Exam 2 Flashcards
What is transcription
DNA -> mRNA
Central Dogma
DNA -> RNA -> Protein
Enzyme for RNA
Ribozyme
RNA vs DNA (just RNA)
RNA:
- Uracil instead of Thymine
- Ribose instead of deoxyribose
- Can fold into different structures
What catalyzes RNA trasnscription?
RNA Polymerase
Functions of RNA polymerase
Catalyzes RNA transcription
Unwinds the strands
Keeps strands seperate
Coding vs non coding strand
Coding: The one that will look like your new strand but you don’t touch
Noncoding: The one you touch but is the opposite of your new strand
What is translation
mRNA -> polypeptide
Steps of eukaryotic transcription and where they’re located
- Transcription: in nuclear envelope
DNA -> Pre-mRNA - RNA processing
Pre-mRNA -> mRNA - Translation: Leaves nuclear envelope
mRNA -> Polypeptide
Done by a ribosome
Prokaryotic transcripts are often
polycistronic (multiple proteins encoded on one mRNA)
Eukaryotic vs Prokaryotic mRNA
Eukaryotic:
- mRNA processing (pre -> mRNA)
- leaves nuclear envelope for translation
- One mRNA for one protein
Prokaryotic:
- No processing (no splicing, 5 prime caps, etc.)
- Polycistronic
Three ways pre-mRNA is processed
- 5’ cap
- Splicing (introns are removed)
- Poly-A tail
Why do we have pre-mRNA processing?
- Protects ends
- Marks ready for translation
What does the 5’ cap bond to?
triphosphate group bridge
What splices the pre-mRNA
Spliceosome
What is a spliceosome made of and how does it work
Made of snRNPs and other proteins. It hydrogen bonds with the introns to form and intron loop
What is alternative splicing and what is the outcome?
Recombines exons to form different patterns. It can distinguish protein functions out of one gene.
What distinguishes pre-mRNA to mRNA and allows mRNA to leave the nucleus?
Nuclear Pore Complex
What adds the poly-A tail to mRNA
Poly-A polymerase
What interacts with mRNA to translate it?
A ribosome
What is a ribosome made of? (overall)
rRNA and ribosomal proteins
UTR
Noncoding regions binding sites where proteins bind to stop translation
5’ UTR
Blocks translation (proteins bind to it)
3’ UTR
Bind to microribosomes at post transcription regulation
What subunits make up the ribosome
Small subunit and bigsubunit
Why are ribosomes so big
They need to bind to 3 tRNA, mRNA, polypeptides, etc.
Polypeptides are made from the
N-terminus to the C-terminus
Three factors used in translation
Initiation, elongation, and release factors
What brings specific tRNAs to the ribosome
Aminoacyl tRNA synthetases
Draw a polypeptide chain being made from n to c terminus
okay
Label all the amino acids accordingly
Okay
Why is there a triplet code?
There are 20 amino acids
1: 4
2: 4 x 4 = 16
3: 4 x 4 x 4 = 64
What does the redundancy of 64 codes when you only need 20
diversity of the last codon, allows to be wobbled by tRNA
Initiation
Starts at 5’ cap, first AUG is the start codon, and is read 3 at a time
What differentiates amino acids?
R groups
Who reads the triplet code in mRNA
tRNA
At the ___’ end of tRNA is where amino acids attatch
3’ end via an ester bond
How are amino acids grouped with triplet codes
The anticodon region reads the mRNA sequence, and an amino acids fits into the attachment site on the 3’ end of the tRNA
What ends the process of translation?
hydrolysis
Chromatin
DNA + protein fiber that organizes and packages genetic material
Histone
Made of 8 proteins, a spool where the DNA is wrapped around
How may wraps per histone
around 1.5
T/F Chromosomes are always condensed
F, condensed only during replication
Homologous
Similar but not identical
Diploid
Two of each chromosome
Humans have __ sets of chromosomes so ____ in total
23 sets, 46
Why is telomerase only active in germ and stem cells
Somatic cells like skin cells should not keep rapidly rejuvenating or else cancer will occur.
Sexual reproduction summarized
Meiosis:
germ-like cells: haploid egg and sperm fertilize to make a diploid zygote
Mitosis: zygote multiples so form an organism full of somatic and germ cells.
Two parts of a chromosome
Centromeres and telomeres
Direction RNA polymerase reads and synthesizes in
Reads: 3’ to 5’
Synthesizes: 5’ to 3’
TATA box
where RNA polymerase binds to before transcription
Direction the ribosome reads and synthesizes during translation
Reads: 5’ to 3’
Synthesizes: n terminus to c terminus
Describe the EPA
E: n-terminus, tRNA ejected
P: connecting polypeptides
A: C-terminus, tRNA enters
What happens during s phase
2 Homologous chromosomes (1 chromatid each) replicated and make 2 homologous chromosomes (2 sister chromatids each)
Which strand needs telomerase to add telomeres to prevent important sequences from being lost?
lagging strand
What attaches to centromeres to separate sister chromatids?
kinetochores attached to long microtubules
Three things that allow for genetic diversity
- Random fertilization
- Independent assortment of maternal and paternal homologs during meiosis I
- Crossing over during meiotic prophase I
Classify as haploid, diploid, and by mass during the stages of cell division
Interphase:
2n, 2x
2n, 4x
Meiosis I:
n, 2x
Meiosis II
n, x
Steps of Meiosis I
Interphase, Prophase I, Metaphase I, telophase I, cytokinesis
Interphase
Interphase: Chromosomes replicate to make sister chromatids in the parent cell
Prophase I
Early Prophase I: Chromosomes condense, nuclear envelope breaks up, spindle apparatus forms, Synapsis of homologous chromosomes (form tetrads)
Late Prophase I: Crossing over of nonsister chromatids
How do holiday junctions work
When it is formed, there is a 50% 50% chance that resolvase slices it to recombine from non sister chromatids. if the out strands are cut, it happens
Chiasma
the located where non-sister chromatids link in recombination
Metaphase I
Tetrads migrate to metaphase plate
At least one holiday junction needs to form for each chromosome before metaphase I, how can the cell tell?
If there is tension when the chromosomes are being pulled apart
Anaphase I
Homologs separate and begin moving to opposite sides of the cell
Telophase I
Cells divide
What happens during meiosis II?
Same as meiosis I but there is no interphase, and four cells are formed. Each with their own nuclear envelope, two chromosomes (each with one chromatid)
What solutions did valence bond theory give
- Considers quantum mechanics
- Separate orbitals can’t form proper geometry, so they hybridize
What does hybridization do
Takes different orbitals and makes them the same size and shape
What are sigma bonds
Covalent bonds between 2 atoms formed when orbitals overlap
What are pi bonds
Bonds made when p orbitals overlaps above and below the internuclear axis
Why is SP3 lower in the energy diagram than P?
It has more s character
Paramagnetic
Molecules with unpaid electrons, attracted to magnetic fields
Diamagnetic
Molecules with paired electrons, not attracted to magnetic fields
When orbitals (wave functions) are inphase
It is constructive and forms a bond
When orbitals (wave functions) are outphase
It is destructive and forms a node (aka antibond)
Valence bond theory vs MO
Valence Bond:
- Each atom’s own orbitals hybridize independently
MO:
- All atomic orbitals combine in one molecule
Molecular Orbital Theory, 4 principles
- S and S combine to for a bonding and antibonding MO (sigma and sigma star)
- Bonding MOs are lower in energer
- Lowest MOs fill first
- The number of AOs equals the number of MOs
Bond Order (equation and use)
Determines strength and length
1/2[(number of electrons in bonding MOs) - (number of electrons in antibonding MOs)]
Why does sp mixing happen?
2s and 2p are closer in energy when the Zeff is lower
Diatomics that will experience sp mixing and wont
Yes: Li2, Be2, B2, C2, N2 (anything isoelectric with N2)
No: O2, F2, Ne2
The more Zeff
The less energy of MO orbitals
Intermolecular vs Intramolecular
Intermolecular:
- Between two or more molecules
- Dipole-dipole interactions and London dispersion forces
- Hold molecules together (determine melting point, boiling point, etc)
- Weak interactions
Intramolecular:
- Inside a molecule
- Covalent
- Hold atoms together to make a molecule
- Very strong
London Dispersion Forces (Vanderwall)
- Instantaneous
- Temporary dipoles because electrons are always moving
- Every molecule has it
- The more there are the higher boiling and melting point
Higher surface area =
More chance of LDF
- They can stack better
Dipole Dipole
Permanent interaction
Electronegative atom
Hydrogren Bond
The strongest dipole-dipole interaction (due to the difference in EN)
Steps to make sure it is hydrogen bond
- Net dipole
- Hydrogen bonded to EN atom
- O, N, Br, F
Ion-Dipole
Interactions like salt and water
Percent Yield
Actual yield/Theoretical Yield x 100 = % yield
Molarity
Moles of solute/Liters of solution
T/F RNA molecules can synthesize sequentially before the first finishes
T
T/F All genes are transcribed at the same efficiency
F, UTR tunes efficiency
Transcribe the RNA from this
5’-AGTCTA-3’
3’-TCAGAT-5’
5’-AGUCUA-3’
Where is hybridization inaccurate?
The theory is inaccurate because it assumes that electrons are localized in bonds between atoms or in lone pairs, “belonging” to one atom. In reality, electrons are delocalized across the entire molecule. As a result of this physical inaccuracy, this theory cannot predict the energies of electrons within molecules.
Best way different cells maintain different functions
Cell specific mRNA transcription
Which amino acid would tRNA with the anticodon 5’-CUU-3’ carry?
Lys
Alpha Helix
Coils like a spring, turns every 3.6 amino acids
C=O groups point down to the C-terminus (positively charged)
N-H groups point up to the N-terminus (negatively charged)
Beta sheet
Two poly peptides stacked on top of one another
Parallel: Same direction
Antiparallel: Opposite directions
Nonpolar amino acids tend to be found in the
interior of proteins
