Nucleic Acids synthesis and DNA packaging Flashcards
what are the rules for protein and nucleic acid synthesis?
- There are a limited number of different monomeric building blocks
- Monomers are added one at a time (ATP needed, H2O released)
- Each chain has a specific starting point
- The primary synthetic produce is often modified
what are the 2 types of nucleic acids?
Deoxyribonucleic acid (DNA): C2 attached to an H group
Ribonucleic acid (RNA): C2 attached to an OH group
mRNA function
carries genetic info from DNA in nucleus to the ribosomes in cytoplasm (where proteins are synthesized)
tRNA function
matches the corresponding amino acids to the ribosomal codons - sequences of 3 nucleotides, on the mRNA strand through its anticodon region to the growing peptide chain
rRNA function
forms the core of the ribosome and catalyzes protein synthesis
what are nucleotides and their parts?
nucleotides: the building blocks of nucleic acids (DNA and RNA)
1. Sugar: Deoxyribose or Ribose
2. Nitrogen base
Purines: adenine (A); guanine (G)
Pyrimidines: thymine (T) or uracil (U) for RNA; cytosine (C)
3. Phosphate: joins sugars via phosphodiester bonds
which bases are purines?
Adenine A and Guanine G
which bases are pyrimidines?
Thymine T or Uracil U and Cytosine C
how does the covalent structure differ between RNA and DNA?
- Sugar: RNA - ribose vs DNA - deoxyribose
- One of the 4 major nitrogen bases: RNA - U vs DNA - T
what is the difference between nucleosides and nucleotides?
Nucleoside = sugar + base
Nucleotide = nucleoside + phosphate
A nucleoside is joined to one or more phosphate groups by ester linkages and thus becomes nucleotides
what are the 4 nucleoside units in RNA?
A - Adenosine
G - guanosine
C - cytidine
U - Uridine
what are the 4 nucleoside units in DNA?
Deoxyadenosine
Deoxyguanosine
Deoxycytidine
Thymidine (not necessarily deoxythymidine because T containing nucleotide is rarely found in RNA)
what are the 5 carbons of the sugar all attached to?
C1’ → base
C2- → sugar (ribose or deoxyribose)
C3’ → next nucleotide
C5’ → phosphate
what is an example of a nucleoside and nucleotide?
nucleoside: deoxyguanosine 3’-monophosphate (3’-dGMP)
nucleotide: adenosine 5’-triphosphate (5’-ATP)
what type of bond are between nucleotides?
covalent bonds (phosphodiester bonds)
what type of bonds are between the nitrogen bases?
hydrogen bonds
how do you join nucleotides together?
Covalent bonds through the 5’-phosphate group of one sugar bonds to the 3’-OH group of the next sugar
From 5’ end → 3’ end (3’end is where new nucleotides are added)
what is the 5’ end and 3’end of a nucleic acid?
5’ end: phosphoryl group attached to the 5’C atom of the sugar
3’ end: a free hydroxyl attached to the 3’C of the sugar
what are the functions of nucleotides?
- Phosphate groups hold energy: 3 high energy phosphate bonds (ie. ATP)
ATP → ADP → AMP to release energy - Signaling: ATP → ADP → AMP → cAMP
cAMP signals “hunger” and turns on enzymes that make ATP
who are key people involved in understanding the structure of DNA and what did they discover?
Erwin Chargaff: purines bind to pyrimidines (A-T and C-G)
Rosalind franklin: X-ray diffraction experiments revealed that DNA has the shape of a coiled spring or helix
In 1953, James Watson and Francis Crick deduced that DNA was a double helix
difference between purines and pyrimidines?
Structure: purines have a DOUBLE-ring structure (6-membered ring fused to a 5-member ring); pyrimidines have a SINGLE 6-membered spring structure
Size: purines are larger than pyrimidines
number of hydrogen bonds between the base pairs A-T and C-G?
Adenine - thymine/uracil with 2 hydrogen bonds; guanine - cytosine with 3 hydrogen bonds
nucleosomes and their important facts
Nucleosomes are complexes of DNA and histones (DNA wraps around the outside of the histone octamers to form nucleosomes)
nucleosomes are the basic units of eukaryotic chromosome structure (chromatin)
joined together by linker DNA to which histone H1 binds to → the histone-DNA complex has the appearance of beads on a string
Digestion of the linker DNA yields the nucleosome core particle
Nucleosomes themselves are arranged in a helical array that further compacts the DNA → further folding then generates the chromosome
histones and their structure
small, positively charged proteins associated with eukaryotic DNA that form chromatin
the 8 histones of the core particle are arranged as an octamer composed of a (H3)2(H4)2 tetramer and a pair of (H2A-H2B) dimers
chromatin
Made up of repeating units containing 200 base pairs of DNA and 2 copies each of histones H2A, H2B, H3, and H4
Made of nucleosomes and consists of a segment of DNA wrapped around a core of histone proteins
difference between histones, chromatin, and nucleosomes and what is their level of compaction?
- Histones: the proteins that bind to DNA to aid in its organization
- Nucleosomes: the specific repeating units formed by DNA wrapped around histones → serve as the building blocks of chromatin
- Chromatin: the overall structure formed from DNA and histones → determining how DNA is packaged in the nucleus
what experiment showed that DNA and not proteins is the genetic, heritable material?
Hershey and Chase Experiments
1. used two different isotopes to label the DNA and protein of the T2 phage/viruses
DNA Labeling: used 32P (phosphorus-32) to label the DNA, as DNA contains phosphorus in its backbone
Protein Labeling: used 35S (sulfur-35) to label the protein coat of the virus, since proteins contain sulfur but DNA does not
2. Allowed both types of labeled phages to infect separate cultures of E. coli bacteria –> After the infection, the researchers used a blender to separate the phage coats from the bacterial cell
3. The mixture was then centrifuged to separate the heavier bacterial cells from the lighter phage coats. The bacteria formed a pellet at the bottom of the centrifuge tube, while the phage coats remained in the supernatant
4. found that the radioactivity was associated with the bacterial pellet, indicating that the DNA had entered the bacteria, but the culture infected with 35S-labeled phages, the radioactivity remained in the supernatant, indicating that the protein did not enter the bacterial cells
summary:
T2 viruses: are made entirely of protein and NDA)
–> injecting its genetic material into a bacterium
–> the viral capsule remains attached to the outside of the cell
–> the viruses were allowed to infect E. coli
–> viral heads were sheared off the bacteria and then centrifuged
–> the infected bacteria contained phosphorus but not sulfur
how much do chromatins reduce DNA length by?
chromatins reduce DNA length by 10,000x
How do the charges of histones affect DNA packaging?
Negative phosphates on DNA are attracted to positive histones
What is the significance of histone tails?
They are exposed and the covalent modification of these tails is crucial for regulation of gene expression
How does a nucleoside become a nucleotide and through what type of bonds?
a nucleoside is joined to one or more phosphate groups by ESTER linkages to become nucleotide
describe the directionality of nucleic acid chains
the two ends are different:
5’ end has a phosphoryl group attached to the 5’C of the sugar
3’ end: has a free hydroxyl group OH- attached to the 3’C of the sugar
by convention, how are nucleic acid sequences written?
from left to right in the 5’ to 3’ direction
ie. 5’ - pCpTpA - 3’
or pCTA or CTA
new nucleotides are added onto which end?
3’ end
what are analogs of nucleotides?
chemically modified versions of standard nucleotides that mimic their structure and function but have slight variations that can affect their incorporation into DNA or RNA, interactions with enzymes, or stability
- they are often used in research, diagnostic assays, and medical treatments (CANCER treatment)
What is the “trojan horse” nucleotide substrate?
a nucleotide substrate that refers to a type of nucleotide analog used in drug development (particularly in antiviral and anticancer therapies) where the “trojan horse” nucleotide substrate is
designed to resemble natural nucleotides enough to be incorporated into DNA or RNA by viral or cancerous cells, but once incorporated these analogs act as poisons and disrupt normal nucleic acid synthesis or function –> ultimately killing the cell or inhibiting DNA replication
what are the 4 types of histones?
H2A, H2B, H3, H4
What is chromatin made up of?
repeating units that contain 200 base pairs of DNA and 2 copies of each histone (H2A, H2B, H3, H4)
How are the 8 histones of the core particle arranged?
they form an octamer composed of a (H3)2(H4)2 tetramer and a pair of H2A - H2B dimers
(aka 2 H3 and 2 H4 form a tetramer together, and 2 dimers of H2A - H2B are formed ==> 8 total)
What is histone H1 and its function?
histone H1 binds to the linker DNA (the stretch of DNA that links nucleosomes together) that connects the core nucleosomes together to form the beads on a string conformation
What are the formations that lead from histones –> chromosome?
- short region of DNA double helix
- beads on a string form of chromatin
- chromatin fiber of associated nucleosomes
- chromatin fiber folded into loops
- entire mitotic chromosome
What is the first parity rule?
The percentage of complementary bases are the same (A and T have same percentage; G and C have the same percentage)
