Lecture Exam 1 Flashcards
What is the central dogma of molecular biology?
DNA–>RNA–>Protein
How has our conception of the central dogma changed over the years?
We now know that there are reverse processes that happen along with the forward processes (Replication, Transcription, Translation)
Nucleotide
basic building block of the nucleic acids, DNA and RNA
Base
molecule that accepts a proton when dissolved in water
DNA Strand
complementary base paired, double strand of nucleic acids that holds all of our genetic information
Double Helix
the typical structure of a DNA molecule in which the two complimentary polynucleotide strands are wound around each other with base-pairing between the strands
Histone
one of a small group of abundunt, highly conserved proteins around which DNA wraps to form nucleosomes, structures that represent the most fundamental level of chromatin packing
Nucleosome
beadlike structural unit of a eukaryotic chromosome composed of a short length of DNA wrapped around an octameric core of histone proteins
Chromosome
long, thread-like structure composed of DNA and proteins that carry the genetic information for an organism becomes visible as a distinct entity when a plant or animal cell prepares to divide
Chromatin
complex of DNA and proteins that make up the chromosomes in an eukaryotic cell
How are nucleosomes moved in the DNA in order to make way for transcription?
Remodeling complexes move histones (nucleosomes) out of the way in order to make way for transcription
What are some examples of histone tail modifications and the enzymes that make the modification?
-Acetylation: adds an acetyl group using the enzyme HAT
-Methylation: adds a methyl group using the enzyme PRC2 to add it. HDAC removes it
-Phosphorylation: adding or removing phosphates using PP
How do modifications to histone tails affect DNA structure and access to the genome?
-Histone modifications regulate chromatin structure and the accessibility of certain regions of the genome
-Requires energy to move the histone and uncoil the DNA that is needing to be replicated
What is DNA topology?
The nature of the supercoiling of a double stranded DNA molecule
What is DNA supercoiling?
-winding up of DNA in a positive (overwound) or negative (underwound) direction
-facilitates compaction of chromosomes
-assists in replication and transcription by opening the double helix slightly
What are topoisomerases and what are the general mechanisms?
-Topoisomerases cleave DNA by cutting opposite strands in a staggered fashion (Catalytic Cycle)
-Mechanism: cuts opposite strands in a staggered fashion, lets DNA through, closes back up (ligation)
Type I vs. Type II Topoisomerases?
-Type I A: strand passage/ 5’ DNA cleavage
-Type I B and C: controlled rotation/ 3’ DNA cleavage
-Type 2 A and B: strand passage/ 5’ DNA cleavage
How does the DNA polymerase copy DNA (directionality, does it need a primer)?
-DNA polymerase reads the DNA in a 3’ to 5’ direction and lays down nucleotides in the 5’ to 3’ direction
-Primers are required for DNA polymerase to know where to begin replication
Replication Origin
nucleotide sequence at which DNA replication is initiated
Leading Strand
at the replication fork, the DNA strand that is made by the continuous synthesis in the 5’ to 3’ direction
Lagging Strand
at the replication fork, the DNA strand that is made discontinuously in short fragments (Okazaki fragments) that are later joined together to form one continuous strand
DNA Helicase
“unzips” DNA; forms replication fork
RNA Primase
makes short RNA primers from a DNA template
Ligase
seals nicks
Okazaki Fragments
short length of DNA, including an RNA primer that are made on the lagging strand during DNA replication. Following primer removal, fragments are rapidly joined together by DNA ligase to form a continuous strand
What does telomerase do?
Telomerase is an enzyme that elongates telomeres, synthesizing the repetitive nucleotide sequences found at the end of eukaryotic chromosomes
What are some examples of DNA damage?
-Depurination: lost the purine base from nucleotide; could lead to a deletion in the strand
-Deamination: uracil is added to the DNA molecule
-Thymine DImer: UV radiation causes thymine dimers to stick together (skin cancer)
What are some examples of DNA repair mechanisms?
-Mismatch Repair: mechanism for recognizing and correcting incorrectly paired nucleotides
-Nonhomologous End Joining: an error-prone mechanism for repairing double strand breaks in DNA by rejoining the two broken ends; often results in a loss of information at the site of repair; results in the loss of DNA sequence
-Homologous Recombination: can repair breaks flawlessly; uses an undamaged, duplicated, or homologous chromosome to guide the repair; no loss of nucleotides
What are some key proteins involved in transcription?
-RNA polymerase: has 3 types that all transcribe different genes
-RNA Polymerase I: most rRNA genes
-RNA Polymerase II: all protein-coding genes, miRNA genes, other noncoding RNA
-RNA Polymerase III: tRNA genes, 5S rRNA gene, genes for other small RNA
-Transcription Factors: control the rate of transcription
-Promoter
-Activator
-Repressor
What are some key differences between RNA polymerase and DNA polymerase?
-DNA polymerase: replicates DNA and makes it into a copy of itself with proofreading capabilities
-RNA polymerase: turns the DNA into a RNA transcript and does not have proofreading capabilities
mRNA
messenger RNA; code for proteins
rRNA
ribosomal RNA; form the core of the ribosomes structure and catalyze protein synthesis
tRNA
transfer RNA; serve as adapters between mRNA and amino acids during protein synthesis
Transcription Factor
a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequencce
Intron
non coding regions that are removed during splicing
Exon
part that is expressed; are stitched together after the introns are cleaved
What are some main differences between eukaryotic and prokaryotic transcription and translation?
-Eukaryotic: transcribe, cap, poly-a tail, splice, export
-Prokaryotic: transcribe, translate, protein; transcription and translation can happen simultanously
What is the gentic code?
3 letter codons correspond to a specific amino acid
Reading Frame
read 3 letters at a time then move on to the next 3 letters to determine what protein it forms
Ribosome
large, macromolecule complex, composed of RNAs and proteins, that translates a mRNA into a polypeptide chain
tRNA Synthtase
enzymes that will grab tRNA amino acids
A/P/E sites
transcript enter–>A site–>P site–>E site–> then the protein is ejected
Polysistronic
prokaryotes
Monocistronic
Eukaryotic; codes for one protein at a time
Polysomes
may be multiple ribosomes working together to make a protein
Proteasomes
large protein machine that degrades proteins that are damaged, misfolded, or no longer needed by the cell; its target protein are marked for destruction primarily by the attachment of a short chain of ubiquitin
What is alternative splicing?
-The production of different mRNAs (and proteins) from the same gene by splicing its RNA transcript in different ways
-You do not have to stitch exons back together each times splicing takes place
What are the levels of regulation of gene expression?
- Transcription Control: DNA being told what RNA gets made
- RNA processing Control: controls what RNA is processed
- mRNA processing control: controls what mRNA gets transported
- Translation control: how much mRNA gets transcribed
- Degradation of mRNA
- Protein Degradation Control
- Protein Activity Control: when is the protein turned on/off
What are repressors, activators, and enhancers in gene expression?
-Repressors: proteins that turn off or reduce gene expression
-Activators: a protein that turns on the genes
-Enhancers: enhances the rate of transcription
How do methylation and histone modifications influence gene expression?
-CpG sites (where Cytosine is 5’ to Guanine) are where methylation can occur
-Patterns of modifications are influencing the traits
-Heritability can influence the epigenome (diseases, smoking, exercise can all effect your offspring)
How does RNA-induced silencing work (miRNA or RNAi)?
miRNA binds to RISC (RNA silencing complex) when there is an extensive match between the small single strand of miRNA and the single strand of mRNA
What are Prader-Willi and ANgelman syndromes? How does gene silencing affect the function of the genes involved and cause disease?
-Both occur in the same region of the genome due to X-inactivation/ gene silencing
-Prader-Willi: insatiable hunger that leads to obesity
-Mom’s copy of X is silenced, dad’s copy is used but broken
-Angelman Syndrome: developmental delays;uncontrollable smiling
-Mom’s copy of X is used but broken, dads copy is off but is fine
What is X-inactivation?
when one copy of a x chromosome is silenced resulting in it being inactive
