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Chemical Foundations
Proteins
Replication
Transcription
Translation
100
What is the difference between affinity and specificity.
Affinity --> how well molecules FIT together, tighter attractions form Specificity --> ability to bind tightly to only one or a few related molecules
100
Peptide bonds form through which reaction?
Dehydration R-O=C--NH-R
100
If double stranded DNA has 14% G (guanine), what percent A (adenine), T (thymine) and C (cytosine) would you expect?
C= 14% A = 36% T= 36%
100
Where does the promoter bind on the DNA molecule and what binds to the promoter
UPSTREAM RNA POLYMERASE
100
What are the three molecules that come together to form translation complex
mRNA, tRNA, rRNA
200
What is the electronegativity associated with the two covalent bonds?
0.4 - 2: POLAR <0.4 : NON-POLAR
200
What is the difference between alpha helices and beta pleated sheets? -# of residues -arrangements
-Alpha helices: 4 residues; B-pleated: 5-8 -Helix VS antiparallel/ parallel formation
200
DNA gyrase belongs to which enzyme family and what is it responsible for?
Topoisomerase II // Ligating pieces on lagging strand together forever <3
200
Downstream consists of RNA polymerase moving in what direction?
In the direction of transcription, towards coding sequence (+ve)
200
What is the difference between the assembled ribosomal size in prokaryotes VS eukaryotes
70S VS 80s
300
How to competitive inhibitors affect the Km and Vmax
Km increases, Vmax the same
300
What are the two amino acids that stabilize U-Turns
Glycine & Proline
300
What adds a primer needed for DNA replication and to what region are the dNTPs added?
DNA Polymerase III; added to free 3'OH group
300
Where are three locations transcription takes place?
Nucleus of cells, mitochondria and chloroplasts
300
What are the 4 characteristics of the genetic code, explain each.
Code is Unambiguous (specific) Each codon specifies 1 aa. Code is Degenerate/redundant 20 diff aa, some encoded by multiple codons = redundancy Code is non-overlapping and continuous The code is read, starting from a fixed starting point, as a continuous sequence of successive triplet bases read in order Code is nearly universal, with certain exceptions (MITOCHONDRIAL EXCEPTIONS)
400
Zinc in the zinc finger motif is coordinated by side chains of which amino acids?
Cys & His
400
Name the aromatic amino acids
Phenylalanine, Tyrosine, Tryptophan
400
DNA's template strand is read from ___ to ____ But the dNTPs are added from ____ to ___
3' to 5' 5' to 3'
400
Describe what each one is needed for during transcription: DNA template RNA polymerase RNA nucleotide triphosphates (rNTP) RNA transcript Transcription factors Enhancers (regulatory sequences)
DNA template - what will be transcribed RNA polymerase - to melt dsDNA and code template strand RNA nucleotide triphosphates (rNTP)- added one at a time to the 3’ end of the growing primary RNA transcript Transcription factors -controls the rate of transcription of genetic information from DNA to mRNA, by binding to a specific DNA sequence. Regulate genes in order to make sure that they are expressed in the right cell at the right time Enhancers (regulatory sequences) - a short (50-1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur.
400
tRNA containing anticodon CCG binds to mRNA codon GGC; how many hydrogen bonds form during this interaction?
3 x 3 = 9 H bonds
500
What are the three components of nucleic acids?
Pentose Sugar Nitrogenous Base ( Attached to C1 ) Phosphate group (Attached to C5)
500
Name the 3 basic amino acids.
What is lysine, arginine, histidine
500
State what each of these structures is used for during DNA replication: - ds DNA template - DNA polymerase - Primase - RNA nucleotide triphosphates - DNA nucleotide triphosphates - Helicase - Single-strand binding proteins - Topoisomerases - DNA ligases
ds DNA template: to replicate DNA polymerases: deoxynucleotide polymerization (extend DNA) & have exonuclease activity to destroy primer Primase: an enzyme that adds a short RNA sequence (primer) at the start of replication RNA nucleotide triphosphates for RNA primer DNA nucleotide triphosphates for DNA polymerization Helicase: assist in unwinding at replication fork (ori) Single-strand binding proteins: bind to DNA to prevent premature reannealing of dsDNA and recoiling Topoisomerases: nicks wound DNA to relieve tension from helicase-induced unwinding, then reseals the nicks DNA ligases: seals the single strand nick, join Okazaki fragments on lagging strand
500
List and describe the 3 post-transcriptional modifications mRNA undergoes:
Methyl cap (5’ end) Polyadenylation (3’ end) Intron removal & exon splicing
500
What is the name of the enzyme that charges tRNA with correct amino acid?
aminoacyl tRNA synthetase enzyme