Flashcards in Biochemistry Lecture 1 - Genetic Material Deck (34):
What is a nucleoside?
A pentose sugar and nitrogenous base without phosphate groups attached to the 5' carbon.
What is a nucleotide?
Consists of a pentose sugar, nitrogenous base, and any number of phosphate groups (nonspecific as to the # of phosphates).
What is a dNTP?
Stands for deoxynucleoSIDE triphosphate. Consists of a pentose sugar, nitrogenous base, and three phosphate groups. They serve as activated precursors to DNA synthesis.
What is an oligonucleotide?
An oligonucleotide are groups of 5-50 linked nucleotides. They can also be called PRIMERS in some contexts.
What is positive supercoiling?
When DNA is twisted around its axis in the same direction as the double helix twist.
What is negative supercoiling?
When DNA is twisted around its axis in the opposite direction as the double helix twist.
What does "relaxed" DNA referred to?
DNA that is not supercoiled.
Describe right vs. left-handed DNA.
Right-handed: DNA helix is twisted clockwise when looking at the 5' to 3' direction.
Left-handed: DNA helix is twisted counter-clockwise when looking at the 5' to 3' direction.
What is topoisomerase?
An enzyme that catalyzes changes in the supercoiling of DNA.
Describe the attributes of Z-DNA.
It is left handed.
It has stretches of alternating purines and pyrimidines.
It reduces the number of negative supercoils.
It has unclear biological consequences but possibly promotes recombination and may play a role in gene expression.
Describe what DNA bending is and examples of what causes it.
DNA bending is when DNA is inherently bent. Caused by: protein interactions (ex. histones), or adenine repeats. Bending can bring distant DNA sites closer together.
What is a pseudogen?
A pseudogen is a genetic sequence located near a functional family that resembles that functional family but is non-coding due to an earlier mutation of the gene.
What is a processed pseudogen?
A processed pseudogen is a pseudogen that was created from RNA (reverse transcript) is inserted back into the genome.
What are proviruses?
DNA copies of retroviruses that have been inserted into the chromosome. Humans have approx. 1,000 of these in the genome.
Describe transposable elements.
These are sequences that can insert copies of themselves in to new genomic locations. Two main classes exist.
What is a SSR?
Simple Sequence Repeats (SSRs) include microsatellites and minisatellites. These repeated sequences are present at the same locations in human chromosomes, but the number of repeated sequences is polymorphic.
What are SINEs?
A dispersed repeat element. Stands for Short Interspersed Repeat Elements. They make up ~10% of human genome. They aren't tandemly repeated. Ex. Alu family includes 1,000,000 members with ~280 nucleotide repeat units and a total size of 1-5 kb.
What are LINEs?
A dispersed repeat element. Stands for Long Interspersed Repeat Elements. Makes up ~20% of human genome. Made up of ~500 nucleotide repeat units. Ex. L1 family.
They are made of 2-5 base pair repeat units and a total size of ~100 base pairs.
Describe minisatellites AKA variable number tandem repeats (VNTRs).
They are SSRs with 14-50 base pair repeat units. These are not transcribed to RNA (they're nonfunctional).
What is a satellite sequence? Where are they found on human chromosomes?
They're 5-100 base pair repeat units (total size several mega-bases) which form a satellite band when separated from DNA on a density gradient. They're found at centromeres or telomeres.
What are telomeres?
Found at the ends of all human chromosomes. Sequence is TTAGGG and are organized in tandem arrays of ~1000 to 1700 copies. They protect coding sequences from being cut off during replication. Known as the "mitotic clock," these indicate senescence (loss of ability to divide, grow). They're synthesized by telomerase (enzyme), a reverse transcriptase. Note: this protein enzyme is typically not expressed in normal cells but is active in tumors.
What is a nucleosome?
A nucleosome is a DNA/Histone complex. They are further ordered into chromatin fibers.
Name the purines.
Name the pyrimidines.
What keeps complimentary DNA strands together?
H-bonding between complimentary bases.
What is the difference between Topo I and Topo II?
Topo I cuts only one strand of the DNA, Topo II cuts both.
Name two anti-tumor drugs that poison DNA topoisomerases.
Campothecin inactivates Topo I, m-AMSA inhibits Topo II. Dovorubin inhibits Topo II indirectly.
What percentage of the human genome codes for proteins?
What is the longest gene known?
Dystrophin gene (Duchenne muscular dystrophy) is 200kb (most range from 1-100 kb)
Are SSRs polymorphic?
What is a SNP?
Single nucleotide polymorphism.
What is the L1 family an example of?