Unit 1 Flashcards
What are the requirements of “genetic material”
- Can replicate
- Controls the expression of traits
- Ability to change/adapt
Do polypeptides or DNA have more potential variation/different combinations?
Polypeptides
What is the nucleotide? What are its 3 components? What bond links them together?
The repeating structural unit of DNA and RNA
Phosphate group, Pentose sugar, nitrogenous base
Phosphodiester bonds
What is Chargaff’s rule?
% adenine = % thymine
% cytosine = % guanine
adenine + guanine (purines) = thymine + cytosine (pyrimidines)
What did Rosalind Franklin discover about the structure of DNA?
X-ray diffraction showed that DNA is helical with more than one strand. 10 base pairs per complete turn.
What direction do DNA strands go in?
A phosphate connects the 5’ carbon of one nucleotide to the 3’ carbon of another
Therefore, strand goes 5’ to 3’
What are some general DNA structural features?
•10 base pairs per complete twist
•the two strands are antiparallel
-one runs in the 5’ to 3’ direction and the other goes 3’ to 5’
•the helix is primarily in right-handed in the B form
How is the double-bonded structure of DNA stabilized?
- Hydrogen bonding between complementary bases (A-T is 2 hydrogen bonds, C-G is 3 hydrogen bonds)
- Base stacking (flattened regions face each other)
What two asymmetrical grooves are on the outside of the helix?
- Major groove
- Minor groove
What different forms of the DNA double helix can form?
•B-DNA, the predominant form found in living cells
•A-DNA and Z-DNA, under certain in vitro conditions
What are some of the features of A-DNA?
•right handed helix
•11 bp per turn
•occurs under conditions of low humidity
•little evidence to suggest it is biologically important
What are some of the features of Z-DNA?
•left handed helix
•12 bp per turn
•may play a role in transcription and chromosome structure
What’s the difference between B-DNA and Z-DNA?
B-DNA
•bases relatively perpendicular to the central axis
Z-DNA
•bases substantially tilted relative to central axis
•sugar phosphate backbone follows zigzag pattern
Can DNA form a triple helix? If so, explain
Yes.
Synthetic DNA oligomers were found to complex to double stranded DNA to form a triplex.
Found to occur in nature during instances of recombination and inactivation of specific genes
Potential tool for therapeutic gene inactivation
Explain the structure of RNA
•RNA strands typically several hundred to thousand nucleotides in length
•Only one of two strands of DNA is used as template in RNA synthesis
Explain RNA secondary structure
•although usually single stranded, RNA molecules can form short double-stranded regions
•secondary structure due to complementary base pairing (A to U, C to G)
•RNA double helices are typically right handed (11-12 base pairs per turn)
What are the 4 RNA secondary structures possible?
- Bulge Loop ||>
- Internal Loop ()
- Multibranched Loop +
- Stem-loop 💡
How do viruses self-assemble?
Viruses with a simple structure can self-assemble when genetic material and capsid proteins spontaneously bind to each other
Explain directed assembly in viruses
Complex viruses undergo a process called directed assembly, requiring proteins not part of the virus itself. These noncapsid proteins help with packaging.
Explain the bacterial nucleoid
Bacterial chromosome is found in the nucleoid, not bounded by membrane so the DNA is direct contact with the cytoplasm
Bacterial chromosomal DNA is usually a circular molecule a few million nucleotides in length
Explain the types of genes found in bacterial chromosomes
- Structural gene sequences (encoding proteins) make up most
- Intergenic regions are non transcribed DNA between adjacent genes
How do loop domains form in bacterial chromosomal DNA?
DNA must be compacted about a 1000-fold in order to fit, causing the formation loop domains
What is additional compaction of bacterial chromosomes called?
DNA supercooling, where loop domains get even more compact
What two main enzymes control supercooling in bacteria
- DNA gyrase (topoisomerase II)
•introduced negative supercoils and relaxes positive supercoils - DNA topoisomerase I
•introduced positive supercoils and relaxes negative supercoils
How do eukaryotic genomes vary in size?
Difference in size is not because of extra genes. Accumulation of repetitive DNA sequences is what makes the difference
What is a nucleosome?
Double stranded DNA wrapped around an octamer of four histone proteins (2 copies of each = 8 total)
What is the H1 linker histone?
It binds to linker DNA and nucleosomes
What are the “beads on a string”?
Connected nucleosomes resemble beads on a string (seven-fold reduction of DNA length)
What is the 30 nm fiber?
When nucleosomes associate with each other to form a more compact structure (another 7-fold)
How does the third level of compaction in eukaryotic chromosomes work?
Third level of compaction involves the interaction between the 30 nm fiber and the nuclear matrix, creating radial loops
What are the two parts of the nuclear matrix?
- Nuclear lamina (fibers that line the inner nuclear membrane)
- Internal matrix proteins (connected to nuclear lamina and fills interior of nucleus)
Describe euchromatin
The less condensed regions of chromosomes
Transcriptionally active
Regions where the 30 nm fibers form radial loop domains
Describe heterochromatin
Tightly compacted regions of chromosomes
Transcriptionally inactive
Radial loop domains compacted even further
What are the two types of heterochromatin?
- Constitutive heterochromatin
•regions that are always heterchromatix and permanently inactive with transcription - Facultative heterochromatin
•regions that can interconvert between euchromatin and heterochromatin
What is condensin?
•plays a critical role in condensation
•in cytoplasm during interphase
•binds to chromosomes and compacts the radial loops
What are cohesins?
•plays critical role in sister chromatid alignment
•meet at centromere then degrades
What are the three replication models?
- Conservative model
•both parental strands stay together after DNA replication - Semiconservative model
•double-stranded DNA contains one parental and one daughter strand following replication - Dispersive model
•parental and daughter DNA are interspersed in both strands following replication
Where does bacterial DNA replication start?
•begins at the origin of replication (bacterial chromosomes only have one)
•DNA synthesis proceeds bidirectionally
When does bacterial DNA replication end?
When replication forks meet at the opposite end
What are the three types of DNA sequences that are functionally significant?
- AT-rich region
- DnaA boxes
- GATC methylation sites
What does the DNA helicase do?
Separates the two DNA strands by breaking down the hydrogen bonds between them
What is DNA gyrase’s role in replication?
Travels ahead of the helicase and alleviates any supercoils that form
What is the role of single stranded binding proteins in replication?
Bind to the separated dna strands to keep them apart
How are RNA primers synthesized?
DNA primase
Explain the different DNA polymerases
•DNA Pol I: composed of a single polypeptide, removes RNA primers and replaces with DNA
•DNA Pol III: composed of ten subunits, workhorse of replication
What is the primosome?
When the helicase and primase are bound to each other
What is the replisome?
The primosome associated with two DNA polymerase
How are the leading and lagging strands replicated?
DNA pol III act in concert to replicate leading and lagging strands
