BIOCHEM EXAM 1

What is the bond angle of water and why is it not 109.5 like a perfect tetraheron?

104.5 - the two lone pairs on the oxygen compress the bond angle slightly

List 3 reasons why water is polar?

• Oxygen is far more electronegative that H - electrons are pulled towards O

• The molecule’s bent shape means the dipole’s don’t cancel - there is net dipole

• O carries partial positive charge and each H carries partial positive charge

Why does the polarity of water matter biologically?

Polarity of water makes an excellent solvent for charged polar molecules. It also enables hydrogen bonding.

Define H bond and how it forms

A H bond forms between a donor and an acceptorD

Define donor/acceptor needed for H bonding

Donor: electronegative atom (x) with an H covalently attached - any NH or OH group

acceptor: electronegative atom (Y) that has a lone pair - S,O,N

Are H bonds strong?

Not really, are an intermediate-strength interaction. However, there are a LOT of them, and they collectively drive protein folding, DNA base pairing, and enzyme-substrate interactions.

Are linear or non-linear H-bonds stronger?

Linear H-bonds are stronger, and about 90% of H-bonds in proteins are linear. Non-linear H-bonds still form but are weaker because of orbital overlap between the lone pair and the H is reduced.

How many H-bonds can one water molecule form?

Up to 4 bonds (2 as donor via H and 2 as acceptors via lone pairs). This is due to tetrahedral geometry around oxygen.

Why does ice have a rigid tetrahedral lattice?

Because of the 4 H-bonding possible from one water molecule

Why does ice float?

When water freezes, it forms a tetrahedral arrangement that maximizes H-bonds, that is locked into rigid, open crystal structures. This repeating pattern creates larger gaps between the molecules (larger than in liquid water), and since it takes up more space overall, mass is spread out meaning a lower density.

How does ice floating protect aquatic animals?

If ice were like other materials and sank when solidified, lakes and rivers would freeze from the bottom up, destroying aquatic life. Instead, the floating layer if ice acts as an insulator, protecting the liquid water and marine life underneath.

Describe liquid water properties related to H bonding.

In liquid water, H-bonds continuously break and reform. Entropy increases with temp, so fewer H-bonds exist per molecule at higher temps.

What is the concentration of water?

55.5M

Define hydrophillic

WATER LOVING - forms favorable H-bonds or ionic interactions with water. Polar or charged groups dissolve readily in water

Define hydrophobic

WATER FEARING - cannot form H-bonds with water. Nonpolar groups do not dissolve, which forces water to form an ordered cage.

Explain the hydrophobic effect and include details about entropy.

When a nonpolar solute is placed in water, water cannot H-bond with it. Instead, water maximizes its own H-bonds by forming a highly ordered shell (cage) around the solute. This ordered cage has a large entropic cost - it is thermodynamically unfavorable. The system minimizes this by clustering nonpolar groups together (reducing the surface area) causing the hydrophobicity to collapse. This drives protein folding and membrane formation. Basically, non-polar molecules dont repel water, water just prefers to not pay the entropic penalty of caging them. Bringing hydrophobic groups together releases ordered water, increasing entropy.

What happens when you add non-polar tail into a polar solvent?

A miscelle will form - hydrophobic tails point inward, and hydrophillic heads face water.

Are ioinic interactions weaker in water or organic solvents, why?

water weakens ionic interactions due to water having a high dielectric constant which shield opposite charges, reducing the electrostatic attraction between them and causing the compound to disassociate. In a nonpolar organic solvent, ionic bonds are stronger becuase of having a low dielectric constant, and cannot shield charged ions, so it stays tightly attracted to one another.

Explain the water and protein-ligand interaction

Water creates a cage-like structute around the protein’s binding site and the ligand, which is restrictive and costs energy. When the ligand enters the protein’s binding pocket, these structured water molecules are pushed out into the bulk solvent. Once released, the water molecules have much more freedom to move around, which means inc in entropy which is favorable. This favorability drives the ligand and protein together to bind.

Ka of a strong acid

Ka>1 - complete dissociation. EX: HCl, H2SO4, HNO3

Ka of a weak acid

Ka<1 - only partially ionized in water. EX: acetic acid, phosphoric acid, carbonic acid, amino acids

What is a buffer

A weak acid/conjugate base pair that resists changed in pH upon addition of small amounts of strong acid or base.

The _ the buffer concentration, the _ moles of acid/base it can absorb before pH changes significantly

higher, more

Why is water a liquid at room temp?

Because of the strength of H-bonding, would be a gas otherwise

_enthalpy is favored

LOW

_entropy is favored

HIGH

Why do bilayers form?

air has O2, CO2, N2, all non-polar, so the non-polar chain faces toward it

Why are there no free H+ protons in solutions?

wh**e always binds to everything, which is why we actually have H3O+ molecules.

In the ionization of water, if any protons are released it will _ _ . If it has to be released, it will be _ _

form water, from water

Solve buffer practice problems in

moles, not concentration

What is the usable pH range for buffers

pH = pka± 1

What is a base in a nucleic acid?

An aromatic heterocyclic molecule that provides the name and identity for different nucelotides

What is a nucleoside?

A base plus a 5 membered sugar ring derived from ribose. These sugar groups provide much of the difference between RNA and DNA

What is nucleotide

Base plus ribose plus phosphate group that links nucleotides together through the phosphate backbone

How many H bonds between A and T/U

2 bonds

How many H bonds between C and G

3 H bonds

What came first, RNA or DNA?

RNA is the initial foundation of life, we know this because it can adopt structure. DNA evolved from RNA, how it has extra bits such as being double stranded

Base pair width is nearly _ within a given conformation of DNA

identical

What 4 thermodynamically forces define the DNA double helix?

base stacking, hydrophobic effect, hydrogen bonding, electrostatic repulsion

What is the primary driving force behind DNA double helix formation?

base stacking interactions driven by the hydrophobic effect

What is base stacking?

favorable interactions between adjacent aromatic bases stacked on top of one another

Why can DNA bases stack on one another?

Bases are flat, aromatic molecules that can form favorable H bonds and pi stacking interactions

Why does base stacking stabilize DNA?

It lowers the energy of the system through favorable interactions between neighboring bases

Why are DNA bases considered relatively hydrophobic>

Their aromatic ring systems are less favorable for interaction with water than the charged sugar-phosphate backbone

Why are the bases buried in the center of the DNA helix?

To minimize exposure to water and maximize stacking interactions

How does the hydrophobic effect contribute to DNA stability?

Base burial releases ordered water molecules into solution, increasing entropy which is thermodynamically favored

What is H bonding contribution to DNA helix

H bonds provide specifity for base pairing. It’s not the primary driving force for DNA formation because bases can form H-bonds with water when DNA is single stranded, so little energy is gained

What forces oppose DNA helix formation?

electrostatic repulsion - negatively charged phosphate groups in the backbone repel one another, but base stacking, the hydrophobic effect, and H bond outweighs the repulsion

Describe the thermodynamic forces that define the DNA double helix

DNA helix formation is driven primarily by base stacking and the hydrophobic effect. Aromatic bases stack together and become buried from water, releasing ordered water molecules and increasing entropy. H bonds between complementary bases provide specifity and contribute to stability. Electrostatic repulsion between negative charge phosphate groups oppose helix formation but is overcome by the favorable stacking interactions and ionic shielding.

What is A form and B form

A form is double helix RNA and B form is double helix DNAW

What is central dogma process

DNA replication, transcription, RNA, translation, protein

What is transcription?

RNA polymerase unwinds and seperates double stranded DNA at the position where transcription occurs. The RNA product is complimentary to the noncoding template strand.

What is mRNA?

messenger RNA, encodes protein sequence

What is tRNA

transfer RNA; carries amino acids to ribosme

what is rRNA?

ribosomal RNA, aids in protein synthesis

What is transcription in the nucleus?

DNA is copied into mRNA inside the cell nucleus

What is the process of translation?

Translation occurs in the ribosome, which contains rRNA and many other proteins. tRNA carries amino acids to the ribosome and binds to its complement in the mRNA template.

What is denaturation?

A quick, reversible process where double stranded nucleic acids are unfolded and dissociate at high temperature. Tm is the melting temp, when it starts to unwind (50% will be folded, other half unfolded). A/T base pair has less H bonding so it will denature faster. If you lower the temp slowly, single strands will go to double helix because its the lowest energy form.

What is annealing?

two single complementary strands of DNA bind together through H bonding to form a double helix. Happens by cooling down slowly. Cooling down rapidly can lead to improper base pairing

What is step 1 of DNA amplification of PCR?

denaturation (92-95) dsDNA denatures and seperates at high temps to form ssDNA

What is step 2 of DNA amplification of PCR?

Annealing (55) primers base pair to ssDNA, actua temp depends on DNA template and primers

Primers concentration is _ than concentration of DNA is amplification

much higher

What is step 3 of DNA amplification of PCR?

extension (72) optimal temp for heat-stable DNA polymerases to work. New strand is synthesized. Repeat from step 1 for number of cycles

What happens when ddNTPS are incorporated?

extension stops

DNA generated by PCR is _ which allows:

unmethylated; allows for the use of restriction enzymes that can free cut at recognition sites, which makes it easier to insert the DNA into plasmids for cloning.