BME 711 Molecular Interactions

Biomolecules: 

organic molecules in living organisms

Organic molecules:

characterized by a carbon-based framework and the presence of carbon-hydrogen bonds

Biomolecules = Building Blocks of Life (how are they created originally (theory)?) (Video)

What is the smallest particle of any element

an atom.

What bond results in molecules usually ?

covalent

bonds (sharing electrons between atoms).

Electrons Four Important Biological Roles

form covalent bonds, create ions when gained or lost, capture and store energy, create free readicals

Covalent Bonds a definition

result when atoms share elctrons. tehse bidns require the most energy to make or break

Nonpolar molecules

have an even distriubution of electrons, ex. fatty acid

polar molecules

have regions of partical charge , ex. water

ionic bonds

are elctrostsatic attractions between ions, ex. sodium chloride

hydrogen bonds

form between a hydrogen atom and a nerby oxygen, nitrogen, or flourine atom, ex. water and otehr water molecules

Van der Waals Forces

weak, nonspecific attractions between atoms

hydrophillic inetractions

molecules that have polar regions or ionic bodns radily inetract with the polar regions of water, they are able to easily disolve in water, ex. salt

hydrophobic interactions

repel watr molecules, ex. phospholipids

Case study with hemorage stoping aprticels

had to make them hydrophillic so they soak in the blood and not repel it

Acid

a molecule that contributes H+ to a solution, pH less than 7

base

a moelcules that decreases the H+ concentrtaion of a solution by combining with free H+, pH greater than 7

classes of Biomolecules

proteins, carbohydrates, lipids, nucelotides

What do Most Biomolecules Contain

• Carbon

• Hydrogen

• Oxygen

What percent of tyhe body mass do biomolecules make up?

more than 90%

Formation of Lipids

Glyercerol + Fatty acid

glycerol

a simple 3-carbon molecules that amkes up the backbone of most lipids

monoglyveride

glycerol plus one datty acid

diglyceride

glycerol plus two fatty acids

triglyceride

glycerol plus three fatty acids

The Miller–Urey experiment generated organic molecules from a mixture of simple inorganic compounds under simulated prebiotic conditions. Which modification would most directly test whether the specific atmospheric composition assumed in the original experiment was necessary for organic synthesis?

A. Increase the electrical discharge intensity while keeping the gas composition constant

• B. Systematically vary the relative concentrations of CH₄, NH₃, H₂, and H₂O while maintaining the same energy input

• C. Increase the volume of the reaction vessel without changing the reactant concentrations

• D. Replace the condenser with a larger condenser while maintaining all chemical conditions

• B. Systematically vary the relative concentrations of CH₄, NH₃, H₂, and H₂O while maintaining the same energy input

The detection of amino acids following a Miller–Urey-type experiment provides evidence that:

A. Complete living cells can spontaneously assemble under prebiotic conditions

• B. Genetic information can emerge directly from inorganic molecules

• C. Some biologically relevant organic molecules can form abiotically under certain environmental conditions

• D. The precise atmospheric composition of early Earth has been experimentally confirmed

• C. Some biologically relevant organic molecules can form abiotically under certain environmental conditions

Suppose a researcher wants to engineer an artificial protocell capable of maintaining an internal chemical environment distinct from its surroundings. Which feature would be most critical to achieving this?

• A. A membrane-bound compartment with selective permeability

• B. A high concentration of extracellular proteins

• C. A rigid extracellular matrix

• D. Randomized distribution of molecules throughout the surrounding solution

• A membrane-bound compartment with selective permeability

Which statement represents the most scientifically appropriate limitation when extrapolating the Miller–Urey results to the origin of life?

• A. Organic molecules cannot form without pre-existing biological catalysts

• B. Formation of organic molecules does not demonstrate the subsequent emergence of self-replication, metabolism, or cellular organization

• C. Amino acids are unrelated to modern biological systems

• D. Electrical energy cannot drive chemical reactions under natural conditions

• B. Formation of organic molecules does not demonstrate the subsequent emergence of self-replication, metabolism, or cellular organization

Consider a hypothetical prebiotic system in which amino acids are produced efficiently but no compartmentalization occurs. Which evolutionary problem would remain particularly difficult to solve?

• A. Production of carbon-containing molecules

• B. Establishment of an internal environment capable of concentrating and coupling chemical reactions

• C. Formation of water

• D. Absorption of ultraviolet radiation

• B. Establishment of an internal environment capable of concentrating and coupling chemical reactions

Why is RNA particularly attractive as a candidate for an early biological information system?

• A. RNA is chemically identical to both proteins and DNA

• B. RNA can simultaneously function as an information-containing polymer and, in some cases, as a catalyst

• C. RNA requires proteins to exist but does not require nucleotides

• D. RNA can only function as a structural component

• B. RNA can simultaneously function as an information-containing polymer and, in some cases, as a catalyst

Which sequence most logically represents a plausible progression from prebiotic chemistry toward primitive cellular systems?

• A. Complex cells → proteins → amino acids → inorganic molecules

• B. Organic monomers → polymers → compartmentalization → emergence/selection of self-replicating systems

• C. DNA replication → organelles → amino acids → lipid synthesis

• D. Proteins → fully developed cells → inorganic molecules → polymers

• B. Organic monomers → polymers → compartmentalization → emergence/selection of self-replicating systems

An engineer constructs two protocell populations. Population A has a membrane but no mechanism for retaining useful metabolites. Population B has a membrane with selective permeability. Assuming equivalent external nutrient concentrations, which population would be expected to provide a stronger basis for sustained internal biochemical reactions, and why?

• A. Population A, because unrestricted diffusion maximizes molecular movement

• B. Population A, because membranes prevent all chemical exchange

• C. Population B, because selective permeability can help maintain concentration gradients and distinct internal chemistry

• D. Population B, because selective membranes eliminate the need for energy-dependent processes

• C. Population B, because selective permeability can help maintain concentration gradients and distinct internal chemistry

Suppose an experiment demonstrates that increasing electrical energy input increases the concentration of organic products. Which additional experiment would provide the strongest evidence that electrical energy is causally responsible for their formation?

• A. Repeat the experiment with a larger reaction vessel

• B. Run an otherwise identical control without electrical discharge

• C. Measure the temperature only at the end of the experiment

• D. Increase the concentration of all gases simultaneously

• B. Run an otherwise identical control without electrical discharge

1. A hypothetical prebiotic system successfully produces amino acids, forms membrane-bound vesicles, and contains RNA-like polymers. Which additional property would most strongly distinguish a chemically organized protocell from a collection of independently formed molecules?

• A. The molecules have different molecular weights

• B. The system can maintain an internal chemical state and support heritable self-replication

• C. The system contains carbon

• D. The system contains water

• B. The system can maintain an internal chemical state and support heritable self-replication

Fatty acids

long chains of carbon atoms bound to hydrogens, with a carboxyl(-COOH) or “acid” group at one end of the chain

saturdated fatty acid

fatty acids have no double bonds between carbonds

monousaturated fatty acids

have one double bond between two of the carbons in teh chain

polyunsaturated fatty acid

have two or more double bonds between carbons in the chain

Eiconsanoides

modified 20-carbon fatty acids with a compelte or partial carbon ring at one end and two long carbon cahin “tails”

Jobs of lipids

quick localized messnegers (inflamation responses, blood clotting), soring energy, boundaries with water, dual nature for cell embrane

steroids

lipids related moleculres whose structure includes four linked carbon rings

cholesterol

the primary source of steroids in the human body

phospholipids

have 2 fatty acids and a phosphate group (-H2PO4)

cholesterol is needed for ?

building cell membranesm producing hormones (like estrogen and testeosterone), synthesizing vitamin D

Are lipids bad?

they are a necessity for life , too much cholesterol in the body can mess with lipid boudndaries and folding. Lipids are needed for many body functions but too many lipds in the body is harmful.

Carbohydrates (CH2O)n

the most common biomolecule, main energy source; structural molecule

Monosaccharides

simple sugars , five(Ribose, docyribose) or six(fructose, gliucose) carbons

Disaccharides

consist of glucose plus another monosaccharide

sucrose

glucose + fructose

maltose

glucose + glucose

polysaccharides

glucose polymers; stored energy

polysaccharides for animals, plants, yeast

Chitin, Glycogen, Cellulose, startch, Dextran

Nucleotide

sonsist of one or more phosphate groups, a 5-carbon sugar, and a carbon-nitrogen ring structure called a nitrigenous base

Nitroigenous Bases

Purines(Adenine A, Guanoine G) and Pyrimidines (Cytosine C, Thymine T, Uracil U)

single nucelotides

include the enegry -transfering compounds ATP (adenosine triphosphate) and ADP (adenosine diphosphate) , as well as cyclic AMP, a molecule important in the transfer of signals betwwen cells

Nucleic acids (Nucleotide polymers)

such as RNA and DNA store and transmit generic information

RNA (Ribonucleic acid)

a single-strand nucelic acid with ribose as the sugar in the backbone, and four bases - adenine, guanine, cytosine, and uracil

DNA (deoxyribonucleic acid)

a double helix, a three dimensional stucture that fiorms when two DNA strands link through hydrogen bonds between complentary base pairs. Deoxyribose is the sugar in the backbone and the four bases are adenine, guanine, cytosine, and thymine

antiparallel oruentation

the 3’ end of one strand is bound to the 5’ end of the second starnd

the genome encodes our bodys funcamental blueprint, process

transcription, mRNA processing, atchament of ribosomal subunits, translation, termination

A researcher wants to use CRISPR-Cas9 to introduce a mutation into a specific gene. Which sequence of events most accurately describes the mechanism presented in the video?

A. Cas9 first randomly cleaves genomic DNA, followed by guide RNA selection of the correct fragment
B. Guide RNA recognizes a complementary DNA sequence, recruits Cas9, and Cas9 cleaves the target DNA
C. Cas9 synthesizes a complementary DNA strand, which then replaces the endogenous gene
D. Guide RNA directly cleaves the DNA while Cas9 functions primarily as a DNA-repair enzyme

B. Guide RNA recognizes a complementary DNA sequence, recruits Cas9, and Cas9 cleaves the target DNA

The natural biological function of the CRISPR-Cas9 system in bacteria is most accurately described as:

A. A mechanism for increasing bacterial mutation rates
B. A DNA replication system that promotes bacterial proliferation
C. An adaptive immune mechanism that protects bacteria from invading genetic material
D. A system used exclusively for repairing spontaneous mutations

C. An adaptive immune mechanism that protects bacteria from invading genetic material

Suppose the sequence of a target gene is changed by a single nucleotide mutation near the intended CRISPR target site. Which component of the CRISPR-Cas9 system would primarily need to be redesigned to retarget the system to the new sequence?

A. Cas9 nuclease
B. Guide RNA
C. DNA polymerase
D. Ribosomal RNA

B. Guide RNA

A CRISPR-Cas9 complex produces a double-strand break in a genomic locus. The cell repairs the break inaccurately, introducing small insertions or deletions. What is the most likely consequence?

A. Permanent gene knockout due to disruption of the coding sequence
B. Increased transcription because Cas9 activates the promoter
C. Conversion of genomic DNA directly into RNA
D. Complete prevention of DNA replication throughout the cell

A. Permanent gene knockout due to disruption of the coding sequence

A biomedical engineer wants to replace a disease-associated DNA sequence with a specific corrected sequence rather than simply disrupt the gene. Which strategy best corresponds to the mechanism illustrated in the video?

A. Deliver Cas9 alone and allow random DNA degradation
B. Deliver guide RNA without Cas9
C. Provide a donor DNA template containing the desired sequence for repair
D. Prevent the cell from repairing the Cas9-induced DNA break

C. Provide a donor DNA template containing the desired sequence for repair

Consider two potential genomic sites:

• Site 1: Highly complementary to the guide RNA and appropriately positioned relative to the PAM

• Site 2: Contains several mismatches to the guide RNA but is otherwise similar

Which statement best describes the engineering concern associated with Site 2?

A. It guarantees more efficient editing than Site 1
B. It may represent a potential off-target site
C. It cannot interact with Cas9 under any circumstances
D. It will automatically become the primary editing site

B. It may represent a potential off-target site

You want to determine whether a newly identified gene contributes to a disease phenotype in cultured human cells. Which CRISPR-Cas9 strategy would provide the most direct initial functional test?

A. Introduce a guide RNA targeting the gene and examine the phenotype following gene disruption
B. Introduce Cas9 without a guide RNA and measure cell growth
C. Increase expression of unrelated genes and compare cell morphology
D. Introduce random DNA fragments and determine whether the phenotype changes

A. Introduce a guide RNA targeting the gene and examine the phenotype following gene disruption

Which feature most directly explains why CRISPR-Cas9 is considered a programmable genome-editing technology?

A. Cas9 can recognize every DNA sequence independently of RNA
B. The DNA sequence recognized by the system can be changed primarily by changing the guide RNA
C. Cas9 randomly mutates the entire genome and researchers select desirable cells
D. CRISPR works only at naturally occurring bacterial DNA sequences

B. The DNA sequence recognized by the system can be changed primarily by changing the guide RNA

A biomedical engineering research team wants to investigate whether a particular mutation causes a cellular disease phenotype. Which experimental approach best uses the principle demonstrated by CRISPR-Cas9?

A. Randomly mutating the entire genome and screening for changes
B. Precisely modifying the suspected genomic locus and comparing the resulting cellular phenotype with an appropriate control
C. Increasing the concentration of Cas9 until all cellular DNA is degraded
D. Removing all RNA from the cell before introducing the target gene

B. Precisely modifying the suspected genomic locus and comparing the resulting cellular phenotype with an appropriate control

A researcher designs a CRISPR-Cas9 system with the following components:

Cas9 + guide RNA + target DNA + donor DNA

Which outcome most appropriately represents the intended sequence of events?

A. Guide RNA cuts donor DNA → Cas9 synthesizes RNA → donor DNA destroys target DNA
B. Guide RNA recognizes target DNA → Cas9 generates a DNA break → cellular repair machinery can use donor DNA to introduce a desired sequence
C. Donor DNA binds Cas9 → Cas9 converts donor DNA into RNA → guide RNA repairs the chromosome
D. Cas9 randomly cuts the genome → donor DNA independently integrates at any genomic location

B. Guide RNA recognizes target DNA → Cas9 generates a DNA break → cellular repair machinery can use donor DNA to introduce a desired sequence

Amino Acids

It has a carboxyl group (-COOH), an amino group (-NH2), and a hydrogen attached to the same carbon. The fourth bond of the carbon attaches to a cariable “R” group

Peptides

the polymers the 20 protein-forming amino acids assemble into

Peptide length ranges

oligopeptide: 2-9

polypeptide: 10-100 amino acids

proteins: >100 amino acids

primarly strcture

the sequence of amino acids in a pepeptide chain

Which statement best explains why the primary structure of a protein is critical for determining its eventual function?

A. The primary structure directly determines the protein's cellular location but not its shape.
B. The amino acid sequence determines the chemical interactions that drive the protein toward a particular three-dimensional structure.
C. The primary structure determines only the number of subunits in a protein.
D. The amino acid sequence has little effect on folding because chaperone proteins determine the final structure.

B. The amino acid sequence determines the chemical interactions that drive the protein toward a particular three-dimensional structure.

Which molecular interaction is primarily responsible for stabilizing the α-helices and β-sheets characteristic of protein secondary structure?

A. Disulfide bonds between cysteine side chains
B. Hydrogen bonds involving the peptide backbone
C. Peptide bonds between amino acid side chains
D. Ionic bonds between different protein subunits

B. Hydrogen bonds involving the peptide backbone

A mutation replaces a hydrophobic amino acid buried within the core of a protein with a highly polar amino acid. Which outcome is most directly expected?

A. The mutation can alter protein folding and potentially reduce protein stability or function.
B. The mutation will always have no effect because only the primary structure determines function.
C. The mutation will necessarily create a new peptide bond.
D. The mutation will cause the protein to form additional quaternary structures.

A. The mutation can alter protein folding and potentially reduce protein stability or function.

What is the primary role of molecular chaperones/chaperonins during protein folding?

A. They determine the amino acid sequence of newly synthesized proteins.
B. They permanently become part of the protein's tertiary structure.
C. They assist proteins in reaching or maintaining appropriate folded states and can help prevent inappropriate aggregation.
D. They replace peptide bonds that have been broken during translation.

C. They assist proteins in reaching or maintaining appropriate folded states and can help prevent inappropriate aggregation.

A therapeutic protein is exposed to a condition that disrupts the interactions maintaining its three-dimensional structure but does not initially break its peptide bonds. Which consequence is most likely?

A. Its amino acid sequence will immediately change.
B. Its biological activity may decrease because its three-dimensional structure has been disrupted.
C. Its primary structure will automatically become a quaternary structure.
D. The protein will necessarily acquire a new biological function.

B. Its biological activity may decrease because its three-dimensional structure has been disrupted.

Enzymes (Lactase)

Catalyze chemical reactions

Membrane transporters (Ion pump) 

Move substances across membranes

Signal molecules (Insulin)

Communicate between cells

Receptors (Growth factor receptor) 

Bind signals and trigger responses

Binding proteins (LDL)

Carry or store molecules

Immunoglobulins (Antibodies)

Protect against pathogens

Regulatory proteins (p53)

Control cellular processes

Structural proteins (Actin)

Support cell shape and structure

Motor proteins (Myosin)

Generate movement within cells

Storage proteins (Ferritin)

Store nutrients or ions

Chaperone proteins (HSP70)

Help other proteins fold properly

Soluble proteins

bind to other molecules (ligands) at their

binding sites through noncovalent interactions.

Specificity (the structure and function

are closely related):

the protein and

ligand need to match (relatively) to

complement each other.

Can we design a protein (agonist) to match a

specific protein/ligand for a desired effect?

Morphine mimics endorphins by binding to opioid

receptors, reducing the neuron excitation.

As a result of noncovalent interactions:(Protein Interactions)

Protein-binding reactions are reversible (P + L PL)

• Affinity: the degree to which a protein is attached to a ligand

• Reversible binding reactions go to a state of equilibrium, where the

rate of binding (P + L→ PL) is exactly equal to the rate of unbinding,

or dissociation (PL → P + L).

Competitors:

related ligands compete for the binding site, and

the one with a higher affinity (Keq=1/Kd) wins.

How is the protein binding

controlled in the body?

Activation

• Inhibition

proteyletics activation

proteins is inactive until peptide fragments are removed

cofactors

required for an active binding site