Biol 3140 Exam 1 - Iowa State University

Cell Theory

• All organisms are made up of one or more cells

• All cells come from pre-existing cells

• The cell is the basic unit of structure and organization that performs life functions

Prokaryotic Cells

• Single-celled organism

• Has no nucleus

• Lacks some membrane-bound organelles

• Has a cell membrane, cytoplasm, and genetic material (ex., ribosomes)

• Has circular DNA

Eukaryotic Cells

• Multi-celled organisms

• Has a nucleus

• Has membrane-bound organelles

• Has a cell membrane, cytoplasm, and genetic material (ex., ribosomes)

• Has linear DNA

How are Cells Studied?

Microscopes

Light Microscopy

• Uses light as an illuminating source

• Has a 1000x maximum magnification

• Uses live or dead specimens

• Uses glass as a lens material

• Has a 0.25um-0.3um resolving power

• Produces colored images

• Used to study internal structure

Electron Microscopy

• Uses electrons as an illuminating source

• Has a 2000000x maximum magnification

• Uses dead or dried specimens

• Uses electromagnets as a lens material

• Has a 0.001um resolving power

• Produces black and white images

• Used to study external surfaces, cell structure, and small organisms

Advantage and Disadvantage of Electron Microscopy

• Advantage: higher magnification and resolution that allows for small details to be analyzed

• Disadvantage: cells have to be dead and thinly sliced for the transmission electron microscopes

Advantage and Disadvantage of Light Microscopy

• Advantage: see live cells in their natural colors

• Disadvantage: details are not as clear as electron microscopy

Nucleus

• Largest organelle

• Information and DNA storage of the cell

• Enclosed in a nuclear envelope (two concentric membranes)

Endoplasmic Reticulum

• Considered an “irregular maze”

• Major site for synthesizing proteins, secreted proteins, and membrane lipids

Golgi Apparatus

• Flattened membrane enclosed sacs

• Helps with synthesis of proteins, modifications, and sorting proteins/lipids during secretion

Mitochondria

• Believed to be evolved from engulfed bacteria

• Contains it’s own DNA

• Reproduce by dividing

• Generate energy from food molecules

Chloroplasts

• Only present in plants and algae

• Carry out photosynthesis

• Make all foods we consume directly OR indirectly

• Believed to be evolved from photosynthetic bacteria

What is a Major Function of Cytoskeletons?

Maintain shape and facilitate organelle movement

Why do Scientists Study Model Organisms?

Understanding them allows us to understand other organisms because we share similar genes with them. It allows us to practice “ethics” by not using humans to do certain experiments. Since we all descended from a common ancestor, these model organisms are more like us than not.

How Do Cells Exploit the Laws of Chemistry and Physics to Survive, Thrive, and Reproduce?

• Use energy from the environment through chemical reactions

• Use thermodynamics for metabolism and replication

• Use a continuous input of energy to maintain themselves

• Based on carbon compounds, so they’re very regulated

How Do Different Atoms Interact to Form Molecules?

By sharing or transferring electrons and creating chemical bonds

Why Do Carbon, Hydrogen, Oxygen, and Nitrogen Prevalent in Living Cells?

They can bond easily to the carbon. Carbon is considered a backbone, because of all the bonds it can form

Covalent Bonds

• Form by the sharing of electrons

• Spatial arrangement of them can be formed by oxygen, nitrogen, carbon

• These molecules have precise 3D structures defined by covalent linkage bond angles and lengths

• The polarity depends on the relative electronegativities of the participant atoms

Noncovalent Bonds

• Weaker interactions than covalent bonds

• Are ionic bonds, hydrophobic bonds, electrostatic interactions, and Van der Waals

• Electromagnetic interactions instead of electron sharing

What is a Unique Property of a Noncovalent Bond?

The electron jumps from one atom to another. These are called salts instead of molecules. They are formed by gain or the loss of electrons (ex., NaCl)

Ionic Bonds

• Formed by the gain or loss of electrons

• Form salts instead of molecules

Hydrogen Bonds

• Gives water special properties

• High boiling point

• The slight positive charge association with the hydrogen atoms is electrically attracted to the slight negative charge of the oxygen atom

• Broken by random thermal motions

What are the Four Major Carbon-Based Molecules Found in All Organisms?

• Sugar

• Fatty acid

• Amino acid

• Nucleotide

What are Sugar’s (Glucose) Major Properties and Functions in Living Cells?

• Can be made into larger molecules

• Can be broken down into smaller subunits

• Common examples are starches, glycogens, and cellulose

• Readily available energy source that can be stored for later

• Pack densely and form polysaccharides

What are Fatty Acid’s Major Properties and Functions in Living Cells?

• Both hydrophobic and hydrophilic (amphipathic)

• The head of them loves water, the tail doesn’t

• Helps to form cell membranes

What are Nucleic Acid’s Major Properties and Functions (DNA/RNA) in Living Cells?

• DNA: held by phosphodiester bonds

• Are subunits of DNA/RNA

• Energy currency

What are Amino Acid’s Major Properties and Functions in Living Cells?

• Subunits of proteins

• 20 different AA in 1 protein

• Held together via peptide bonds in proteins

How are Different Macromolecules Built-In Cells?

They are added to one end of a chain via condensation reactions, which releases water

How do Cells Use Energy?

All cells get energy from the sun, and they use it for chemical reactions and processes

How do Cells Obtain and Store Energy?

Photosynthetic cells obtain energy from the sun and then create organic molecules. Animal cells get energy from food, using chemical bond energy

What are Catabolic Reactions?

The breakdown of large molecules into smaller components (ex., digestion of food; breakdown of glucose)

What are Anabolic Reactions?

Chemical reactions create complex molecules from smaller ones, using ATP as a main energy source for these reactions (ex., protein synthesis; building muscle mass)

How do Enzymes Catalyze Chemical Reactions in Cells?

They reduce the energy needed to initiate spontaneous reactions

What are the Major Differences Among Different Activated Carriers?

• ATP is the more widely used carrier

  • The two outermost phosphate groups are held by high energy phosphoanhydride bonds

  • Interconverting ATP to ADP occurs in a cycle

    • ADP —→ ATP releases H2O and ATP —→ ADP requires H2O

  • The terminal phosphate of ATP can be transferred to other molecules, occurring in coupled reactions

• CoA is another carrier

  • Has a thioester bond with high energy

  • Releases a lot of energy when hydrolyzed

• Activated carriers are important because they store and transfer energy for cells to use

How are Different Activated Carriers Used by Cells?

They transfer energy, electrons, or chemical groups in order to power different reactions. They store energy in an easily accessible/exchangeable form

How are Biological Polymers Synthesized in Cells?

They are synthesized by joining small building blocks together through covalent bonds, releasing water molecules in the process. Dehydration synthesis is key. Driven by ATP hydrolysis

What Determines the Shape of a Protein?

• Folding via noncovalent bonds inside of the protein

  • Hydrophobic forces help fold into compact structures

• Stability is determined by combined strength of the bonds in the protein

What are the Differences of Primary, Secondary, Tertiary, and Quaternary Protein Structures?

• Primary structure: the linear sequence of amino acids in a polypeptide chain

• Secondary structure: local folding patterns like alpha helices and beta sheets formed by hydrogen bonds

• Tertiary structure: overall 3D shape of a single polypeptide chain due to interactions between side chains, the noncovalent bonding that occurs

• Quaternary structure: arrangement of multiple polypeptide chains to form a functional protein complex

What are Enzymes?

Proteins that speed up chemical reactions in living things. They are responsible for building some substances and breaking down others. All living things have enzymes and our bodies naturally produce them. They convert substrates into products

How do Proteins Bind to Other Molecules?

• Binds through a specific region on their surface called a binding site

• The binding site interacts with the target molecule using a combination of weak, noncovalent bonds

  • ex., hydrogen bonds, ionic bonds, Van der Waals, and hydrophobic interactiojns

• There is a highly specific “lock and key” fit between the protein and molecule

What Determines the Specific Binding of Proteins to Other Molecules?

Determined by the 3D structure of the protein. This is also determined by the amino acid sequence

What Domain of an Antibody is Responsible for the Specific Binding of an Antigen?

The amino-terminal variable or V domains of the heavy and light chains

Antibody

• Y-shaped with two identical antigen-binding sites

• Held via disulfide bonds

• Produced by the immune system in response to foreign molecules

Condensation

Builds a larger molecule (polymer) from smaller ones (monomers) by removing a water molecule

Hydrolysis

Breaks down large molecules into smaller ones by adding a water molecule

Spontaneous Reaction

• Occurs naturally

• ΔG < 0

• Releases energy into surroundings

• Products have a lower energy than reactants

Nonspontaneous Reaction

• Does not occurs naturally

• ΔG > 0

• Needs an external energy source

• Products have a higher energy than reactants

How Do Enzymes Lower Activation Energy?

• Positioning of substrates to favor the reaction 

•  Straining bonds within the bound substrate 

•  Rearrangement of electrons in the substrate

•  Formation of covalent bond between substrate and enzyme

Allosteric Regulation of Enzymes

• Enzymes have 2 binding sites on the surface

  • Active site - binds substrate (not this one)

  • Regulatory site - binds regulatory molecule

• Binding on the regulator conformationally changes protein

• Increases activity (activator) or inhibits activity (inhibitor)

Ion-Exchange Chromatography

Separates molecules based on their charge. Often used to purify proteins or nucleic acids

Gel-Filtration Chromatography

Separates molecules based on their size

Affinity Chromatography

Separates molecules based on their specific binding interactions

SDS-Page

Separates proteins based on their molecule weight using denaturing

2D-Page

Separates proteins based on their isoelectric (pH at which a molecule has no net charge) point

Mass Spectrometry

Used to identify and sequence protein by determining the price masses of peptide derived from them

What is an Advantage and Disadvantage of X-Ray Crystallography?

• Advantage: can provide high-resolution, detailed three-dimensional images of the arrangement of atoms within a crystal

• Disadvantage: it relies on the formation of high-quality protein crystal

What is an Advantage and Disadvantage of NMR Spectroscopy?

• Advantage: can solve dynamic protein structures in solution

• Disadvantage: NMR becomes increasingly challenging as the size of the protein complex increases

What is an Advantage and Disadvantage of Cryo-Electron Microscopy?

• Advantage: can visualize biological macromolecules and complexes at high resolution without the need for crystallization 

• Disadvantage: can not visualize smaller proteins