BIOMG 3320 Exam Questions Fall 2024
Bond between phosphate and sugar? **** phosphodiester
Bond between sugar and base? **** glycosidic
Non-covalent interactions? **** H bonding, base stacking, electrostatic interactions
Chargaff rules? **** purine content = pyrimidine content
adenine = thymine
guanine = cytosine
Do base compositions differ between species? **** Yes - have different ratios
Bacterial genome? _ micrometer, _______ DNA molecule, _____ million base pairs, _________
genes, _____ packed with genes, plasmids (Y/N), transposons (Y/N) **** 1; circular; 5; 5,000;
densely
plasmids (Y)
transposons (N)
Eukaryotic genome? __ micrometers, contains a _______, many __________ chromosomes,
chromatin (Y/N), 10^_ to 10^ _ base pairs, _______ - _______ genes, _________ packed with
genes, Transposons (Y/N) **** 10; nucleus; linear
chromatin (Y)
10^7 to 10^11
6,000-30,000 genes
not densely packed with genes
transposons (Y)
Termination codons? **** UAA, UGA, UAG
Initiation codon? **** AUG (methionine)
Level 1 logic of degeneracy in the code? **** some mutations won't change the encoded a.a.
sequence
ie. ACA, ACU, ACC, ACG all encode the same amino acid
,Level 2 logic of degeneracy in the code? **** amino acids with similar properties can have
similar codons
ie. Ser and Thr
Solving the code part 2? **** incorporation of a.a. into polypeptides in response to random
polymers of RNA
Exceptions to the genetic code? **** mitochondrial genomes, chloroplasts and viruses
Modern Sanger sequencing **** incorporation into DNA terminated future chain growth and
flourescently labels the DNA
4 things needed for modern Sanger sequencing? **** DNA polymerase
DNA template
fluorescent ddNTPs
primer
Primer does/does not require label? **** does not
Where does the labeling come from? **** fluorescent chain terminating ddNTPs
4 separate reactions? **** No - one reaction has all dNTPs and all ddNTP
ddNTPs higher/lower concentration than dNTPs? **** lower
What is the general process of Illumina sequencing? **** digital camera - each pixel of the
camera is equivalent to a full Sanger sequencing reaction
What 2 things do you start with? **** 1. pool of DNA fragments with lots of different
sequences
2. identical adapters ligated to each unique DNA fragment
What is the glass lawn? **** ssDNA that act as primers and base pair with adapters
What do you use to create clusters? **** PCR to amplify the flour signal
What do sequences within a single cluster have in common ? **** same sequence
DNA molecules in different clusters? **** different sequences
Still use DNA polymerase? **** Yes
, Normal dNTPs present? **** No
Key concept? **** polymerize one base at a time, snap a pic, remove flour, remove 3' block,
polymerize one base, snap a pic, remove flour...
Restriction endonucleases function? **** digest foreign DNA
How can you use restriction endonuclease? **** for recombinant DNA technology - can cut
and paste gene into a bacterial promoter of an operon and initiate replication to manufacture a lot
of that gene
3 major steps in bacterial transcription? **** initiation, elongation, termination
Initiation? **** promoter recognition and binding, formation of closed complex, transition to
open complex, promoter clearance
What does sigma do? **** promoter recognition
Elongation? **** loses sigma, gains NUSA
What does NUSA do? **** elongation factor used for productive elongation
Termination? **** polymerase detaches from DNA (p-dependent and p-independent)
p-independent termination? **** intrinsic termination by a hairpin sequence
p-dependent termination? **** ATP dependent helices recognizes rut elements and binds
nascent transcript and migrates toward polymerase
operon? **** a functioning uit of genomic DNA containing a cluster of genes under the control
of one promoter
What does lac operon do? **** encodes a protein called galactosidase that cleaves lactose
Lac operon - no lactose high glucose? **** lac repressor binds operator --> transcription of
galactisodase is blocked
Lac operon - high lactose no glucose? **** cAMP binds CAP activator and enables DNA
binding: lactose binds lac repressor and is released from operator--> transcription of
galactisodase occurs
Bond between phosphate and sugar? **** phosphodiester
Bond between sugar and base? **** glycosidic
Non-covalent interactions? **** H bonding, base stacking, electrostatic interactions
Chargaff rules? **** purine content = pyrimidine content
adenine = thymine
guanine = cytosine
Do base compositions differ between species? **** Yes - have different ratios
Bacterial genome? _ micrometer, _______ DNA molecule, _____ million base pairs, _________
genes, _____ packed with genes, plasmids (Y/N), transposons (Y/N) **** 1; circular; 5; 5,000;
densely
plasmids (Y)
transposons (N)
Eukaryotic genome? __ micrometers, contains a _______, many __________ chromosomes,
chromatin (Y/N), 10^_ to 10^ _ base pairs, _______ - _______ genes, _________ packed with
genes, Transposons (Y/N) **** 10; nucleus; linear
chromatin (Y)
10^7 to 10^11
6,000-30,000 genes
not densely packed with genes
transposons (Y)
Termination codons? **** UAA, UGA, UAG
Initiation codon? **** AUG (methionine)
Level 1 logic of degeneracy in the code? **** some mutations won't change the encoded a.a.
sequence
ie. ACA, ACU, ACC, ACG all encode the same amino acid
,Level 2 logic of degeneracy in the code? **** amino acids with similar properties can have
similar codons
ie. Ser and Thr
Solving the code part 2? **** incorporation of a.a. into polypeptides in response to random
polymers of RNA
Exceptions to the genetic code? **** mitochondrial genomes, chloroplasts and viruses
Modern Sanger sequencing **** incorporation into DNA terminated future chain growth and
flourescently labels the DNA
4 things needed for modern Sanger sequencing? **** DNA polymerase
DNA template
fluorescent ddNTPs
primer
Primer does/does not require label? **** does not
Where does the labeling come from? **** fluorescent chain terminating ddNTPs
4 separate reactions? **** No - one reaction has all dNTPs and all ddNTP
ddNTPs higher/lower concentration than dNTPs? **** lower
What is the general process of Illumina sequencing? **** digital camera - each pixel of the
camera is equivalent to a full Sanger sequencing reaction
What 2 things do you start with? **** 1. pool of DNA fragments with lots of different
sequences
2. identical adapters ligated to each unique DNA fragment
What is the glass lawn? **** ssDNA that act as primers and base pair with adapters
What do you use to create clusters? **** PCR to amplify the flour signal
What do sequences within a single cluster have in common ? **** same sequence
DNA molecules in different clusters? **** different sequences
Still use DNA polymerase? **** Yes
, Normal dNTPs present? **** No
Key concept? **** polymerize one base at a time, snap a pic, remove flour, remove 3' block,
polymerize one base, snap a pic, remove flour...
Restriction endonucleases function? **** digest foreign DNA
How can you use restriction endonuclease? **** for recombinant DNA technology - can cut
and paste gene into a bacterial promoter of an operon and initiate replication to manufacture a lot
of that gene
3 major steps in bacterial transcription? **** initiation, elongation, termination
Initiation? **** promoter recognition and binding, formation of closed complex, transition to
open complex, promoter clearance
What does sigma do? **** promoter recognition
Elongation? **** loses sigma, gains NUSA
What does NUSA do? **** elongation factor used for productive elongation
Termination? **** polymerase detaches from DNA (p-dependent and p-independent)
p-independent termination? **** intrinsic termination by a hairpin sequence
p-dependent termination? **** ATP dependent helices recognizes rut elements and binds
nascent transcript and migrates toward polymerase
operon? **** a functioning uit of genomic DNA containing a cluster of genes under the control
of one promoter
What does lac operon do? **** encodes a protein called galactosidase that cleaves lactose
Lac operon - no lactose high glucose? **** lac repressor binds operator --> transcription of
galactisodase is blocked
Lac operon - high lactose no glucose? **** cAMP binds CAP activator and enables DNA
binding: lactose binds lac repressor and is released from operator--> transcription of
galactisodase occurs
