BIOL 112 Week 1: Cell Theory and Diversity

• Week 1
• BIOL 112 - Lecture Content
• January 6

Cell Theory

• All living organisms consist of cells.
• The cell serves as the fundamental unit of life.
• Cells can only be created from pre-existing cells.

Cell Diversity

• There are 3 domains of cells: Bacteria (prokaryote), Archaea (prokaryote), and Eukaryotes.
• Prokaryotes constitute most living organisms.
• Some cells exist as unicells, while others form parts of multicellular organisms.
• There are many more lineages of unicellular eukaryotes than multicellular ones.

Bacteria

• Has a cell wall
• Has a cell membrane
• Nucleoid stores the DNA
• Plasmids are other genetic material locations
• Circular DNA
• Has ribosomes
• Does not have golgi bodies
• Does not have endoplasmic reticulum
• Does not have vesicles
• Does not have chloroplasts
• Does not have mitochondria
• 200nm - 750µm or 0.5 - 3µm is its general size
• Building blocks are proteins

Eukaryotes

• Has a cell membrane

• Has a cell wall - sometimes

• Nucleus stores the DNA

• Mitochondria and chloroplasts are other genetic material locations

• Linear DNA however the mitochondria and chloroplasts have circular

• Has ribosomes

• Has golgi bodies

• Has endoplasmic reticulum

• Has vesicles

• Has chloroplasts - sometimes

• Has mitochondria

• 0.2µm to several m or 10-100µm is its general size

• Building blocks are proteins

• January 8

• Cells are the smallest unit of life because:

  • They are organized and contained in membranes.
  • They are separated from the external environment
  • Eukaryotes possess internal membrane-bound compartments.
  • They contain DNA which carry instructions for growth, development, reproduction, ect.,
  • DNA is heritable and makes evolution possible
  • They can harness energy for growth, development, feeding, reproduction, membrane transport, and homeostasis.

Endosymbiotic Theory

• Mitochondria and chloroplasts originated from free-living bacteria that were ingested but not digested by cells containing nuclei.
• Mitochondria evolved from alpha-proteobacteria capable of aerobic respiration.
• Chloroplasts evolved from photosynthetic cyanobacteria.

Evidence for Endosymbiotic Theory

• Chloroplasts and mitochondria contain small circular DNA.
• Size mirrors bacteria.
• Cyanobacteria possess internal membranes resembling thylakoid membranes of chloroplasts.
• Genes on circular chromosomes resemble bacterial genes.

Summary Points

• Both bacteria and eukaryotic cells are contained within membranes, composed of the same macromolecules, have DNA, and harness energy through metabolic reactions.

• Prokaryotes represent most organisms on Earth

• Most eukaryotes are unicellular.

• Cells display far more diversity than textbook diagrams indicate.

• Bacteria typically lack internal membrane-bound compartments, are smaller, can be unicellular or multicellular, and possesses circular DNA.

• All cell types share membranes, DNA as a genetic code, ribosomes, and the four macromolecules, proteins, nucleic acids, lipids, and carbohydrates

• Many exceptions exist to the rules governing eukaryote and prokaryote differences.

• January 10

Molecules in a Cell

• Ions constitute about 1%
• Small organic molecules account for 10-20%
• Proteins, nucleic acids, carbohydrates and lipids make up 80-90%

Organic Molecules

• Must contain at least one carbon-hydrogen bond

Proteins (Polypeptides)

• Examples: Hormones, Enzymes, Cytoskeleton, Transport Proteins
• Monomers: Amino Acids
• Covalent Bond Type: Peptide Bond

Nucleic Acids

• Examples: DNA, RNA
• Monomers: Nucleotides
• Covalent Bond Type: Phosphodiester Bond

Carbohydrates

• Examples: Fiber - Cell Wall, Cellulose, Starch, Glycogen
• Monomers: Monosaccharides
• Covalent Bond Type: Glycosidic Bond

Lipids

• Examples: Phospholipids, Triglycerides (fat, oil)
• Monomers: Fatty Acids
• Covalent Bond Type: Ester Linkage

Nucleic Acids

• DNA monomers are deoxyribonucleotides

• RNA monomers are ribonucleotides

• Ribose (RNA) and deoxyribose (DNA) are 5 carbon sugars

• Carbon atoms of sugars are numbered, indicated with a prime symbol - 5' (5 prime)

• Monomers are polar

• New monomers are always added to the 3' OH end

• Proteins (polypeptides)

  • Monomer has N and C ends, amino and carboxyl, directionality, and new amino acids added to C end and growth.
  • Growth occurred in the N to C direction.

• Carbohydrates

  • Chains of sugars also have directionality
  • In starch, the C4 of a new glucose molecule is added to the C1 carbon of the first monomer

Lipids: - Do not have the same directionality / polarity as polypeptides, nucleic acids, and carbohydrates - It is not a chain as the head it very different from the tail

Phospholipids

• Composed of polar, hydrophilic head due to charged functional groups & polar covalent bonds
• Have non-polar, hydrophobic tail caused by regions with non-polar covalent bonds
• Are amphipathic

Hydrophilic Molecules

• Interact with water
• Have polar bonds or are uncharged
• Usually have hydrophilic properties

Hydrophobic Molecules

• Have weak interactions with water
• Have non-polar bonds and are uncharged

Amphipathic Molecules

• Consist of hydrophobic and hydrophilic regions

Macromolecule Locations & Function

• DNA, produced in the nucleus, is centralized & contains critical information.
• Proteins are found throughout the cell and perform functions like DNA packaging, enzymatic breakdown and transport.
• Carbohydrates provide shorter-term energy storage & form cell wall components.
• Lipids are in all membranes. Some cells contain cytoplasmic lipid droplets.

Summary

• Asymmetrical molecules exhibit polarity.

• Nucleic acids, proteins & carbohydrates exhibit directionality, synthesized as chains, and have one end where new monomers are added for that polymer growth

• Lipids have no directionality.

• January 13

Hydrophobic Molecules

• Form weak interactions with water.
• Diffuse easily across biological membranes if they're small enough
• Includes steroid hormones and waxes
• Are uncharged and non-polar

Cell Membrane

• Semi-permeable barrier.

• Creates entity separate from environment.

• Requires intake of matter from the environment in the form of food and energy

• Requires expulsion of waste matter from the environment

• Contains lipids and proteins that move laterally within the membrane, called the Fluid Mosaic Model.

• January 15

Structure of Phospholipids

• Cell membrane (membrane bilayer)
  • They mainly have heads and double tails - cylindrical shape
• Liposomes
  • Mixed type of lipids - larger heads and double tails / smaller heads and double tail
  • Also forms a bilayer
  • Usually created artificially
  • Has an aqueous cavity
• Micelles
  • Bulky heads and single tails - cone shape
  • No aqueous cavity

Thermodynamics

• Thermodynamics Drive Phospholipid Formation
  • △G = △H - T△S
  • Free energy of system (G) depends on enthalpy (H) and entropy (S)
  • Reactions are Spontaneous when △G is negative
    • Enthalpy measures heat released / absorbed by process.
    • Entropy relates to disorder/randomness.
    • Entropy increases can drive very low free energy
    • Enthalpy impacts system stability but less than entropy.

Bond/Interaction Type

• Strongest to weakest:
  • Covalent (not an interaction)
  • Ionic
  • Ion - Permanent Dipole (Ion-PD)
  • Hydrogen Bonding (H-bond)
  • Permanent Dipole - Permanent Dipole (PD-PD)
  • Ion - Induced Dipole (Ion-ID)
  • Permanent Dipole - Induced Dipole (PD-ID)
  • Induced Dipole - Induced Dipole (ID-ID)

Hydrophobic Effect

• Non-polar groups are mostly buried away from water
  • Applies to membranes, proteins, and nucleic acids
• Increases system stability
• Driven by entropy
  • Water molecules interacting directly with fatty acids are highly ordered
    • This is less free, meaning it has lower entropy, and is less sable
• Entropy of lipids offset by the water increase
  • Phospholipids are more ordered - decrease in entropy, but water molecules a less ordered - increasing entropy, making it more stable

Summary

• Phospholipids spontaneously form higher order structures in water

• Shapes of higher order structures and aqueous cavities depends on the shapes of the phospholipids Hydrophobic effect is critical for lipid bilayers and nucleic acids.

• Entropic force drives this, and it can be described as: when phospholipids are dispersed in water, each has a cage (low motional freedom)

• When phospholipids form a bilayer, water is ‘trapped' high motional freedom/high entropy) Contributes to stability, but cannot influence entropy.

• January 20

Diffusion

• Net movement of molecules across a membrane from high to low concentration.
• Result of random kinetic movements
• Equilibrium is without net movement; molecule movement never stops

Reasons for Diffusion

• Energetically favorable
• Increased entropy is a cause, as molecules become less clustered / more organized

Osmosis

• Diffusion of warter from high to low concentration
• From low to high solute concentration
• The solute concentration in extracellular space determines the diffusion of water

Molecules and Diffusion

• Diffusion allows small, nonpolar, small / polar molecules through the lipid bilayer:
  • Can be simple / facilitated.
  • Moves along concentration gradient.
  • Two-way directional.
  • Never stops moving.
• Polar, charged and large molecules use proteins for transport
• Charged molecules are overly bulky as they are surrounded by “hydration shells".

Membrane Transport

• Uses protein channels or carriers for small, charged and large, polar molecules
• Active Transport takes energy
  • Transport against electrochemical gradient
  • Transporter protein required (pumps)
• Passive transport not require energy input
  • Transport along concentration gradient,
  • Simple diffusion - small, non-polar molecules diffuse across membrane unaided
  • Facilitated diffusion - large, charged, polar molecules use transporter protein

Channel Proteins

• Provide a hydrophilic passage for ions, small, polar molecules
• Channels can "open" / "gated" depending on chemical signals
• Usually selective to molecule like ions, small, polar molecules
• Transport via channel occurs faster than carrier proteins

Carrier Proteins

• Carrier proteins are “gated".
• Transports specific molecules, more specific than channels
• Opens / closes
• Protein changes shape to open or close

Transport

• Primary Active: ATP aids molecules against concentration.
  • Sodium (3) is pumped outside cell (against the concentration gradient).
  • Potassium (2) is pumped into cell against its gradient.
• Secondary Active:ATP creates electro-chemical gradient to transport molecules against it.
  • Protons flowing down concentration drives transport up the concentration.

January 27

Proteins Role: - Regulation - Transport - Signalling - Force generation - Catalysts - Structure - Transcription - Translation Proteins (polypeptides are an N or C terminus): - There is a peptide bond between a carboxyl or amine group - Direction matters for consistency - This means they're synthesizing N/C terimus

Structure

• Primary (1°): linear polypeptide chain, amino acids bonded together, all backbone structure is the same and determined overall 3D structure
• Secondary (2°): interactions between acids, including the alpha helix and beta pleated sheet, hydrogen bonds stabilize backbone
  • Alpha helix is a carbonyl backbone group where hydrogen connects to the amide group
  • Beta Pleated Sheets involves the hydrogen bonds between carboxyl or amide groups
• Tertiary (3°): 3D shape with non-covalent interactions with side chains, side chains stabilized disulfide bonds of cysteine
• Quaternary (4°): results through subunit proteins (complexes), hydrophobic interactions and amino acid chains and protein subunits

January 29

• Protein Folding and Thermodynamics:Reaction is spontaneous
  • AG is negative
  • Entropy H2O increases
  • Enthalpy decreases
  • Bond strength
  • Protein Stability
• Side Chain Polarity
  • Hydrophobic with no polarity
  • +/ basic charged
  • Charged or acidic

Protein Folding

• Affected by relative stability and interactions, strong bond = increases stability and side chains
• Interior in the protein
  • Charged and polar parts are more attracted to the water and the other ones interact with the nonpolar side chain
• Shape and size increase in folding and stability
• Denaturing is unfolding with activity loss that regains

How Side Chains Affect Protein Folding

• Stability is influenced by interactions of side chains
  • Stronger bonds have more stability
• Location in protein effects it
  • Exterior versus Interior chains will have H2O interactions versus nonpolar bonding
• Side chain size influences folding and stability
• Denaturing and Unfolding
  • Denaturing is unfolding
  • With loss of biological activity
• Happens with non covalent disruptions noncovalent disrupt

February 3

• Change in structure is a change in activity as well

Conformation

• Molecule shape changes for transport and binding of glucose/Na+ to induce change

Enzymes

• Have Substrate and active Site
  • Site shape changes depending on type
• Enymes need Alosteric and Active sites and active shape

Regulation of Enzymes With Molecules

• Molecules can change active site shapes
• Binding or substrate prevention or promotion
• Inhibitor prevents molecule connection
• Activator adds connection

February 17 - Nucleic Acids - Unit 2

Nucleosides contain sugars and nucleobases

• Nucleotide is same with phosphate
• Nucleotides added to 3 prime end
• All phsophates are on the 5 prime carbon
• RNA has hydroxy and DNA has none (one less)
• RNA has uracil
• DNA has thymine

DNA vs RNA

RNA has the Uracil and a Hydrogen

• MacroAssembly of DNA
• The double strand has 3-hydroxyl and phosphates

DNA Helix:

• Grooves and Binding

Recognizing DNA- different Proteins

• Major Grooves (big)
• Minor gRooves (small)

February 5th

• Geometry of Chargoff means that the bonds are stacking in a way that makes it regular
• Distances b/w strands
• T and A are held together by 2 hydrogen bonds
• C/G = Held By 3 ID-DI and PD-PD

Hydrophobic Effect

• DNA is present.
• Strands provide freedom to allow water interaction = Water is freed when it strands increase the interactions and increase the entropy
• Bases of nitrogen are used and sealed from water to be less table

Key Elements of Double Helic

• H bonds
• Phosphate
• Interaction
• Biological Info

InfoMolecule:

• DNA for everything to be passed
• Synthesis:
• Translation and Transcription

Genes:

-Transcription/ RNA that aren't translated

Gene COntains:

• A promoter and regions to say "hey"
• Terminator with sequences for termination, and sequences that transcribe into message to make amino acids

Promoter:

• Pol moves from promoter to terminator reading from 3 > 5 (the other way around)

February 10:

• Transcription start sites:

  • top strand
  • the one on bottom and swaps U/T

• Starts with synthesisi zation

  • with enymes and help, on promoter

Eukaryotic/Bacterial Transcription and Translation - simultaneous

• in the separate sections-nucleus vs cytoplasm
• Transciption = 3 steps

polymerase

Starts the transcription

• Stop by releasing and passing through teriminator called mRNA

• Has subnuits, makes the RNA tranfers, multiple channels (that pull apart the helix)

• Sigma creates the area for binding + start of tranfer + 1, catalytic area

Recriutemtn-Eukaryotic

• polymerase binds, activation and transcription of factors

February 12: - DNA- RNA

In grooves - Amino Acids

Transcription:

• can bind and make transcripts

Eukaryotic TRansiption"

• New, but Modified 5 End, exons / intons- the transcipt ends here

Splicing:

  - introns
   - removed vs exons
    -  proteins in the cell recognize and remove

• Each trancribe one
  • tranncribe
    • protein w ribosome
    • a RNA, and structure

February 24

Translation

• Required components
  • Messenger rna (via transfer) with sequences for the ribosomal movements
• RIbOSOME/transfer and synthetase
• elognation / initiation factos + release factors
• TRNA has ribosomes and proteins! (small/large subu)

TRna is a product of transcription .

• trnas + ribosoem = the tranasport
• ribosiomes will combine

Translation Elements

Untranslated regions with code

• bacterial region hairpins

5 Cap

• The site Binds
• site

FEBraru 25

• Delivers animoa cids / tthe three amino acid pair

• They intereact

• the structure of the amino acids

• There is directional bonding Aug makes M uAC cna take the amino acids

linking / binding

• ribsoesm have subu Small, large (3)
• Genetic Codons:
• "unversal"
• mRNA code
• redudnant
• codon
• "begin reading"

Repsonsible for starating coding (AUG)

• RNA- code / template

February 26

• TRanslation in Polypeptides:

1 Step - mRNA bond the Sites : - trna and ribsomes (shine)

• 2 step translantion with ribos s-
• Trna comes and synthesis from the aug - the bond is helped via enzymes The process stops wiht the proteins recofinizing when there are release signals

March 3

• no information