Nucleic Acids synthesis and DNA packaging

Question 1

what are the rules for protein and nucleic acid synthesis?

Answer 1

1. There are a limited number of different monomeric building blocks
2. Monomers are added one at a time (ATP needed, H2O released)
3. Each chain has a specific starting point
4. The primary synthetic produce is often modified

Question 2

what are the 2 types of nucleic acids?

Answer 2

Deoxyribonucleic acid (DNA): C2 attached to an H group
Ribonucleic acid (RNA): C2 attached to an OH group

Question 3

mRNA function

Answer 3

carries genetic info from DNA in nucleus to the ribosomes in cytoplasm (where proteins are synthesized)

Question 4

tRNA function

Answer 4

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

Question 5

rRNA function

Answer 5

forms the core of the ribosome and catalyzes protein synthesis

Question 6

what are nucleotides and their parts?

Answer 6

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

Question 7

which bases are purines?

Answer 7

Adenine A and Guanine G

Question 8

which bases are pyrimidines?

Answer 8

Thymine T or Uracil U and Cytosine C

Question 9

how does the covalent structure differ between RNA and DNA?

Answer 9

1. Sugar: RNA - ribose vs DNA - deoxyribose
2. One of the 4 major nitrogen bases: RNA - U vs DNA - T

Question 10

what is the difference between nucleosides and nucleotides?

Answer 10

Nucleoside = sugar + base
Nucleotide = nucleoside + phosphate
A nucleoside is joined to one or more phosphate groups by ester linkages and thus becomes nucleotides

Question 11

what are the 4 nucleoside units in RNA?

Answer 11

A - Adenosine
G - guanosine
C - cytidine
U - Uridine

Question 12

what are the 4 nucleoside units in DNA?

Answer 12

Deoxyadenosine
Deoxyguanosine
Deoxycytidine
Thymidine (not necessarily deoxythymidine because T containing nucleotide is rarely found in RNA)

Question 13

what are the 5 carbons of the sugar all attached to?

Answer 13

C1’ → base
C2- → sugar (ribose or deoxyribose)
C3’ → next nucleotide
C5’ → phosphate

Question 14

what is an example of a nucleoside and nucleotide?

Answer 14

nucleoside: deoxyguanosine 3’-monophosphate (3’-dGMP)
nucleotide: adenosine 5’-triphosphate (5’-ATP)

Question 15

what type of bond are between nucleotides?

Answer 15

covalent bonds (phosphodiester bonds)

Question 16

what type of bonds are between the nitrogen bases?

Answer 16

hydrogen bonds

Question 17

how do you join nucleotides together?

Answer 17

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)

Question 18

what is the 5’ end and 3’end of a nucleic acid?

Answer 18

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

Question 19

what are the functions of nucleotides?

Answer 19

1. Phosphate groups hold energy: 3 high energy phosphate bonds (ie. ATP)
   ATP → ADP → AMP to release energy
2. Signaling: ATP → ADP → AMP → cAMP
   cAMP signals “hunger” and turns on enzymes that make ATP

Question 20

who are key people involved in understanding the structure of DNA and what did they discover?

Answer 20

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

Question 21

difference between purines and pyrimidines?

Answer 21

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

Question 22

number of hydrogen bonds between the base pairs A-T and C-G?

Answer 22

Adenine - thymine/uracil with 2 hydrogen bonds; guanine - cytosine with 3 hydrogen bonds

Question 23

nucleosomes and their important facts

Answer 23

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

Question 24

histones and their structure

Answer 24

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

Question 25

chromatin

Answer 25

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

Question 26

difference between histones, chromatin, and nucleosomes and what is their level of compaction?

Answer 26

1. Histones: the proteins that bind to DNA to aid in its organization
2. Nucleosomes: the specific repeating units formed by DNA wrapped around histones → serve as the building blocks of chromatin
3. Chromatin: the overall structure formed from DNA and histones → determining how DNA is packaged in the nucleus

Question 27

what experiment showed that DNA and not proteins is the genetic, heritable material?

Answer 27

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

Question 28

how much do chromatins reduce DNA length by?

Answer 28

chromatins reduce DNA length by 10,000x

Question 29

How do the charges of histones affect DNA packaging?

Answer 29

Negative phosphates on DNA are attracted to positive histones

Question 30

What is the significance of histone tails?

Answer 30

They are exposed and the covalent modification of these tails is crucial for regulation of gene expression

Question 31

How does a nucleoside become a nucleotide and through what type of bonds?

Answer 31

a nucleoside is joined to one or more phosphate groups by ESTER linkages to become nucleotide

Question 32

describe the directionality of nucleic acid chains

Answer 32

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

Question 33

by convention, how are nucleic acid sequences written?

Answer 33

from left to right in the 5’ to 3’ direction
ie. 5’ - pCpTpA - 3’
or pCTA or CTA

Question 34

new nucleotides are added onto which end?

Answer 34

3’ end

Question 35

what are analogs of nucleotides?

Answer 35

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)

Question 36

What is the “trojan horse” nucleotide substrate?

Answer 36

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

Question 37

what are the 4 types of histones?

Answer 37

H2A, H2B, H3, H4

Question 38

What is chromatin made up of?

Answer 38

repeating units that contain 200 base pairs of DNA and 2 copies of each histone (H2A, H2B, H3, H4)

Question 39

How are the 8 histones of the core particle arranged?

Answer 39

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)

Question 40

What is histone H1 and its function?

Answer 40

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

Question 41

What are the formations that lead from histones –> chromosome?

Answer 41

1. short region of DNA double helix
2. beads on a string form of chromatin
3. chromatin fiber of associated nucleosomes
4. chromatin fiber folded into loops
5. entire mitotic chromosome

Question 42

What is the first parity rule?

Answer 42

The percentage of complementary bases are the same (A and T have same percentage; G and C have the same percentage)