Exam 1 Review (1-3)

Focuses on the learning objectives

Identify the most abundant functional groups found
in biomolecules

Amino (-NH3)

Hydroxyl (-OH)

Sulfhydryl (-SH)

Carboxyl (-C=OO^-)

Phosphoryl (P=OOO^-)

Methyl (-CH)

Polar

molecules that have a partial positive charge on one side and a partial negative charge on the other, leading to an unequal distribution of electrons

ex) H2O

Nonpolar

molecules that have an equal distribution of electrical charge, resulting in no partial positive or negative charges. ex) lipids

Name the four major classes of biomolecules,

Carbohydrates

Lipids

Proteins

Nucleic acids

What biomolecules form polymers?

Carbohydrates

Proteins

Nucleic Acids

Primary cellular function of carbohydrates

Energy source/storage

Cell recognition

Provide structural support

Primary cellular function of lipids

Forms cell membranes

Energy conversion/storage

Cell signaling

Primary cellular function of proteins

Act as catalysts

Structural support

Store & transmit genetic info

Primary cellular function of nucleic acids

Store & transmit genetic information

Enzyme catalysis

Signal transduction

Energy conversion

Explain the role of pathways in living systems

Coordinate & control complex processes in response to environment

Series of linked biochemical rxns where product of 1 rxn = reactant for the next

Identify the three components of a nucleotide

5C sugar

Phosphoryl group

Nitrogenous base

Compare and contrast the overall functional role of DNA and RNA

DNA → permanent storage for an organisms genetic info

RNA → temporary working copy that executes the instructions to build; transcriptome (mRNA), Translation (tRNA & rRNA)

Both → store, encode, or transmit the genetic instructions required to build and maintain living organisms

Define the Central Dogma of molecular biology

Describes the flow of genetic information within a biological system

DNA → RNA → Protein

Transcriptome

Collection of DNA transcripts (RNA) generated by DNA transcription

Proteome

Set of proteins produced by mRNA translation either in entire organism or tissue

Identify the relationship between protein structure and function

Proteins 3D shape dictates its ability to recognize, bind, & interact with other molecules

Endothermic

A reaction absorbs heat from the surroundings

+ΔH (unfavorable/nonspont.)

Breaking of noncovalent interactions

Exothermic

Reaction releases heat

-ΔH (favorable/spont.)

Formation of noncovalent interaction

0th Law of Thermodynamics

Thermal equilibrium- if 2 bodies are in thermal equilibrium with a third body, they are also in equilibrium with each other

1st Law of Thermodynamics

Conservation of energy- Energy is conserved, but can be converted between types

Energy (E) can be neither created nor destroyed.

• Energy can only be converted from one form to another

• ΔE=q-W

2nd Law of Thermodynamics

Entropy- In all spontaneous processes, the entropy of the universe increases

3rd Law of Thermodynamics

Absolute zero- the entropy of a system approaches a constant value

as the system approaches absolute zero

Enthalpy

Total heat content/bond energy of a system

-ΔH = favorable/spontaneous

Entropy

ΔS

Number of ways energy can be distributed (resonance in Ochem); disorder

+ΔS = favorable/spontaneous

Gibbs Free Energy

ΔG

Energy available for work

-ΔG = favorable/spontaneous

Gibbs Free Energy Relation to ΔH & ΔS

ΔG = ΔH - TΔS

ΔG < 0

Rxn favorable

Equilibrium favors products (forward rxn)

Energy released

Exergonic

ΔG > 0

Rxn unfavorable

Equilibrium favors reactants (reverse rxn) Energy absorbed Endergonic

Exergonic

-ΔG

Rxn spontaneous

Energy released to surroundings

Endergonic & Coupled in Biological Systems

ΔG

Rxn non-spontaneous

Energy absorbed/required

Can be coupled to an exergonic rxn to become overall favorable

Common Coupling Rxn

ATP Hyrdolysis → ΔG = -30.5 kj/mol

Explain why ATP hydrolysis produces a large standard free energy change, in terms of electrostatic charge repulsion and product stabilization.

Due to the repulsion between negatively charged phosphate groups in ATP (-ΔH).

When ATP is hydrolyzed, the release of one phosphate group decreases this repulsion and allows for better stabilization of the products → more possible resonance forms , leading to a more favorable reaction.

Hydrogen Bonds

Responsible fro unique properties of water

H “shared” bt 2 eneg atoms

ΔH is - & favorable, attractive

H Bond Donor

Atom that has H bonded

H Bond Acceptor

Has lone pair

Electrostatic Interactions

Attractive or repulsive forces

Strength of bond depends on charge, distance bt charges, and environment bt them

Dipole-dipole

Ionic interactions

Salt bridge → ion-ion bt + and - charged atoms

Van der Waals

Temporarily occur between the dipoles of nearby electrically neutral molecules

Depend strongly on distance bt 2 atoms

Very weak individual attraction

Hydrophobic Effect

Occur bt nonpolar molecules

Do not for H bonds w/ water

Play important role in protein folding rxns

Driven by water’s tendency to maximize its own internal H bonding and entropy

Strength of 4 IMF

Strongest: Electrostatic (salt-bridge #1, dipole #2) → 0.25nm

Moderate Strong: Hydrogen Bonding → 0.30nm

Weak: van der Waals → 0.3-0.6nm

Variable: Hydrophobic Effect

Relate pH to the concentration of H+ or OH–

pH = -log[H+]

pOH = -log[OH-]

[H+] increases = pH decreases

[OH-] increases = pH increases

Interpret titration curve for a weak acid

Use the Henderson-Hasselbalch equation to determine pH or the ionization state of a weak acid

pH = pKa + log [A-]/[HA]

pKa = -logKa

Relate ionization state to a group's capacity for electrostatic and hydrogen-bonding interactions.

The ionization state of a group affects its ability to participate in electrostatic interactions and hydrogen bonding. Higher ionization states generally enhance a group's capacity to form such interactions due to the presence of charged species.

Key structural differences bt DNA & RNA an their link to function

DNA: dbl stranded w/ deoxyribose sugar, N base, and uses Thymine, longer

RNA: single stranded w/ ribose sugar, N base, and uses Uracil, shorter

1° structure of DNA

Sequence of polymers (polarity 5’→3’)

Unique arrangement of deoxyribonucleotides/ribonucleotides arranged in a single chain

Usually depicted as single letters in a row

2° structure of DNA

Complementary H bonding interactions

2 comp. strands of DNA bind (anneal)

Double helix

Causes backbone (sugar phosphate) to adopt a particular shape

Restate Chargaff’s rule and explain typical base pairing in DNA structure.

The amount of adenine = amount of thymine, and the amount of cytosine = amount of guanine, leading to complementary base pairing (A-T and C-G) that stabilizes the DNA double helix.

Called Watson-Crick base pairs

A-DNA

Right handed helix

Wider turn

Compact and compressed

Areas of active transcription

B-DNA

Physiological form

Right handed helix

Z-DNA

Left handed helix

Narrower turn

Areas of active transcription

Zigzag backbone

Helical twist

Optimizes H bonding

Propeller twist

Optimizes stacking

Base stacking

Most important stabilizing interaction in nucleic acids

Impact of strand length on T_m

Longer the strand = higher the T_m

More H bonds

More stacking

More Van der Waals

IMF are additive

Impact of ionic strength on T_m

Higher ionic strength = higher T_m

The backbone carries - charges → + ions in solution neutralize the - charges, reducing the repulsion between the strands and stabilizing the double helix structure.

Higher [salt] = higher T_m = higher stability

Higher heat required to denature strands

Counter ion Condensation

Impact of A-T vs G-C content on T_m

Higher G-C content increases T_m due to more hydrogen bonds and stronger base stacking interactions → more stable compared to A-T pairs.

Positive supercoiling

Right strand twists over left

DNA overwound in same direction as natural right handed helix

Increase physical stress of DNA

Negative supercoiling

Left strand twists over right, causing DNA to be underwound, which relieves physical stress and facilitates strand separation during processes like replication and transcription.

Linking number

Number of times a strand of DNA winds in the right-handed direction around the helix in an imaginary plane

Lk = Tw + Wr

Twist

Measures the winding of DNA strands around each other

Writhe

Measures crossing of DNA strands

Explain how linking number, twist, and writhe are related

The linking number (Lk) is the sum of the twist (Tw) and writhe (Wr) of a DNA molecule, showing how the DNA strands are intertwined.

Identify the histone proteins and the structures they form.

Histone proteins are the core components of nucleosomes, which are structures formed by DNA wrapped around histone octomers.

These proteins include H2A, H2B, H3, and H4, and they play a critical role in the compaction and organization of chromatin.

Key elements in DNA condensation

Structural proteins

Chemical/ionic factors

Enzymatic macheinery

Explain how a plasmid can transfer genetic material from one cell to another

Conjugation

Transformation

Transduction

List the elements of a plasmid that make it useful for producing
recombinant DNA

Origin of Replication

Selectable marker

Multiple cloning sites

Promoter region

Explain the role played by restriction enzymes in the production of recombinant DNA

Act as molecular scissors that cut DNA at a specific sequence, allowing the isolation of genes and splicing them into other DNA molecules

Add a vector and insert

Explain the cut-and-paste cloning and identify what is happening in each step

1st → restriction enzymes cut the DNA at specific sites

2nd (cut)→ the desired DNA fragment is isolated and a vector (like a plasmid) is prepared by cutting it with the same restriction enzyme.

3rd (paste) → the DNA fragment is inserted into the vector, which is then introduced into a host cell for replication.

Predict the expected size of a colony PCR product based on primer binding sites relative to the insert within a plasmid and interpret agarose gel results

Equals the exact number of base pairs from the 5′ start of the forward primer to the 5′ start (or 3′ end) of the reverse primer on the plasmid map, spanning the distance between their binding sites