Biological Organization and Cell Structure

• BioUnit 1 (1502)

L1 Objectives - Cell Theory + Prokaryotes

• Levels of biological organization depend on each other: cell → multi-cell → population → community.
• Emergent properties apply to biological organisms due to arising in a level of organization that cannot be predicted from understanding what is below it.
• All properties of living systems involve cell organization, reproduction and growth, and homeostasis.

Basic Cell Theory

• All living organisms are composed of one or more cells.
• Cells are the basic building blocks of life.
• New cells come from pre-existing cells.
• Two defining characteristics of prokaryotic cells are no nucleus and a single-chamber compartment.
• They have a high surface area to volume ratio.

Structure and Composition of Bacterial Cell Walls

• Gram-positive bacteria have a thick cell wall of peptidoglycan, which stains purple.
• Gram-negative bacteria have a thin cell wall with a capsule, which stains pink.
• Shape, environment, niche, metabolic requirements, and outputs can inform bacteria type.

L2 Objectives - Prokaryotes vs. Eukaryotes

• Prokaryotes: "before nucleus", single chamber without membrane bound organelles and decreased surface area to volume ratio.
• Eukaryotes: "true nucleus", have effective surface area by having membrane-bound compartments.

Eukaryotic Structure

• Nucleus houses DNA.
• Nuclear envelope: double membrane that maintains a nuclear environment distinct from the cytoplasm.
• Lamina: cytoskeletal structure that supports the nuclear envelope.
• Pore complex: structural transport between the nucleus and cytoplasm allowing selective two-way exchanging of material.
• Rough Endoplasmic Reticulum: (ribosomes) protein synthesis, interconnected network of membranes continuous with the nuclear envelope.
• Smooth Endoplasmic Reticulum: lipid synthesis and detoxification.
• The rough ER connects to the smooth ER which connects to the Golgi apparatus.
• Golgi apparatus packs and reprocesses protein and lipids connected to organelles by vesicles.
• Secretory vesicles transport to the plasma membrane for expulsion via exocytosis.
• Endocrine vesicles form the plasma membrane to the endocytic system.
• Lysosomes degrade macromolecules and works at low pH containing enzymes.
• Peroxisomes facilitate lipid breakdown and other metabolic processes and contain hydrogen peroxide.
• Mitochondria are the "powerhouse of the cell" using glucose and ATP for cellular respiration.
• Nucleolus is the area where rRNA is made, and ribosomes are constructed.

Plant Cell Structure

• Plastids: chloroplasts (photosynthesis), amyloplasts (starch storage).
• Chromoplasts (pigments).
• Central vacuole provides structural support.
• Cell wall: primarily cellulose and has both primary (1°) and secondary (2°) structures.
• Plasmodesmata: channels between walls, connecting cells.

Eukaryotic Evolution Theories

• Endosymbiont: absorbed smaller cell.
• Inside Out- symbiosis within cell.

L3 - Chemical Basics/Overview

• Refers to Chemical Bonds
• Ionic bonds involve complete electron transfer.
• Covalent bonds involve sharing of electrons, either equally or unequally.
• Hydrogen bonds involve hydrogen bonded to fluorine, oxygen, or nitrogen (DNA).
• Van der Waals forces are weak bonds between atoms close together.
• The strength of the bonds: VDW & H-bond < covalent < Ionic.

L4 Objectives - Carbs/Macromolecules

• Organic molecules:
• Contain carbon in living organisms, made of carbon, hydrogen, oxygen, and less abundant phosphorus and sulfur.
• Carbohydrates, lipids, proteins, and nucleic acids are macromolecules and basic building blocks of life.

Hydrocarbons and their Different Forms

• Alkanes/alkenes/alkynes.
• Benzene rings.
• Two common variations with H2O: dehydration synthesis (H2O out) and hydrolysis (H2O in, aids in breakdown of starches).
• Macromolecule polymers are also considered polymers.
• Polymers are macromolecules assembled from monomers through polymerization, held together by covalent bonds.
• Carbohydrates' structural features:
• Composed of (CH2O)n, where n is the number of carbons in the molecule.
• Components includes: monosaccharides, used to describe models as linear or random.
• Structural support
• energy storage
• biochemical intermediates

Isomer Types

• Isomers have the same formula:
• Structural isomers (aldoses vs. ketoses) have different arrangements.
• Enantiomers are mirror images that cannot be rotated.
• Stereo- isomers differ chemically and physically.
• Mono/di/polysaccharides have structured features.
• Monosaccharides are linear or glucose rings (alpha/beta).
• Disaccharides have a dehydration synthesis between 1-4 carbons in 2 monosaccharides by glycosidic bonds; connects sugar molecules (carbs) to another group.
• Polysaccharides are chains of monosaccharides with glycosidic bonds.

Common Polysaccharides and Their Types

• Amylose: a plant starch with alpha 1-4 linkages.
• Glycogen: an animal starch with alpha 1-4 linkages, branched energy storage.
• Chitin: insect exoskeleton with beta 1-4 linkages, which animals cannot digest; modified.
• Cellulose: plant cell wall structure with beta 1-4 linkages, unmodified.

L5 Objectives - Proteins/NA/Lipids

• Structural features in lipids H2O insoluble and amphipathic (polar and nonpolar regions).
• Fatty acids/triglycerides/phospholipids/sterols.
• Unsaturated fats have kinks produced by double bonds which can be removed through hydrogenation (adding H+).
• Triglycerides store energy efficiently with 1 glycerol and 3 fatty acids and ester bonds.
• Phospholipids - membrane building bilyr selectively permeable with a polar head and nonpolar tail.
• Liposomes/micelle are membrane-bound.
• Steroids have a framework of 4 carbon rings and contain functional groups that vary by lipid molecule.

Amino Acids

• Building blocks of proteins with a basic structural feature
• Has carbon, hydrogen, oxygen, and nitrogen, contains amino carboxyl and unique side chain.
• Over 20 in proteins.
• Amino acid groups are charged polar including cysteine, serine, tyrosine, threonine, asparagine, and glutamine.
• Polar amino acids end in -OH.
• Positively charged polar amino acids include lysine, arginine, and histidine.
• Amino acid polymerization uses peptide bonds is synthesized by ribosome between the oxygen of a carboxyl group, hydrogen of an amine group, and creates a C-N bond.
• Polymerization has monomers combined to form polymers.

Structure of Proteins

The Protein has Four Levels

• Primary (1°): AA sequence codes via DNA sequence.
• Covalent or peptide (N-N) and disulfide bonds.
• Secondary (2°): Arrangement of neighboring AA in alpha helix or beta sheet; hydrogen bonds hold.
• Tertiary (3°): Overall 3D folding, 1 peptide chain with charge-charge (salt bridge, ionic bonds), disulfide covalent bonds, forms cysteine AA that makes SH.
• Quaternary (4°): Protein with +1 peptide.
• Not all proteins will have hemoglobin.
• Domain is a structural subdivision of a protein with specified function.
• Structure: features contribute to protein folding.
• Conformational structures have flexibility in the final folded proteins.
• Protein folding: linear chain of amino acids (polypeptide chain) twists into 3D structure to become active.
• 6-NA : DNA/RNA
• Nucleic acids (NA) have a basic structure:
• NA= 3 phosphate groups + sugar + N base.
• Chain of nucleotides forms DNA.

DNA vs RNA

• DNA - deoxyribonucleic acid, hereditary material (all living, some viruses).
• RNA - ribonucleic acid, more diverse hereditary material (intermediate between DNA + protein).
• DNA polymers uses phosphodiester bonds.
• Sugar phosphate backbone with dehydration synthesis between P groups.
• A and G are Purines (pure as gold).
• Holds DNA together.
• Base pairing involves hydrogen bonds between bases
• C and G = 3 bonds; -A and T = 2 bonds.

Basic Principles of DNA

• Replication explained.

• 5' 3' writing.

• 1 direction.

• EXACT copy.

• Uses pre-existing strand.

• Hydrolysis of P bonds in nucleotide triphosphate gives energy.

• Chargoff's Rule: When DNA is analyzed, A=T and G=C; different organisms have different ratios of A/T and G/C.

• Leading/Lagging & Replication fork.

• Leading: continuous strand in 5' → 3'.

• Lagging: staggered replication and creation of okazaki fragments

• Occurs in a 3' → 5'.

• Replication fork: ½ of replication bubble (helix splits)

• Different protein enzymes are involved in DNA replication.

• Helicase unwinds the DNA helix, and topoisomerase relaxes it.

• Primase adds an RNA primer, so DNA polymerase III can be added.

• DNA polymerase III puts in nucleotides and proofreads, corrects, removes, and replaces nucleotides from RNA.

• DNA polymerase I replaces the RNA primer with DNA and proofreads existing strand.

• Ligase seals nicks in okazaki lagging to form phosphodiester bonds.

L7 DNA Cont.

• Basic organization of DNA in prokaryotes and eukaryotes:
• Prokaryotes: very little DNA, circular chromosomes.
• Eukaryotes: multiple linear chromosomes, DNA organized around histone (protein) in nucleosome (structure); wants more control in replication.
• Telomeres: specific repetitive DNA sequence (can be replicated without consequences).
• Telomerase: enzyme lengthens, RNA dependent DNA polymerase, RNA primer, and enzyme structure.
• Extends the 3' end of lagging end and complementary to telomere sequence.
• Gene expression
• Gene = unit of heredity; unit of DNA encodes for RNA → protein.
• Transcription (DNA → mRNA).
• Translation (mRNA → protein).

Differences in Gene Expression in Prokaryotes and Eukaryotes

• Prokaryotes: replication and transcription occur invivo in the cytoplasm but are coupled in one place.
• Eukaryotes: replication is regulated at multiple levels during transcription in the nucleus to translation in the cytoplasm in diff compartments.

Transcription

• Initiation: RNA polymerase binds to promoter (TATA box).
• Elongation: Adds nucleotides 5'→3'.
• Coding strand acts as non-template while the template is used as blueprint for complementary RNA molecule.
• Termination: Newly made RNA is released from RNA polymerase with an enzyme and is signaled on the terminator.
• Then RNA polymerase and mRNA falls off.

Roles of Different Protein Enzymes

• In transcription, RNA polymerase uses a DNA template as a guide to form RNA nucleotides into a polymer, but no primer is needed.
• Polymerase I: transcribes rRNA.
• Polymerase III: transcribes tRNA and rRNA.
• Transcription factors bind to special DNA to activate/inhibit transcription.

mRNA Processing Steps in Eukaryotes (pre-mRNA -> mRNA)

• Add 5' cap and poly A tail for protection and regulation.

• Undergoes splicing.

• Spliceosomes remove introns.

• SURNPs/spliceosome exons are expressed and become proteins and transforms pre-mRNA.

• mRNA exits nucleus to be translated into protein.

• Alternative splicing allows single gene to produce multiple different proteins in different combinations of exons.

• Different mRNAs are expressed to express different proteins.

Translation (mRNA+ Protein)-

• Initiating, tRNA binds to P site initiating complex.
• Begins anticodon to mRNA and reads/writes tRNA.
• Scans for START codon (AUG).
• The small ribosome binds to mRNA.
• Elongation A-P-E site peptide chains are formed.
• Termination: stop codon (UAA / UAG / UGA) causes release factor to enter A site and the ribosomal subunit falls off, releases from the ribosome.

Roles of Ribosome

• Ribosomes the small ones that read and write the code that is translated to peptides.
• Ribosomes binds mRNA and tRNA.
• Catalyzes peptide bonds to form polypeptides.
• tRNA carries genetic info from DNA (codons).
• tRNA delivers AA that matches anticodon to codon.
• rRNA- structural and catalytic component of ribosome; adds in peptide bond formation.
• Initiation factors help assemble mRNA starts at the start codon.
• Elongation factors assist tRNA movement and AA addition.
• Inosine: often found in tRNA, flexible in base pairing.
• Aminoacyl-tRNA synthetase attaches AA on the 3' end of tRNA.

Importance of Protein Folding

• 2° structures in RNA - hairpin loops/stems, local folding by H binds with 1 same strand that's crucial for RNA function.
• Chaperonins help proteins that misfold to fold correctly with ER and cytoplasm.
• Wobble Hypothesis: 3rd position in codon often not as important as first 2 for specific AA.
• Frameshift: shift 1 letter, and it can be completely different proteins. RNA is self-binding and creates versatile traits through proteins.
• Why mRNA is so versatile is because RNA is not able to fold as proteins do.

Explore the levels of biological organization, emergent properties, and cell theory. Investigate the functions of cellular structures such as the endoplasmic reticulum, Golgi apparatus, lysosomes, and mitochondria. Learn about plant-specific organelles like amyloplasts and plasmodesmata.