1
Q
7 Characteristics of life
A
Reproduction
Growth & Development
Responds to Environment
Metabolism/E
Genetic material (DNA) as info
Made of 1/1+ cells
Evolution over generations
Homeostasis
2
Q
How do cells vary?
A
Diversity: shape, size, function (electrical/photosynthetic) -> determined by proteins, DNA packaging (nucleus vs nucleoid)
3
Q
Prokaryotes Vs. Eukaryotes
A
DNA packaged: nucleoid (prok) & nucleus (euk)
Membrane bound organelles: no (prok) & yes (euk)
Cytoskeleton: No (pro) & Yes (euk)
Cell wall: yes (pro) & Yes only in plants/fungi (euk)
4
Q
What do all cells have in common?
A
DNA, ribosomes, plasma membrane (phospholipids/proteins)
5
Q
Model System
A
A whole organism we use in a laboratory
↳ biological species extensively studied to understand particular biological phenomena, with the expectation that discoveries made in that organism will provide insight into the workings of other organisms.
6
Q
Benefits of Model systems
A
Relatively easy to maintain in lab, Reproduce quickly,
Many replicates (Statistical
analysis)
Vary conditions (targeted
experiment)
7
Q
types of model systems
A
heba (cell culture), ecoli, mice, yeast, fruit flies, nematodes
8
Q
Protein
A
Polymer built from amino acids that provides cells with their shape, structure, and performs most of
their activities.
9
Q
Amino Acid
A
Small organic molecule containing both an amino group and a carboxyl group; building block of
proteins.
10
Q
Peptide Bond
A
Chemical bond between the carbonyl group of one amino acid and the amino group of another.
11
Q
Polypeptide:
A
Linear polymer composed of multiple amino acids. Proteins are made of one or more long polypeptide
chains.
12
Q
Amino Acid Sequence
A
The order of amino acid subunits in a protein chain (primary structure)
13
Q
Polypeptide Backbone
A
Repeating sequence of –N–C–C– atoms forming the protein core; side chains attach here
14
Q
N-Terminus
A
The end of a polypeptide chain carrying a free α-amino group.
15
Q
C-Terminus
A
The end of a polypeptide chain carrying a free carboxyl group (–COOH)
16
Q
Side Chain (R groups)
A
Portion of an amino acid not in peptide bonds; gives each amino acid unique properties.
17
Q
Electrostatic Interactions
A
Forces attracting opposite charges, e.g., ionic bonds.
18
Q
Van der Waals Attractions
A
Weak interactions due to fluctuating charges between atoms close together
19
Q
Hydrophobic Interactions
A
Nonpolar molecules cluster to avoid disrupting water’s H-bond network. push together membrane phospholipids and fold proteins into a compact,
globular shape.
20
Q
Name the non-covalent interactions that facilitate protein folding.
A
Hydrophobic interactions
van der waals
electrostatic interactions
hydrogen bonding
21
Q
How does amino acid sequence determine protein shape and function?
A
AA Sequence encodes each residue’s chemical properties, which drive folding interactions. These interactions produce a stable 3D shape that defines function. Mutations can alter properties
22
Q
What is an Alpha Helix?
A
Folding pattern where a single polypeptide twists into a rigid cylinder stabilized by hydrogen bonds between every 4th amino acid; found in keratin (hair, nails, skin).
23
Q
What is a Beta Sheet?
A
Folding pattern where neighboring polypeptide regions align side by side with hydrogen bonds, forming a flat/pleated structure; found in silk and amyloid fibers.
24
Q
What stabilizes alpha helices and beta sheets?
A
Stabilized by hydrogen bonds between backbone N–H and C=O groups, not R groups.
25
How to identify helix vs. sheet?
Helices are twisted, sheets are flat and rigid.
26
Where are alpha helices and beta sheets located in the cell?
Alpha helices often in membrane proteins; beta sheets in many proteins, depends on R group chemistry and environment.
27
What is Primary Structure in proteins?
Linear sequence of amino acids.
28
What is Secondary Structure in proteins?
Local folding into alpha helices and beta sheets.
29
What is Tertiary Structure in proteins?
Complete 3D structure of a single polypeptide, includes side chain interactions.
30
What is Quaternary Structure in proteins?
Complex of multiple polypeptide chains, e.g., hemoglobin (4 subunits).
31
What are the levels of protein structure?
Primary: sequence; Secondary: helices/sheets; Tertiary: 3D fold; Quaternary: multiple chains together.
32
What is a Protein Domain?
Compact, stable protein segment that folds independently and usually has a specific function; evol conserved across species.
characteristic and stable 3D structure, often consisting of alpha-helices, beta-sheets
33
What is an Intrinsically Disordered Sequence?
Region lacking defined structure, flexible, keeps domains close or links proteins together.
34
What is the function of domains vs. disordered regions?
Domains: perform functions; Disordered: flexible connectors, scaffolds, bring domains/proteins together.
35
What is a Protein Subunit?
Monomeric unit within a larger protein complex.
36
What is a Dimer?
Protein with 2 similar subunits.
37
What is a Trimer?
Protein with 3 similar subunits.
38
What is a Tetramer?
Protein with 4 similar subunits, e.g., hemoglobin.
39
What is the difference between Homo and Hetero?
Homodimer = identical subunits; Heterodimer = different subunits.
40
What is a Protein Filament?
Long fibrous structures formed by monomer assembly; structural/movement roles.
41
What is a Tubular Sheet?
Beta-sheet structures forming hollow tubes, e.g., ER tubules.
42
What is a Hollow Sphere?
Empty spherical protein structure, natural or engineered (e.g., viral capsids).
43
What is a Globular Protein?
A spherical, water-soluble protein that performs functional roles such as enzymes, transport (e.g., hemoglobin), and signaling unlike fibrous proteins
44
What is a Fibrous Protein?
Long, skinny protein; insoluble in water, structural roles: providing support, strength, & elasticity. (e.g., Extracell M, cytoskeleton).
45
How do proteins assemble into higher structures?
Filaments: Actin fibers of the cytoskeleton; support and restrict cell membrane.
Hollow tubes: Tubulin subunits form microtubules for 3D support/transport.
Spheres: Viruses w/ protein shells (capsids) for protection.
46
What is a Protein?
Polymer built from amino acids that provides cells with their shape, structure, and performs most of their activities.
47
What is an Amino Acid?
Small organic molecule containing both an amino group and a carboxyl group; building block of proteins.
48
What is a Peptide Bond?
Chemical bond between the carbonyl group of one amino acid and the amino group of another.
49
What is a Polypeptide?
Linear polymer composed of multiple amino acids. Proteins are made of one or more long polypeptide chains.
50
What is an Amino Acid Sequence?
The order of amino acid subunits in a protein chain (primary structure).
51
What is a Polypeptide Backbone?
Repeating sequence of –N–C–C– atoms forming the protein core; side chains attach here.
52
What is the N-Terminus?
The end of a polypeptide chain carrying a free α-amino group.
53
What is the C-Terminus?
The end of a polypeptide chain carrying a free carboxyl group (–COOH).
54
What is a Side Chain?
Portion of an amino acid not in peptide bonds; gives each amino acid unique properties.
55
What is a Polar molecule?
Molecule/bond with uneven electron distribution.
56
What is a Nonpolar molecule?
Molecule lacking positive/negative charge separation; generally insoluble in water.
57
What are Hydrogen Bonds?
Weak noncovalent interaction between H (partially +) and N/O (partially –).
58
What are Electrostatic Interactions?
Forces attracting opposite charges, e.g., ionic bonds.
59
What are Van der Waals Attractions?
Weak interactions due to fluctuating charges between atoms close together.
60
What are Hydrophobic Interactions?
Nonpolar molecules cluster to avoid disrupting water’s H-bond network.
61
What is a Backbone Model?
Shows overall polypeptide chain organization for comparing structures.
62
What is a Wire Model?
Shows side chain positions; useful for predicting activity-related residues.
63
What is a Ribbon Structure?
Highlights backbone folds of the polypeptide.
64
What is a Space-Filling Model?
Shows protein surface contours; reveals exposed amino acids.
65
How to draw an amino acid at neutral pH?
Include amino group (–NH3+), carboxyl group (–COO–), H, and side chain (R) attached to central carbon.
66
What is a schematic of a polypeptide chain?
4 amino acids linked; identify backbone (–N–C–C–), peptide bonds, N-/C-termini, and side chains.
67
What are the chemical characteristics of side chains?
1) Polar Negatively charged, 2) Polar Positively charged, 3) Nonpolar, 4) Uncharged polar.
68
What types of interactions are involved in folding?
Van der Waals, hydrophobic interactions, H-bonds, ionic bonds.
69
How is protein shape determined?
Amino acid sequence encodes chemical properties → drives folding → stable 3D structure → function.
70
What is denaturation and renaturation?
Denature: The loss of a protein 3d structure (& function) due to disrupted weak bonds, often caused by heat, pH, or chemicals. It is usually irreversible, but sometimes reversible if conditions return to normal. Renature: protein refolds; may need chaperones.
71
What are the different protein models?
Backbone, wireframe, ribbon, and space-filling models show different structural features.
72
Why regulate protein activity?
Proteins drive nearly all cellular processes. Regulation ensures correct timing, location, and amount of activity to prevent waste, imbalance, or harm.
73
What are the four levels of protein regulation?
1) Gene expression (how much protein is made) 2) Protein degradation (protein lifetime) 3) Localization (where the protein is in the cell) 4) Direct activity regulation (chemical modifications or interactions).
74
What are 7 ways proteins are controlled?
1) Regulation by other molecules 2) Allosteric sites influence each other 3) Phosphorylation 4) Other covalent modifications 5) GTP binding proteins 6) ATP hydrolysis (motor proteins) 7) Protein complexes (machines).
75
What is feedback inhibition?
End product of a pathway inhibits an early enzyme. Prevents excess product buildup. Example: Final product acts as allosteric inhibitor.
76
Why is negative feedback more common?
It acts almost instantly, is reversible, and maintains balance. Positive feedback amplifies signals and is harder to control.
77
How does phosphorylation work?
Kinase transfers phosphate from ATP to protein. Covalent modification alters protein activity.
78
How does phosphorylation alter activity?
Phosphorylation can activate or inactivate a protein, change its shape, or trigger signaling cascades.
79
What is the difference between phosphorylation and allosteric regulation?
Phosphorylation: covalent, enzymatic. Allosteric regulation: non-covalent, reversible binding.
80
How many proteins are regulated by phosphorylation?
About 1/3 of ~10,000 proteins in a typical mammalian cell are phosphorylated at any time.
81
What is allosteric regulation?
Non-covalent; regulates protein shape and activity.
82
What is competitive inhibition?
Non-covalent; regulates activity by blocking substrate binding.
83
What is phosphorylation?
Covalent; regulates activation state (on/off).
84
What is ubiquitination?
Covalent; regulates degradation (tags proteins for destruction).
85
What are acetylation and palmitoylation?
Covalent; modifies protein activity or localization.
86
What are GTP binding proteins?
Non-covalent; regulate activation state via GTP/GDP switch.
87
How are GTP-binding proteins regulated?
Active when bound to GTP; inactive when GTP is hydrolyzed to GDP. Differs from phosphorylation because whole GTP is bound, not a phosphate added.
88
What is a protein machine?
Complex of proteins working together for efficiency. Examples: Ribosome, Replisome, Spliceosome: achieve a level of coordination, regulation, and functional capability that single proteins cannot.
89
What are the functions of membrane proteins?
1) Transport – channels, pumps for molecule movement 2) Anchors – link cytoskeleton to ECM 3) Receptors – detect and transmit signals 4) Enzymes – catalyze reactions at the membrane.
90
How do proteins associate with the plasma membrane?
• Transmembrane – span bilayer (α-helix or β-barrel) • Monolayer-associated – anchored by α-helix to one side • Lipid-linked – covalently bound to lipid tail • Protein-attached – interact indirectly via other proteins.
91
Why do proteins cross membranes as α-helices?
Hydrogen bonding within helix shields hydrophilic bonds; stable in hydrophobic core.
92
Why are multipass proteins amphipathic?
Hydrophobic residues face lipid tails; hydrophilic residues face inward to form a pore.
93
Describe the β-barrel arrangement.
β-strands form a cylinder. Hydrophobic residues face lipids, hydrophilic residues line the pore interior.
94
Why do cells need a support network for the plasma membrane?
Membrane is thin & fragile; support prevents rupture and maintains shape.
95
What is the difference between plant and animal membrane reinforcement?
Plants: Cell wall (cellulose) Animals: Cell cortex (actin + proteins).
96
What is the cell cortex of red blood cells?
Dense spectrin mesh attached to membrane proteins; gives biconcave shape & flexibility.
97
What are four ways protein diffusion is restricted?
1) Tethering to cortex (inside) 2) Anchoring to ECM (outside) 3) Binding to proteins on neighboring cells 4) Barriers (tight junctions).
98
How do tight junctions restrict protein diffusion?
Seal between epithelial cells prevents crossing; maintain polarity between apical & basal surfaces.
99
What is the structure and components of glycocalyx?
Carbohydrate-rich layer with glycoproteins, glycolipids, proteoglycans.
100
What are the functions of glycocalyx?
Protects from damage, lubricates for motility, enables cell recognition (lectins binding sugars).
101
How do WBCs roll and migrate to infection?
Endothelial lectins bind WBC glycoproteins (weak adhesion → rolling). Integrins strengthen binding → WBC stops & migrates across endothelium.
102
What is a protein standard (ladder/marker)?
Mixture of proteins with known molecular weights used to estimate size of unknown proteins.
103
What is a lysate?
Solution containing cellular components released after breaking open cells.
104
What is a homogenate?
Mixture produced by physically disrupting tissue or cells to release proteins and organelles.
105
What is a detergent?
Molecule that disrupts lipid bilayers, solubilizes membranes, and surrounds hydrophobic protein regions.
106
What is a micelle?
Sphere formed by detergents (amphipathic molecule) with hydrophobic tails inside and hydrophilic heads outside.
107
What is acrylamide/polyacrylamide gel (PAGE)?
Matrix used in electrophoresis to separate proteins by size.
108
What is an antibody?
Immune protein that specifically binds an antigen; used for protein detection in Western blotting.
109
What is densitometry?
Measurement of band intensity on a blot to quantify protein expression.
110
What is a Western blot?
A technique to detect specific proteins in a sample. Proteins are separated by gel electrophoresis, transferred to a membrane, and detected with antibodies.
111
How is a Western blot used in cell biology?
It identifies the presence, size, and relative abundance of proteins. This reveals changes in protein expression, modifications, or signaling pathways relevant to health and disease.
112
Why is equal loading necessary in Western blotting?
Equal amounts of protein must be loaded in each lane to ensure valid comparisons. A loading control (like actin) verifies equal loading across samples.
113
What are the steps of the Western blot procedure?
1) Prepare cell lysate 2) Run proteins on SDS-PAGE 3) Transfer proteins to nitrocellulose membrane 4) Block membrane 5) Incubate with primary antibody 6) Add enzyme-linked secondary antibody 7) Visualize bands.
114
How to make a lysate or homogenate?
Break open cells mechanically (grinding, sonication) or chemically. Detergents solubilize membranes and release proteins.
115
What is the role of detergents in lysates?
Detergents disrupt lipid bilayers and form micelles around hydrophobic protein regions, making them soluble.
116
Why denature and negatively charge proteins?
SDS unfolds proteins and coats them with negative charges. This ensures separation by size only during electrophoresis.
117
How to load and run PAGE?
Samples are pipetted into gel wells and separated by an electric field. Smaller proteins migrate faster through the polyacrylamide matrix.
118
What is the difference between PAGE and agarose gels?
PAGE: high-resolution protein separation by size. Agarose: larger pores, mainly used for DNA/RNA separation.
119
Where do proteins migrate on PAGE?
Larger proteins move slowly and remain near the top of the gel. Smaller proteins travel farther toward the bottom.
120
What is a protein standard?
Also called a ladder or marker. It contains proteins of known sizes to estimate the molecular weight of unknown proteins.
121
Why transfer proteins to a membrane?
The membrane provides a stable surface where proteins can be detected with antibodies, unlike the fragile gel.
122
What is an antibody?
An immune system protein that binds specifically to an antigen. In Western blotting, antibodies detect target proteins.
123
What is the difference between primary and secondary antibodies?
Primary binds the protein of interest. Secondary binds the primary and is enzyme-linked for visualization.
124
Why is the secondary antibody enzyme-linked?
To enable visualization of the primary antibody binding to the target protein.
125
Why is the secondary antibody enzyme-linked?
The enzyme produces a detectable signal (chemiluminescence or fluorescence), amplifying visibility of the protein bands.
126
How is a Western blot developed?
After antibody binding, a substrate reacts with the enzyme on the secondary antibody to produce light or color, making bands visible.
127
How are Western blots quantitated?
Band intensity is measured by densitometry. This quantifies relative protein expression between samples.
128
How to summarize treatments?
• List all experimental conditions tested
• Identify which lanes are controls (no treatment or baseline)
• Note which lanes have treatments alone or in combination
129
How to identify protein level trends?
• Compare protein of interest band intensity across treatments vs controls
• Loading control should remain relatively constant — if it doesn’t, note variation
• Ask: Does the protein of interest increase, decrease, or stay constant?
130
How to link protein trends to biology?
• Increased phosphorylation = protein activation
• Decreased phosphorylation = inhibition or deactivation
• Relate these changes back to the biological mechanism being tested (growth, inhibition, signaling cascade)
131
How to use densitometry?
• Circle and measure both protein of interest and loading control bands
• Plot ratio of phospho-protein (or protein of interest) / loading control
• Each lane = one bar per protein of interest
• Taller bars = stronger relative signal
• Interpret graph trends to confirm regulation across treatments
132
What is binding specificity?
The ability of a protein to selectively bind to one (or very few) molecules due to the precise fit between its binding site and the ligand.
133
What is a ligand?
A molecule that binds to a specific site on a protein.
134
What is a binding site?
A region on the protein surface, often a cavity or groove, that interacts with a ligand using noncovalent bonds and amino acid side chains.
135
What is equilibrium?
State where forward and reverse reaction rates are equal, so there is no net chemical change.
136
What is the equilibrium constant (Keq)?
The ratio of product to substrate concentrations when a reversible reaction reaches equilibrium.
137
What is an enzyme?
A protein that catalyzes a specific chemical reaction.
138
What is a catalyst?
A substance that accelerates a reaction by lowering its activation energy. Enzymes act as catalysts in cells.
139
What is an active site?
The region on an enzyme where a substrate binds and is transformed during catalysis.
140
What is a substrate?
The molecule upon which an enzyme acts.
141
What are products?
The molecules generated by a biochemical reaction, such as an enzymatic transformation.
142
What is activation energy?
The energy barrier that must be overcome for a chemical reaction to occur.
143
Why does protein activity depend on specific binding?
Proteins must fit their ligands precisely, allowing enough noncovalent bonds for stable, selective binding.
144
How do proteins interact with other molecules?
Via binding sites shaped by amino acid side chains forming multiple weak interactions.
145
What bonds facilitate ligand-protein interactions?
Hydrogen bonds, ionic attractions, van der Waals forces, hydrophobic interactions.
146
What is the difference between weak and strong ligand associations?
Weak: few bonds, transient. Strong: many bonds, tight fit, long-lasting.
147
What is the role of side chains in binding pockets?
They determine the shape and chemical environment of the binding site, enabling specific ligand recognition.
148
What is the significance of non-binding protein regions?
Provide stability, orientation, flexibility, and support protein function.
149
How to identify equilibrium in a diagram?
Rates: forward = reverse. Concentrations: plateaus where reactants and products stop changing.
150
What does Keq reveal about molecular interactions/binding?
High Keq = strong binding affinity. Low Keq = weak binding.
151
What is the function of an enzyme?
Enzymes lower activation energy, speeding up reactions without altering ∆G.
152
How to calculate K (equilib constant)
Concentration of P over concentration of R
153
154
Why are enzymes essential?
They allow biological reactions to occur at rates fast enough to sustain life.
155
What is the effect of enzymes on activation energy?
Enzymes stabilize the transition state, lowering the energy barrier to reaction.
156
How to read an enzyme vs no enzyme graph?
Enzyme reduces activation energy peak. ∆G remains the same since reactant and product energies don’t change.
157
What is the equation for enzymatic reaction?
S+E, E+P →ES→EP→ E+P
158
What are the two mechanisms of enzyme action?
1) Strains substrate toward transition state. 2) Brings substrates together in proximity and correct orientation (increase rxn likelihood).
159
What are the four main functions of the plasma membrane?
Selective barrier, receiving information, import/export of molecules, movement/expansion.
160
List the 7 subcellular compartments enclosed by internal membranes.
Mitochondrion, transport vesicle, ER, nucleus, peroxisome, lysosome, Golgi.
161
What are two shared features of all membrane lipids?
Hydrophobic tail(s) (1 or 2) and hydrophilic head.
162
How do unsaturated and saturated fatty acids differ?
Saturated = all single C–C bonds; unsaturated = one or more C=C double bonds.
163
Why is a lipid bilayer self-sealing?
It’s energetically favorable — hydrophobic tails avoid water, so tears reseal.
164
How does the plasma membrane act as a two-dimensional fluid?
Lipids/proteins move independently within the bilayer; fluidity allows signaling, diffusion, fusion.
165
How is the plasma membrane flexible?
Entire bilayer can bend → allows 3D shapes, vesicles, cell deformation.
166
What are the 4 types of lipid motility? Which are spontaneous?
Lateral diffusion ★, flexion ★, rotation ★, flip-flop (non-spontaneous).
167
What two properties of hydrocarbon tails affect fluidity?
Tail length (shorter = more fluid) and saturation (unsaturated = more fluid).
168
How does this support the fluid mosaic model?
The membrane is fluid + a mosaic of lipids and proteins; the model holds up.
169
Compare a liposome, micelle, and plasma membrane.
Micelle = single layer, hydrophobic core; Liposome = bilayer with aqueous interior; Plasma membrane = bilayer enclosing cytoplasm.
170
Where does phospholipid synthesis begin?
Endoplasmic reticulum (ER).
171
How are new phospholipids added and distributed in ER?
Synthesized in cytosolic leaflet by enzymes → inserted asymmetrically → scramblases flip lipids for symmetry.
172
Compare flippases vs scramblases.
Scramblases: ER; random transfer; symmetric membrane; not curved. Flippases: Golgi; specific transfer to cytosolic side; asymmetric; curved.
Molec Bio
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