Student's Study Guide for Lesson Nineteen Identification and Structure of Genomic Information by Dr Jamie Love 2002 - 2010

Sir Archibald Garrod suggested that some human diseases were caused by "______ errors of metabolism".

Beadle and Tatum, irradiated Neurospora with X-rays and produced "_______" that would die unless their medium was supplemented with B6.
A particular ____ codes for the synthesis of one particular enzyme.
The "one gene - one ______ hypothesis" and it is the foundation of molecular genetics but becomes "one gene - one _______".

Frederick Griffith mixed dead (heat killed) lethal bacteria with live harmless bacteria and injected the mixture into mice. The mice died! These "transformed" bacteria remained lethal and passed the lethal trait to their offspring, therefore, this "transforming material" is the _______ material. Oswald Avery lysed (broke open) the lethal bacteria and separated the bacterial components into its ____ - lipids, polysaccharides, proteins and nucleic acids. He discovered that only the nucleic acids ___________ the harmless bacteria into lethal ones. He discovered that "RNA-free" solution of nucleic acids was still able to transform harmless bacteria into lethal bacteria so Avery proved that ___ is the genetic material!

James Watson and Francis Crick discovered the _________ of DNA (using important data collected by Rosalind Parkers) and published their discovery in 1953.

All genetic information is contained in nucleic acids and these are made of three types of _________ …

1. Sugars - actually a five-______ sugar called a "pentose".
2. Inorganic phosphate - just PO₄ acting as a ______.
3. Bases - sometimes described as "nitrogenous bases".

Carbon 1 (C1) is where the ____ is attached. Carbon 2 (C2) tells you if it is a ribose or deoxyribose. In deoxyribose "de oxy" is missing. Carbon 3 (C3) is the point of attachment for more ___________. Carbon 4 (C4) completes the ____ via an oxygen which bridges to the carbon 1 (C1). Carbon 5 (C5) hangs away from the ring and is the point of attachment for its ____________.

Phosphates and sugars make up the "________" of DNA and RNA.
They form a chain that runs from a ________ on the previous molecule, to C3 (the right foot and hip) through C_ (the right shoulder) to C5 (the right hand holding a mitten for grabbing the ___ molecule).

There are two types of nitrogenous _____.

Pyrimidines are a single _________ ring of carbons and nitrogens. Pyrimidine

Purines are ______ rings made of a pyrimidine with a pentagon added. Purine

We refer to the carbon 1 in sugar as "carbon one _____" and the carbon in the bases simply as "carbon one".
We use the abbreviation ' (a little dash of an apostrophe) to signify prime so the sugar runs 3' to 5' with the 4' shoulder in between.

DNA has ____ different bases (and abbreviations).

Adenine (A) and guanine (G) are _____ which are distinguished and identified by the oxygen (O) or ammonia (NH₂) attached at specific positions.

Adenine

Guanine

Thymine (T) and cytosine (C) are __________ and distinguished and identified by the oxygen (O), ammonia (NH₂) or methyl (CH₃) attached at specific positions.

Thymine

Cytosine

RNA (ribonucleic acid) does not have _______. Instead, it has the base ______ (U).

Uracil

Sugar's carbon one (1') is the site where bases are attached.
Any base (A, G, C, T or U) can attach to either sugar (ribose or deoxyribose) to form a "double molecule" called a __________.

The bond linking these molecules (sugar and base) is called a _________ ____.

If the sugar is ribose we have a ______________ but if the sugar is deoxyribose we have a deoxyribonucleoside.

Here (below) are the four ribonucleosides. Notice that they all have a hydroxyl group (OH) at the ___ position.

_________	_______
_________	________

Below are the four deoxyribonucleosides. Notice that they do NOT have a ________ group (OH) at the C2' position.

_____adenosine	Deoxy_________
Deoxyguanosine	Deoxycytidine

_________ can be attached to the sugar though the 5' carbon to give a "triple molecule" of phosphate, sugar and base called a __________.
[Nucleoside stops at sugar but nucleotide takes a phosphate.]
Nucleotides are the fundamental "units" of the larger molecules of DNA and RNA.

Here are the four ribonucleotides (made of ribose with a _________ at the 5' carbon and one of the four possible bases on the 1' carbon).

_________	_________
_________	__________

Here are the four _________________ (made of deoxyribose with a phosphate at the 5' carbon and one of the four possible bases on the 1' carbon).

______________	________________
______________	_______________

Nucleoside diphosphates have a ____ of phosphates (PO₃-PO₄) and nucleoside triphosphates have a triplet of phosphates (PO₃-PO₃-PO₄) attached to the 5' carbon of the sugar.

Adenosine triphosphate (___) is often called the "power molecule" of life because it is the most common source of chemical energy for living things! ATP is made of an ______ base attached to a ribose via ___ (adenosine) with a ____________ (PO3-PO3-PO4) attached at the sugar's 5'. These extra phosphates (the second and third phosphates) are linked to each other by very energetic bonds called _____________ linkages. ("Pyro" is Latin for "____".) Large amounts of energy are released when ATP is hydrolyzed. ["Hydrolyzed" means when _____ (hydro) is used to lyse (brake) it.] All nucleoside triphosphates are high energy and ______ but once they lose their second and third phosphates (ATP->ADP + P ->AMP + P) the remaining nucleoside monophosphate is very stable and can no longer provide any energy.

DNA is deoxyribonucleic ____. RNA is ribonucleic ____.
A molecule that releases hydrogens is said to be an acid (by definition) and by releasing the hydrogens it takes on a negative charge (by the laws of electrostatics).
The __________ in DNA and RNA cause these molecules to have a (net) negative charge (and the reason they are acids).

Nucleic acids are polymers (chains) of nucleotides called _______________. This drawing shows the double bonds of the phosphates that were missing in the previous drawings. It also shows, in red, the negative charges near the __________. This linkage is between the __ of one sugar and the __ of another sugar with its one phosphate (PO4-1) acting as the linker. One of the phosphate's four oxygens is attached to the 5' carbon via an _____ bond. [An ester is a part of a molecule that has one double-bonded _____ attached only to the central atom, phosphorous in this case, and the other oxygen linking the central (phosphorous) atom to a different atom (the C5' in this case) via an oxygen.] The other oxygen from the PO4-1 forms an ester bond with the ___ of the previous sugar. The two sugars are tied together by a ______________ ____ - a bond made using two ester with a phosphorous in the middle. Polymers of nucleic acids (DNA and RNA) are __________ joined by phosphodiester bonds.

A stick diagram reminds us of the zigzag backbone of the sugar-phosphates. The terminal OH, represented on the 3' extreme, is the ___ OH in the backbone. Only one phosphate is free (at the _ end).

A simpler representation is to type the sequence with the phosphates and bases abbreviated, all in a straight line. It shows all the phosphates including the one at the 5' end. The other side of the molecule does NOT have a phosphate so it must have a hydroxyl (OH) there.

Accept that, "sequences of bases are ______ written such that the left side is the 5' end (with a dangling phosphate) and the right hand side is the 3' end (with the OH group).

DNA is usually composed of a ____ of strands!

Chargaff discovered that the DNA from any particular cell has ___ amounts purines and pyrimidines.
The amount of adenine (A) equals that amount of _______ (T) and the amount of guanine (G) equals the amount of cytosine (C). This is called "Chargaff's rule".

DNA is a ______-helix composed of two strands of polynucleotides. DNA is like a ladder with the sugar-phosphate backbone of the two polynucleotides as the supporting _____ of the ladder and with the bases as the rungs (steps). The bases forming the _____ are bound to each other by "hydrogen bonds". Hydrogen bonds are relatively ____ bonds but when you have several (many) working together they can hold things together. The hydrogens on the bases cause hydrogen bonds form between a specific purine and a specific pyrimidine. Adenine (A) and thymine (T) form ___ hydrogen bonds between them. Guanine (G) and cytosine (C) form _____ hydrogen bonds between them. Each nucleotide is attached to the next nucleotide by a _________ group (PO4) linking the 5' carbon (5'C) of one sugar to the 3' carbon (3'C) of the next sugar.

Notice that the strand on the right is in an _______ orientation to the one on the left. We say the stands are "____________" meaning they run in opposite directions. All double-stranded DNA is antiparallel (because that is the only way to match the bonding made by the bases). Adenine cannot form its two hydrogen bonds with thymine unless thymine is __________ "upside down". The same is true for the guanine-cytosine bonds.

The phosphodiester bonds and sugars have a restricted orientation that cause them to ____ a small amount in order to line up with the opposite, complementary strand. The result is that the two strands wrap around each other in a double _____. The diameter of this double-helix is only __ angstroms. (An angstrom, is roughly the diameter of a hydrogen atom and precisely 10-10 of a _____.) Adjacent bases are separated by 3.4 ________ along the helix axis and ____ 36 degrees from each other. The helical structure repeats after ___ nucleotides. (10 nucleotides x 36o per nucleotide interval = 360o per interval) So there are 34 angstroms per ________.

The molecule on the left is ______ right-handed DNA. The second image is a ____-handed helix and is not the normal, natural form of DNA. Notice how its twists the _____ way. DNA has "grooves" (indented areas) running along the ______ of the helix caused by the bulky sugars and phosphates on the exterior and the less bulky bases inside. One groove is _______ than the other so they are called the "minor groove" and "major groove".

Right-handed DNA (Correct)

Left-handed DNA (WRONG!)