CHEM 314 Quiz 4 Flashcards
Nucleotides are composed of what 3 components?
sugar, base, phosphate
Does RNA or DNA have an OH at the 2’ location?
RNA
What is the general structure of a purine?
It has 2 rings
What is the general structure of a pyrimidine?
it has 1 ring
Which nucleotides are purines?
Adenine (A) and Guanine (G)
Which nucleotides are pyrimidines?
Cytosine (C), Thymine (T), and Uracil (U)
Which nucleotide is in DNA only?
Thymine (T)
Which nucleotide is in RNA only?
Uracil (U)
What is different about adenine and guanine?
Adenine has 2 rings but has an NH2 group on top. Guanine has 2 rings but has a =O on top and an NH2 on the side
What is different about cytosine, thymine, and uracil?
cytosine is a single ring but has an NH2 on top and a =O on the side. thymine is a single ring that has a =O on top and on the side, AND a methyl. uracil is a single ring that has a =O on top and on the side
How do you abbreviate bases of DNA with different numbers of phosphates?
Mono = MP, Di = DP, and Tri = TP. For example: adenine with 2 phosphates would be dADP
How do you abbreviate bases of RNA with different numbers of phosphates?
Mono = MP, Di = DP, and Tri = TP. For example: adenine with 2 phosphates would be ADP
Where do nucleotides link together?
At the 3’ and 5’ locations
In a double helix, how do strands run?
Two strands ru antiparallel (5’ –> 3’, and 3’ –> 5’)
What are the features of a double helix?
Purine and pyrimidines are on the inside, while sugars and phosphates are on the outside (polar and charged, exposed to H2O)
Is DNA hydrophobic?
Yes, it is hydrophobic and protected from H2O because we are mostly made from H2O
What are the secondary structures of RNA?
single strands, bulge, stem, internal loop, and hairpin
3D structures of RNA are…
as diverse as their functions
What are some types of RNA?
Transfer RNA (tRNA), messenger RNA (mRNA), and ribozyme RNA (RNA enzyme)
How can you tell major and minor grooves of a helix apart?
Major grooves have a wide open space, while minor grooves are more narrow. These alternate
What happens at the major groove?
DNA binding to other proteins and enzymes
What do prokaryotic chromosomes look like?
circular and highly compacted. They can go from relaxed DNA to a supercoil
What do eukaryotic chromosomes look like?
linear and compact. They wrap around histone proteins to save space
How to nucleosomes turn into chromosomes?
nucleosomes compact against each other and ‘fold’ into chromosomes
Which base pairs have the most H-bonding capability?
AT (DNA), AU (RNA), and GC (DNA and RNA)
What is the difference between base stacking and base pairing in a DNA double helix?
Base stacking occurs between bases on the SAME strand. Base pairing occurs on bases on DIFFERENT strands –> antiparallel
In addition to base stacking and pairing, what is another IMF that stabilizes the double helix?
Hydrophobic effects nonhydrogen bonded atoms of nitrogenous bases are relatively polar and are forced away from water towards the center of the helix, leaving polar sugar/phosphate backbone on exterior to interact with aqueous environment
What is the DNA compaction strategy utilized by prokaryotic cells?
DNA supercoiling –> helix coiling on itself. To uncoil, use topoisomerase
What is the DNA compaction strategy utilized by eukaryotic cells?
Coil DNA around histone proteins. Histone has a + charge and DNA has a - charge so they are good binding partners
What type of covalent bond controls primary structure of proteins?
peptide bonds
what secondary structure controlled by H bonds in protein?
H-bond: backbone alpha helix and beta sheets
what tertiary structure controlled by hydrophobic effect in proteins?
nonpolar amino acids are inside globular proteins
What type of covalent bond controls the primary structure of carbs?
glycosidic
What secondary structure controlled by H bonds in carbs?
H-bond: linear strands (cellulose)
What type of covalent bond controls primary structure of nucleic acids?
phosphodiester
What secondary structure controlled by H bonds in nucleic acids?
H-bond: between base on different strands
Why is RNA capable of more diverse functions than DNA?
Because RNA is single stranded and base pairs within a single strand, it adopts more diverse tertiary structures, which are directly associated with their functions. 3D shape is the primary determinant of a biomolecules function
What amino acids would you expect histones to be primarily composed of?
positively charged amino acids - arginine, lysine, and some histidine
What are the requirements of DNA replication?
- preexisting DNA template
- primer with complementary sequence to DNA template
- 4 deoxynucleotide triphosphates (dATP, dCTP, dGTP, and TTP)
- DNA polymerase
- Mg 2+
Is the net reaction of DNA replication spontaneous?
Yes, it has an overall negative delta G
What direction is replication?
bidirectional
What method does DNA replication use?
Semiconservative - so you get 2 new daughter strands
What directions are leading and lagging strands?
The leading strand is continuous with the synthesis of a new strand, while the lagging strand is dis-continuous with the synthesis of a new strand
are okazaki fragments on the leading or lagging strand?
lagging
What is the purpose of Mg 2+ in DNA replication?
It helps stabilize the system
What enzyme unzips the circular DNA double helix in replication initiation?
helicase
What provides a starting point for DNA synthesis?
primers
What is the purpose of single stranded binding proteins (SSBPs)?
They stabilize single stranded DNA near replication because otherwise it would not be as efficient.
After elongation in DNA replication, what is the purpose of the enzymes: DNA polymerase 1 and DNA ligase?
DNA polymerase 1 replaces RNA nucleotides from primers with DNA nucleotides (proof reads). DNA ligase forms a phosphodiester bond between DNA fragments after DNA polymerase 1
What are 2 ways in which the fidelity of DNA replication is maintained? (how does the cell ensure there are few mistakes in DNA replication)
Many proofreading mechanisms
DNA polymerase III discriminates between right and wrong base pairs
How is DNA replication affected by amino acid substitution in the beta-clamp protein that made the clamp hold more loosely?
It would slow down. DNA polymerase would ‘fall off’ and have to start again
How is DNA replication affected by the absence of single strand binding proteins?
Without SSBPs, DNA would want to base pair with itself, forming secondary structure. Formation of secondary structure would prevent the DNA polymerase from adding new nucleotides onto the strand. Thus, replication would be slower or would stop entirely.
How would DNA replication be affected by high FM of polIII for dNTP’s?
High KM means weak affinity for dNTP substrate. This would slow rate of replicatino as dNTP wouldn’t bind as well for strand elongation
How would DNA replication be affected by low KM of polIII for dNTPs?
Low KM means high affinity for dNTP substrate. This would speed up the rate of replication as dNTP would bind well for strand elongation
How would DNA replication be affected by low concentration of NTPs (the substrate for primase)?
DNA replication would slow down. Primase doesn’t have enough substrate, thus it will take longer to assemble primers.
How is it possible for DNA polymerase to have such a high degree of fidelity?
DNA polymerase, in addition to catalyzing addition of base pairs, also has proofreading, or exonuclease activity. The poly erase can recognize mismatched base pairs, and cleave these bonds. It can then catalyze addition of the correct nucleotide.
What makes the addition of a deoxynucleotide triphosphate to a growing stand of DNA so favorable?
Hydrolysis of a pyrophosphate into 2 inorganic phosphates is a very favorable follow-up reaction that would make the overall delta G more negative by removing product, lowering the reaction quotient Q
What is meant when we say that DNA synthesis on the leading strand is continuous, and DNA synthesis on the lagging strand is discontinuous?
Synthesis on the leading strand proceeds in longer stretches, as the template strand moves in parallel to the movement of the replication fork. On the lagging strand, synthesis is discontinuous because it proceeds in shorter fragments, as the template strand is drawn out in loops away from the replication fork.
To observe DNA synthesis on a substrate with primers and templates in vitro, what additional reaction components must be added?
dNTPs, DNA polymerase, and Mg 2+
What are the requirements for transcription?
- preexisting DNA template
- primer NOT required because synthesis initiates from and NTP
- 4 nucleotide triphosphates (ATP, CTP, GTP, UTP)
- RNA polymerase
- Mg 2+
What stops transcription?
stop codons
What is the start codon to begin transcription?
ATG
What are the 2 termination mechanisms for transcription?
intrinsic and rho dependent
Intrinsic
- no enzyme required
- sequence on RNA strand: G,C followed by A, U - repeats
- sequence on template DNA strand: G,C –> A,T - repeats
Rho dependent
- enzyme required
- sequence on RNA strand: C rich sequence
- sequence on template DNA strand: G rich sequence
What prevents transcription under normal conditions?
repressor protein, LacI, bound to control site
What is the same between DNA replication and transcription?
Both utilize a nucleic acid polymerase, use nucleotide triphosphate building blocks, use a nucleic acid template, and create a new nucleic acid template
What is different about DNA replication and transcription?
- only 1 DNA strand can act as a template in transcription
- RNA polymerase does not require a primer
- UTP versus TTP as a building block, and ribose versus deoxyribose in the building blocks
- initiation requires origin in replication and a promotor in transcription
What are the subunits that make up RNA polymerase?
Sigma, 2 alpha, beta, beta prime, and omega
What subunits make up the core polymerase? What is their function?
2 alpha, beta, beta prime, and omega - they catalyze the formation of new phosphodiester bonds
What is the purpose of the omega subunut?
It recognizes and binds the promotor sequence on the coding strand in the DNA template
Under what conditions is the regulatory gene, LacI, expressed?
LacI is always expressed meaning that it is transcribed and translated at all times - the gene is under the control of a constitutive promotor which means it is expressed under all environmental conditions
What determines whether or not the repressor protein LacI is bound to the regulatory site laco?
Under non-starved conditions, LacI has a high affinity for laco. The presence of an inducer small molecule is present in solution under starved conditions, and it binds to the LacI protein, causing a conformational change. Under these conditions, the LacI no longer has a high affinity for laco and doesn’t bind to the regulatory site
What are codons?
3 letter codes for amino acids
start: AUG
Anticodon loop
mRNA codon forms complementary base pairs to 3 bases in the anticodon loop
What are the 3 binding sites on tRNA?
E, P, and A. These are in between the 50S and 30S subunits
What are the steps in translation?
initiation, elongation, and termination
What is required for the initiation process?
Proteins called initiation factors (IF1, IF2, and IF3)
IF2
GTP dependent (requires energy)
What is the rate limiting step in translation?
Formation of the 70S initiation complex
What delivers correct aa-tRNA to the A site in elonation?
Elongation factor Tu (EF-Tu). It is GTP dependent (requires energy)
What is catalyzed by RNA within peptidyl transferase center (P site)?
peptide bond formation
what direction does protein synthesis in elongation go?
N –> C direction
What is a good leaving group?
AMP
What is common in the tRNA codon?
inosine, which can pair with either A, U, or C. Base pairing behavior - wobble base
what subunits make up the bacterial ribosome?
30S and 50S
Which subunit is the mRNA associated with?
30S small
which subunits are the tRNA binding sites associated with?
E, P, and A are associated with both 30S and 50S
in which binding sites is mRNA base-paired to the tRNA?
P and A
which binding site is the peptide exit tunnel channel closest to?
P
Which subunit is the peptidyl transferase center associated with?
50S
How does the ribosome ‘recognize’ the mRNA to be translated?
Ribosome RNA in 30S base pairs with the ribosomal binding site (RBS) which is upstream of start codon. The RBS in prokaryotes is usually AGGAGGU
What is the role of IF2?
Initiation factor that delivers initiator tRNA to P site on 30S subunit
What is the role of EF2?
Elongation factor that delivers charged tRNA to A site of 70S ribosome
What is the role of EFG?
elongation factor that assists moving tRNAs from
A–>P+P–>E sites after peptide bond
How are stop codons recognized?
mRNA stop codons recognized in A site by release factor proteins. Rf proteins have similar shape to tRNA and can form complementary interactions with UAA, UAG, UGA codons
How do release factors catalyze the release of the complete peptide?
H2O across the ester bond between the AA and tRNA
