Chapter 6.1 Flashcards
(42 cards)
What are the two forms of nucleic acids in the eukaryotes?
- Deoxyribonucleic acid (DNA)
- Ribonucleic acid (RNA)
What is a nucleoside?
A nucleoside is a 5 carbon sugar (pentose) bonded at Carbon 1 to a nitrogenous base by a covalent bond.
What is a nucleotide?
A nucleotide is a nucleoside with one or more phosphates attached to Carbon 5 of the sugar. Often these molecules are named for the nitrogenous base and the number of phosphates (ATP is adenosine triphosphate!). Nucleotides are the building blocks of DNA.
Why are nucleotides high energy molecules?
Almost all of the energy stored in nucleotides comes from the phosphate groups. The presence of negatively charged phosphates next to one another results in large repulsion and high potential energy locked in the molecule.
What is the difference between ribose and deoxyribose? (know structure and numbering)
Ribose is a 5 carbon saccharide. Deoxyribose is very similar, it just has an -H instead of an -OH on carbon 2.
What are the names of the 5 nitrogenous bases of which DNA and RNA are collectively built?
- Adenine
- Guanine
- Cytosine
- Thymine - DNA only
- Uracil - RNA only
Describe the backbone of DNA.
The backbone of DNA is composed of alternating sugar and phosphate groups. These sugars and phosphates are connected with 3’-5’ phosphodiester bonds. That is to say, a phosphate group links the 3’ carbon of one sugar to the 5’ carbon of the next sugar through a phosphate bond.
Remember, phosphate has a negative charge, so DNA and RNA strands are actually pretty negatively charged overall.
Describe the polarity of DNA.
DNA as a long linear molecule that is considered by the enzymes that work on it to “start” with the 5’ end and “end” with the 3’ end. Because of the one way nature of DNA enzyme activity, DNA is said to have polarity. 5’ end has OH or phoshphate and 3’ end has free OH
How do we write the base sequence of a DNA or RNA strand?
DNA base sequences are written from 5’ to 3’ (left to right) using one letter abbreviations for the nitrogenous bases present. For example, 5’-ATG-3’ would be how you write the base sequence for a DNA molecule consisting of those three nucleotides. If you are given a DNA base sequence that is written 3’ to 5’, it might not be a bad idea to flip it so it’s easier to compare to other base sequences.
Is DNA double or single stranded
Double stranded
Generally speaking, is RNA double or single stranded?
Single stranded
What does it mean when we say the two strands of DNA are antiparallel?
Remember, the 5’ to 3’ directionality is very important for the enzymes interacting with DNA. Antiparallel refers to the fact that the 5’ to 3’ direction for one strand is opposite of the other one.
What are the two classes of the nitrogenous bases that make up DNA?
- Purines: Adenine and Guanine
- Pyrimidines: Cytosine, Uracil, and Thymine
What are the nitrogenous bases? Aromatic or no?
The nitrogenous bases are a collection of nitrogen containing aromatic bases. These bases make up the interior fundamental language of DNA.
What are the main components of a DNA strand?
- Phosphate groups in the backbone
- Deoxyriboses in the backbone
- Nitrogenous bases in the middle.
What is the Watson-Crick model of DNA structure?
- The two strands of DNA are antiparallel. When one strand has polarity 5’ to 3’ down the page, the other has 5’ to 3’ up the page.
- The sugar Phosphate backbone is on the outside of the helix and the nitrogenous bases are on the inside
- The bases only pair with complementary bases via hydrogen bonds. A always goes with T and C always goes with G
- Because of the specific pairing, the amount of A’s is always equal to the amount of T’s nad the amount of C’s is always equal to the amount of G’s
What are major and minor grooves?
Major and minor grooves are grooves in DNA that arise as a result of the double helix. These grooves are used as binding sites by proteins
What does it mean to denature DNA?
Denaturing DNA is when you disrupt the hydrogen bonds holding the bases together and the two strands of DNA separate.
What does it mean to reanneal DNA?
Reannealing DNA is when DNA is brought back together after it has been denatured.
What is probe DNA?
Probe DNA is a strand of DNA with a known sequence. It is used in various testing and laboratory applications to learn about your mystery DNA.
What is a nucleosome?
A nucleosome is the name for a histone with DNA wrapped around it.
What are the two types of chromatin?
- Heterochromatin
- Euchromatin
What is Heterochromatin?
Heterochromatin refers to DNA that is wrapped tightly around histones. Heterochromatin is dark when viewed under microscope and is transcriptionally silent, meaning RNA polymerase cannot interact with Heterchromatin to make mRNA.
What is Euchromatin?
Euchromatin refers to DNA that is wrapped loosely around histones. Euchromatin is light when viewed under microscope and is transcriptionally active, meaning RNA polymerase can interact with euchromatin to make mRNA.
