Cell Molec: Lecture 1 Learning Objectives

Handmade, not AI

List the fundamental properties shared by all cells, their importance and identify examples

1. Plasma Membrane: A selectively permeable lipid boundary separates the cell from its surroundings, maintains a distinct internal environment, and regulates exchange and signaling. EX: phospholipid bilayer in all cells. EX: The bacterial plasma membrane encloses the cytoplasm; in eukaryotes, it also contains transporters and receptors.

2. Genetic Material: DNA stores heritable instructions. It can be copied before division, expressed, and changed by mutation, allowing continuity and evolution. EX: transcription of genes to mRNA, replication of DNA during cell division. EX: A bacterial circular chromosome is copied before binary fission; eukaryotic linear chromosomes are replicated before mitosis

3. Ribosomes: Complexes of RNA and proteins that synthesize proteins by translating mRNA into amino acid sequences. They are essential for producing proteins, as well as for cell function and growth. EX: ribosomes in prokaryotes are free-floating in the cytoplasm; in eukaryotes, they can be found both free and attached to the endoplasmic reticulum.

4. Cytosol: The aqueous component of the cytoplasm where metabolic reactions occur, supporting cellular processes and providing a medium for molecular diffusion. EX: The cytosol contains enzymes, ions, and small molecules necessary for cellular function.

Describe the structure of a virus

Genetic material surrounded by a protein capsid and sometimes a lipid envelope. The only thing missing is the ability to reproduce on their own; they use host cell machinery to replicate.

Which form of microscopy is described?

Visible light passes through the specimen; naturally colored material or stains absorb light. It provides a quick, inexpensive view of tissue and cellular morphology and works well for fixed, stained specimens. Transparent specimens often need staining, which is often toxic; resolution is limited. At best, some larger organelles such as mitochondria may be seen

Bright-field light microscopy

Which form of microscopy is described?

Differences in refractive index and phase shifts are converted to differences in light intensity. Makes highly transparent, unstained specimens visible; it allows easy, moderate-cost observation of living cells and growth. Produces a characteristic glowing halo/ring artifact around structures; less sharp and less three-dimensional than DIC.

Phase contrast light microscopy

Which form of microscopy is described?

Split light beams passing through regions of different refractive index interfere to create high contrast and apparent depth. Unstained living cells; sharper images without the phase-contrast halo; high-quality, three-dimensional-looking surface/detail. More specialized and expensive than phase contrast; the image has pseudo-3D relief rather than a true measured 3D reconstruction.

Differential interference contrast (DIC) microscopy

Which form of microscopy is described?

Fluorochromes absorb excitation light and emit longer-wavelength light. Dyes, fluorescent proteins, or fluorochrome-conjugated antibodies label selected targets. Highly specific localization of cells, organelles, proteins, gene expression, or metabolic activity; several colors can identify several targets. Requires a fluorescent label and appropriate filters; excitation can bleach fluorophores and damage living cells; resolution remains limited by light unless a specialized super-resolution method is used.

Fluorescence light microscopy

Which form of microscopy is described?

An electron beam replaces visible light. TEM records electrons transmitted through thin sections; SEM scans electrons from the surface. Greatest resolution among the listed methods. TEM reveals internal ultrastructure; SEM gives detailed cell-surface topography. Expensive and time-consuming. Extensive preparation and vacuum conditions mean specimens are fixed/dead; not suited for observing growth.

Electron microscopy (EM)

Which forms of microscopy keep specimens alive while observing them?

Phase-Contrast, DIC, and Fluorescence Microscopy

Select the best microscopy for the experimental goal: Best possible resolution to view subcellular structure

Electron microscopy (EM)

Select the best microscopy for the experimental goal: High-contrast specimen; keeping cells alive does not matter

Bright-field microscopy

Select the best microscopy for the experimental goal: Observing a living organism or cell as it grows

Phase-contrast microscopy

Select the best microscopy for the experimental goal: Use fluorochrome-conjugated antibodies to highlight particular structures

Fluorescence microscopy

Select the best microscopy for the experimental goal: Observe an organism with high-quality three-dimensional image appearance

DIC microscopy

Describe the viral structure and size

Typical size is about 5-300 nm. Contains A DNA or RNA genome enclosed by a protein capsid; some also possess a host-derived lipid envelope bearing surface proteins that determine host/cell specificity by binding host-cell receptors.

Compare viruses with cells

They lack ribosomes, organelles, cytoplasm, and a true cellular plasma membrane, and they cannot reproduce or independently transcribe and translate their genomes. They are obligate intracellular parasites that hijack a host cell’s machinery

Compare prokaryotes with eukaryotes

-Prokaryotes are unicellular organisms that lack a nucleus and membrane-bound organelles, whereas eukaryotes are multicellular (or unicellular) organisms with a defined nucleus and specialized organelles. Prokaryotes typically have circular DNA, while eukaryotes have linear DNA organized into chromosomes.

-Prokaryotes are often 1 um, eukaryotes are often 10 um

-Prokaryotes replicate by binary fission and eukaryotes replicate by mitosis

-In prokaryotes, oxidative phosphorylation occurs on plasma membrane, in eukaryotes, occurs on inner mitochondrial membrane

-Prokaryotes = bacteria + archaea

-Eukaryotes = plants and animals

-Eukaryotes can be unicellular and multicellular, prokaryotes can only be unicellular

-Both have ribosomes, make ATP via glycolysis or cellular respiration, have cytoplasm, and a plasma membrane

What are the tenets of cell theory

1. All organisms are composed of one or more cells

2. The cell is the structural unit of life

3. Cells only arise from pre-existing cells

What spin speed is required for mitochondrial contents to form a pellet?

20,000 g

What spin speed is required for ribosomes to form a pellet?

200,000 g

What spin speed is required for nucleus components to form a pellet?

500-1,000 g

What spin speed is required for the microsomal fraction?

50,000-100,000 g

How does density relate to the spin speed?

The larger denser particles pellet at a lower spin speed

Order the cellular components from most dense to least dense: Mitochondria, ribosomes, microsomes, nucleus

nucleus, mitochondria, microsomes (plasma membrane, smooth ER, rough ER), ribosomes.

Compare the size of prokaryotic cells, eukaryotic cells, mitochondria, and macromolecues using micrometers, nanometers, and angstroms

-Prokaryotic cells, eukaryotic cells, and mitochondria are measured in micrometers. Eukaryotes ~ 10-100 um in diameter, prokaryotes ~ 0.1-5um, and mitochondrion ~ 1-2 um.

-Viruses and organelles smaller than mitochondria/ DNA fragments are nanometer-scale and measured in nanometers. Viruses are 0.005-0.03 um.

-Proteins and other macromolecular features are angstrom-to-nanometer scale.

Rank the conversions from smallest to largest. Nanometer, angstrom, and micrometer

Angstrom, nanometer, micrometer.

1 um = ______ nm

1000

1 nm = ________ A

10

1 um= _____A

10,000

Autologous Transplant

A self-transplant, immune rejection is less likely, but patient-derived cells may retain the disease-causing mutation. EX: Mesenchymal stem cell transplant

Allogenic transplant

A transplant that uses cells from another person; donor availability and immune matching matter, and rejection or graft-versus-host disease can occur. A hematopoietic stem cell transplant is usually this; it is donated, and rejection is likely.

Are plasma membranes present in bacteria, plants, and animals? What is the function of the plasma membrane?

Yes; selective boundary, transport, and signaling is the function

Are cell walls present in bacterial, plant, and animal cells? What is their function?

-Bacterium; usually yes

-Plant cell; yes

-Animal cell; no, and the ECM provides support and signaling

Function: shape and extracellular protection

Is the nucleus a structure present in the bacterium, plant cell, and animal cell? What is the function of it?

-Bacterium; no DNA is in the nucleoid

-Plant cell; yes

-Animal cell; yes

Function: stores linear chromosomes

Is mitochondria a structure present in the bacterium, plant cell, and animal cell? What is its function?

-Bacterium; no

-Plant cell; yes

-Animal cell; yes

Function: oxidative phosphorylation and ATP

Is the rough ER a structure present in the bacterium, plant cell, and animal cell? What is the function of it?

Bacterium; no

Plant cell; yes

Animal cell; yes

Function: synthesis/ folding of secret and membrane proteins

Is the smooth ER a structure present in the bacterium, plant cell, and animal cell? What is its function?

-Bacterium; no

-Plant cell; yes

-Animal cell; yes

Function: lipid/steroid synthesis and detoxification

Is the Golgi apparatus a structure present in the bacterium, plant cell, and animal cell? What is its function?

-Bacterium; no

-Plant cell; yes

-Animal cell; yes

Function: modification, sorting, and packaging of proteins and lipids

Are lysosomes a structure present in the bacterium, plant cell, and animal cell? What is its function?

- Bacterium: no

-Plant cell; lytic vacuole performs related functions

-Animal cell; common

Function: acidic degradation of endocytosed/ phagocytosed and cellular material

Are peroxisomes a structure present in the bacterium, plant cell, and animal cell? What is its function?

-Bacterium; no; membrane-bound peroxisome

-Plant cell; yes

-Animal cell; yes

Function: H2O2-linked detoxification, fatty acid metabolism, roles in photosynthesis

Are transport vesicles a structure present in the bacterium, plant cell, and animal cell? What is their function?

-Bacterium; no

-Plant cell; yes

-Animal cell; yes

Function: cargo through endomembrane system; transport of proteins and lipids between organelles and to the plasma membrane

Is a cytoskeleton a structure present in the bacterium, plant cell, and animal cell? What is their function?

-Bacterium; no, simpler cytoskeletal proteins

-Plant cell; complex cytoskeleton

-Animal cell; complex cytoskeleton

Function: provides structural support, regulates cell shape, and aids in cellular movement and transport.

Is a central vacuole a structure present in the bacterium, plant cell, and animal cell? What is their function?

-Bacterium; no

-Plant cell; yes

-Animal cell; no, small vesicles/vacuoles may occur

Compare prokaryotes, plant cells, and animal cells possible energy/carbon sources

Prokaryotes: Extremely diverse; sunlight, reduced organic carbon, and inorganic compounds; some use nitrogen-containing compounds

Plant cells: Light is captured for photosynthesis; plants also oxidize carbohydrates as chemical fuel

Animal cells: Organic molecules from food, especially carbohydrates and fats

Compare prokaryotes, plant cells, and animal cells location of ATP synthesis and how energy is captured.

Prokaryotes: Glycolysis and the Krebs cycle occur in the cytoplasm; Electron transport and oxidative phosphorylation occur at the plasma membrane.

Plant cells: Photosynthesis in chloroplasts produces energy-rich carbohydrates; mitochondria use respiration to convert chemical energy into ATP

Animal cells: Glycolysis in the cytosol, the Krebs cycle, and oxidative phosphorylation in mitochondria convert chemical energy to ATP.

Compare prokaryotes, plant cells, and animal cells fixation capabilities

Prokaryotes: Some can fix CO2; some can fix Nitrogen; some others utilize organic carbon. These abilities are not present in every prokaryote

Plant cells: Fix CO2 through photosynthesis. Plants generally do not fix atmospheric N2 themselves. They may obtain fixed nitrogen from bacteria.

Animal cells: Cannot fix carbon or nitrogen; they rely on organic compounds.

Primary culture

Cells removed directly from an organism/tissue and cultured for the first time. Usually a heterogeneous population with a limited proliferative lifespan.

Secondary culture

Cells transferred/subcultured from a primary culture into a new vessel. It may be more selected/adapted than the original primary culture but is still usually finite unless immortalized.

Cell line

A cultured population maintained through repeated passages. In the lecture’s emphasis, an established/continuous cell line contains changes that permit indefinite proliferation; HeLa is an example.

Name the culture type as described by its advantages and limitations:

Advantages: Most closely resembles the tissue of origin and retains more physiologically relevant traits

Limitations: Finite lifespan, donor-to-donor variability, smaller cell numbers, and possible mixture of cell types

Primary culture

Name the culture type as described by its advantages and limitations:

Advantages: Expands cell number and allows continued experiments beyond the original vessel

Limitations: Can undergo senescence and phenotypic drift; later passages may resemble the tissue less closely.

Secondary culture

Name the culture type as described by its advantages and limitations:

Advantages: Large populations, long lifespan, repeatability, experimental continuity, and more standardized material.

Limitations: Can be abnormal, genetically unstable, or less representative of the original tissue

Cell line

What culture type best aligns with the experimental goal?

Large cell population with greater replicative capacity/lifespan

Continuous cell line; Its cells can proliferate extensively or indefinitely

What culture type best aligns with the experimental goal?

Repeat the same experiment many times with cells as consistently similar as possible

A cloned/ standardized cell line. A stable line reduces donor and passage-to-passage variation; a cloned line can be genetically very similar. Mutation and drift can still occur

What culture type best aligns with the experimental goal?

Cells that resemble the original tissue as closely as possible

Primary culture. It is obtained directly from tissue and has undergone the least culture adaptation.

What culture type best aligns with the experimental goal?

Balance tissue resemblance with modest expansion

Early-passage secondary culture. It provides more cells than the original primary vessel while remaining closer to primary tissue than a heavily adapted continuous line

What is in the pellet and the supernatant after removing the pellet, after the spin of 500-1000 g?

Pellet: Nuclei plus unbroken cells and large cellular debris Supernatant: Mitochondria, lysosomes/peroxisomes, membrane fragments, ribosomes, soluble proteins

What is in the pellet and the supernatant after removing the pellet, after the spin at 20,000 g?

Pellet: Mitochondrial fraction; may also include lysosomes and peroxisomes

Supernatant: Microsomes/membrane vesicles, ribosomes, large complexes, soluble cytosolic proteins

What is in the pellet and the supernatant after removing the pellet, after the spin at 50,000-100,000 g?

Pellet: Microsomal fraction: small vesicles formed from fragmented ER and other membranes

Supernatant: Ribosomes/ large protein complexes and soluble cytosolic proteins

What is in the pellet and the supernatant after removing the pellet, after the spin at 200,000 g?

Pellet: Ribosomes and other large macromolecular complexes

Supernatant: Cytosol; soluble cytoplasmic proteins and small molecules

What will be isolated/retained in a pellet after the steps are taken:

Homogenize → spin at ~500–1,000 × g → collect the pellet → wash and re-spin the pellet at the same low speed to improve purity.

Nuclei only

What will be isolated/retained in a pellet after the steps are taken:

Homogenize → 1,000 × g → discard/retain nuclear pellet separately → take supernatant → 20,000 × g → collect and wash the pellet

Mitochondria only

What will be isolated/retained in a pellet after the steps are taken:

Homogenize → 1,000 × g and remove pellet → spin supernatant at 20,000 × g and remove mitochondrial pellet → spin resulting supernatant at ~50,000–100,000 × g → collect/wash pellet.

Microsomes only

What will be isolated/retained in a pellet after the steps are taken:

Homogenize → sequentially remove nuclear, mitochondrial, and microsomal pellets → ultracentrifuge remaining supernatant at ~200,000 × g to pellet ribosomes/large complexes → retain final supernatant.

Cytosol only

Cell differentiation

Most cells in a multicellular organism contain essentially the same genome, but different cell types express different combinations of genes. Differential gene expression produces different proteins, organelles, shapes, and functions—for example, a muscle cell specializes in contraction whereas a pancreatic β cell specializes in insulin secretion. THIS PROCESS enables tissues and organs to divide labor, while stem cells provide self-renewal and replacement of damaged or short-lived cells.

Pluripotent vs multipotent

Pluripotent cells can form nearly every body cell type from all three embryonic germ layers, but not an entire organism with extraembryonic tissues. Multipotent cells can form several related cell types within a limited lineage; for example, hematopoietic stem cells make blood-cell types but do not normally make epidermis.

Autologous vs Allogenic

An autologous transplant uses the patient’s own cells, so immune rejection is less likely, although patient-derived cells may retain a disease-causing mutation. An allogeneic transplant uses cells from another person; donor availability and immune matching matter, and rejection or graft-versus-host disease can occur.

Which cell source/method best aligns with the following advantage and major concern?:

Advantage: Often more accessible, clinically established in some settings, and lower teratoma risk than pluripotent cells. Can be autologous or allogeneic depending on source.

Concern: Limited range of cell types. Choose when the needed tissue lineage matches the adult stem cell; allogeneic marrow is common, while patient-derived MSC approaches can be autologous.

Adult stem cells

Which cell source/method best aligns with the following advantage and major concern?:

Advantage: Least differentiated; can generate virtually any body cell type

Concern: Ethical issues, immune mismatch if from another embryo, and teratoma risk. Choose when broad developmental potential is essential and these concerns are controlled.

Embryonic stem (ES) cells

Which cell source/method best aligns with the following advantage and major concern?:

Advantage: Avoids embryo use; can be patient-specific/autologous and is useful for disease modeling, drug testing, and replacement-cell development.

Concern: Teratoma risk if undifferentiated cells remain; reprogramming/genetic abnormalities; patient-derived cells may carry the disease mutation unless corrected.

Induced pluripotent stem (iPS) cells

Which cell source/method best aligns with the following advantage and major concern?:

Advantage: Avoids embryos and the pluripotent intermediate; potentially lowers teratoma risk and can be patient-specific.

Concerns: Conversion may be incomplete or inefficient; choose when a direct lineage change is known, such as pancreatic acinar cell → β-like cell

Transdifferentiated/directly reprogrammed cells

Which cell source/method best aligns with the following advantage and major concern?:

Advantage: Creates pluripotent cells genetically similar to the patient—an autologous-like strategy that may reduce immune mismatch

Concern: Requires oocytes and embryo creation, raises ethical/technical issues, does not perfectly match mitochondrial DNA, and retains pluripotent-cell teratoma risk.

Somatic cell nuclear transfer (SCNT)

What is the best stem-cell method given the experimental/therapeutic goal?:

Repopulate bone marrow after ablation

Hematopoietic adult stem cells; often easiest to obtain but they are allogenic; they are multipotent for blood lineages and are the established lineage-appropriate source

What is the best stem-cell method given the experimental/therapeutic goal?:

Model a patient’s inherited disease in many potential cell types without using an embryo

Patient-dervied/ Autologous iPS cells (Induced pluripotent stem cells). They retain the patient genotype, are pluripotent, and can be differentiated into relevant cells. Gene correction can provide an isogenic control.

What is the best stem-cell method given the experimental/therapeutic goal?:

Generate the broadest possible range of body cell types

ES or iPS ( embryonic stem or Induced pluripotent stem cells) cells. Both are pluripotent. ES cells are embryo-derived; iPS cells avoid embryo use and can be patient-specific.

What is the best stem-cell method given the experimental/therapeutic goal?:

Convert one available adult cell directly to another while avoiding pluripotency

Transdifferentiation/ direct reprogramming. The process bypasses a pluripotent intermediate and therefore reduces the concern that residual pluripotent cells form teratomas.

What is the best stem-cell method given the experimental/therapeutic goal?:

Create pluripotent cells with the patient’s nuclear genome using an oocyte

Somatic cell nuclear transfer (SCNT- derived cells). The transferred somatic nucleus supplies the patient nuclear genome.

What is the best stem-cell method given the experimental/therapeutic goal?:

Minimize immune rejection

Autologous cells, if biologically appropriate. Self-derived cells are less likely to be recognized as foreign. The original genetic disease may need correction first.

What is the best stem-cell method given the experimental/therapeutic goal?:

Lowest likelihood of forming a teratoma among listed adult, ES, iPS, and transdifferentiated options

Lineage-restricted adult stem cells or fully transdifferentiated cells. Teratomas are particularly associated with residual pluripotent ES/iPS cells. Transdifferentiated cells do not pass through pluripotency.

Based off the potency and method, what is the cell source?:

• Usually multipotent, tissue-specific cells that self-renew; examples include hematopoietic, epidermal, and mesenchymal stem cells.

Adult stem cells

Based off the potency and method, what is the cell source?:

• Pluripotent cells isolated from a blastocyst. Least differentiated.

Embryonic stem cells

Based off the potency and method, what is the cell source?:

• Differentiated somatic cells reprogrammed back to a pluripotent state, then directed to a desired lineage.

Induced pluripotent stem (iPS) cells

Based off the potency and method, what is the cell source?:

• One mature cell type is converted directly into another without passing through pluripotency.

Transdifferentiated/ directly reprogrammed cells

Based off the potency and method, what is the cell source?:

• A patient somatic-cell nucleus is transferred into an enucleated egg; resulting blastocyst-derived ES-like cells carry the patient nuclear genome.

Somatic cell nuclear transfer (SCNT)

Determine the model organism based on why researchers use it:

Very rapid, inexpensive growth; simple genetics; easy DNA manipulation; large populations.

Escherichia coli (bacterium);

-Why: Fundamental prokaryotic processes, DNA replication/transcription/translation, bacterial metabolism, plasmids, and recombinant protein production.

Determine the model organism based on why researchers use it:

Eukaryotic cell cycle, secretion/endomembrane trafficking, organelles, chromosome biology, metabolism, and gene-function screens.

Saccharomyces cerevisiae (budding yeast);

-Why: Single-celled eukaryote; rapid growth; strong genetics; many pathways conserved with animals.

Determine the model organism based on why researchers use it:

Plant development, photosynthesis, chloroplasts, hormones, environmental responses, and plant genetics.

Arabidopsis thaliana (mustard plant);

-Why: Small plant, short generation time, many offspring, compact sequenced genome, easy genetic work

Determine the model organism based on why researchers use it:

Cell lineage, programmed cell death/apoptosis, development, aging, and observing cells in a whole transparent animal

Caenorhabditis elegans (nematode);

-Why: Transparent multicellular animal with an invariant cell lineage, short generation time, and simple nervous system.

Determine the model organism based on why researchers use it:

Inheritance, development and pattern formation, signaling pathways, neurobiology, and genetic screens in an animal

Drosophila melanogaster (fruit fly);

-Why: Short generation time, many offspring, powerful genetics, visible phenotypes, conserved developmental pathways.

Determine the model organism based on why researchers use it:

Mammalian development, physiology, immunology, cancer, organ systems, disease mechanisms, and preclinical therapeutic testing.

Mus musculus (mouse);

-Why: Mammalian anatomy, physiology, immunity, and genes resemble humans; transgenic/knockout disease models are available.

A filter with pores of what size would be able to filter out bacteria, while allowing water to pass through?

400 nm

True/False: The difference between deoxyribose and ribose occurs at the 3’ carbon

False; the difference occurs at the 2' carbon, where ribose has a hydroxyl group and deoxyribose has a hydrogen.

Where do H bonds occur between two nucleotides?

Between an electronegative atom and a H bound to another electronegative atom (F, O, or N)

A and T have ___H bonds. C and G have ___ H bonds.

2, 3

How do C and G related to melting and annealing temperature?

C and G pairs, having three hydrogen bonds, contribute to higher melting and annealing temperatures compared to A and T pairs.

High pH means ____ H+ concentration.

low; likely to deprotonate functional group

Low pH means ___ H+ concentration.

High; likely to protonate the functional group

Deoxyribose has a ____ in the 2 prime carbon position

Hydrogen

Ribose has a ___ in the 2 prime position

Hydroxyl group

Purines have ___ rings and pyrimidines have ____ rings.

two; one

Nucleotide vs Nucleoside

A nucleotide is a building block of nucleic acids, consisting of a nitrogenous base, a sugar (ribose or deoxyribose), and one or more phosphate groups, while a nucleoside consists only of the base and sugar without the phosphate.