Chapter 14-17 Flashcards
What’s the structure of a nucleotide?
-phosphate group, sugar (pentose), and nitrogenous base
What’s a nucleoside of a nucleotide?
The nitrogenous base and the sugar
How do ribonucleotides and deoxyribonucleotides differ?
-The sugar in ribonucleotides is ribose
-The sugar in deoxyribonucleotides
-Their 2’ carbon substituents are different
describe the structure of a polynucleotide? Mention phosphodiester bond and sugar-phosphate backbone. Can you describe how a polynucleotide has a 5’ to 3’ orientation?
-made up of a chain of nucleoside triphosphates (or nucleotides), held together by phosphodiester bonds: the phosphate of one nucleotide covalently bonds to the sugar of another
-each end of the polynucleotide is different: 5’ is phosphate, and 3’ is -OH and nucleic acid codes are always read from 5’ to 3’
Can you describe complementary base pairing in nucleic acids? Mention the type of bond involved and how many bonds are between each base pair.
-Complementary base pairing is the pairing between the nitrogenous bases of two polynucleotides (DNA) with the association being between a pyrimidine (C,T,U) and a purine (G,A)
-This is linked together by hydrogen bonds
-C is with G: 3 H-bonds
-A is with T: 2 H-bonds
Can you describe the levels of structure in RNA (up to quaternary structure)?
1)Primary structure: the sequence in which the bases (U, A, C, G) are aligned.
2)Secondary structure: the 2-D analysis of the [hydrogen] bonds between different parts of RNA. In other words, where RNA becomes double-stranded (tRNA, and
3)tertiary structure is defined as the three-dimensional arrangement of RNA building blocks, which include helical duplexes, triple-stranded structures
4)Quaternary structure arises from the association of multiple macromolecular chains
What are the characteristics of DNA that allows it to act as genetic material? What are the types of information that is stored in DNA?
1) Its capability for replication
2) Its semiconservative
3) It stores information, transfers it and expresses genetic information
- genetic information, nucleic acids hold the instructions for protein synthesis,
What are ribozymes? What reactions do rRNA and spliceosomes catalyze?
-specific folding of RNA allows them to have specific functions such as ribozymes
-rRNA catalyzes peptide bond formation
-certain ribozymes called spliceosomes catalyze reactions during RNA splicing
Which bases are
purines? Pyrimidines?
pyrimidine = (C,T,U)
and a purine = (G,A)
What are some of the many functions of RNA? (4 specific examples) Why is RNA capable of producing many functional classes?
-mRNA: used to make a protein (recognizes amino acid sequence)
-tRNA: facilitates translation during protein synthesis
-Spliceosomes: catalyze the reactions during RNA splicing
-rRNA: catalyzes peptide bond formation
-They’re capable of these different functions because of the 4 levels of structure
Compare coding vs. non-coding RNAs.
1) Coding RNAs generally refers to mRNA that encodes protein to act as various components including enzymes, cell structures, and signal transductors.
2) Noncoding = cellular regulators
What is Chargaff’s Rule? How did Watson, Crick and Franklin’s discovery of the double-stranded
nature of DNA explain the rule?
-A & T always have same % because they’re paired together
-G & C have the same % for the same reason
-The uniform diameter of the double helix suggests that purines must be paired with pyrimidines
What was Rosalind Franklin’s experiment and what did it show them?
-An X-ray diffraction photo of DNA was produced and it showed;
1) DNA has a helical shape
2) The width of the helix
3) the spacing of the nitrogenous bases
What is the process of replication?
-It’s the process of copying a double-stranded piece of DNA in a cell prior to cell division?
Why is DNA semi-conservative?
because one of the old strands form the original piece of DNA can be used as a template for the new strand of DNA
Can you describe the experimental design (4 steps), and results obtained for the Meselson-Stahl experiment (the bacterial experiment with N14 & N15) in 1958? Explain how the results contributed to our understanding of the mechanism of DNA replication
-Experimental design:
1) bacteria cultured in medium with N15 isotope
2) bacteria transferred to medium with N14 isotope
3) DNA sample centrifuged after first replication
4) DNA sample centrifuged after second replication
-Results: parent cell made two daughter cells that had one strand from the parent, then each of these daughter cells made two each, 2 of which were completely new and the other two contained DNA from the daughter cell
-Explains the semi-conservative properties of DNA replication
What are the steps in DNA polymerization in Prokaryotes?
1) replication begins at sites called origins of replication
2) proteins recognize the strand of origins of replication and attach to the DNA splitting the two strands which create a replication bubble
3) parent DNA copied in both directions from origin at same time until whole chromosome is replicated
What are the building blocks used in prokaryotic DNA polymerization?
1) Origin of replication (DNA sequence that starts replication)
2) Replication Fork: exists at each end of the replication bubble (2 replication forks)
3) Replication Factory: contains 12 enzymes and other proteins
4) DNA polymerase III and I
What are the enzymes used by the replication factory (in order of use)? (8)
1)Helicase
2)SSBP
3)Topoisomerase
4)Primase
5)DNA polymerase III
6)Rnase H
7)DNA polymerase I
8)DNA ligase
What are the steps of the replication factory in prokaryotes and what does it do? (6 steps)
1) Helicase unzips the strands at the origin and SSBP adheres to separated strands to prevent annealing
2) Tension is released by using Topoisomerase to break, swivel and rejoin DNA strands
3) Primase synthesizes a primer (short chain of RNA) and DNA Polymerase catalyzes the polymerization of DNA nucleotides
4) DNA polymerase III adds complementary DNA nucleotides to the free 3’ end of strand (elongated from 5’ to 3’) & a sliding clamp makes sure the polymerase stays in contact with the template strand
5) Rnase H degrades RNA primer by hydrolyzing its phosphodiester bonds & DNA pol I adds nucleotides to any exposed 3’ ends (leading and lagging)
6) DNA ligase glues fragments of DNA on the new strand to make a continuous polynucleotide strand
What are the 5 main differences between Prokaryotic and Eukaryotic DNA replication?
1) Eukaryotes have linear chromosomes (prokaryotes = circular)
2) Eukaryotes have many origins of replication per chromosome (prokaryotes have one)
3) Eukaryotes have over 11 different polymerases (prokaryotes have pol III and pol I)
4) Both have okazaki fragments but they’re present for longer in prokaryotes because they have less base pairs than eukaryotes
5) Eukaryotes require telomeres to protect the ends of their strands
What are telomeres?
short repeated DNA sequences (TTAGGG)
What happens to telomeres after each replication event?
They get shorter and shorter as we get older and more replication events occur because they act as a buffer to prevent erosion (not completely)
What are the 2 protective functions of telomeres?
1) prevent the activation of DNA damage
2) provide some protection against the organism’s genes shortening
What is the function of a telomerase enzyme in eukaryotes and where are they found?
function:
-they extend the length of telomeres
found in:
-germ cells
-cells within embryos/fetuses
-certain tumor cells
How is telomerase implicated in the difference between replication in somatic cells versus germ line cells?
normal shortening of telomeres may protect organisms from cancer by limiting the number of divisions that somatic cells can undergo
How is the copying of DNA so remarkable in its speed and accuracy? (list 3 reasons)
1) the high specificity of base pairing
2) DNA polymerases proofreading and error checking mechanisms
3) Other enzymes can fix missed errors
How can DNA pol fix “wrong” nucleotides?
It has exonuclease abilities meaning it can cleave off nucleotides and replace them with the correct nucleotide
What are 5 things that can damage DNA? (RRXUO)
1) reactive chemicals
2) radioactivity
3) x-rays
4) UV light
5) other harmful toxins (i.e. mycotoxins, asbestos, nanoparticles)
Which enzymes repair external damage and repair mismatched nucleotides? (3)
1) Nuclease enzyme
2) DNA pol
3) DNA ligase
How do we know which strand has the right sequence?
The parent strand is methylated (daughter DNA isn’t)
What are the 4 steps of DNA excision repair?
1) mismatched base pairs detected by enzymes
2) nuclease enzyme cuts damaged strand at 2 points releasing the damaged section
3) DNA pol places correct nucleotides in the gap
4) Ligase seals the nucleotides together
How does UV light damage DNA in skin cells?
UV covalently cross links two adjacent pyrimidines distorting the DNA molecule (this creates Pyrimidine dimers)
What is the disease XP and what is it caused by?
it’s an inherited disease that causes hypersensitivity to light and it’s caused by a defect in nucleotide excision repair mechanism
What are 3 forms of chromosome coils?
1) loop domain structure
2) loop anchor
3) double helix
Why is it important that chromosomes coil?
So that nothing fragments off during replication
What is the complex of DNA and proteins called?
Chromatin
What is a nucleosome?
It’s a basic unit of DNA packaging, unfolded chromatin if you will (beads on a string separated by linker DNA)
How does DNA change as it’s packaged and moved around the cell?
1) DNA double helix
2) Histones (proteins with positively charged amino acids) coil the double stranded DNA (1st level of packaging)
3) Nucleosomes (unfolded chromatin) present during interphase
4) Fibers: folding of nucleosomes that allow for interactions between histone tails and linker DNA (present during interphase)
5) Looped domains: Folding of the fibers (also fold during replication)
What diameter of chromatid (2 chromatids make a chromosome) is most appropriate for cell division?
700 nm (metaphase)
Why are even higher levels of DNA packaging are achieved in cells? and when are they achieved? (IPM - phases)
-The entire DNA strand must fit within the nucleus of a cell, so it must be very tightly packaged to fit
-Interphase: highly extended
-Prophase: chromatin coils/folds (condenses)
-Metaphase: short and thick chromosomes
How is DNA spatially organized in the nucleus?
Looped domains of chromatin attach to the nuclear envelope during interphase
Why does chromatin of each chromosome occupy a specific restricted area within the nucleus
it’s so that there is no entangling of the chromatin fibers
What is the form of chromatin known as heterochromatin?
They are regions of highly condensed chromatin making them inaccessible to transcriptional machinery
What is the form of chromatin known as euchromatin?
They are regions of less tightly packed chromatin making them easier to transcribe
What makes chromatin more condensed or less condensed?
Depends on the number of histones and how closely packed they are
What was Beadle and Tatum’s experiment on neospora? And what did their results show?
-They bombarded Neospora cells with X-Rays to generate mutants then placed the offspring of the mutants into tubes containing a certain medium
-Results: each mutant (3 classes of genetic mutants) had a defective gene that wasn’t able to produce one enzyme “one gene - one enzyme” and this showed that enzymes are coded by and for genes
What were the 2 main flaws with the one gene - one enzyme hypothesis and what was it turned into?
1) not all genes encode enzymes
2) many genes encode proteins without enzymatic properties
–> was then turned into the one gene - one polypeptide model
What was wrong with the one gene - one polypeptide model? (2)
1) Eukaryotic genes can each code for polypeptides using alternative splicing
2) Quite a few genes code for RNA molecules
What is transcription?
the synthesis of RNA using information in DNA (no change in language)
What is translation?
synthesis of polypeptides using information from mRNA (there’s a change in language - nucleic acids to amino acids)
what is a transcription unit?
The stretch of DNA downstream from the promoter that’s transcribed into an RNA molecule
What are some prokaryotic genes?
-regulatory sequences (includes promoter)
-Coding region (Exon)
What are some eukaryotic genes?
-Regulatory sequences (includes promoter)
-Coding regions (Exon)
-Non-coding regions (Introns)
What’s the difference between RNA polymerase in eukaryotes and in prokaryotes?
-Doesn’t require a primer to start
-Eukaryotes: have 3 known RNA pols
1) RNA pol I: transcribes ribosomal RNAs (rRNA)
2) RNA pol II: transcribes protein-coding genes (mRNA)
3) RNA pol III: transcribes small RNAs (tRNA, rRNA, etc.)
-Prokaryotes: have only 1 known RNA polymerase
what does 1+ mean on a gene?
transcription start site
what does upstream mean and what components on the gene are upstream?
-Upstream means before the start site (denoted with negative numbers)
-The promoter is upstream
What does downstream mean and what components of the gene are downstream?
-Downstream means after the start site
-RNA coding region
-termination site
What direction is the synthesis of a new strand? (non template strand)
5’ to 3’
Where does gene expression occur in prokaryotes and in eukaryotes?
Prokaryotic gene expression (both transcription and translation) occurs within the cytoplasm of a cell due to the lack of a defined nucleus; thus, the DNA is freely located within the cytoplasm. Eukaryotic gene expression occurs in both the nucleus (transcription) and cytoplasm (translation)
What are the major steps of transcription? (3 - IET)
1) Initiation: RNA pol binds to DNA
2) Elongation: RNA pol generates an RNA transcript
3) Termination: Primary transcript and RNA pol released
What is the role of an RNA polymerase in the process of transcription?
-It’s the enzyme responsible for the transcription of DNA into RNA
-It pries the two strands apart and uses one as the template strand
-It then hooks together the RNA nucleotides as they base pair along the DNA template strand
Aside from synthesizing different types of polynucleotides, how else is RNA polymerase different from DNA polymerase?
DNA pol: requires a primer to begin
RNA pol: does NOT require a primer to begin
What are transcription factors?
-they help recruit RNA pol and initiate transcription at the promoter
What is the promoter sequence?
-they are specific 6-base sequences present at -35 and -10 (prokaryotes) which indicate which is the coding strand eukaryktes (TATA BOX)
What are the components of an initiation complex?
RNA pol + transcription factors
What role do histone proteins play in transcription? (HINT: Histone code theory)
-They help determine whether a gene will be transcribed. Histone code is a theory that transcription is regulated by the chemical residues on the tails of histones
Can you describe how pre-RNA molecules are processed into mature functional molecules?
-pre-RNA must go through post transcriptional modification before it can be used in for translation as mRNA
-Modifications involve:
-addition of 5’ cap and 3’ poly-A tail (both ends of the mRNA are altered)
-excision of introns and splicing of exons back together
What is 5’ cap?
modified guanine nucleotide
What is 3’ Poly-A tail?
-It’s a polyadenylation signal
-Synthesized upon the transcription of (AAUAAA)
-An enzyme adds 50-250 A nucleotides making a poly-A tail after transcription
What is a polyadenylation signal and what are its roles (3)?
-it’s a stretch of repeats of AAUAAA
-Poly-A tail
1) facilitates export of mRNA from nucleus
2) protects mRNA from degradation by hydrolytic enzymes
3) helps ribosomes attach to 5’ end of mRNA
Can you describe mRNA splicing using the terms introns and exons? What is the general structure of the spliceosome and the role it plays in splicing?
-Introns are removed by a complex made of proteins and snRNAs called spliceosomes and then they splice together the exons to make a mature mRNA
What’s the signal for RNA splicing?
it’s a nucleotide sequence at the end of each intron and they’re recognized by small nuclear ribonucleoproteins
What and where are 5’ and 3’ untranslated regions (UTRs) of an mRNA?
-UTRs are:
1) nucleotides that precede and follow the start and stop codon
2) sequences within the gene that won’t be translated into amino acids
-introns as well as 3’ and 5’ UTRs are part of exons –> all of these are UTRs
What are the 4 main differences between transcription in eukaryotes and prokaryotes?
1) Prokaryotes have 1 kind of RNA pol whereas eukaryotes have 3
2) Initiation:
-Prokaryote: RNA pol binds to promoter of gene
-Eukaryote: transcription factor binds to promoter first then recruits RNA pol (they then form the transcription initiation complex_
3) Eukaryotes have pre-mRNA containing introns and exons that needs to be converted into a mature RNA before being able to use it for transcription
4) Eukaryotes have post-transcriptional modifications which involves splicing 5’ cap & a 3’ Poly-A tail is added
Can you describe the process of alternative splicing in eukaryotes and its role? Why does this explain a possible role for introns?
-Introns enables a single gene to encode more than one polypeptide; this is called evolutionary splicing
-This means the number of different proteins a eukaryote can produce is greater than it’s number of genes
Can you describe the mRNA genetic code and the characteristics of the genetic code discussed in class?
-Each sequence of 3 nitrogenous bases in mRNA is a codon that codes for specific amino acids
What determines the amino acid?
the specific order of nitrogenous bases
How many codons does a ribosome read at a time?
1 codon (3 nitrogenous bases)
What’s the start codon?
AUG
What are the stop codons?
UAA, UGA, and UAG
Can you describe the structure of a tRNA mentioning the amino acid attachment site and anticodon?
-each tRNA molecule is approximately 80 nucleotides long
-3D conformation is possible due to stretches of complementary bases that can H-bond together
-3’ end = attachment site
-other end is a nucleotide triplet that can base pair with an anticodon on an mRNA
What’s the function of tRNA?
to transfer amino acids from cytoplasmic pool of amino acids to a growing polypeptide in a ribosome
What are the 3 steps of tRNA charging (mention the enzymes used)?
1) Amino acid and tRNA enter active site
2) Using ATP, synthase catalyzes the covalent bonding of amino acid and tRNA
3) tRNA, now charged with its amino acid, is released by the synthase
What provides energy in the process of tRNA charging (covalent bonding of amino acid and tRNA)?
The hydrolysis of ATP
What do aminoacyl-tRNA synthetases’ do?
-correctly match tRNA to its specific amino acid
Why are there only 45 tRNAs when we have 61 codons?
-this is due to the wobble rule which implies that complementary base pairing becomes more relaxed
-tRNAs bind to more than one codon
If you had to have a mutation for one of the pairs in your codon, which would it be?
the third pair (third base doesn’t have to be properly matched; wobble rule)
Why does the wobble base pairing occur only in the third nucleotide of the codon (first nucleotide of the anticodon)?
Because there is redundancy in the genetic code: the first two nucleotides are conserved but the third can vary
What is the structure and functions of the ribosome?
FUNCTIONS:
-synthesis of polypeptides occurs in ribosomes
-they facilitate coupling of tRNA anticodons with mRNA by holding them close together
STRUCTURE:
-large subunit (above strand of mRNA)
-small subunit (below strand of mRNA)
What do the protein components of ribosomes do?
stabilize the ribosome
Where are the subunits of the ribosome assembled in eukaryotes?
In the nucleolus
What’s the difference b/w ribosomes in prokaryotes and eukaryotes?
Eukaryotic ribosomes are slightly larger
How many binding sites do ribosomes have and what are they? (hint: APE)
1) A site: aminoacyl-tRNA binding site
2) P site: peptidyl-tRNA binding site
3) E site: exit site
What are the 3 steps of translation? And what does each step require?
1) Initiation
2) Elongation
3) Termination
–> THEY ALL REQUIRE PROTEIN FACTORS
Describe the first step of translation: Initiation (4 small steps)
1) small ribosomal subunit binds to 5’ cap of mRNA strand
2) slides downstream until start codon
3) initiator tRNA carrying methionine, h-bonds with start codon
4) initiator tRNA sits in P site while A site is vacant
What provides energy for the first step of translation: initiation?
the hydrolysis of GTP
What direction is a polypeptide synthesized in?
N-terminus to C-terminus
Describe the second step of translation: elongation (3 steps).
1) Codon recognition: anticodon of incoming aminoacyl tRNA base pairs w/ complementary mRNA codon in A site
2) A peptide bond is formed b/w new amino acid at A site and carboxyl end of polypeptide at P site (catalyzed by rRNA)
3) ribosome translocates the tRNA from A to P site which requires energy from GTP hydrolysis
Describe the third (last) step of translation: termination.
-elongation continues until stop codon reaches A site
-stop codons UAA, UGA, UAG aren’t translated, they only act as signals
What’s a polyribosome?
several ribosomes translating the same RNA simultaneously (it allows cells to produce proteins rapidly)
How can transcription and translation be used to amplify gene expression and why that is important in cells?
-level of a bacterial protein can quickly be amplified by multiple transcription and translation events occurring concurrently on the same DNA template
-IDK
Can you describe the various types of locations where proteins are transported (protein targeting)?
1) Stay free in cytosol; free ribosomes –> proteins that function in the cytosol
2) Ribosomes bound to rough ER –> proteins of the endomembrane system, and ribosomes synthesizing secreted proteins (insulin, hormones, etc.)
Can you describe one type of signal used to alert a transport system to bring a protein to the correct destination?
SRP (signal-recognition particle) binds to signal peptide, temporarily stopping translation, then it brings to a receptor built into ER. SRP leaves, synthesis resumes. Cleaving enzyme cuts off signal peptide. Completed peptide leaves.
