Chemistry of the Cell
What is valence?
Number of electrons needed to stabilize outer orbitals
What are the four macromolecules? Name the monomers
Nucleotides -> nucleic acids
Amino acids -> proteins
Monosaccharides -> polysaccharidesWhat enzyme is used for DNA synthesis?
DNA Polymerase III
What is transcription?
Copy DNA base sequences into RNA base sequences
What is translation?
Interpret RNA base sequence into amino acid sequence
What is the importance of water?
1. Water is polar and cohesive
2. Water stabilizes temperature
3. Water is an excellent solvent
What reaction joins two activated monomer together?
Condensation
Why does DNA Pol III require deoxynucleoside TRIphosphate?
dNTP provides high energy when phosphate bonds are broken. This breakage favors formation of phosphodiester bond.
RNA Pol II
Why has life on Earth developed a 3-nucleotide (triplet) codon system?
64 possible amino acids when 20 amino acids are necessary for life on Earth. This allows for degeneracy and minimizes the harmful effects when mutations occur?
What are selectively permeable membranes made of? What is the importance of a membrane?
Phospholipids.
Membranes keep contents in and materials out
What are the four levels of protein folding? What type of bonds are in each level of protein folding?
Primary -> Secondary -> Tertiary -> Quaternary
Primary: linear
Secondary: hydrogen bonding
Tertiary: side chain interactions (disulfide bonds via cysteine residues, ioninc bonds)
Quaternary: two or more polypeptides interacting to form a complex
What is the function of DNA Pol I?
To remove the RNA bases, so that the strands can be DNA
What are the different types of RNA? Name their function
mRNA encode for proteins
tRNA carry amino acids onto the mRNA, which synthesizes a polypeptide chain
rRNA make up parts of the ribosome
What tRNA position allows for degeneracy?
The wobble position allows for imperfect pairing therefore nitrogenous bases that can't match before no can.
There's an inosine (modified purine) that allows for degeneracy, which minimizes the harmful effects when mutation happens
What are the five molecular principles of life on Earth?
1. Importance of carbon
2. Importance of water
3. Importance of selectively permeable membranes
4. Importance of synthesis by polymerization
5. Importance of self-assembly
What monosaccharides make up lactose? Why can't humans digest lactose?
Beta-D-galactose + Beta-D-glucose. Humans don't have the enzyme that recognizes the Beta glycosidic bond, therefore we can't digest it.
What are the 5 ingredients needed in PCR?
1. Template DNA strand
2. A pool of dNTPs
3. Taq DNA Polymerase
4. DNA primers
5. Adjustable heating/cooling equipment
mRNA needs protection when leaving the nucleus. What are the two protections?
5' cap is the addition of a “backward” methylated guanosine nucleotide
3' polyA tail: multiple adenine nucleotides added to the 3' end
What proteins are involved in the Elongation and Termination part of translation?
Bonus: Can you name the stop codons?
Elongation Factor carries GTP and the amino acyl tRNA
Release factor carries the stop codon
UAA: U Are Annoying
UGA: U Go Away
UAG: U Are Gone
Why do we need a match to combust gas if the end result is energetically favorable?
Gases are stable and the match is the "motivator" to get the reaction going (Potential energy turned into kinetic energy)
Name the two groups that modify histones, ultimately regulating access to DNA
Acetyl group on histone tails -> histones hold onto DNA loosely -> have access to DNA
Methyl group on histone tails -> histones tightly grip onto DNA -> less access to DNA
Describe the problem faced by DNA Polymerase III when copying a double stranded DNA.
Bonus: How do you solve this?
DNA Pol III can only CONTINUOUSLY synthesize the template strand that goes 3' to 5'. This is the leading strand.
The strand that goes 5' - 3' is the lagging strand because DNA Pol III has to work backwards.
The short RNA primers discontinuously added onto the lagging strand are called Okazaki fragments and DNA ligase glues them together.
Why does the final mRNA NOT line up with the original gene (that it was transcribed from)?
The final mRNA spliced out the introns
Initiation: 4G recruits 40S of ribosome. 60S is recruited and assembles the ribosome. First tRNA starts at the P site.
Elongation: Elongation factor brings amino-acyl tRNA into the A site, growing polypeptide chain is added onto the amino acid of the A site. Elongation factor breaks the GTP and moves the tRNAs down their sites
Termination: Release factor brings the stop codon and translation stops