When does transcription continue until?
until RNA POL encounters sequence known as terminator where transcript is released
3.3
What is promoter recognition mediated by in bacteria?
protein called SIGMA FACTOR that associates with RNA POL and facilitates binding to specific promoters
3.3
Why is sigma binding transient?
once transcription is initiated, sigma factor dissociates and RNA POL continues transcription on its own
3.3
Describe promoter recognition in eukaryotes.
requires 6 proteins called GENERAL TRANSCRIPTION FACTORS that assemble at promoter of gene and 1+ TRANSCRIPTIONAL ACTIVATOR PROTEINS which each bind to a specific DNA sequence known as an enhancer
3.3
What do transcriptional activator proteins help control?
when and in which cells transcription of a gene will occur
- able to bind with enhancer DNA sequences and proteins that allow transcription to begin
- therefore, needed for transcription
3.3
What happens once transcription initiation takes place?
successive ribonucleotides are added to grow the transcript in the process of elongation
3.3
Describe the bubble transcription takes place in.
the strands of DNA duplex are separated and the growing end of RNA transcript is paired with template strand, creating RNA-DNA duplex
3.3
Describe polymerization.
- incoming ribonucleoside triphosphate is accepted by RNA POL only if it undergoes proper base pairing with base in template DNA
- RNA POL orients 3’ end of growing strand so oxygen iin hydroxyl group can attack innermost phosphate of triphosphate of incoming ribonucleoside, competing for the covalent bond that drive the reaction that creates phosphodiester bond attaching incoming nucleotide to 3’ end of growing chain
- reaction releases pyrphosphate (P-P group), cleavage of this molecules makes reaction irreversible and next ribnucleoside triphosphate that complements template is brought in
3.3
What does transcription require to take place?
- template DNA
- supply of ribnucleoside triphosphate
- RNA POL
3.3
What is RNA POL?
large multi-protein complex in which transcription occurs
- transcription bubble forms and transcription takes place inside polymerase
- RNA POL contains structural features that separate DNA strands, allow RNA-DNA duplex to form, elongate transcript, release finished transcript, and restore original DNA helix
- it’s a molecular machine capable of adding thousands of nucleotides to a transcript before dissociating from template
- very accurate
3.4
What is a primary transcript?
initial RNA transcript that comes off the template DNA strand that contains complement of every base that was transcribed from DNA template
- for protein-coding genes, this means primary transcript includes info needed to direct ribosome to produce protein corresponding to the gene
3.4
What is mRNA?
RNA molecule that combines with ribosome to direct protein synthesis
carries genetic info from DNA to ribosome
3.4
Describe the relation between primary transcript and mRNA.
primary transcript is mRNA
as the 3’ end of primary transcript is still being synthesized, ribosomes bind with special sequences near its 5’ end and begin the process of protein synthesis
3.4
Why does transcription and translation take place at the same time in bacteria?
there’s no nuclear envelope to spatially separate transcription from translation
3.4
Describe a feature of primary transcripts for protein-coding genes in prokaryotes that is not shared with eukaryotes.
contain genetic information for synthesis of two or more different proteins
- these proteins usually code for successive steps in biochemical reactions that produce small molecules needed for growth or for successive steps needed to break down a small molecules used for nutrients or energy
3.4
What is polycistronic mRNA?
molecule of mRNA that codes for multiple proteins
3.4
Does transcription and translation occur at the same time in eukaryotes?
nuclear envelope is a barrier between processes of transcription and translation
transcription occurs in nucleus
translation occurs in cytoplasm
separation allows for complex chemical modification of primary transcript called RNA PROCESSING
3.4
What does RNA processing do?
converts primary transcript into finished mRNA which can then be translated by ribosome
3.4
What are the three main types of chemical modification in RNA processing?
- addition of 5’ CAP
- polyadenylation: adding a polyA tail to 3’ end
- splicing: introns are excised from RNA strand and exons are spliced together
3.4
Describe the addition of 5’ cap.
- attached by unusual linkage
- 5’ cap consists of modified nucleotide called 7-methylguanosine
- enzyme attached modified nucleotide to 5’ end of primary transcript “backwards
3.4
How is 5’ cap linked to RNA transcript?
by triphosphate bridge between 5’ carbons of both ribose sugars
normal linkage between two nucleotides: phosphodiester bond
3.4
What is 5’ cap essential for?
translation because in eukaryotes, ribosome recognizes an mRNA by its 5’ cap
without the cap, ribosome would not attach to mRNA and translation would not occur
3.4
Describe polyadenylation.
- addition of a string of ~250 consecutive A-bearing ribonucleotides to 3’ end, forming a polyA tail
- important in export of mRNA into cytoplasm
3.4
What stabilizes RNA transcript?
- 5’ cap
- polyA tail
they protect the two ends of transcript and increase stability until translation
3.4
What are introns?
interspersed noncoding regions
3.4
What are exons?
regions of protein-coding sequence
3.4
What is RNA splicing?
removal of noncoding introns, catalyzed by a complex of RNA and protein known as spliceosome
3.4
Describe splicing.
- spliceosome brings specific sequence within intro into proximity with 5’ end of intron at 5’ splice site
- proximity enables a reaction that cuts RNA at 5’ splice site and the cleaved end of intron connects back on itself, forming a loop and tail called a lariat
- spliceosome brings 5’ splice site close to splice site at 3’ end of intron
- 5’ splice site attacks 3’ splice site, cleaving the bond that holds that lariat on transcript and attaching ends of exons to each other
- result: exons are connected and lariat is released and broken down into its constituent nucleotides
3.4
What is alternative splicing?
presence of multiple introns allows for this process in which primary transcripts from same gene can be spliced in different ways to yield different mRNAs and therefore different proteins
- more than 80% human genes are alternatively spliced
- spliced forms differ in whether a particular exon is or is not removed from primary transcript along with its flanking introns
- allows same transcript to be processed in diverse ways to produce mRNA molecules with different combos of exons coding for different proteins
3.4
What is ribosomal RNA?
- makes up bulk of ribosomes
- essential in translation
- in eukaryotic cells, genes and transcripts for rRNA are concentrated in nucleolus
3.4
What is a nucleolus?
distinct, dense, non-membrane-bound spherical structure observed within the nucleus
3.4
What is transfer RNA?
carries individual amino acids for use in translation
3.4
What is small nuclear RNA (snRNA)?
essential component of spliceosome required for RNA processing
3.4
What are microRNA (miRNA) and small interfering RNA (siRNA)?
two major type of small regulatory RNA
- inhibit translation or cause destruction of RNA transcript
