Chapter 13 Notes

Question 1

What is DNA?

Answer 1

A chain (polymer) of nucleotides
-each nucleotide is made of a sugar (ribose), a phosphate group, and a base

Question 2

What are the bases of DNA? What is important to know about hydrogen bonds in DNA?

Answer 2

Purine (Adenine, Guanine): 2 rings
Pyrimidine (Cytosine, Thymine): 1 ring
-some are hydrogen bond acceptors (-O=C+): cytosine & thymine
-others are hydrogen bond donators (C+ = -O - - - H - N): Nitrogen bonded to a carbon

Question 3

What are you referring to when referring to a prime? Where is the phosphate group attached to?

Answer 3

The carbon within a ribose
- 1’, 2’, 3’, 4’, 5’
-attached to 5’ carbon

Question 4

What does a DNA polymer contain?

Answer 4

(1) a sugar-phosphate backbone
(2) a series (sequences) of bases

Question 5

What is important to know about the sequence of a DNA strand?

Answer 5

The sequence determines the identity of the DNA strand
-A DNA strand has a polarity & a sequence

Question 6

Who helped us understand the structure of DNA?

Answer 6

-Erwin Chargaff & colleagues collected data about nucleotide content in DNA of various species (realized that Adenine & thymine are similar and Guanine & Cytosine are similar)
-Rosalind Franklin was about to obtain an X-ray diffraction picture of a DNA sampl. Watson & Crick solved the structure of DNA

Question 7

What does 1/h and 1/p mean in the structure of DNA?

Answer 7

-1/h: where h is the height of each base pair along the helix
-1/p: where p is the pitch of the helix

Question 8

What is the pitch of the helix?

Answer 8

The distance along the axis that one turn makes
- 34 A^degrees, distance/turn

Question 9

What is important to know about hydrogen bonds?

Answer 9

They form within the structure of DNA, between bases on opposite strands
-they are not set in stone, different arrangements are possible

Question 10

What is the Watson-Crick base pairing theory?

Answer 10

-base pairs are obligatory double-stranded DNA
— non Watson-Crick basepairing is possible, but not in double stranded DNA

Question 11

What is important to know about B-DNA?

Answer 11

-The pitch is 34 A^degree, with 10 base pairs per turn
-its physiologically, meaning its more physiologically relevant to us compared to A-DNA
-the major and minor grooves within the DNA are more prominent

Question 12

What structure is similar to A-DNA?

Answer 12

Double-stranded RNA

Question 13

What has to happen to express genes or copy DNA?

Answer 13

DNA is folded/packaged, meaning you have to unpack the DNA

Question 14

What is the difference between the modes of DNA replication: conservative vs semiconservative?

Answer 14

Conservative: does not require DNA melting
-one daughter cell gets parental DNA, the other gets the synthesized DNA
Semiconservative: ripping DNA apart all at once
-one base at a time, needs a lot of energy

Question 15

What is known as genetic fingerprinting?

Answer 15

The Polymerase Chain Reaction (PCR)
-for genetic finger printing, some information regarding the sequence of DNA must be known

Question 16

Why are two PCR primers designed?

Answer 16

They’re designed in order to replicate some of the DNA that does NOT encode proteins

Question 17

Why is PCR used?

Answer 17

To obtain large amounts of DNA fragments, each resulting fragments lies between two primers

Question 18

What do restriction enzymes do?

Answer 18

They can cut DNA at specific sequences, usually palindromic sequences

Question 19

What is a palindromic sequence?

Answer 19

Reading the same sequence from front to back, back to front (if 5’—3’ is the same as 3’—5’)

Question 20

What happens to a circular plasmid when it is cut with restriction enzymes?

Answer 20

It is cut but either of them separately or both
-the fragments are run on an agarose gel
-the markers then indicate the fragments length and approximate positions of the cut sites on the plasmid

Question 21

DNA manipulation: can we use restriction enzymes to swap DNA fragments?

Answer 21

Bacteria can be engineered to harbor and express a gene of interest.
-strategy was used by Genetech in the mid 1980s to synthesize insulin

Question 22

The central dogma of molecular biology- how are genes expressed through DNA

Answer 22

DNA contains the genetic information, leads to transcription of RNA

Question 23

The central dogma of molecular biology- how are genes expressed through RNA?

Answer 23

Functions in catalytic and structural capacities in cellular processes
-RNA serves as a template, catalyst, and structural “scaffolding” in peptide bond formation during translation

Question 24

The central dogma of molecular biology- how are genes expressed through proteins?

Answer 24

Responsible for most of the cellular functions: catalysis, structure, import/export, nutrient metabolism

Question 25

What does protein synthesis consist of?

Answer 25

Repeated information of a covalent bond between two amino acids
-amino acids are the building block of proteins/proteins are the polymers of amino acids

Question 26

What is peptide bond formation?

Answer 26

A condensation reaction catalyzed by the ribosome
-peptide bonds are also called amide bonds, which means each covalent bond in protein synthesis are amide bonds

Question 27

What are DNA and RNA strand?

Answer 27

They are complementary to each other
-the complementary strands run in the opposite polarity

Question 28

How does a DNA react in an agarose gel?

Answer 28

If DNA is (-) then it will run to (+)