BIOMG 3350 Final Exam Review 2024
Describe the structure of a nucleotide. What is the difference in the structure between
RNA and DNA? How are nucleotides connected in DNA? ** answer** pentose sugar
phosphate group connected at the fifth carbon
nitrogenous base connected at the first carbon
OH at carbon 3
DNA has H at carbon 2
RNA has OH at carbon 2
Nucleotides are connected by a 3',5' phosphodiester linkage. This means that the 3
carbon of one nucleotide is connected to the phosphate on the 5 carbon of another
nucleotide.
What is the usual key feature of the origin of DNA replication for bacteria? ** answer**
AT-rich segments because these bonds are easier for helicase to separate. AT has only
two hydrogen bonds, while CG has three hydrogen bonds.
Describe the steps of DNA replication. Be sure to discuss leading and lagging strands.
** answer** 1. Helicase separates DNA strands (breaks the H-bonds holding bases
together)
- helicase movement causes a replication fork
2. Topoisomerases (DNA gyrase) reduces strain and supercoils, allowing helicase to
continue separating
3. Single Strand Binding proteins (SSBs) stabilize/protect the isolated strands
4. RNA primer (needed to start DNA replication) is added by primase
5. DNA polymerase III adds nucleotides in the 5' to 3' direction
- the leading strand has 5' to 3' synthesis in the same direction as the replication fork
movement. continuous
- the lagging strand has 5' to 3' synthesis in the opposite direction as the replication fork
movement. Because of this the lagging strand needs multiple RNA primers to form
Okasaki fragments. discontinuous
6. DNA polymerase I removes the RNA primer and replaces it with DNA
7. DNA ligase seals the nicks after the RNA primer is replaced with DNA
What are the purines and pyrimidines? What's the difference? ** answer** pyrimidines
- thymine, cytosine, uracil
,purines - adenine, guanine
pyrimidines are 1 six carbon ring structures.
purines are 2 ring structures (1 six carbon, 1 five carbon)
DNA can be highly distorted during replication/transcription, but is resolved by this
enzyme ** answer** topoisomerase
What are important structural components of chromosomes? ** answer** centromere =
a DNA sequence that functions during cell division as an attachment point for proteins
that link the chromosome to the mitotic spindle
telomeres = sequences at the ends of eukaryotic chromosomes that help stabilize the
chromosome (highly repetitive sequences associated with these)
gene = a segment of a DNA molecule that containsthe information required for the
synthesis of afunctional biological product, whether protein orRNA
Why don't bacterial cells have telomeres? ** answer** Bacterial cells are circular, while
eukaryotic cells have exposed ends (and thus need to be protected by these
sequences).
introns and exons ** answer** In most eukaryotic genes, coding regions (exons) are
interrupted by noncoding regions (introns). During transcription, the entire gene is
copied into a pre-mRNA, which includes exons and introns. During the process of RNA
splicing, introns are removed and exons joined to form a contiguous coding sequence.
~99% of human genome does not code for genes
what are the functions of the four classes of RNA? ** answer** several classes of
RNA:
- ribosomal RNAs (rRNAs) = components of ribosomes
- messenger RNAs (mRNAs) = intermediates in protein synthesis
- transfer RNAs (tRNAs) = adapter molecules that translate the information in mRNA
into a specific amino acid sequence
- noncoding RNAs (ncRNAs) = wide variety of functions
Why is RNA less stable than DNA? ** answer** It has an extra Hydroxyl Group (OH)
on the 2' carbon making it more likely to participate in chemical reactions
The proximity of the OH group to the phosphodiester bond means that the H may react
with the phosphate group, causing the bond between two nucleotides to break
, How in DNA denatured? Can this be fixed? ** answer** denaturation, or melting, of the
double helix:- due to pH extremes or high temperatures (useful in experiments) -
disrupts hydrogen bonds and base-stacking interactions
Yes, can be fixed. anneal = process by which two strands spontaneously rewind when
temperature or pH is returned to its normal range- two-step process
What are the adenine nucleotides? ** answer** Nucleotides Carry Chemical Energy in
Cells
hydrolysis of nucleoside triphosphates provides chemical energy- ATP is the most
widely used. ADP also
cAMP are is another nucleotide that is a secondary messenger
Describe the structure of the strand (macro-level structure) of DNA and RNA **
answer** DNA is primarily a right-handed two-stranded helix (secondary
structure),whereas RNA has lots of secondary and tertiary structure (interactionsbeyond
just a helix) but is a single strand.
Describe DNA repair (proofreading, mismatch, and damage) ** answer** DNA is
degraded by nucleases.
exonuclease = enzyme that can remove nucleotides from the strand starting from one
end of the strand.
endonuclease = enzyme that can remove nucleotides from the middle of the strand
Proofread: During DNA synthesis, most DNA polymerases "check their work," fixing the
majority of mispaired bases in a process called proofreading. DNA pol I and DNA pol III
have 3' to 5' exonuclease capabilities. This allows them to proofread and remove
incorrectly matching nucleotides and replace them right away.
Mismatch repair: Immediately after DNA synthesis, any remaining mispaired bases can
be detected and replaced in a process called mismatch repair. First, a protein complex
(group of proteins) recognizes and binds to the mispaired base. A second complex cuts
the DNA near the mismatch, and more enzymes chop out the incorrect nucleotide and a
surrounding patch of DNA. A DNA polymerase then replaces the missing section with
correct nucleotides, and an enzyme called a DNA ligase seals the gap.
- in this case, the DAUGHTER STRAND is corrected, not the parent strand. In bacteria,
original and newly made strands of DNA can be told apart by methylation state. An old
DNA strand will have methyl groups attached to some of its bases, while a newly made
DNA strand will not yet have gotten its methyl group. (thus, the methylated strand is not
edited, but the non-methylated strand is).
Describe the structure of a nucleotide. What is the difference in the structure between
RNA and DNA? How are nucleotides connected in DNA? ** answer** pentose sugar
phosphate group connected at the fifth carbon
nitrogenous base connected at the first carbon
OH at carbon 3
DNA has H at carbon 2
RNA has OH at carbon 2
Nucleotides are connected by a 3',5' phosphodiester linkage. This means that the 3
carbon of one nucleotide is connected to the phosphate on the 5 carbon of another
nucleotide.
What is the usual key feature of the origin of DNA replication for bacteria? ** answer**
AT-rich segments because these bonds are easier for helicase to separate. AT has only
two hydrogen bonds, while CG has three hydrogen bonds.
Describe the steps of DNA replication. Be sure to discuss leading and lagging strands.
** answer** 1. Helicase separates DNA strands (breaks the H-bonds holding bases
together)
- helicase movement causes a replication fork
2. Topoisomerases (DNA gyrase) reduces strain and supercoils, allowing helicase to
continue separating
3. Single Strand Binding proteins (SSBs) stabilize/protect the isolated strands
4. RNA primer (needed to start DNA replication) is added by primase
5. DNA polymerase III adds nucleotides in the 5' to 3' direction
- the leading strand has 5' to 3' synthesis in the same direction as the replication fork
movement. continuous
- the lagging strand has 5' to 3' synthesis in the opposite direction as the replication fork
movement. Because of this the lagging strand needs multiple RNA primers to form
Okasaki fragments. discontinuous
6. DNA polymerase I removes the RNA primer and replaces it with DNA
7. DNA ligase seals the nicks after the RNA primer is replaced with DNA
What are the purines and pyrimidines? What's the difference? ** answer** pyrimidines
- thymine, cytosine, uracil
,purines - adenine, guanine
pyrimidines are 1 six carbon ring structures.
purines are 2 ring structures (1 six carbon, 1 five carbon)
DNA can be highly distorted during replication/transcription, but is resolved by this
enzyme ** answer** topoisomerase
What are important structural components of chromosomes? ** answer** centromere =
a DNA sequence that functions during cell division as an attachment point for proteins
that link the chromosome to the mitotic spindle
telomeres = sequences at the ends of eukaryotic chromosomes that help stabilize the
chromosome (highly repetitive sequences associated with these)
gene = a segment of a DNA molecule that containsthe information required for the
synthesis of afunctional biological product, whether protein orRNA
Why don't bacterial cells have telomeres? ** answer** Bacterial cells are circular, while
eukaryotic cells have exposed ends (and thus need to be protected by these
sequences).
introns and exons ** answer** In most eukaryotic genes, coding regions (exons) are
interrupted by noncoding regions (introns). During transcription, the entire gene is
copied into a pre-mRNA, which includes exons and introns. During the process of RNA
splicing, introns are removed and exons joined to form a contiguous coding sequence.
~99% of human genome does not code for genes
what are the functions of the four classes of RNA? ** answer** several classes of
RNA:
- ribosomal RNAs (rRNAs) = components of ribosomes
- messenger RNAs (mRNAs) = intermediates in protein synthesis
- transfer RNAs (tRNAs) = adapter molecules that translate the information in mRNA
into a specific amino acid sequence
- noncoding RNAs (ncRNAs) = wide variety of functions
Why is RNA less stable than DNA? ** answer** It has an extra Hydroxyl Group (OH)
on the 2' carbon making it more likely to participate in chemical reactions
The proximity of the OH group to the phosphodiester bond means that the H may react
with the phosphate group, causing the bond between two nucleotides to break
, How in DNA denatured? Can this be fixed? ** answer** denaturation, or melting, of the
double helix:- due to pH extremes or high temperatures (useful in experiments) -
disrupts hydrogen bonds and base-stacking interactions
Yes, can be fixed. anneal = process by which two strands spontaneously rewind when
temperature or pH is returned to its normal range- two-step process
What are the adenine nucleotides? ** answer** Nucleotides Carry Chemical Energy in
Cells
hydrolysis of nucleoside triphosphates provides chemical energy- ATP is the most
widely used. ADP also
cAMP are is another nucleotide that is a secondary messenger
Describe the structure of the strand (macro-level structure) of DNA and RNA **
answer** DNA is primarily a right-handed two-stranded helix (secondary
structure),whereas RNA has lots of secondary and tertiary structure (interactionsbeyond
just a helix) but is a single strand.
Describe DNA repair (proofreading, mismatch, and damage) ** answer** DNA is
degraded by nucleases.
exonuclease = enzyme that can remove nucleotides from the strand starting from one
end of the strand.
endonuclease = enzyme that can remove nucleotides from the middle of the strand
Proofread: During DNA synthesis, most DNA polymerases "check their work," fixing the
majority of mispaired bases in a process called proofreading. DNA pol I and DNA pol III
have 3' to 5' exonuclease capabilities. This allows them to proofread and remove
incorrectly matching nucleotides and replace them right away.
Mismatch repair: Immediately after DNA synthesis, any remaining mispaired bases can
be detected and replaced in a process called mismatch repair. First, a protein complex
(group of proteins) recognizes and binds to the mispaired base. A second complex cuts
the DNA near the mismatch, and more enzymes chop out the incorrect nucleotide and a
surrounding patch of DNA. A DNA polymerase then replaces the missing section with
correct nucleotides, and an enzyme called a DNA ligase seals the gap.
- in this case, the DAUGHTER STRAND is corrected, not the parent strand. In bacteria,
original and newly made strands of DNA can be told apart by methylation state. An old
DNA strand will have methyl groups attached to some of its bases, while a newly made
DNA strand will not yet have gotten its methyl group. (thus, the methylated strand is not
edited, but the non-methylated strand is).
