Week 1 Flashcards
Nucleic acids are found in the following 3 locations in a human cell:
Explain fundamentals of nucleic acids
nucleus, chloroplasts, mitochondria
What is the purpose of nucleic acids?
Explain fundamentals of nucleic acids
to store and express genetic info
What is the central dogma?
Explain the central dogma of molecular bio
flow of information from DNA to RNA to protein
What is transcription?
Explain the central dogma of molecular bio
DNA to RNA
What is translation?
Explain the central dogma of molecular bio
RNA to protein
What is replication?
Explain the central dogma of molecular bio
When DNA replicates itself
What is reverse transcription, and when is it used?
Explain the central dogma of molecular bio
RNA to DNA. It is used in the PCR technique and by viruses
What is the difference between nucleotides and nucleosides?
Describe the structure, properties, and forms of DNA
Nucleotides are the building blocks of DNA (composed of nitrogenous base, sugar, and phosphate group). NucleoSIDEs (just nitrogenous base plus sugar)
State the order of structure of building DNA
Describe the structure, properties, and forms of DNA
Nucleoside –> Nucleotide –> Nucleic Acids –> DNA
What is the significance of a phosphodiester bond in regards to DNA/RNA?
Describe the structure, properties, and forms of DNA
It is responsible for stablizing the backbone of the structure
What is Chargaff rule?
Describe the structure, properties, and forms of DNA
states the amount of purines is equal to pyridimines
What type of bond links the sugar and nitrogenous base?
Describe the structure, properties, and forms of DNA
N-Glycosidic linkage
How many hydrogen bonds link adenine and thymine?
Describe the structure, properties, and forms of DNA
2
How many hydrogen bonds link cysteine and guanine?
Describe the structure, properties, and forms of DNA
3
What charge is a histone and why is this significant?
Assess the histones
it is positive and since DNA is negatively charged, they can interact to form chromatin
What is a nucleosome?
a section of DNA wrapped around a group of proteins (like a histone)
What are the five classes of histones?
Assess the histones
H1, H2A, H2B, H3, H4
Explain the organization of DNA into chromosomes.
Explain the organization of DNA into the chromosomes
DNA –> “bead on a string” nucleosomes –> 30nm chromatin –> chromosome extended form –> chromosome condensed –> paird metaphase chromosome
What is Tm (melting temperature)?
It is the temperature at which 1/2 of the DNA is unwinded
What are the forms of DNA?
Describe the structure, properties, and forms of DNA
B form (most popular), A form, Z form
What is B form DNA?
Describe the structure, properties, and forms of DNA
most common form of DNA. Double-stranded, right-handed, 10 bps per turn
What is A form DNA?
Describe the structure, properties, and forms of DNA
dehydrated B form DNA, right-handed, 11 bps per turn, 20 degree twist
What is Z form DNA?
Describe the structure, properties, and forms of DNA
left-handed, 12 bps per turn
Transitions between which two forms of DNA is crucial for gene expression?
Describe the structure, properties, and forms of DNA
B and Z
What must be modified for gene expression?
Histone modification (like methylation)
This process weakens the DNA-histone interactions and makes DNA accessible to factors needed for transcription.
Lysine acetylation
This process is catalyzed by histone acetyltransferases (HATs) and is important for transcription activation
Histone acetylation
This type of chromatin is densely packed and is genetically inactive.
Heterochromatin
mRNA accounts for what percent of total RNA?
5%
Describe what monocistronic is and how it relates to RNA.
Eukaryotic RNA is monocistronic meaning it only codes for one gene. This is opposite of prokaryotic RNA which is polycistronic.
How many subunits does the prokaryotic RNA poly have and name them.
5 subunits. 2 alpha, 1 beta, 1 beta prime, 1 omega
Which subunits of pro RNA pol are responsible for enzyme assembly?
alpha and omega
Which subunit of pro RNA pol are responsible for template binding?
beta prime
Which subunits of pro RNA pol are responsible for 5’ to 3’ polymerase activity?
beta
What is the holoenzyme?
it is the core enzyme plus the sigma subunit. together this makes the pro RNA pol
What is the name of the subunit responsible for the RNA polymerase recognizing the promoter?
the sigma factor
In prokaryotes, what are the names of the promoter regions of the DNA strand?
Pribnow box, -35 sequence
What is the name of the enzyme which is responsible for uncoiling the supercoiled DNA during transcription?
DNA topoisomerase
Which direction does transcription occur?
5’ to 3’
In regards to prokaryotes, describe the differences between Rho dependent/independent termination.
Rho dependent is when a Rho factor binds to the rut site on the RNA. Rho independent utilizes a hairpin loop with a string of uracil residues (week A/U bonds)
Name the 3 distinct type of eukaryotic RNA polymerases and their function.
- RNA Polymerase I (rRNA)
- RNA Polymerase II (mRNA)
- RNA Polymerase III (tRNA)
In eukaryotes, what is the name of the promoter region for RNA Polymerase II?
TATA box
This is required for initiation of transcription, recruitment of RNA pol II, and for recognition of the promoter.
General Transcription Factors (GTFs), specifically transcription factor IID (TFIID)
Can eukaryotic RNA polymerases recognize promoter regions on their own?
No; they need GTFs
What is Transcription Factor IID?
a GTF which binds to DNA and allows the RNA poly II to come and start transcription
What type of factor is responsible for binding proximal and distal regulatory elements?
Special Transcription Factors (STFs)
What are enhancers?
They help increase the rate at which transcription occurs. They can be located thousands of base pairs away from the promoter region.
Name one modification during RNA processing.
*7-Methylguanosine-triphosphate cap added to 5’ end of mRNA
*3’ Poly-A tail
T/F Blood is classified as part of the extracellular fluid (ECF)
False; (Whole) blood is composed of red and white cells and plasma; therefore blood has both ECF and ICF. Plasma by itself would be considered to be part of the ECF
A mutation in the promoter region of DNA will likely cause which process to be defective?
initiation of transcription. Mutations in the promoter typically prevent formation of the RNA Polymerase II transcription initiation complex
What is the Pribnow box?
a sequence on the DNA strand used in prokaryotic transcription initiation
What is Rho protein factor?
a protein involved in prokaryotic transcription termination
What is the sigma protein factor?
the subunit of prokaryotic RNA polymerase that recognizes and binds the prokaryotic promoter
What is pKa?
it is the extent of dissociation of a weak acid in water. it is a constant.
The lower the pKa the __ the acid.
stronger
What type of bond links amino acid residues?
peptide bond (a type of amide bond)
The peptide bond links which carbon and which nitrogen on the amino acid residues?
amino N and carboxylic acid C
Name the two secondary protein structures. How are both of the structures stabilized?
Beta sheets and alpha helices; hydrogen bonds
Cysteine can form ____ bonds which is important for ____ protein structure.
disulfide bonds; tertiary
Glycine’s R group is ___.
H
What is a structural motif?
smaller combos of 2nd structures
Kd is ____ related to binding affinity?
inversely
The formation of covalent bonds linking amino acids on a growing polypeptide chain is catalyzed by the ____ which is a component of the ___ ribosomal subunit.
28S rRNA riboenzyme; 60S
Name the stop codons.
UGA, UAA, UAG
Eukaryotic Translation Initiation: ribosomal subunit binds with the ___ and ____ at the mRNA 5’ cap to form _____.
eIF, Met-tRNA, preinitiation complex
Eukaryotic Translation Elongation: initial tRNA moves to the ___ site of the ribosome. _____ catalyzes the formation of peptide bond. ____ assists in elongation.
A, peptidyl transferase, Eef-2
Name the prokaryotic ribosomal subunits.
30S, 50S, 70S
Name the eukaryotic ribosomal subunits.
40S, 60S, 80S
The _____ sequence is upstream of the start codon and is needed to start prokaryotic translation.
Shine-Dalgarno
Macrolide abx such as azithromycin are affect bc they inhibit ____.
peptidyl transferase (used in translation)
Proteins from the rough ER travel to the _____ to get processed further.
golgi
After proteins leave the rough ER and golgi complex they then travel to either ____, ____, or ____.
lysosomes, cellular membrane, or outside of the cell
If ubiquitin is added to a cell what is its fate?
It will travel to a proteasome where it will be degraded
If pKa > pH, then which form of the weak acid will be favored? deprotonated or protonated?
protonated form.
What is the name for a combination of 2 alleles on the same chromosome?
Haplotype
____ is the presence of two or more variant forms likely due to a single nucleotide polymorphism.
Polymorphism. DOESN’T IMPLY AFFECT ON PHENOTYPE
____ is the rearrangement (anywhere from (2 to >100,000 bp) in the order sections of DNA.
Structural variant. Think of this as the broader term which includes variants such as CNV, microsatellites, etc.
___ is a large (1kb-1Mbp) homologous DNA sequence present in different amounts.
Copy Number Variant (CNV)
____ are tandemly (next to each other) repeated sequences of 2-4 nucleotides
Microsatellites
Allele frequency is defined as
of “A” alleles in population/TOTAL # of alleles in population
Odds ratio is defined as
odds of disease in presence of allele/ odds of disease in absence of allele
What is NMD?
Nonsense mediated mRNA decay. It is a surveillance system which regulates gene expression by identifying and degrading mRNA which contains PTCs or premature termination codons.
____ is a form of alternative splicing that involves the exclusion of specific exons from mature mRNA.
Exon skipping
____ occurs when a single functional copy of a gene is not sufficient to produce the normal phenotype or function.
haploinsufficiency
___ is a mechanism where a mutated allele interferes with the function of a normal allele resulting in a dominant phenotype even if only one allele is affected.
dominant negative
Consanguinity results in a/n ___ in # of affected homozygotes and a/n ____ in # of heterozygotes for _____.
increase, decrease, autosomal recessive
What is incomplete penetrance?
when an individual can have genes, but not show any symptoms
What is variable expressivity?
range of expression for a phenotype, all individuals have the same genotype
What is genetic anticipation?
a phenomenon in which the severity and onset of a disease becomes earlier and earlier with generations. Typically due to trinucleotide repeat expansion
What is pleiotropy?
mutations in a single gene cause diverse phenotypic symptoms in different organ systems
___ is a quantitative measurement used to calculate disease risk. It is expressed as a percentage.
Penetrance
____ is a qualitative measurement used to show the degree to which a particular genotype is expressed as a phenotype.
Expressivity
____ is mutations in different genes produce the same disorder.
Locus Heterogeneity
___ is mutations in the same gene produce the same disorder.
Mutational (allelic) heterogeneity
What chromosomal aberration is indicated by “ins”?
insertion
What chromosomal aberration is indicated by “inv”?
invertion
What chromosomal aberration is indicated by “t”?
translocation
What chromosomal aberration is indicated by “ter”?
terminal
What chromosomal aberration is indicated by “r”?
ring chromosome
What chromosomal aberration is indicated by “i”?
isochromosome
