BIO 81 Exam 1 Study Guide

What are the criteria for being a living organism?

• complexity and organization at different levels

• highly regulated

• abilities to respond to the environment

• grow and develop

• metabolize

• reproduce

• capacity to evolve

Compare and contrast a hypothesis vs. a theory and give an example of each.

Hypothesis - a potential explanation made from an observation, can be supported or falsified by data, and a good hypothesis makes predictions that can be tested

• ex: "If a student studies with music, then their test scores will decrease." (This is a prediction that can be tested through a controlled experiment).

Theory - a general explanation of a natural phenomenon supported by a body of experiments

• ex: The Theory of Evolution by Natural Selection (This is a widely accepted, extensively verified explanation for the diversity of life on Earth)

Explain the purpose and steps of the Scientific Method.

The Scientific Method is a systematic, logical approach used by scientists to discover how things work and to solve problems.

Its primary purpose is to minimize human bias and ensure that results are reliable, reproducible, and based on objective evidence rather than intuition or guesswork.

Steps:

1. make observations

2. ask a question

3. formulate a hypothesis

4. make predictions

5. design experiment

6. collect and interpret data

7. draw conclusions

8. possibly peer review and publish the study

What are the first and second laws of thermodynamics, and how do they apply to living organisms?

First law of thermodynamics - Energy can be neither created nor destroyed; it can only be transformed from one form to another

• Living organisms transform energy from the environment into chemical energy that cells can utilize. They give off heat as a by-product.

Second law of thermodynamics - The degree of entropy (disorder) in the universe tends to increase

• Living organisms are highly organized and need a lot of energy to remain that way. The cell gives off energy as heat, causing small molecules in the environment to move more. This increase in movement increases the entropy (disorder) of the entries system.

What does it mean to say that a cell is life’s functional unit?

A cell is the simplest entity that can exist as an independent unit of life. While many organisms are multicellular, life can take on a single-celled form as well. All cells have a discrete boundary that separates their interior from the external environment, and they also have the ability to harness materials and energy from that environment.

How does the central dogma help us to understand how mutations in DNA can result in disease?

DNA directs the formation of proteins that do the cell’s work. Mutations in DNA can be transcribed and translated into proteins with altered structure and, therefore, different functions. Changes in protein function can cause the cell to work improperly, or fail althogether, resulting in some cases in disease. In some cases, however, altered proteins improve the function of the cell.

What was Stanley Miller’s experiment, and what is its significance in understanding the origins of life?

Experiment: Stanley Miller’s experiment was designed to simulate Earth’s early atmosphere. He began by heating liquid water to produce water vapor. This water vapor then mixed with other gases thought to be present on early Earth, including methane, ammonia, and hydrogen gas. To simulate lightning, Miller passes a spark through the mixture of gases. The gas mixture was then cooled, allowing liquid water to form again and dissolve any molecules that were synthesized. These were collected at the bottom of the apparatus and obtained through a sampling valve for analysis.

Results: As the experiment proceeded, reddish material accumulated at the bottom of the apparatus. Analysis showed that this material included a number of amino acids, the building blocks that make up proteins, which are the key structural and functional molecules that do much of the work of the cell.

What are atoms made up of? Describe each component.

Protons - positively charged particles, in the nucleus

Neutrons - neutral particles, in the nucleus

Electrons - negatively charged particles, orbit around the nucleus in regions called orbitals

What are isotopes?

Atoms of the same element that have different number of neutrons

Describe the 4 different types of bonds, and give examples of each.

Polar covalent - shared pair of electrons between atoms with very different electronegativities

• ex: water

Non-polar covalent - shared pair of electrons between atoms with similar electronegativities

• ex: hydrocarbons, gases (O₂, H₂, and N₂)

Ionic - two ions with opposite charges associate with each other due to their difference in electronegativity

• ex: electrolytes such as K⁺, Na⁺, and Cl^-

Hydrogen - a weak attraction between a partial positive hydrogen and a partial negative electronegative atom

• ex: base pairing in DNA, alpha-helices and beta-sheets in proteins, cohesive properties of water

What are the differences between structural isomers, Cis-trans isomers, and Enantiomers?

Structural isomers - Atoms are connected in a completely different order (e.g., branching vs. straight chain)

Cis-trans isomers - Geometric isSame connectivity, but rigid bonds (like \(C=C\)) prevent rotation, forcing groups to be on the same side (cis) or opposite sides (trans)

Enantiomers - Non-superimposable mirror images, usually involving a chiral center (carbon with four different groups)

Why do salts dissolve in water?

The partial positive charge on H⁺ associates with the negative charge on the Cl^-.

The partial negative on the O^- associates with the positive charge on the Na⁺.

What are the four emergent properties of water that contribute to Earth’s suitability and explain why those properties do so?

1. Cohesive behavior - due to hydrogen bonding, water molecules stick together (cohesion) and to other substances (adhesion). This allows for capillary action, enabling plants to transport water and nutrients against gravity from roots to leaves.

2. Ability to moderate temperature - water has a high specific heat, meaning it resists changes in temperature by absorbing or releasing large amounts of heat with little change in its own temperature. This stabilizes ocean temperatures for marine life and keeps terrestrial climates moderate.

3. Expansion upon freezing - water is less dense as a solid (ice) than as a liquid. Ice floats, insulating the liquid water below, which prevents oceans and lakes from freezing solid and allows aquatic life to survive winter.

4. Versatility as a solvent - due to its polarity, water is the "universal solvent" capable of dissolving many substances. This allows water to act as a transport medium for nutrients in biological fluids (blood, sap) and facilitates chemical reactions necessary for metabolism.

What would be the effect on the water molecule if oxygen and hydrogen had equal electronegativity?

The molecules would become nonpolar, losing its charge separation and the ability to form hydrogen bonds.

• water would lose properties like cohesion, surface tension, and its ability to act as a solvent

• would make it unsuitable for life

Why does water make a great solvent?

Its polarity and ability to form hydrogen bonds.

• The water molecule (H₂O) has a partial negative charge near the oxygen atom and a partial positive charge near the hydrogen atoms, allowing it to attract, break apart, and surround charged or polar substances like salts and sugars.

What is cohesion? Give an example.

The tendency of molecules of the same type to stick together (due to hydrogen bonds)

• ex: surface tension, water transport in plants

What is adhesion? Give an example.

The tendency of two different molecules to stick together (due to hydrogen bonds)

• ex: water transport in plants (water molecules adhere to plant wall)

How does water regulate temperature?

Hydrogen bonds make water resist changes in temperature

• high specific heat capacity and high heat of vaporization

Why is table salt iodized?

Some trace elements are required to prevent diseases. A lack of iodine causes the thyroid gland to swell (this is cqalled goiter)

What is pH and how is it measured?

pH is a measure of the concentration of protons in a solution

• Low H⁺ concentration means basic

• High H⁺ concentration means acidic

What are the four most common elements in organic molecules?

Carbon, oxygen, hydrogen, and nitrogen

What features of carbon allow it to form diverse structures?

• Behaves as if it has 4 unpaired electrons

• Carbon atoms can bond with other carbon atoms to form large carbon chains that branch or form rings

• Can form double bonds (limits the flexibility of the molecules and their structural options)

What are hydrocarbons? What are some of their properties?

a molecule composed entirely of carbon and hydrogen atoms

• are nonpolar/hydrophobic

• can exist in many forms (e.g., linear chains, rings, branched chains)

• are the primary components of fats and fossil fuels

What are the four major classes of biological macromolecules and what are their functions?

1. carbohydrates (sugars + starches)

   1. provide a source of energy and make up the cell wall in bacteria, plant, and algae cells

2. proteins (structural molecules, enzymes)

   1. act as catalysts to facilitate chemical reactions and also provide structural support of the cell

3. nucleic acids (DNA, RNA)

   1. encode and transmit genetic information

4. lipids (fats, oils, waxes)

   1. store energy, act as signaling olecules, and make up the membranes of the cell

How is diversity achieved in polymers? Use proteins as an example.

Through numerous combinations of subunits

• proteins for example, are a polymer of amino acid subunits

• any combination of subunits can be made, each resulting in a different protein

• in this way, polymers are capable of displaying virtually limitless diversity

What is the amino group, its properties, and the macromolecule(s) it’s found in?

-NH₂

properties:

• polar, positively charged at the pH of the cell, behaves as a base, hydrophilic

commonly found in:

• amino acids, proteins

What is the amide group, its properties, and the macromolecule(s) it’s found in?

-C(=O)NH-

properties:

• polar, hydrophilic

commonly found in:

• proteins

What is the carboxyl group, its properties, and the macromolecule(s) it’s found in?

-COOH

properties:

• polar, negatively charged at the pH of a cell, behaves as an acid, hydrophilic

commonly found in:

• fatty acids, amino acids, proteins

What is the carbonyl group, its properties, and the macromolecule(s) it’s found in?

>C=O

properties:

• polar, hydrophilic

commonly found in:

• carbohydrates, proteins

What is the hydroxyl group, its properties, and the macromolecule(s) it’s found in?

-OH

properties:

• polar, hydrophilic

commonly found in:

• carbohydrates, proteins, nucleic acids

What is the sulfhydryl group, its properties, and the macromolecule(s) it’s found in?

-SH

properties:

• polar, forms S-S disulfide bonds

commonly found in:

• the amino acid cysteine, proteins

What is the methyl group, its properties, and the macromolecule(s) it’s found in?

-CH₃

properties:

• nonpolar

commonly found in:

• amino acids, proteins, nucleic acids

What is the phosphate group, its properties, and the macromolecule(s) it’s found in?

-OPO₃H₂

properties:

• polar, negatively charged at the pH of a cell, hydrophilic

commonly found in:

• phospholipids, nucleic acids, ATP

What is a dehydration synthesis reaction? Anabolic or catabolic? Give an example.

builds polymers by releasing a water molecule (anabolic)

• ex: formation of maltose (glucose + glucose)

What is a hydrolysis reaction? Anabolic or catabolic? Give an example.

breaks polymers into monomers by adding a water molecule (catabolic)

• ex: breaking down maltose (glucose + glucose)

What are saccharides, monosaccharides, disaccharides, and polysaccharides? Give examples of each.

Saccharides - the simplest carbohydrate molecule (sugar)

Monosaccharides - a simple sugar; the monomers that make up large carbohydrates

• ex: ribose, glucose, fructose

Disaccharides - a double sugar

• ex: lactose in milk (glucose + galactose), maltose (glucose + glucose), sucrose (glucose + fructose)

Polysaccharides - a polymer of simple sugars; provide long-term energy storage or structural support

• ex: starch, cellulose, chitin, glycogen

What is the bond that attaches one monosaccharide to another?

Glycosidic bond

• covalent

• formed between carbon 1 of one monosaccharide and a hydroxyl (-OH) in a different monosaccharide molecule

What are the two classifications of monosaccharides based on the location of the carbonyl group and number of carbons?

Aldose - contains an aldehyde group (-CHO) at the end of the carbon chain

Ketose - contains a ketone group (C=O) typically at the second carbon

What are the four classifications of polysaccharides? Which are for storage and which for support?

1. starch (storage)

2. glycogen (storage)

3. cellulose (support)

4. chitin (support)

What is starch? Found in plants or animals?

A storage polysaccharide of plants and consists entirely of glucose monomers

• The simplest form of starch is amylase

What is glycogen? Found in plants or animals?

A storage polysaccharide in animals

• Vertebrates store glycogen mainly in liver + muscle cells

What is celulose?

A major component of the tough wall of plant cells, a polymer of glucose w/ different glycosidic linkages

• major source of insoluable fiber

What is chitin?

Found in the exoskeleton of arthropods, also provides structural support for cell walls of fungi

What are alpha and beta glucose ring structures? What are their oritentations?

Alpha and beta glucose are cyclic isomers of glucose that differ only in the orientation of the hydroxyl (-OH) group on the first carbon (C1)

• alpha are helical polymers, are more reactive and easily broken down by enzymes

• beta are straight polymers, less reactive due to structure, and require different enzymes for breakdown

What are lipids, their types, and their properties?

fatty, oily, waxy compounds that are soluble in organic solvents and insoluble in polar solvents such as water

types: triglycerides, phospholipids, sterols

properties:

• most hydrophobic

• mostly made of hydrocarbons

What are triglycerides?

• composed of 1 glycerol molecule and 3 fatty acid molecules

• assembled via dehydration synthesis

What is the difference between saturated and unsaturated fats?

Saurated

• no double bonds

• maximum # of hydrogens attached to each carbon

• solid at room temperature

• primarily animal fats

Unsaturated

• has one or more double bonds

• fewer than a maximum of 3 hydrogens

• liquid at room temperature

• plant-based oils, nuts, seeds, fish

How are saturated fats solid at room temperature while unsaturated fats are liquid?

Saturated fats are solid at room temperature because their straight molecular chains pack tightly together, allowing for strong intermolecular attractions.

• have greater van der Waals forces cause they’re straight and can pack together tightly

Conversely, unsaturated fats remain liquid because double bonds create "kinks" in their chains, preventing dense packing and keeping the molecules fluid.

What are Van der Waals Forces and how do they relate to fatty acids?

the attraction of temporarily polarized molecules that is formed from opposite charges

• the hydrocarbon chains in fatty acids have nonpolar covalent bonds

• the longer the hydrocarbon tial, the greater teh strength of van der Waals forces

What is hydrogenation?

converts unsaturated fats to saturated fats

• creates trans fats, a type of unsaturated fat that is even less healthy than saturated fats

What are steroids and their properties? Give examples.

The precursor molecule for cholesterol and steroid hormones

• composed of a carbon skeleton with 4 rings and varying functional groups

• ex: cholesterol, synthetic anabolic steroids, estrogen, testosterone

What is cholesterol and its functions?

• a sterol

• component of membrane

• the “base steroid” from which your body produces other steroids

What are phospholipids and their functions?

• a major component of all cell membranes

• amphipathic

structure:

• one glycerol molecule

• two fatty acids

• one phosphate

• one choline molecule

What are proteins and their functions? Give examples.

the key structural and functional molecule that does the work of the cell, providing structural support and catalyzing chemical reactions

functions:

• structural support, storage, transport, cellular communications, movement, defense against foreign substances

examples:

• transport proteins, enzymatic proteins, contractile and motor proteins, cell membrane proteins

Describe the structure of a protein.

• apha carbon (central C)

• animo group (-NH₂)

• carboxyl group (-COOH)

• hydrogen atom

• R group (side chain)

What is the type of bond that connects amino acids together to form a protein?

peptide bond

• covalent bond

• alpha carboxyl chain attaches to the next alpha-amino region

What are the two ends of a protein?

1. amino end (N-terminus)

2. carboxyl end (C-terminus)

Describe the four levels of structure of a protein (include the bonds at each level).

primary structure

• sequence of amino acids in a protein

• held together by covalent peptide bonds

secondary structure

• results from repeating hydrogen bonding interactions between atoms of the polypeptide backbone

• hydrogen bonds form between the amino hydrogen and carboxyl oxygen in the peptide backbone

• alpha-helix structure:

  • polypeptide backbone is twisted in a right-hand coil

• beta sheet structure:

  • polypeptide chain folds back and forth on itself, forming a pleated sheet

tertiary structure

• determined by interactions between R groups, rather than interactions between backbone constituents

• interaction between R groups: hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions

• the 3D shape enables the protein to carry out its specific function in a cell

• has disulfide bridges (a strong covalent bond between the sulfur atoms of two cysteine amino acid residues within a protein)

quaternary structure

• results when several polypeptide chains form one macromolecule

• held together by hydrogen bonding and London dispersion forces

• ex: collagen and hemoglobin

What is a protein or peptide backbone?

The protein backbone, also known as the peptide backbone, is the fundamental structural framework of proteins. It consists of a continuous chain of amino acid residues linked together by peptide bonds, forming the primary structure of a protein molecule.

• The protein backbone is composed of a repeating pattern of nitrogen, carbon, and oxygen atoms, with the side chains of the amino acids protruding from the backbone.

What is a disulfide bridge?

a strong covalent bond between the sulfur atoms of two cysteine amino acid residues within a protein

• these bonds play a crucial role in stabilizing the tertiary and quaternary structures of proteins, holding them in their functional 3D shapes

How can proteins become denatured? What is denaturation of a protein?

definition: the unfolding of proteins by chemical treatment or high temperatures

• the separation of paired, complementary strands of nucleic acids

• a denatured protein is biologically inactive

can become denatured through alterations in pH, salt concentration, temperature, or other environmental factors

What are chaperonins?

a protein that shield a slow-folding protein ntil it can attain proper three-dimensional structure

What are nucleic acids and their properties? Give some examples.

a polymer of nucleotides that encodes and transmits genetic information

• nucleic acids determine the primary structure of each protein in a cell

roles:

• DNA and RNA

the monomers of nucleic acids are nucleotides

What are nucleotides and their two classifications?

monomers of nucleic acids

composition:

• one phosphate group (or more)

• one pentose sugar (deoxyribose or ribose)

• one nitrogenous base

pyrimidine bases (have a single ring)

• cytosine, thymine, uracil

• CUT the Pie (CUT = Pyrimidines)

purine bases (have a double ring)

• guanine, adenine

• Pure As Gold (AG = Purines)

What is the bond that forms the sugar-phosphate backbone of DNA and RNA?

phosphodiester bond

• forms when a phosphate group in one nucleotide is covalently joined to the sugar unit in another molecule

• ocurs via dehydration reaction

• links 5’ phosphate to 3/ hydroxyl to form covalent bonds

• forms a sugar-phosphate backbone

How does base pairing stabilize the double helix of DNA?

the arrangement of atoms allows precise hydrogen bonding

Define a cell.

the smallest unit of life that can function independently

• every living thing is made up of one or more cells

• biochemical processes take place inside cells to carry out basic functions of life

What is cell theory?

Cell theory states:

1. All organisms are made of cells

2. The cell is the fundamental unit of life

3. Cells come from preexisting cells

What are the common features of all cells?

They all have genetic material, ribosomes, cytoplasm, and cell membrane

Compare prokaryote and eukaryote cells.

Prokaryotes (Archaea & Bacteria)

• single-celled, no nucleus, no membrane-bound organelles, reproduce asexually, the most ancient form of life

• Archaea: more similar to eukaryotes than bacteria, can survive in extreme environments

• Bacteria: cell walls containing peptidoglycan, found in nearly every environment

Eukaryotes (Eukarya)

• has a nucleus, has membrane-bound organelles, larger, more complex

Compare plant and animal cells.

In animal cells, but not in plant cells:

• lysosomes

• centrioles

• flagella (in some plant sperm)

In plant cells, but not in animal cells:

• cell wall

• chloroplasts

• central vacuole

Similarities:

• bound by a membrane

• contains membrane-bound organelles

How do metabolic requirements set upper limits on the size of a cell?

surface-to-volume ratio

• as a cell grows, its volume increases faster than its surface area

• Small cells have a high surface area relative to volume, enabling efficient nutrient uptake and waste disposal.

What are vesicles and how do they work?

small membrane-enclosed sac that transports substances within the cell

how vesicles work:

• bud off an organelle, taking a piece of the membrane and internal contents of the organelle from which they derive

• they then fuse with another organelle or the cell membrane, reforming a continuous membrane and unloading their contents

exocytosis

• a vesicle from the cytoplam fuses with the cell membrane and empties its contents into the extracellular space or delivers protein to the cell membrane

endocytosis

• a vesicle buds off from the cell membrane, bringing material from outside the cell into that vesicle

What is the nucleus, its structures, contents, and functions?

contains most of the cell’s genes and is usually the most conspicuous organelle

• site of transcription (DNA → RNA)

• RNA is exported from the nucleus

• produces ribosomes necessary for protein synthesis

• coordinates the replication of DNA during cell division

Nuclear Envelope - encloses the nucleus, separating it from the cytoplasm

• is a double-membrane; each membrane has a lipid bilayer

Nuclear Pores - protein channels in the nuclear envelope that allow molecules to move into/out of the nucleus

• essential for the nucleus communicating w/ the rest of the cell

• (mRNA out & ribosomal proteins in/out)

Nuclear Lamina - a meshwork of intermediate filaments (lamins) and proteins lining the inner nuclear envelope

Describe DNA and RNA in the nucleus.

DNA

• organized into discrete units called chromosomes

  • each chromosome is composed of a single DNA molecule associated w/ proteins

• chromatin - a complex of DNA and proteins that gives chromosomes their structure

  • condenses to form discrete chromosomes as a cell prepares for division

RNA

• nucleolus - a distinct, dense, non-membrane-bound structure within the nucleus that contains the genes and transcripts for ribosomal RNA

• RNA is synthesized in the nucleus

• mRNA leaves the nucleus through a nuclear pore

• binds to a ribosome so protein synthesis can start

What is the endomembrane system?

an interconnected network of lipid bilayer membranes within eukaryotic cells that works together to modify, package, and transport lipids and proteins

• It facilitates cellular traffic and compartmentalization but excludes mitochondria and chloroplasts

• Key components include the nuclear envelope, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vesicles, and the plasma membrane

What organelles are in the endomembrane system and which are not?

IN Endomembrane System

• nuclear envelope

• endoplasmic reticulum (ER)

• Golgi apparatus

• lysosomes

• vesicles and vacuoles

• plasma membrane

NOT in Endomembrane System

*These operate independently and do not exchange vesicles

• mitochondria (Responsible for ATP production)

• chloroplasts (Found in plants for photosynthesis)

• peroxisomes (Metabolic compartments that break down fatty acids, which do not receive vesicles from the Golgi)

• nucleolus (Located inside the nucleus but distinct from the membrane system)

What are the names and function of the major organelles of the endomembrane system in eukaryotic cells?

Nucleus - encloses the cell’s genetic information and is the site of transcription

Endoplasmic Reticulum (ER) - an organelle in which proteins and lipids are synthesized

Golgi apparatus - modifies proteins and lipids produced by the ER and acts as a sorting station as those molecules move to their final destinations

Lysosomes - contain enzymes that break down macromolecules

What are ribosomes and their functions?

Particles made of ribosomal RNA and protein that synthesize proteins

• Note: they are not membrane-bound organelles

They carry out protein synthesis in two locations:

• in the cytosol (free ribosomes)

• on the outside of the ER or nuclear envelope (bound ribosomes)

Consists of a small subunit (reads mRNA) and a large subunit (joins amino acid)

What are antibiotics and how do they work?

Antibiotics are powerful medications that treat bacterial infections by either killing bacteria directly

• They work by targeting specific structures or processes in bacteria—such as cell wall formation, protein synthesis, or DNA replication—that human cells do not have, or inhibiting their growth and reproduction

Many antibiotics bind to bacterial ribosomes or cell walls

• Penicillin prevents bacteria from building cell walls, causing them to burst

• Some antibiotics interfere with the machinery bacteria use to create essential proteins, stopping them from multiplying

• Specific drugs break down the bacterial cell membrane, causing essential components to leak out

• Other antibiotics prevent bacteria from copying their DNA, stopping reproduction.

What is the endoplasmic reticulum and its functions?

An organelle composed of a network of membranes that is involved in the synthesis of proteins and lipids

Structure:

• has a complex network of interconnected tubules and flattened sacs

• cisternae - flattened, sac-like, membrane-bound compartments

• lumen - fluid-filled inner compartment inside the cisternae

Rough ER

• has attached ribosomes that secrete glycoproteins

• primarily involved in protein synthesis and modification

• distributes transport vesicles

• all cells have at least some rough ER for the production of transmembrane and organelle proteins

Smooth ER

• lacks ribosomes

• extension of rough ER

• important for lipid and steroid synthesis

• large proportion in specialized cells

• involved in metabolic processes like lipid synthesis, carbohydrate metabolism, and detoxification of drugs and poisons

What is the Golgi apparatus and its functions?

An organelle that modifies proteins and lipids produced by the ER and acts as a sorting station as they move to their final destination

Structure:

• flattened membranous sacs

  • cisternae - flattened sacs that are the internal space of the Golgi

• cis face - receiving side (closest to ER)

• trans face - shipping side (closest to plasma membrane)

• Different regions of the Golgi have different enzymes that catalyze specific reactions

Functions:

• Modifies proteins and lipids received from the ER

• Packages/sorts proteins and lipids into vesicles for transport

• Synthesizes carbohydrates that’ll be added to proteins and lipids

• The edges of cisternae bud off as vesicles carrying proteins or modified sugars to the cell membrane

Describe the protein production pathway.

Transcription

• In the nucleus, RNA polymerase converts a DNA gene sequence into messenger RNA (mRNA), which is then processed.

Export

• The mature mRNA molecule exits the nucleus via nuclear pores to the cytoplasm.

Translation

• Ribosomes read the mRNA, and tRNA brings amino acids to build the polypeptide chain.

Protein Folding & Modification

• The ribosome moves to the endoplasmic reticulum and “reads” the mRNA instructions

• Protein moves to the Golgi complex for additional processing and sorting

Transport & Secretion

• Protein moves to the plasma membrane to be secreted

What are lysosomes and their functions?

A vesicle derived from the Golgi apparatus that contains hydrolytic enzymes that break down macromolecules

• These macromolecules are either damaged or unneeded

• Maintains a pH of 5

Digestion through phagocytosis:

• forms a food vacuole

autophagy - Use enzymes to recycle the cell’s own organelles and macromolecules

How do lysosomes illustrate the importance of compartmentalizing certain reactions in different spaces in the cell?

They have an acidic environment (pH of about 5), and this environment works well for degrading macromolecules, which is one of the functions of lysosomes.

These reactions must be confined to lysosomes because many of the cell’s proteins required for cellular function would unfold or degrade at such a low pH.

What are some genetic disorders associated with lysosomal disorders?

Tay Sachs Disease - A neurodegenerative condition resulting in physical and mental deterioration

• missing an enzyme in lysosomes that breaks down lipids

• Result: lipids accumulate in the brain, which leads to mental and physical deterioration

Niemann-Pick Disease - Causes lung, liver, and spleen dysfunction, alongside neurological symptoms

• also causes a lipid accumulation, but in the spleen, liver, lungs, bone marrow, and brain

What are peroxisomes and their functions?

Self-replicating oxidative organelles

• aid in digestion

• originate at the ER

• contain enzymes that digest and then oxidize certain toxic molecules

• break down fatty acids

• produce cholesterol and some lipids

What are vacuoles and their functions?

Membrane-bound, fluid-filled organelle found in the cytoplasm of plant, fungal, and some animal and bacterial cells

Structure:

• space within a cell, enclosed by a membrane

Function:

• storage (holds water, ions, nutrients, proteins, pigments)

• turgor pressure for structural support in plants

Why are mitochondria and chloroplasts are not considered in the endomembrane system

They are self-replicating organelles with their own DNA and double-membrane structures, likely originating from engulfed prokaryotes (endosymbiotic theory).

Unlike the endomembrane system (ER, Golgi, vesicles), they function independently and are not part of the cell's membrane trafficking, protein synthesis, or transport network.

What are mitochondria, their structure, and their functions?

Harness energy from chemical compounds (such as sugars) and turns it into ATP

• found in almost all eukaryotic cells

• grow and reproduce inside the cell

• contain their own DNA and ribosomes

Structure:

• has a double membrane

• Outer membrane: a highly permeable membrane containing proteins called porins that allow the movement of ions and small molecules

• Inner membrane: less permeable and highly folded into structures called cristae

  • Cristae increase the surface area for biochemical reactions

• Inner membrane space: the space between the outer and inner membranes, which is critical for creating a proton radient for ATP production

• Matrix: fluid-filled inner compartment containing enzymes for the citric acid cycle, mitochondrial DNA, and ribosomes

Function:

• Energy production (cellular respiration)

• Metabolic signaling and synthesis (involved in the synthesis of heme groups (for hemoglobin) and steroids, & the production of reactive oxygen species (ROS) for signaling)

What are chloroplasts, their structure, and their functions?

Organelles that convert energy from sunlight into energy stored in sugar molecules

• contain their own DNA and ribosomes

• sugar made in chloroplasts travels to the mitochondria, which extracts the energy to use in cellular process

Structure:

• Double membrane envelope

• Stroma: space inside the chloroplast, surrounding the tylakoids

• Thylakoid system: a collection of membranous sacs containing chlorophyll

• Grana: tightly packed stacks of thylakoids, designed to maximize light absorption

• Lumen: space inside the thylakoid membranes

Function:

• Photosynthesis (converts light energy, CO₂, and water into glucose and oxygen)

• Produces glucose that can then be used to produce ATP for energy

Are mitochondria present in animal cells, plant cells, or both?

Both

What are four similarities between mitochondria and chloroplasts?

1. not part of the endomembrane system

2. have a double membrane

3. have proteins made by free ribosomes

4. contain their own DNA

Describe the endosymbiont theory, discuss the evidence.

proposes that eukaryotic organelles—specifically mitochondria and chloroplasts—originated as free-living prokaryotes (bacteria) that were engulfed by a larger host cell

• The theory suggests that an anaerobic host cell engulfed an aerobic proteobacterium, which evolved into the mitochondrion, giving rise to all eukaryotes. Later, one of these aerobic, nucleated cells engulfed a photosynthetic cyanobacterium, which evolved into the chloroplast, giving rise to plants and algae.

Evidence:

• Mitochondria and chloroplasts contain their own circular DNA, similar to bacterial chromosomes

• These organelles have their own ribosomes (70S) that closely resemble bacterial ribosomes in size and structure, rather than the 80S ribosomes found in the surrounding eukaryotic cytoplasm.

• Mitochondria and chloroplasts reproduce independently within the cell through a process similar to binary fission, the same method used by bacteria.

• Both organelles are surrounded by two membranes—an inner membrane belonging to the original bacterium and an outer membrane derived from the host cell's vesicle.

• They are roughly the same size as prokaryotic cells.

What is the cytoskeleton, what is it composed of, and what are the functions?

The cytoskeleton provides a structural framework for the cell

• Extends through the cytoplasm

• Organizes the cell’s structures and activities

• Anchors organelles

• Structural support

• Cell movement

• Aids in digestion

• Organelle transport

Composed of 3 molecular structures:

1. microfilaments

2. microtubules

3. intermediate filaments

What is polymerization and depolymerization?

Polymerization is the chemical process of linking small molecules (monomers) together to form long, complex chain molecules called polymers

• exothermic (releases heat)

• synthesis of new material

Depolymerization is the reverse process, breaking down polymers back into their constituent monomer units or oligomers, often used in chemical recycling to recover raw materials

• endothermic(requires energy input)

• recovery of raw materials

What are microfilaments, their structure, function, and importance in the cytoskeleton?

Microfilaments (also called actin filaments) are the thinnest components of the eukaryotic cytoskeleton that are dynamic, polar structures that enable cell motility, maintain cell shape, facilitate muscle contraction, and divide cells during cytokinesis

Structure:

• Size: the thinnest and shortest (abt 7nm in diameter)

• Composition: made of globular protein subunits called G-actin (globular actin)

• Arrangement: G-actin monomers polymerize to form long, flexible, helical polymers called F-actin (filamentous actin)

• Helix Structure: two parallel F-actin strands twist around each other

  • twisted double helix of actin subunits

• Polarity: they have distinct plus (+) and minus (-) ends

  • allows them to grow (polymerize) and shrink (depolymerize) rapidly, often utilizing ATP

Function:

movement and muscle contraction

• Cell shape and structure:

  • form a 3D network called the cortex

    • area of cytoplasm just beneath the cell membrane

    • bundles of microfilaments make up the core of microvilli of intestinal cells

• Cell movement:

  • Enable movement by lengthening and shortening (amoeboid, pseudopod extension, cytoplasmic streaming)

• Muscle contraction:

  • Working with motor protein myosin, they slide past each other to cause muscle fiber contraction

• Cell division:

  • Form the contractile ring (cleavage furrow) that pinches an animal cell into two during cytokinesis

• Intracellular transport:

  • Act as tracks for myosin-based movement of organelles and vesicles within the cytoplasm.

What are actin and myosin? What are the purposes/functions?

The primary motor proteins that are responsible for muscle contraction and cell motility

Actin - globular proteins that link together to form long, spiralling chains

• thin and smooth

• serve as the “tracks” along which myosin travels

• Role: acts as the track along which myosin moves during contraction

• Additional functions: part of the cytoskeleton, maintains cell shape, aids in endocytosis, facilitates cell motility

Myosin - motor proteins that convert ATP to mechanical force

• thick and rough

• acts like a motor, using its heads to “walk” along actin filaments

• Role: convert chemical energy (ATP hydrolysis) into mechanical energy

Interactions:

• The myosin head binds to actin, forming cross-bridges to pull the actin filaments, known as the sliding filament mechanism

Play a role in:

• muscle contraction

• cellular mobility

• intracellular transport

• cell division

What makes up the core of microvilli of intestinal cells?

Bundles of microfilaments

What is the cortex in a cell?

The cell cortex (or actin cortex) is a specialized, thin network of actin filaments, myosin motors, and actin-binding proteins located directly beneath the plasma membrane of most animal cells. It acts as a structural scaffold to maintain cell shape, regulate surface tension, and facilitate movement, division, and structural integrity.

It acts as a mechanical shell that regulates cell shape, surface tension, and rigidity while enabling cell division (cytokinesis) and migration.