Chapter 4 Flashcards
Nucleotides are built from what 3 things?
- A sugar (Deoxyribose for DNA & ribose for RNA)
- An aromatic base (nitrogenous base)
- 1-3 phosphate grouo
G & A are what?
Purines
C, T, & U are what?
Pyrimidines
Nucleosides contain what?
A sugar & a base (purines or pyrimidines)
Nucleotides contain what?
A sugar, base (purine or pyrimidine), & 1-3 phosphate groups where if it has 3 its called nucleoside triphosphate (NTP where N is a purine or pyrimidine)
The __________ & __________ make up the backbone of DNA
Sugar & phosphate
Nucleotides in DNA chain are covalently lined by _____________ bonds between the 3’ hydroxyl group of one dexoribose and the 5’ phosphate group of the next dexoribose
Phosphodiester bonds
In a polynucleotide, the end of the chain with a free 5’ phosphate group is written _______ with other nucleotides written in the 5’ to 3’ direction
First
In DNA H-bonded pair always consist of a __________ plus a _________
Purine, pyrimidine so we can actually calculate the # of purines if we know the # of pyrimidines (A+G = T+ C)
Annealing (hybridization)
The binding of two complementary strand of DNA into a double-stranded structure
Denaturation (melting)
The separation of strands
DNA strand are always antiparallel & the _____ end is always written first
5’
___________ is used to stabilize prokaryotes chromosomes
DNA gyrase
What is the telomere sequence that is found at the end of DNA?
5’-TTAGGG-3’
Intergenic DNA
Are composed of noncoding DNA
Single nucleotide polymorphisms (SNPS)
Are essentially mutations, they are single nucleotide changes (predicted that there is one for every 1,000 base pair) & usually occur in noncoding regions of the genome)
Single nucleotide polymorphisms (SNPS)
Are essentially mutations, they are single nucleotide changes (predicted that there is one for every 1,000 base pair) & usually occur in noncoding regions of the genome) & they can lead to specific traits & phenotypes like how some ppl can’t taste PTC & others can
Copy number variations (CNVs)
Are structural variations in the genome that lead to different copies of DNA sections
Tandem repeats
Where short sequences of nucleotides are repeated one right after the other from as little as 3 to over 100 times
Synonyms
Two or more codons coding for the same amino acids & are degenerate (each codon only specifies one amino acid)
Is DNA replicat onserative, semiconservative, or disperative?
Semi-conservative (The old strand is used to make the new strand)
Helicase enzyme uses the energy of ______- hydrolysis to break the DNA strand for replication
ATP
Polymerization occurs in the __________ direction
5’ to 3’
DNA polymerase requires a __________ to make a copy strand (daughter strand)
Template
DNA polymerase requires a _______ to start replication
Primer
Replication forks grow away from the ________ in both directions & each fork contains a leading strand & a lagging strand
Origin
Replication of the leading strand is ___________ and leads into the replication fork while replication of the lagging strand is ___________ resulting in Okazaki fragments
Continuous, discontinuous
Eventually, all RNA primers are replaced by DNA & the fragments are joined by an enzyme called ________ ligase
DNA ligase
DNA polymerase 3
Is responsible for the super fast accurate elongation of the leading strand & also has proofreading functions
Exonuclease
“cutting a nucleic acid chain at the end”
Endonuclease
Will cut a polypeptide acid chain in the middle of the chain, usually at a particular sequence
What are the two types of endonucleases?
- Repair enzymes
- Restriction enzymes
Repair enzymes
Removes chemically damaged DNA from the chian
Restriction enzyme
Are endonucleases found in bacteria & are made to destroy the DNA of infecting virus thus restricting the host range of the virus
Telomeres
Are disposable repeats at end of chromosomes & are consumed 7 shorten during cell division
Genetic mutations
Are any alterations of the DNA sequence of an organism’s genome
Ionizing radiation (such as X-rays, alpha particles, and gamma rays) can cause _______ breaks
DNA
Mutagen
Any compound that can cause mutations (& biological agents like viruses, transposons, etc can also cause mutations& arent mutagens)
What are the type of mutations?
- Point mutations
- Insertions
- Deletions
- Inversions
- Amplifications
- Translocation & rearrangements
- Loss of heterozygosity
Point mutations
Are single base pair substitutions (ex. A in place of G)
What are the different types of point mutations
- Transitions
- Transversions
Transitions
Substitution of a pyrimidine for another pyrimidine or substitution of a purine for another purine
What are the types of point mutations?
- Missense mutation
- Nonsense mutation
- Silent mutation
Missense mutation
This causes one amino acid to be replaced with a different amino acid
Nonsense mutation
A stop codon replaces a regular codon & prematurely shortens the protein
Silent mutation
A codon is changed into a new codon for the same amino acid, so there is no change in the protein’s amino acid sequence
Insertion
Refers to the addition of one or more extra nucleotides into the DNA sequence
Deletion
The removal of nucleotides from the sequence
What two types of mutations cause a frame shift in the sequence?
Insertion & deletion
Frameshift mutations
Mutations that cause a change in the reading frame
An inversion
When a segment of a chromosome is reversed end to end (The chromosome undergoes breakage and rearrangement within itself)
Insertions, deletions,, & inversion can be caused by _____________
Transposons
Chromosome amplification
When a segment of a chromosome is duplicated
Translocations
Results when recombination occurs between nonhomologous chromosomes
Transposons
Mobile genetic elements in the genomes (genetic mobility)
Loss of heterozygosity
When a deletion occurs in a diploid organism & deletes the normal copy of the gene & the only remaining copy is the mutated version
Hemizygous
When there is only one gene copy in the diploid organism
Haploinsufficiency
A diploid organism has only a single - functional copy of a gene and this single copy is not enough to support a normal state
Inborn errors of metabolism
Are a group of genetic diseases that involve disorders of metabolism
What are the different types of DNA repair mechanisms?
- Direct reversal
- Homology- dependent repair
- Excisionm repair
- Post-replication repair
- Double-stranded break repair
- Homologous recombination
Direct reversal
DNA damages that are directly repaired
Homology-dependent repair
Using the second strand (undamaged strand) of the DNA double-strand to make a complementary repair on the other strand
What are the two types of homology-dependent repair?
- Excision repair
- Post-replication repair
Excision repair
Occurs before DNA replication & removes defective bases or nucleotides & replacing them
Post-Replication repair
Are repairs that happen before & during DNA replication & use the mismatch repair pathway to target mismatched base pairs that slipped through the DNA proof reading process
Double-stranded break repair (DSB)
Its caused by reactive oxygen species, ionizing radiation, UV light or chemical agents & its goal is reattach and fuse chromosomes that have come apart because of it
What are the two ways that a double-strand repair can work?
- Homologous recombination
- Nonhomologous recombination
Homologous recombination
Process where one sister chromatid can help repair a DSB in the other
Nonhomologous end joining
Process of just reconnecting the broken chromosomes at the end
mRNA (coding RNA)
Carries genetic information to the ribosome where it can be translated into proteins each unique polypeptide is created based on the codon on the mRNA
Transfer RNA (tRNA) (non-coding RNA)
Is responsible for translating the genetic code & carries amino acids from the cytoplasm to the ribosome to be added to a growing protein
Ribosomal RNA (rRNA) (non-coding RNA)
Are the major components of the ribosome
RNA polymerase 1 transcribes most _______
rRNA
RNA polymerase 2 transcribe ___________
hnRNA (which results in mRNA), most snRNA, & some miRNA
RNA polymerase 3 transcribe ________
tRNA, long ncRNA, siRNA, some miRNA, & some rRNA
Translation
Is the synthesis of polypeptides according to the amino acid sequence dictated by the sequence of codons in mRNA
Wobble Hypothesis
States that the first two codon-anticodon pairs obey normal base pairing rules, but the 3rd position is more flexible which is why there is smaller numbers in tRNA
What are the most common wobble base pairs?
- G-U
- I-U
- I-A
- I-C
Amino acid activation (tRNA loading)
A process where two high energy phosphate bonds are hydrolyzed to provide the energy to attach an amino acid to its tRNA molecule
What are the 3 steps in the amino acid activation process?
- An amino acid is attached to AMP to form aminoacyl AMP
- The pyrophosphate leaving group is hydrolyzed to 2 orthophosphate
- tRNA loading, an unfavorable reaction is driven forward by the destruction of the high energy aminoacyl - AMP bond created in step 1
Aminoacyl-tRNA synthetase enzymes
Are used to attach the appropriate amino acid to each tRNA molecule
What are the two main functions that amino acid activation serves?
- Specific & accurate amino acid delivery
- Thermodynamic activation of the amino acid
What are the binding site in the ribsome?
- A site - where each new tRNA delivers its amino acid
- P site- where the growing polypeptide chain is located during translation
- E site- where a now empty tRNA sits prior to its release from the ribosome
What are the binding site in the ribsome?
- A site - where each new tRNA delivers its amino acid
- P site- where the growing polypeptide chain is located during translation
- E site- where a now empty tRNA sits prior to its release from the ribosome
A —> P —> E
What are the main differences between eukaryotic & prokaryotic translation?
The ribosome is larger & has different components than the prokaryotic ribosome, the mRNA must be processed before it can be translated, & the N-terminal amino acid is different
Cap independent translation
A eukaryote starting translation in the middle of an mRNA molecule (without the requirement of the 5’ cap of the mRNA)
Regulation of gene expression occurs where?
In transcription
What are the 3 most commonly used way to regulate gene expression?
DNA methylation, chromatin remodeling, & RNA interference
What are the two ways the DNA methylation turns off eukaryotic gene expression?
- Methylation physically blocks the gene from transcriptional proteins
- Certain proteins bind methylated Cp5 groups & recuit chromatin remodeling proteins that change the winding of DNA around histones
Gene imprinting
When only one allele of a gene is expressed
Regulation of _____________ is the primary method of regulation of gene expression in prokaryotes
Transcription
Anabolic enzymes whose transcription is inhibited in the presence of an excess amount of products are __________
Repressible
Catabolic enzymes whose transcription can be stimulated b the abundance of a substrate are called ___________
Inducible enzymes
The Lac Operon is __________ since the enzymes it codes for are part of lactose catabolism
Inducible
