BMB 251H - Molecular and Cell Biology I - Exam I

Spring 2026 - Dr. Lindner, PSU

Cell needs

Eat food, Eliminate waste, Avoid danger, Reproduce, KNOW how to do these things

Plasma membrane composition

Phospholipid bilayer proposed of lipids and proteins

What do membrane proteins transport in and out of the cell?

Sugars, Amino acids, peptides, amines, Ions

RNA world hypothesis

RNA came first, but DNA was more stable, so it was preferred

DNA

Hereditary information transferred to progeny in the form of a double-helix of nucleotide chains

What makes the backbone of DNA unique?

Big whopping negative charge

What is responsible for the directionality of DNA and RNA?

Asymmetry of monomers

What is each replicated DNA copy composed of?

A double-helix of one old strand and one new strand

Replication

One strand of DNA is replicated into two new strands

Transcription

DNA is “un-zipped” to form strand(s) of RNA

Translation

The amino acid sequence of RNA is “read” and translated to create proteins

Exceptions to Central Dogma

Hypothesized to be no exceptions to the true central dogma, however Watson’s model does contain exceptions

Four major methods of gene mutation

Mutation (Replication error), Duplication, Shuffling, Horizontal Gene Transfer

Cell Endosymbiosis Hypothesis

Speculation of how mitochondria / chloroplasts made their way into eukaryotic cells. Started as prokaryotic endosymbionts that travelled into the cell and were engulfed, resulting in a second membrane

Elements that make up 99% of living matter

C, H, O, N

Rarer, essential elements that make up 0.9% of living matter

P, S, Cl, Ca, K, Na, Mg

Trace elements that make up <0.1% of living matter

V, Cr, Mn, Fe, Co, Ni, Co, Ni, Cu, Zn, Mo, Se, I, F

Bond types/interactions in order of strength

Covalent Bonds (Disulfide is Strongest), Ionic (Electrostatic) Interactions, Hydrogen Bonds, Van der waals Attraction

How strong are covalent bonds in comparison to the cell’s thermal energy?

100x stronger

How weak are non-covalent bonds compared to covalent bonds?

95% weaker

Polymer of carbohydrate

Polysaccharide

Polymer of amino acids

Protein

Polymer of nucleotides

Nucleic Acid

Methyl

-CH3

Hydroxyl

-OH

Carboxyl

COO-

Carbonyl

C=O

Amine

NH3+

Sulfhydryl

SH

Phosphate

PO3

Affinity

Measure of relative time molecules stay together

Cell Composition

30% chemicals, 70% water

What type of bonding is responsible for base pairing in DNA?

Hydrogen Bonding

Energy favorability of condensation reactions

Energetically unfavorable

Energy favorability of hydrolysis reactions

Energetically favorable

Where can functional groups be found on sugars?

From carbons 3-8

Nucleotide Formula

Phosphate, 5-carbon sugar, purine/pyrimidine base

Amphiphilic

One end of the molecule is hydrophilic and the other end is hydrophobic

Purines

Two rings, Adenine and Guanine

Pyrimidines

One ring, cytosine, thymine, uracil

How do nucleotides store energy

Phosphoanhydride Bonds

Catabolic Pathways

Break down molecules to generate energy

Anabolic Pathways

Use building blocks to synthesize molecules

Is oxidation or reduction favorable?

Oxidation is favorable, reduction is unfavorable

How are energetically unfavorable reactions managed

Energetically unfavorable reactions are coupled with energetically favorable reactions to manage the energy requirement

Activated Carrier Molecules

ATP, NADH, NADPH, FADH2, Acetyl CoA

Which electrons carriers are used for catabolic redox?

NAD+ and NADH

Which electron carriers are used for anabolic redox?

NADPH and NADP+

How do cells release energy to properly utilize food sources?

Stepwise release of energy and storage in electron carriers

Where does glycolysis take place?

Cytoplasm/Cytosol

Where does the Citric Acid Cycle take place?

Mitochondria

Where does oxidative phosphorylation take place?

The membrane of mitochondria

Where does fatty acid oxidation take place?

Mitochondria

What goes in and out of glycolysis?

In: Glucose (C6H12O6), 2 ATP ; Out: 2 NADH, 4 ATP, 2 Pyruvate

What goes in and out of the citric acid cycle?

In: Pyruvate modified to Acetyl CoA ; Out: 3 NADH, 1 GTP, 1 FADH2, 2 CO2

What is the final electron acceptor in the electron transport chain?

Oxygen

What does the process of fatty acid oxidation do?

Breaks down fatty acyl CoA to acetyl CoA, feeding into the citric acid cycle until completely degraded

What kind of energy ultimately powers most biological processes?

Light energy

What energetically favorable process is paired to the energetically unfavorable reaction of ATP synthesis?

The electron transport chain

How are peptide bonds formed?

A condensation reaction between the C-terminus of one amino acid and the N-terminus of another

Where is the phi angle of protein folding?

Between the alpha carbon and the adjacent Nitrogen atom

Where is the psi angle of protein folding?

Between the alpha carbon and the adjacent Carbon atom

Aspartic Acid Charge/Polarity

Negative

Glutamic Acid Charge/Polarity

Negative

Arginine Charge/Polarity

Positive

Lysine Charge/Polarity

Positive

Histidine Charge/Polarity

Positive

Asparagine Charge/Polarity

Polar

Glutamine Charge/Polarity

Polar

Serine Charge/Polarity

Polar

Threonine Charge/Polarity

Polar

Tyrosine Charge/Polarity

Polar

Alanine Charge/Polarity

Non-Polar

Glycine Charge/Polarity

Non-Polar

Valine Charge/Polarity

Non-Polar

Leucine Charge/Polarity

Non-Polar

Isoleucine Charge/Polarity

Non-Polar

Proline Charge/Polarity

Non-Polar

Phenylalanine Charge/Polarity

Non-Polar

Methionine Charge/Polarity

Non-Polar

Tryptophan Charge/Polarity

Non-Polar

Cysteine Charge/Polarity

Non-Polar

Aspartic Acid 3-Letter Code

Asp

Glutamic Acid 3-Letter Code

Glu

Arginine 3-Letter Code

Arg

Lysine 3-Letter Code

Lys

Histidine 3-Letter Code

His

Asparagine 3-Letter Code

Asn

Glutamine 3-Letter Code

Gln

Serine 3-Letter Code

Ser

Threonine 3-Letter Code

Thr

Tyrosine 3-Letter Code

Tyr

Alanine 3-Letter Code

Ala

Glycine 3-Letter Code

Gly

Valine 3-Letter Code

Val

Leucine 3-Letter Code

Leu

Isoleucine 3-Letter Code

Ile

Proline 3-Letter Code

Pro

Phenylalanine 3-Letter Code

Phe

Methionine 3-Letter Code

Met