LAST SET OF LECTURES (13-17)

Question 1

what are the two types of nucleic acid

Answer 1

RNA and DNA

Question 2

what are the funtions of nucleic acid

Answer 2

-storage of info
-transfer of info
- expression of genetic info
-CO-ENZYMES: essential parts of many enzymes, and
necessary for their function
-SIGNALING MOLECULES: cAMP
-TRANSFER OF CHEMICAL ENERGY in all cells: i.e. ATP, GTP and ADP.

Question 3

how do nucleic acids hold “the instructions” for the creation of one living organsism

Answer 3

protein
synthesis.

Question 4

How is DNA replicated for cell division

Answer 4

mitosis or
meiosis

Question 5

What makes up a nucletoide (monomer of nucleic acid)

Answer 5

nitrogenous base, sugar pentose, and one or more phosphate group(s)

Question 6

what are the nitrogenous bases that make up nucleotides

Answer 6

Pyrimidines
 1-ring molecule
 Cytosine (has an amino gorup) (both), Thymine (methyl group)
(T in DNA)/Uracil (dbl bonded O) (U in RNA)
Purines
 2-ring molecule
 Adenine ( amino group and HC) (both) and
Guanine (NH and NH2) (both)

CG AND AT

Question 7

what are the sugar backbones in nucleic acids. WHat makes them different?

Answer 7

Deoxyribose and Ribose

The only difference between the sugar in DNA and RNA is that DNA lacks an oxygen
atom on the second carbon of its ring.

Question 8

how do yu differentiate the carbons of the sugar carbons from the attached nitrogenous base?

Answer 8

• the carbons on the sugar ring have a prime (’) after them.
• Therefore, the different carbon is the 2’ carbon and the carbon that sticks up
  is the 5’ carbon.

Question 9

what makes the structural backbone of the nucleic acid

Answer 9

the sugar and phosphate groups of a nucleotide

Question 10

what is a phosphosiester bond

Answer 10

, the phosphate
group of 1 nucleotide
covalently bonds with the sugar
of another nucleotide. This is a dehydration synthesis rx

Question 11

T or F each end of a polynucleotude strand is different

Answer 11

True

 One side ends with a phosphate group
attached to the 5’ carbon.
 The other side ends with a hydroxyl group
attached to the 3’ carbon.
* These are thereby referred to as the 5’ end and
3’ end respectively.

Question 12

nucleic acid codes are always read in the ___ to ___ direction

Answer 12

5’, 3’ (OH)

Question 13

what is the main diff between RNA and DNA

Answer 13

RNA
single stranded.It has one strand of
polynucleotides that
twists around itself.
DNA
double stranded. It has 2 strands of polynucleotides
linked together by hydrogen bonds
between their nitrogenous bases.

Question 14

why is RNA useful ?

Answer 14

RNA is the product of transcription of specific DNA sequences called genes.
Some RNA strands are used
to carry out specific tasks
(e.g. tRNA, rRNA and
ribozymes).
Others are used to determine the
sequence of amino acids that
comprise the primary structure of
a protein (mRNA).

Question 15

recall two types of RNA

Answer 15

mRNA
A complimentary
RNA strand to a gene (in red)
used to make a protein
tRNA
Facilitate the process of
translation during protein
synthesis

Question 16

define ribozymes. How can RNA be ribozymes

Answer 16

Ribozyme: Ribonucleic acid enzyme
 rRNA in the large subunit of the ribosome
catalyzes peptide bond formation during
translation.

RNA can associate with itself in
complementary base-pairing and fold into
more complex conformations.

• This specific folding is what allows RNA to
  serve specific functions in cells such as
  ribozymes.

Question 17

define spliceosomes

Answer 17

 Certain ribozymes called spliceosomes
catalyze reactions during RNA splicing

Question 18

what is particular about the double stranded DNA order?

Answer 18

• Each of DNA’s two
  strands have a 5’
  and a 3’ end.
• The directions of
  each strand are
  inversed relative to
  the other.
• The backbones run
  in opposite 5’ → 3’
  directions.
  THE TWI POLYNUCLETOIDES ARE ANTIPARALLEL

Question 19

how many hydrogen bonds are formed between nitrogebous bases

Answer 19

C and G form 3 H bonds
Thymine and Adenine form 2 H bonds

Question 20

What was determined by A.Hershey and M. Chase

Answer 20

• when bacteriophages (composed of DNA
  and protein), infect bacteria, their DNA
  enters the host bacterial cell.
• but most of their protein did NOT enter
  the host bacterial cell.
• served to prove that DNA is the hereditary
  material.

Question 21

What is Chargaff’s rule?

Answer 21

Since A and T always base-pair
together:
 % of A is equal to the %
of T
Since G and C always base-pair
together:
 % of G is equal to the %
of C
Chargaff’s rule remained unexplained until the discovery of the
double helix structure of DNA.

Question 22

How did Watson, Crick and Franklin’s discovery of the double-stranded nature of DNA explain this rule

Answer 22

The uniform diameter of the double helix
suggested that purines must be paired with
pyrimidines.
-This finding explained Chargaff’s rule.

Watson and Crick hinted that since DNA bases can form pre-determined pairs, one
strand can be used as a template for creating another a built-in replication
mechanism.
DNA replication is semi-conservative.
Each newly formed daughter strand
is formed from part of the original
strand and is partly new (making it
not fully conservative to semiconservative).

Question 23

Why do cells replicate DNA

Answer 23

➢ Growth and development
➢ Tissue Renewal (ex: skin cells, red blood cells)
➢ Germ Cell Production

Question 24

DNA replication is semi conservative. What does this mean?

Answer 24

Semiconservative replication entails the replication of one parental strand to give its complementary strand and the replication of the other parental strand to give its complementary strand; each parental strand then stays with its newly replicated, complementary strand

Question 25

How many chromosomes are in one somatic cell in humans

Answer 25

46

Question 26

How do prokaryotes syntheisze new DNA (BRIEF UNDERSTANDING)

Answer 26

- At the origins of replication, short stretches of DNA that have a specific sequence of nucleotides - proteins that intiiate DNA replication recognize the sequence and attach to the DNA, seperating the two strands and opening at replication "bubble" - Parent DNA will be copied to both direction from the origin at the same time until the whole chromosome is replicated - Each end of a replication bubble has a replication fork. Since replication happens in both direction from the origin, there are one at each end of the bubble - enzymes and other proteins partake in replicating the DNA

Question 27

define replication fork

Answer 27

, a Y-shaped region where the parental strands of DNA are being unwound.

Question 28

what are the DETAILED steps of prokaryote DNA replication (replication factory)

Answer 28

1. Unzipping the double stranded DNA - Helicase (enzyme): unzips the complementary polynucleotide strands at the origin of replication -SSBP (sing-stranded building protein) Adhere to the seperated polynucleotide strands ti prevent reannealing (strands "zipping" back up) 2. Release the tension (Separation of the polynucleotide strands leads to supercoiling in the DNA molecule ahead of the replication fork. ) - Topoisomerase (enzyme) Helps relieve this strain by breaking swiverling and rejoining DNA strands. 3. Synthesizing the new strand - Primase (enzyme) synthesize a primer (short chain of RNA) and uses parental DNA as a template - DNA ploymerase (enzyme) Catalyzes the polymerization of DNA nucleotides 4. Synthesize the new complementary DNA strand - DNA polymerase III (enzyme) Adds complementary DNA nucleotides to the free 3' end of the strand. Complementary DNA strands can only be elongated in the 5' to 3' direction - Sliding clamp Ensures DNA Pol III maintains contact witht he template strand during the polymerization process 5. The fifth step is to remove the RNA primers and replace them with DNA nucleotides - Rnase H (enzyme) Recognizes RNA-DNA hybrid segments and degrades the RNA primer by hydrolyzing its phosphodiester bonds - DNA polymerase I (enzyme) adds DNA nucletoides to any exposed 3' ends on the leading and lagging strands 6. Gluing of the lagging strands together - DNA ligase (enzyme) attaches adjacent fragments of DNA on the newly synthesized strands to make a continuous polynucleotide strand

Question 29

T or F DNA Polymerase can only add nucleotides to the 3’ end of an existing polynucleotide strand

Answer 29

T

Question 30

Because DNA pol III can only add nucleotides to an open 3’ end, what is the implications on the two replication forks: ➢Leading strand ➢Lagging strand (Each replication fork has a leading strand and a lagging strand)

Answer 30

* Along one template strand, DNA Pol III can synthesize a complementary strand continuously in the mandatory 5’ → 3’ direction. This new DNA strand is called the leading strand. * To elongate the other new strand in the mandatory 5’ to 3’ direction, DNA pol III must work along the other template strand in the direction away from the replication fork. The new DNA strand synthesized in this way is called the lagging strand.

Question 31

What is pertitnent about a leading strand (STEP 4 replication factory)

Answer 31

* Only one RNA primer is required for each leading strand * it will be synthesized continuously in same the direction of the replication fork’s movement. * As the parent DNA unwinds, the opening space in front of the leading strand allows continuous adding of nucleotides to an open 3’ end.

Question 32

what is pertienent about a lagging strand? (STEP 4 replication factory)

Answer 32

* the lagging strand is synthesized discontinuously, as a series of segments. * Lagging strands grow in the opposite direction from the movement of the replication fork. * They are produced in short segments called Okazaki Fragments as the parent template strand is slowly more and more exposed. * DNA Polymerases can only add nucleotides to the 3’ end of a polynucleotide strand which has and exposed hydroxyl group. * So even though the replication fork is moving away from the origin, the lagging strand can only grow by Okazaki fragments in the direction towards the origin of replication

Question 33

T or F not every okazaki fragment requires a new primer

Answer 33

F Each Okazaki fragment requires a new primer.

Question 34

What is the DNA replication complex

Answer 34

The various proteins that participate in DNA replication actually form a single large complex, a “DNA replication machine.” Many protein-protein interactions facilitate the efficiency of this complex.

Question 35

how does the DNA replication complex move

Answer 35

The DNA replication complex may not move along the DNA; rather, the DNA may move through the complex during the replication process.

Question 36

What is the difference between dna replication in eukaryotes and prokaryotes

Answer 36

* Eukaryotic DNA contains many more base pairs: (6 billion in humans) compared to prokaryotic DNA (~ 5 million). * Replication therefore takes longer than for prokaryotes (a few hours in humans). * Eukaryotic DNA is in multiple linear strands unlike the circular DNA of prokaryotes. * The ends of these linear strands are vulnerable to damage and are therefore protected by telomeres (DNA extensions).

Question 37

what are telomeres

Answer 37

* Telomeres are short repeated DNA sequences (TTAGGG) at both ends of a linear DNA strand which contain no genes.

Question 38

t or f, telomeres do not get shorter with each replication event

Answer 38

False, they do * The end of the molecule on each lagging strand is left un-replicated and the exposed section on the parent strand breaks off.

Question 39

what are the two protective functions of telomeres

Answer 39

➢ Specific associated proteins prevent the activation of DNA damage signaling. ➢ Provides some protection against the organism’s genes shortening.

Question 40

true or false, telomeres acts as a buffer and completely prevent the erosion of near the ends of chromosome

Answer 40

false * Telomeres acts as a buffer. However, telomeres do not completely prevent the erosion of genes near the ends of chromosomes; they merely postpone it.

Question 41

what is telomerase

Answer 41

Telomerase is an enzyme which can extend the length of telomeres.

Question 42

where is telomerase found

Answer 42

➢ Germ cells (undergo meiosis to make gametes) ➢ Cells within embryos/fetuses ➢ Certain tumor cells

Question 43

fun fact: Stem cells in adults don’t have telomerase, so the ends of their DNA get shorter with time.

Question 44

what is an advantage of normal shortening of telomerase

Answer 44

Normal shortening of telomeres may protect organisms from cancer by limiting the number of divisions that somatic cells can undergo. Many cancer cells seem capable of unlimited cell division, as do immortal strains of cultured cells.