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71 Cards in this Set

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  • Back
  • 3rd side (hint)
Information flows from _____ to _______.
Information flows from nucleic acid to protein.
DNA --> RNA --> protein
Differences between transcription and translation in prokaryotes vs. eukaryotes (basic)
Prokaryotes: no nucleus, no processing of the mRNA after transcription
Eukaryotes: transcription in the nucleus, mRNA is processed after transcription (one gene can be processed in different ways ex: hormones)
________ are the building blocks of RNA and DNA
What are the three parts of a nucleotide?
Phosphate group, pentose sugar, and nitrogenous base (purine or pyrimidine)
What carbon on the pentose sugar does the phosphate group bond to? The nitrogenous base?
Phosphate group bonds to the 5' carbon, and the base bonds to the 1' carbon.
What carbon is the oxygen removed from in deoxyribonucleic acid?
The 2' carbon
What is the difference between a purine and a pyrimidine?
A purine has two rings, while a pyrimidine has one ring made of a 6-membered N-containing ring.
Big word = small carbon number
A binds with ___, creating ___ hydrogen bonds.
C binds with ___, creating ___ hydrogen bonds.
A binds with T or U, creating 2 hydrogen bonds.
C binds with G, creating 3 hydrogen bonds.
Stack C on its pair.
What bases are purines and which are pyrimidines?
A and G are purines, C,T, and U are pyrimidines.
How do purines and pyrimidines attach to the pentose sugar?
Purines: C1 to N9
Pyrimidines: C1 to N1
How can one figure out how much DNA is in a molecule?
Look for all the thymine (RNA replaces thymine with uracil)
What does DNA have that RNA doesn't?
What does the abbreviation UMP stand for?
Uridine monophosphate - abbreviation for a ribonucleotide
U refers to a nucleotide base
What does the abbreviation dAMP stand for?
Deoxyadenosine monophosphate - abbreviation for a deoxyribonucleotide
How is a nucleotide formed?
A base attaches to the C1 on a pentose sugar, then the sugar is phosphorylated by kinases on the 5' carbon.
Need three parts
What enzymes phosphorylate molecules? Which dephosphorylate molecules?
Kinases phosphorylate, phosphotases dephosphorylate
What is the complimentary DNA sequence to this strand of DNA?
On a strand of DNA, which end is the phosphate group located at? Which end has the poly A tail?
The phosphate group is at the 5' end, and the poly A tail is at the 3' end.
What type of bond links nucleotides in DNA? What carbons does it link together?
A phosphodiester bond links each nucleotide, connecting the 3' end of one sugar to the 5' end of the next.
True or false: A strand of DNA is polar.
The 5' end is different from the 3' end.
What are the three principle types of RNA?
Messenger RNA (mRNA) - encodes for proteins
Ribosomal RNA (rRNA) - forms part of the ribosome structure
Transfer RNA (tRNA) - adaptor for protein synthesis
What are the four key features of hybridized DNA?
1. The two strands are antiparallel.
2. A helix forms.
3. Major and minor grooves form.
4. A sugar-phosphate backbone runs along the outside.
Hybridized DNA is dsDNA
Why are two strands of DNA able to hybridize?
Because the bases of one nucleic acid strand can form highly specific hydrogen bonds. Ex: A and T/U (2 H-bonds), and G and C (3 H-bonds)
Which is stronger, the bonds between A and T/U or between G and C?
G and C (3 vs. 2 bonds)
Chargoff's ratio: If a cell's DNA is found to be 23% guanine, how much of the DNA is adenine? Cytosine? Thymine?
23% Cytosine
27% Adenine
27% Thymine
%G = %C
%A = %T
True or false: Proteins can be modified after translation.
True or False: DNA is a rigid, immobile molecule.
The genetic code is a sequence of _______.
What is a codon?
A codon is a sequence of 3 bases which code for a single amino acid.
True or False: All codons code for some amino acid.
False; stop codons
What is the 'degeneracy' of the genetic code?
A single amino acid can be coded for by multiple codons; often, the first two bases are sufficient
What are 'synonymous codons'?
Different codons that encode the same amino acid
Condons with similar _______ often code for amino acids with similar ________.
Sequences; properties
How many stop codons are there?
What is the start codon? What amino acid does it encode?
AUG encodes for methionine; it marks the start of the protein coding sequence on mRNA
True or false: In eukaryotic mRNA processing, introns are spliced out and exons are then linked together.
When are introns included in the mRNA transcript?
After transcription until before translation (processing)
What are genes?
Parts of the DNA sequence that encode for proteins.
Of the following DNA strands, which is the coding strand? The template strand? The mRNA transcript?
A is the coding strand.
B is the mRNA strand.
C is the template strand.
True or False: DNA is made up entirely of genes.
False; DNA contains 'regulatory sequences' that bind to a variety of regulatory factors.
Because of differential RNA processing, a single gene can show (3):
1. Multiple start sites for transcription.
2. Multiple polyadenylation sites (poly A tail)
3. Multiple patterns of intron splicing.
True or false: A single gene can give rise to multiple proteins.
What is a mutation?
An alteration in the normal; a wild-type sequence of a DNA molecule.
What types of mutations are considered 'readable'?
Missense, frameshift
What type of mutation causes a truncated protein?
Nonsense mutation - encodes for a stop codon too early in translation.
What is a missense mutation?
The substitution of one base for another, which can result in the substitution of one amino acid for another.
What type of mutation causes sickle cell anemia?
Missense mutation.
What about the genetic code makes it possible for a missense mutation to not have an effect on the protein's structure?
The degeneracy of the code - if the third base is changed, it is still possible for the correct AA to be called because multiple codons can call for the same AA.
What is a nonsense mutation?
When a normal codon specifying an AA is replaced by a stop codon, creating a truncated protein.
What is a frameshift mutation?
The insertion or deletion of a nucleotide (inserting or deleting a single base pair); results in a non-functional protein.
Ex: ACA UGA AUG CGU , now add a G:
What is RNA polymerase?
The enzyme that makes mRNA from the DNA template.
You should know this.
Why are deathcap mushrooms poisonous?
They inhibit RNA polymerase.
What is constitutive gene expression?
Constant basal expression aka housekeeping genes
What is regulated gene expression?
When gene expression levels are responsive to cellular signals.
What molecules are responsible for regulating gene expression?
Inducers and repressors
What is a promoter?
A site, often near where transcription begins on the DNA template, that powerfully controls the expression of the gene.
True or False: A promoter is always part of the coding sequence on DNA.
What do differences between strong and weak promoters depend on?
They depend on the sequence of the promoter itself and on how well this sequence matches a consensus sequence. The less the promoter matches the consensus sequence, the less likely it is to attract initiation factors.
Define the following terms:
upstream, downstream, domain, and +1 base.
Upstream is prior to the gene in question, and downstream is after the gene. A domain is a specific sequence of genes with a specific function. The +1 base is the first base to be transcribed on the DNA template.
In a chromatin, what element is acidic? Which is basic?
The DNA is acidic (with a negatively charged backbone), and the proteins are basic (and positively charged).
What are the steps (in order) of chromosome wrapping?
1. Naked DNA
2. Nucleosomes
3. 30 nM fiber
4. Loops
5. Condensed chromatin
6. Mitotic chromosome
Naked nucleosomes make 30nM fibers loops that are condensed into chromosomes.
How many DNA base pairs are in nucleosome core (associated with histone proteins)?
146 base pairs
What is the region that separates core histones in a nucleosome?
The linker region
What are the four core histone proteins in a nucleosome?
H2A, H2B, H3, H4
How many histone proteins are found in a nucleosome core associated with 146 base pairs of DNA?
Eight, forming an octamer. There is one pair of each of the four core histones, H2A, H2B, H3, and H4.
How does a nuclease digest help scientists discover the length of the linker region in nucleosomes?
The nuclease enzyme cuts DNA where it is most exposed, in the linker region, then the fragments can be separated by size on agrose gel and the linker region can be calculated.
How does one calculate the linker region?
Subtract the smaller piece from the next biggest, then subtract 146. Ex:
Fragment sizes: 1000, 800, 600, 400, 200
Difference: 200 (protein occurs every 200 bps)
200-146 = 54 base pairs.
What transcriptional activity occurs with the following chromatin structures?
a. decompaction
b. normal
c. compaction
a. Induced
b. Basal level of expression
c. Repressed
What are specificity factors?
Factors that alter the specificity of RNA polymerase for a given promoter or set of promoters. They guide RNAP to the proper sequence.
What are repressors and activators?
Repressors impede the access of RNA polymerase to the promoter, and activators enhance the interaction between RNAP and the promoter.
How does modifying the protein core of a nucleosome affect gene expression?
It changes the compaction of the protein and therefore, changes gene expression.
The mass of the histone proteins in chromatin are _______ the mass of the DNA.

a. greater than
b. less than
c. equal to
c. equal to