Midterm 3 (20-27) - BIS 2A

DNA =

deoxyribose + phosphates + four bases

purines

adenine and guanine

pyrimidines

cytosine, uracil, thymine

Ribose has:

four OH groups.

Deoxyribose has:

three OH groups.

In DNA, deoxyribose connects:

5' to 3'.

nucleoside

ribose and base, no phosphate

nucleotide

ribose, nitrogenous base, phosphates

Bases connect to the ___ OH group.

1'

lesson from 100 years of DNA chemistry (-1950)

components and covalent connectivity of DNA

Chargaff's rule

percentage of G always equaled C and percentage of A always equaled T

Why is the constant ration of A to T (and G to C) in plant, animal, prokaryotic, and fungal genomes really significant?
a) It means the fraction of bases that are purines always balances the fraction
that are pyrimidines
b) It is what defines the difference between DNA and RNA
c) It suggests that A is somehow “paired” with T and G is paired with C
d) It suggests that purines pair with purines and pyrimidines pair with pyrimidines

c)

Watson-Crick model told us about:

replication, coding, repair, and recombination in DNA.

Watson-Crick model

DNA is a helix w/ width of purine plus a pyrimidine and a sugar phosphate backbone on the outside

features of Watson-Crick model

- two strands, anti-parallel
- H bonding between strands, A-T and G-C always base paired
- base pairs stacked = plates parallel

A-T and G-C make the ___________, with ___________________.

same shape, same length and width

DNA redundancy

each strand has equivalent information, this is essential to function as genetic material

Why is information on each DNA strand redundant?

Base pairing rules what is inserted - two identical copies are made, sequence can be copied again and again

If one strand is 5' TGCCCTAT 3', the complementary strand is:
a) 5’ TATCCCGT 3’
b) 5’ ATAGGGCA 3’
c) 5’ ACGGGATA 3’
d) 5’ TGCCCTAT 3’

b)

DNA and RNA read, written, and synthesized:

5' to 3'.

DNA could be single stranded and only transiently double-stranded during replication, but:

this has a high mutation rate (viruses).

How does DNA 'pay' to elongate its 3' end?

By releasing free phosphates: dNTP > dNMP + PPi

dNTPs can only be added to:

a preexisting 3' OH.

DNA synthesis always needs a:

primer.

Lagging strand synthesis requires:

constant addition of RNA-based primers.

Leading strands run:

long and continuously.

Lagging strands are:

short patches that are made and then joined later.

Okazaki fragments

the short sequences of DNA nucleotides made to be joined later (lagging strand)

DNA polymerase I

removes RNA primers and replaces them with DNA nucelotides

DNA polymerase III

synthesizes daughter strands

helicase

separates parent DNA strands

ligase

contacts Okazaki fragments

primase

generates RNA primers

telomerase

lengthens telomeres by adding many copies of a short repetitive sequence to the ends of chromosomes

topoisomerase

reduces super-coiling of DNA by cutting the backbone, allowing helices to operate

Synthesis of the leading strand is simple, because:

only adding complementary bases is needed.

Synthesis of the lagging strand is complicated because:

RNA primers constantly need to be added to follow the add to 3' rule.

For the leading strand, a ___ is needed at the origin of replication.

primer

All replication proteins are:

bounded together.

clamp loader

loads on clamps - helps keep replicative polymerase on its template

When helicase unwinds DNA, there are two __________ generated.

replication forks

How many DNA polymerases would be in this picture, and where?

How many primers would be in this picture and how many primases?

When does DNA polymerase III drop off the template?

When it meets the 5' end of the primer

Where does DNA polymerase I start replicating?

3' OH ends

DNA polymerase I is:

a polymerase and a exonuclease

DNA polymerase I replaces RNA with:

DNA.

What is an issue at the end of lagging strand synthesis on linear chromosomes?

Each time, the chromosome will get smaller as it replicates, losing DNA.

Do somatic cells have telomerase?

No, only embryonic and gremlin cells do

Telomerase is a ______________.

reverse transcriptase - its a DNA polymerase that reads an RNA template.

What replication-related problem is solved by telomerase?
a) The inability of the cell to initiate DNA synthesis without building on a pre-existing “primer”.
b) The inability of the cell to terminate replication of a circular template.
c) The requirement for a “promoter” to initiate DNA synthesis

What is circled in green?

The phosphate group

What is circled in blue?

The sugar

What is circled in red?

The nitrogenous base

What kind of bio molecule is DNA?

Nucleic acid

What are DNA monomers called?

Nucleotides

Carbon atoms in a sugar are labeled using:

1', 2', 3', 4', 5'

Which carbon atom in the sugar is attached to the nitrogenous base?

The 1' carbon

Which carbon atom in the sugar is attached to the phosphate group?

The 5' carbon

glycosidic bond

the bond between the 1' carbon and the nitrogenous base in a nucleotide

Is the glycosidic bond polar or non-polar?

Polar (C-N electronegativity)

What is the purpose of DNA?

Storing genetic information

What part of the DNA stores genetic information?

The nitrogenous base

What four nitrogenous bases are in DNA?

Adenine, guanine, cytosine, and thymine

What four nitrogenous bases are in RNA?

Adenine, guanine, cytosine, and uracil

What is the difference between purines and pyrimidines?

Purines have two rings while pyrimidines have one ring

What is the difference between the 5' and 3' end of a pentose sugar?

The 3' end has a hydroxyl group attached and the 5' end has a phosphate group attached

How many hydrogen bonds occur between adenine and thymine?

Two

How many hydrogen bonds occur between guanine and cytosine?

Three

DNA is ____________.

double-stranded

DNA runs __________.

anti-parallel

What is the name of the bond that connects two nucleotides?

Phosphodiester bond

What atoms are involved in the phosphodiester bond?

Oxygen and phosphorous

Is the phosphodiester bond polar or non-polar?

Polar (O-P electronegativity)

Two nucleic acid motors are joined by:

coupling an exergonic reaction with an endergonic reaction.

exergonic reaction in joining nucleic acid monomers

hydrolysis of the phosphoanhydride bond between phosphate groups

endergonic reaction in joining nucleic acid monomers

3' -OH group and phosphate attached to 5' (= phosphodiester bond)

Do nucleic acids have a charge?

DNA and RNA are negatively charged (because of the phosphate groups)

Where does DNA replication begin?

At the origin of replication (ORI)

What enzyme binds to the ORI?

Helicase

Why might eukaryotic organisms have more than one origin of replication?

So that DNA replication can occur in a shorter amount of time (DNA is large)Wh

What interaction holds DNA strands together?

Hydrogen bonds

What does the blue triangle represent?

Helicase

When helicase is unwinding DNA, what potential issue could arise?

The DNA can become over-twisted in front and under-twisted behind

What enzyme can resolve supercoiling in DNA?

Topoisomerase

What direction does DNA polymerase III move along the template strand?

3' to 5'

What direction does DNA polymerase III synthesize the daughter strand?

5' to 3'

What enzyme informs DNA pol III where to begin daughter strand synthesis?

Primase

How does the cell obtain the same strands of DNA every time DNA is replicated?

A-T and G-C, base-stacking and base-pairing, ways to find errorsQ

Which would be the consequence of DNA replication without ligase?
A) It would result in lots of ‘nicks’ or breaks in the DNA sugar-phosphate backbone.
B) Only the leading strand would be replicated, as the cell would be unable to replicate the lagging strand.
C) Replication would stall once all the nucleotides had been used up in the cell.
D) Replication would be unable to start.
E) The cell would need to repair multiple incorrectly paired bases between the template and newly synthesized strands of the DNA.

A)

The phosphodiester bond between the 5' -PO4 and 3' -OH is not formed in the Okazaki fragment. Which enzyme is inhibited or malfunctioning?
A) DNA polymerase III
B) Primase
C) Helicase
D) DNA Polymerase I
E) Ligase

E)

A piece of double-stranded DNA has 30% A. What will be the % G?
A) 30%
B) 40%
C) 20%
D) 70%
E) Indeterminate from the given information.

C)

The nitrogenous base is linked to the ribose or deoxyribose sugar via a __________ at the _ carbon.
A) Glycosidic bond, 5’
B) Peptide bond, 2’
C) Hydrogen bond, 4’
D) Phosphoanhydride bond, 3’
E) Phosphodiester bond, 1’
F) None of the above

F)

How so mutations occur? (1)

Through replication errors

Replication errors can be:

mistakes or replication of a damaged template.

How do mutations occur? (2)

Through erroneous repair of DNA damage

Cancer is caused by:

somatic mutations.

risk factors for cancer

genotoxin exposure, age

Replicative DNA polymerase produces a mutation:

1/10^6 times

DNA polymerase proofreading

enzyme's groove must fit the base pair or it will start over