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Biophysics > Midterm > Flashcards

Midterm Flashcards

1
Q

Time scale of chemical reactions

A

1s to 1ps

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2
Q

Length scale of a eukaryotic cell
Bacterial cell
Nanotechnology
Protein
Radius of DNA

A

1mm to 1um
1um
1um to 1nm
1nm
1nm

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3
Q

Size of prokaryotic cell
No. of base pairs
No. of genes

A

1um
10^6-10^7 base pairs
500-5000

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4
Q

What is the size of a eukaryotic cell?
No. of base pairs?
No. of genes?

A

> 10um (up to 3m long)
10^7-10^10 base pairs
5000-50000 genes

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5
Q

What is the size of the E. coli genome?
Worm
Baker’s yeast
Fruit fly

A

4.2 * 10^6 base pairs (4200 genes)
97 * 10^6 base pairs (20 000 genes)
12 * 10^6 base pairs (6300 genes)
137 * 10^6 base pairs (14 000 genes)

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6
Q

What is the size of the genome of a plant? Mouse
Human

A

1.4 * 10^8 base pairs (26 000 genes)
3 * 10^9 base pairs (24 000 genes)
3.2 * 10^9 base pairs (24 000 genes)

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7
Q

What is life? Aspects of life?

A

There is no strict definition. Aspects of life are: metabolism, growth, energy consumption, out of equilibrium system. Boundary, distinction between inside and outside. Ability to reproduce, with variability, to enable evolution.

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8
Q

What are the three domains of life?

A

Archae, bacteria and eukaryota/eukaryotes

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9
Q

Prokaryotic cell vs. eukaryotic cell?

A

Eukaryotic cells have a nucleus, prokaryotes do not. In general, eurkaryotic cells tend to be large and have more distinct compartments.

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10
Q

What is the central dogma of molecular biology?

A

DNA transcribes into RNA which translates into proteins

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11
Q

What is the size (height) of a base pair in double-stranded RNA?
And in double-stranded DNA?
What are the radiuses?

A

2.8 A
3.4 A
12 A for RNA and 10 A for DNA

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12
Q

How many naturally occuring amino acids?

A

20

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13
Q

What are the building blocks of DNA?

A

Building blocks are nucleotides: sugar-phosphate backbone with nucleobases A, T, C and G. The sugar is deoxyribose. Two strands combine to form double helix

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14
Q

How is RNA different from DNA?

A
  • The sugar is ribose, i.e. it has the 2’ hydroxyl
  • It uses uracil instead of thymine
  • It is often single-stranded (but can fold into complex shapes that are locally double-stranded)
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15
Q

What are the “traditional” roles of RNA (in the central dogma)?

A

Messenger RNA: mRNA
Transfer RNA: tRNA
Ribosomal RNA: rRNA

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16
Q

What are the building blocks of proteins?

A

Amino acids, which are composed of
- Alpha-carbon
- Amino group
- Carboxyl group
- Side chain

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17
Q

How many amino acids does a small protein have?

A

100 amino acids

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18
Q

What is the length of a hydrogen bond?
And a covalent bond?

A

0.3 nm
0.1 nm

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19
Q

What is the typical time step in MD simulations?

A

1-2 fs

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20
Q

What is Anfinsen’s hypothesis?

A

The sequence of a protein uniquely determines its 3D structure. The native state of the protein is
- Unique
- Stable
- Kinetically accessible

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21
Q

What energies are involved in protein folding?

A

Delta G = Delta H - T Delta S
Enthalpy/energy contributions (the Delta H term) tend to stabilize the folded protein. Contributions are hydrogen bonds, salt bridges, van der Waals interactions, etc.
Entropy (the Delta S term) tens to favor the unfolded protein, since the peptide chain has many more confirmations in an unfolded than in the folded, native state. However, solvent entropy can complicate things.

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22
Q

What is Levinthal’s paradox?

A

Assuming even a small number of degrees of freedom per residue (= #dof), there is a huge number of possible configurations, order of (#dof)^(Number of amino acids)
Randomly sampling of these configurations will take extremely long to find the native state.
In reality, there is a non-trivial free energy landscape, which leads to a “folding funnel”

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23
Q

What are “molecular dynamics” simulations?

A

Simulate macromolecules (e.g. proteins, DNA, RNA) classically. Typically at the level of atoms, where every atom is a point mass, with a certain van der Waals radius, partial charge and with specific chemical bonds.

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24
Q

What are terms in a molecular dynamics force field?

A

E_pot(r) = E_bond + E_angle + E_dehidrals + E_elec + E_vdW
Bond, angle, and dehidral interactions are called “bonded” (and represent chemical bonds).
Electrostatic and van der Waals interactions are called “non-bonded”.
r = (x_1, y_1, z_1, …, x_N, y_N, z_N)
N = number of atoms, which includes the macromolecule(s), but also ions and water(1)

25
Q

What time scales are accessible by MD?

A

Typical simulation step = 1 fs.
For a not too large protein and water box, running for
1 ns is relatively easy (takes a day on a laptop)
100 ns to 1us is state-of-the-art (days to weeks on a cluster)
1 ms is possible, for small systems, using supercomputers

26
Q

How do you get the starting positions and velocities for a MD simulation?

A

Starting positions:
Get structure from the PDB, i.e., high-resolution crystallography, cryoEM or NMR.

Starting velocities: Randomly draw velocities from a Maxwell-Botzmann distribution.

27
Q

Why does yeast have the “same problems” as humans?

A

Both are eukaryotes.

28
Q

Analogy DNA and cassette tape

A

Linear storage medium. Different positions encode different messages. Need a “player” to read out message

29
Q

What is missing in many protein animations

A
  • Crowding
  • Thermal motion
30
Q

How does yeast “prepare for being heated”?

A

Express a large set of proteins called heat shock proteins (HSPs)

31
Q

What processes, other than heat response, are the HSPs involved in?

A

Infection, cancer and neurodegeneration

32
Q

How many molar is 1 molecule in a prokaryotic cell?

A

1nM

33
Q

What is a ligand? What are examples of protein-ligand interactions?

A

Ligand = binding partner. Typically binds specifically at a binding site.
Examples range from ions, small molecules (metabolites, drugs, inhibitors, etc.) to other macromolecules, e.g. another protein or DNA/RNA.

34
Q

How do you describe a simple binding equilibrium?

A

Reaction “A binds to B”: A + B <-> AB
Law of mass action: K = [AB]/[A][B] = Ka = 1/Kd = kon/koff
Fraction bound: Y = [AB]/([A]+[AB])=[B]/(Kd+[B])

Graph is Fraction bound vs [Ligand], looks like a logarithm and Kd is the ligand concentration at Y = 1/2

35
Q

What is the protein folding problem?

A

Translation between sequence and structure

36
Q

What has most of protein engineering been like so far?

A

Small changes to existing proteins (= naturally occurring proteins), of which there are ~10^21.

37
Q

How does David Baker want to go beyond evolution?

A

Design completely new proteins from scratch, E.g. for a 100 amino acid protein, there would be 20^100.

38
Q

What are the grand challenges that we can tackle with designed proteins?

A
  • Protein-based materials
  • Drug delivery
  • Smart therapeutics
  • Universal vaccine
  • Expand the alphabet (i.e. use new, non-natural amino acids)
39
Q

What is cooperativity? What is allosterity?

A

Cooperativity: binding at one side influences binding at other sides;
It can be positive and negative (i.e. binding at one site helps or hinders binding at the next)

Allosterity = an event (e.g. binding) has influence on another process at a physically distinct site (e.g. on binding at a different site)

39
Q

What is cooperativity? What is allosterity?

A

Cooperativity: binding at one side influences binding at other sides;
It can be positive and negative (i.e. binding at one site helps or hinders binding at the next)

Allosterity = an event (e.g. binding) has influence on another process at a physically distinct site (e.g. on binding at a different site)

40
Q

What are models for cooperative protein ligand binding?

A

Hill model:
- n binding sites
- All-or-nothing binding

MWC or “concerted” model:
- R and T state
- Independent binding with different affinities
- Presence of the ligand shifts equilibrium to higher affinity state

KNF or “sequential” model:
- Ka1, Ka2, etc.
- Different association constants for subsequent binding events

41
Q

What are the roles of RNA in the central dogma?

A

Messenger RNA (mRNA) = “carbon copy” of the DNA message, to be translated by ribosomes
Ribosomal RNA (rRNA) = Integral part of the ribosome that catalyzes protein synthesis; is a ribozyme
Transfer RNA (tRNA) = adaptor molecule composed of RNA that serves as the physical link between the mRNA and the amino acid sequence of proteins. 3-nucleotide codons on the mRNA are recognized by 3-nucleotide anticodon in the tRNA that carries (covalently attached) the matching amino acid.

42
Q

What are regulatory mechanisms prominently involving RNA beyond the central dogma?

A
  • Ribozymes = catalytically active RNAs, first seem in self-splicing introns
  • RNA interference (RNAi) = suppresses gene expression in a process involving double-stranded RNA and several protein complexes (DICER, RISC)
  • Riboswitches = RNAs, often in the 5’ untranslated region (5’ UTR) of mRNA. Have an aptamer region and allosteric conformational changes in the expression platform will trigger changes in gene expression.
  • CRISPR/Cas = Mechanism where DNA gets cut site specifically by an endonuclease (Cas9) where the binding site is specified by the sequence of a guide RNA.
43
Q

What is the RNA world hypothesis?

A

The hypothesis that there was a stage in the evolutionary history on life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. In the RNA world, RNA is both the storage medium for genetic information (a tole taken over by DNA in “modern” cells) and also catalyzes chemical reactions, including the ones necessary for replication (a role mostly carried out by proteins in current cells).

44
Q

How many virus-like particles on earth?

A

10^31 virus-like particles

45
Q

What is the ion atmosphere?

A

Salt solution around a nucleic acid (or other charged object in solution).
It contains mobile ions, such as Na+ and Cl-, that remain in dynamics exchange

46
Q

What are anions? Cations? Coions? Counterions? Monovalent ions? Divalent ions?

A

Anions: negatively charged ions
Cations: positively charged ions
If you have some larger charged “object” in solution (here: DNA or RNA), the coions have the same charge as the “object (negative for DNA/RNA) and the counterions have the opposite charge (positive for DNA/RNA).
Monovalent ions have one elementary charge (z = +- 1), divalent ions two (z = +- 2), etc.

47
Q

What are principles of the ion atmosphere? How is it different from ligand binding?

A

For the ion atmosphere, you have overall charge neutrality, i.e. the charge of the macromolecule and its ion atmosphere will sum to zero.
In contrast, ligand binding is dominated by mass action and chemical affinity to a specific binding site.

48
Q

What are viruses?

A

Viruses are obligate parasites. They need a host cell to replicate, in particular since they do not make their own ribosomes and therefore can’t make their own proteins.

49
Q

How do viruses store the genome?

A

Viruses store their genomic information either as DNA or RNA, in either single or double-stranded form. The Baltimore classification distinguishes viruses based on how they store the genetic information and based on the intermediates/pathways that occur in mRNA production.

50
Q

What are retroviruses?

A

“Work against the central dogma”
They have a ssRNA genome that is reverse transcribed (by a viral enzyme called reverse transcriptase) into DNA. This DNA is then integrated into the host cell’s genome (by another viral enzyme called integrase).

51
Q

How did viruses originate?

A

There are different hypotheses:
- “Viruses first/early”: Initial life forms were simple and virus-like and co-evolved with more complex cells.
- “Regressive hypothesis”: Certain, more complex cells lost some of their functionality (in particular their ribosomes) and became viruses, relying on other cells for replication.
- “Escaped gene hypothesis” / “Progresive hypothesis”: Certain genetic elements gained the ability to move between cells and viruses.

52
Q

What is the fundamental reaction achieved by the CRISPR/Cas system?

A

Cut double-stranded DNA in a defined location/sequence.

53
Q

What are components of CRISPR/Cas?

A

An endonuclease enzyme (most famously Cas9, but there are others), an RNA that specifies the sequence to cut (“guide RNA”) and the target DNA.

54
Q

What does the CRISPR/Cas system do in nature?

A

“Adaptive immune system” of bacteria against phages.

55
Q

Why are people so excited about it for applications in the lab?

A

Gives ability to program CRISPR/Cas at defined DNA sequence fro genetic engineering.

56
Q

What happens after CRISPR/Cas reacts?

A

The resulting double-strand break gets repaired by the cellular repair machinery, either via non-homologous end-joining or homologous recombination. In that process, new DNA can be inserted if an appropriate sequence is added.

57
Q

What are typical dissociation constants?

A

1 nM to 1 mM: protein-protein interactions, moderate protein-small molecule interactions
1 pM to 1 fM: tight protein-ligand interactions, drugs are made here

Biophysics (2 decks)

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