Exam 1 Flashcards
Lecture 1-7
what are the steps to convert DNA to protein?
DNA undergoes transcription where it is converted to pre-mRNA, RNA processing then converts the pre-mRNA into mRNA that is transported to the cytoplasm where it is translated into an amino acid chain
replication vs transcription vs translation vs RNA splicing
replication: DNA -> DNA
transcription: DNA -> RNA
translation: RNA -> protein
RNA splicing: pre-mRNA -> RNA
what are the 4 levels of DNA winding to form chromosomes?
- nucleosomes: DNA wrapped tightly around an octamer of histone proteins
- nucleosomes then wind into a 30-nm fiber
- the fiber anchors to the nuclear matrix to then form radial loop domains
- loops are wound into final chromosome form
how do histone proteins bind to DNA?
histone proteins contain many positively charged amino acids that bind electrostatically to the negatively charged phosphates on the DNA backbone, 2 of each of the 4 histones form the octamer and H1 histones bind nucleosomes together
nucleotide vs nucleoside
nucleotide: base + sugar + phosphate
(adenosine mono/di/triphosphate)
nucleoside: base + sugar
(adenosine/deoxyadenosine)
DNA vs RNA
DNA: contains deoxyribose (one OH, one H), thymine, double stranded, 5’ to 3’
RNA: contains ribose (two OH), uracil, single stranded, 5’ to 3’
what kind of bonds make up a DNA strand?
bases face inward and form hydrogen bonds with their complementary base, phosphates of one bind to the sugar of the other to form a phosphodiester bond as the backbone
how many hydrogen bonds form between each base pairing?
A-T forms 2 hydrogen bonds, G-C forms 3 hydrogen bonds
what is Chargaff’s rule?
adenine is similar to thymine and guanine is similar to cytosine, this is because A/G (purines) bind to T/C (pyrimidines) in order to ensure a consistent diameter of the helix
how does acetylation/methylation alter how active a DNA strand is?
acetylated histones have weaker interactions with the DNA, allowing for a higher rate of transcription to take place
what is the C-value paradox?
the idea that there is no correlation between genome size and organism complexity
where are the bacterial and eukaryotic chromosomes located in the cell?
bacterial: nucleoid
eukaryotic: nucleus
telomeres vs centromeres vs kinetochores
telomere: a region of repetitive DNA sequence at the end of chromosomes to keep them from shortening
centromeres: site of chromosome segregation during meiosis and mitosis
kinetochores: area that links centromere to spindle during meiosis and mitosis
euchromatin vs heterochromatin
euchromatin: less condensed region of chromosome, transcriptionally active
heterochromatin: tightly condensed region of chromosome, transcriptionally inactive
what is the function of the Shine-Delgarno sequence in prokaryotes?
it pairs with regions of rRNA to position the ribosome correctly to start translation, facilitates mRNA binding to ribosome
which type of bond is created by ribosomes?
peptide bonds
what are the four levels or proteins in structures?A
primary: an amino acid sequence
secondary: amino acid sequence folded into an a helix or B-sheet
tertiary: polypeptide chain with one or more secondary structures attached
quaternary: two or more polypeptides combined in a protein
what does alternative splicing allow eukaryotes to do?
produce more than one gene product from one gene
what does it mean for an amino acid to be degenerate?
there is more than one codon that specifies that single amino acid
what are ribosomes composed of?
rRNA subunits (large and small) and proteins
how can you identify what amino acid is attached to a tRNAs anticodon?
tRNAs anticodon is 3’ to 5’ and is the opposite of the amino acid pair
3’ GGC 5’
CCG = proline
C-terminus vs N-terminus
N-terminus: the first amino acid in a polypeptide chain that has an exposed amino group
C-terminus: last amino acid that has an exposed carboxyl group
what is true of bacterial promoters?
site for RNA polymerase binding that signals the beginning of transcription, cis-acting DNA sequences
what are the three types of genetic transfer?
conjugation: transfer of DNA from one bacterium to another following direct cell-to cell contact through sex pilus, relaxosome initiates this transfer
transduction: transfer DNA between bacteria cells via a bacteriophage
transformation: process by which a bacterium will take up extracellular DNA released by dead bacteria
what are competent cells and what are the different types?
competent cells are cells that contain fertility factor and that can participate in transformation, F+ cells can transfer DNA to F- cells
what are plasmids?
small circular pieces of DNA, separate from the bacterial chromosome
what are the parts of the COVID virus?
envelope protein (E): guides assembly and release
nucleocapsid protein (N): inner surrounding layer that protects RNA
ACE2 receptors: acts as the recognition site that interacts with COVID virions to initiate their entry into cells
what role does RNA polymerase play in transcription?
RNA polymerase sigma factor recognizes and binds to the promoter on the DNA sequence and forms a short open complex within the enzyme, forming a RNA strand, RNA polymerase moves 3’ to 5’, RNA is synthesized 5’ to 3’
what role does DNA polymerase III play in replication?
DNA Polymerase III synthesizes new DNA using the RNA primers on both leading and lagging strands
what role does DNA polymerase I play in replication?
removes the primers on the lagging strand a fills in the gaps between okazaki fragments with DNA
what role does DNA ligase play in replication?
joins okazaki fragments together after the DNA polymerase I has already filled gaps
what roles does primase play in replication?
makes RNA primers, one on leading strand and many on lagging strand
what role does helicase play in replication?
unwinds the DNA double helix by breaking hydrogen bonds between the bases
what role does topoisomerase II (DNA gyrase) play in replication?
relaxes supercoiling in front of the helicase that unwinds it, promotes negative supercoiling
what role do single-stranded DNA binding proteins play in replication?
keeps the two DNA strands separated until after they are copied
what role do B-clamps play in replication?
keeps the DNA polymerase III attached to the DNA strand
what does topoisomerase I do?
relaxes negative supercoils by breaking one strand and rotating the DNA
what does reverse transcriptase do?
makes a DNA copy from RNA
what role does telomerase play in replication?
telomerase contains protein and RNA, the RNA is complementary to the DNA sequence of the telomeric repeat, allowing telomerase to bind to the 3’ overhang which allows room for the DNA sequence to continue to the very end of the chromosome
what role does TFIID play in transcription?
recognizes the TATA box of the core promoter
what role does the mediator play in transcription?
mediator appears to regulate the ability of TFIIH to phosphorylate CTD of RNA pol II and phosphorylate the CTD itself, plays a pivotal role in the switch between transcriptional initiation and elongation
what role does the splicosome play in transcription?
spliceosome is composed of several subunits known as snRNPs, each snRNP contains small nuclear RNA and a set of proteins, remove introns and covalently link exons of RNA
what role does aminoacyl-tRNA synthetase play in translation?
attach amino acids to tRNAs
what occurs at each site of the ribosome during translation?
aminoacyl site: aminoacyl-tRNA binds to the mRNA
peptidyl site: tRNA recognizes and binds to its corresponding codon in the ribosome and the tRNA transfers the appropriate amino acid to the end of the growing amino acid chain
exit site: the discharged tRNA exits the ribosome after it has released its amino acid into the growing polypeptide chain
what are the three steps of pre-mRNA post-translational processing to produce mature mRNA?
addition of 5’ cap, addition of 3’ poly A tail, and excision of introns
how can you tell where on DNA transcription of mRNA has started and stopped? where would translation start and stop on the mRNA?
transcription starts at the start of the mRNA
translation starts at AUG and stops at UAG, UAG does not code for any amino acids
transposons vs retrotransposons
transposon: the TE is removed from original site and transferred to a new site by a “cut and paste” mechanism
retrotransposon: TE is transcribed into RNA, then reverse transcriptase makes a second copy in DNA
what does the enzyme DICER do?
recognizes double stranded RNA and cuts it into short double stranded pieces, forming siRNAs
what role does TFIIH play in transcription?
phosphorylates the C-terminal domain of RNA polymerase to initiate elongation
what role does a poly-A tail play in transcription?
poly-A tail is a string of adenine nucleotides at the 3’ ends of mature mRNA, this tail is important for mRNA stability and translation
what function do tRNAfmet (in prokaryotes) or tRNAimet (in eukaryotes) have?
they are always used to decode the first amino acid codon in all proteins synthesized
excessive innate immune responses are a potential problem with mRNA vaccines, this problem can be reduced by thorough removal of contaminating ________?
double stranded RNA
