Final
Transcription & RNA Processing
RNA processing
Eukaryotes only
5' Cap
Happens as RNA is synthesized
Protects mRNA
3' Poly-A tail
Cleavage factor binds
Cut RNA downstream
Poly-A Polymerase adds A LOT of A's to 3' end
~100-300
Splicing
Removes introns
Joins exons
Splicesome
snRNA + proteins
Alternative splicing
makes many proteins from one gene
Transcription
Prokaryotes
Location
Cytoplasm
Transcription and Translation coupled here
Initiaton
promotor = specific sequece on DNA
RNA polymerase binds to promotor
Unwinds DNA
Forms transcription bubble
Helicase unwinds DNA at promotor
Topoisomerase keeps it from rewinding and relieves stress
Elongation
RNA polymerase adds complementary nucleotides
A-U
C-G
RNA synthesis in the 5' --> 3' direction
Termination
Termination factor reached
Newly synthesized mRNA released
Eukaryotes
Location
Nucleus
goes to cytoplasm for translation
Initiation
Promotor region
Promotor = TATA box
Enhancer sequences
Transcription factors bind to promotor sequnce
recruits RNA Polymerase II to bind to promotor
Helicase unwinds DNA at promotor
forms transcription bubble
Topoisomerase keeps it from rewinding and relieves stress
Elongation
RNA polymerase reads 5' --> 3'
synthesizes complementary RNA 3' --> 5'
U --> T in RNA
Termination
RNA polymerase reads termination factor
Cleavage factors cut RNA transcript
RNA polymerase detaches
DNA Structure & Replication
Double helix model (Watson & Crick)
Antiparallel strands (5′→3′ / 3′→5′)
Sugar-phosphate backbone
Nitrogenous bases: purines (A, G) vs pyrimidines (T, C)
Complementary base pairing: A–T (2 H-bonds), G–C (3 H-bonds)
Phosphodiester bonds (covalent, between nucleotides)
Hydrogen bonds (between bases)
Enzymes in DNA Replication
Helicase – unwinds DNA
Topoisomerase – relieves tension ahead of fork
Single-Stranded Binding Proteins (SSBPs) – stabilize separated strands
Primase – adds RNA primers
DNA Polymerase III – synthesizes new strand (5′→3′)
Sliding clamp – increases DNA pol processivity
DNA Polymerase I – removes RNA primers & fills gaps
Ligase – seals nicks between Okazaki fragments
Overview
Semiconservative replication model
Meselson-Stahl experiment (14N vs. 15N labeling)
Replication origin (ORI)
Replication fork
Bidirectional replication
Replication bubble
Leading vs Lagging Strand
Leading strand synthesized continuously
Lagging strand synthesized discontinuously
Okazaki fragments
Directionality matters: DNA pol adds only to 3′ end
Features of Replication
High speed (E. coli: 2000 nt/sec)
High fidelity (1 error per 10⁶ bases, proofreading)
Requires dNTPs as substrates
Polymerases need a primer to begin synthesis
Griffith's transformation experiment
Hershey & Chase bacteriophage experiment
DNA vs. protein as genetic material
Chargaff's rule (A = T, C = G)
Translation & Protein Trafficking
mRNA -> Protein
Eukaryotes
mRNA Processing: Capped, spliced, poly-A-Tail
larger ribosomes
Prokaryotes
No mRNA processing
smaller ribosomes
Steps of Translation
1. Initiation
Small ribosomal subunits bind to mRNA at start codon (AUG)
tRNA carries methionine to start codon
Large ribosomal subunit joins to form complete ribosome.
2. Elongation
Ribosome moves along mRNA, reading codons.
Matching tRNAs bring amino acids.
Amino acids are joined by peptide bonds
3. Termination
Ribosome reaches a stop codon (UAA, UAG, UGA).
Release factor binds
Ribosomal subunits separate.
Secretory Pathway
Signal peptide directs ribosome to ER membrane.
Protein enters ER lumen ).
Travels to Golgi Apparatus in vesicles.
Golgi further modifies, sorts, packages.
Final vesicle sends protein to:
Plasma Membrane
Lysosome
Cel Membrane
Permanent change in DNA sequence
Types of Mutations
Point Mutations
Silent
No change in amino acid
Missense
Changes one amino acid
Nonsense
Creates premature stop codon
Frameshift Mutations
Insertion
Deletion
Reading frame shift
Two types of Ribosomes
Free Ribsomes
Bound Ribosomes
Cell Energy
Energy Transfer in Cells
Laws of Thermodynamics
1st Law: Energy is transferred and transformed, not created or destroyed.
2nd Law: Energy transfer increases entropy.
Types of Metabolic Pathways
Catabolic Pathways (Cellular Respiration: breakdown of glucose for ATP)
Anabolic Pathways ( Photosynthesis: synthesis of glucose using light energy)
Cellular Respiration: ATP Production
Stages of Cellular Respiration
Glycolysis (Cytoplasm)
Outputs: Pyruvate, ATP (net 2), NADH
Inputs: Glucose, ATP, NAD+
Pyruvate Oxidation (Mitochondrial Matrix)
Outputs: Acetyl-CoA, NADH, CO₂
Inputs: Pyruvate, NAD+
Citric Acid Cycle (Krebs Cycle) (Mitochondrial Matrix)
Inputs: Acetyl-CoA, NAD+, FAD
Outputs: ATP, NADH, FADH₂, CO₂
Oxidative Phosphorylation (ETC + Chemiosmosis) (Inner Mitochondrial Membrane)
Inputs: NADH, FADH₂, O₂
Outputs: ATP (32-34), H₂O
Electron Transport Chain (ETC) & Chemiosmosis
Proton (H⁺) gradient in the intermembrane space drives ATP Synthase.
ATP is generated by oxidative phosphorylation.
Photosynthesis: ATP & Energy Transfer
Light-Dependent Reactions (Thylakoid Membrane)
Electron transport & proton pumping to create ATP and NADPH.
Calvin Cycle (Stroma)
ATP & NADPH used to fix CO₂ into glucose.
Comparison to Cellular Respiration
Both processes use electron transport chains.
ATP is generated using a proton gradient in both mitochondria and chloroplasts.
ATP: The Energy Currency
ATP Hydrolysis: ATP → ADP + Pᵢ (Releases energy)
ATP Synthesis: ADP + Pᵢ → ATP (Requires energy)
ATP used in:
Mechanical Work (Motor Proteins)
Transport Work (Active Transport)
Chemical Work (Biosynthesis)
Cell Structure
Eukaryotic Organelles & Functions
Nucleus – Stores DNA, controls gene expression
Ribosomes – Protein synthesis (free ribosomes → cytoplasmic proteins; rough ER ribosomes → secreted/membrane proteins)
Rough Endoplasmic Reticulum (RER) – Modifies & folds proteins, has ribosomes
Smooth Endoplasmic Reticulum (SER) – Synthesizes lipids, detoxifies drugs, stores calcium
Golgi Apparatus – Modifies, sorts, & packages proteins for secretion
Lysosomes – Digest macromolecules & waste (contains hydrolytic enzymes)
Peroxisomes – Breaks down fatty acids & detoxifies harmful substances
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Peroxisomes Breaks down fatty acids & detoxifies harmful substances
Chloroplasts (plants only) – Photosynthesis (light energy to chemical energy)
Vacuoles – Storage & water balance (large in plants, small in animals)
Cytoskeleton – Provides structure & facilitates cell movement (microtubules, microfilaments, intermediate filaments)
Prokaryotic vs. Eukaryotic Cells
Eukaryotic Cells (Plants, Animals, Fungi, Protists)
Have nucleus (DNA enclosed in membrane)
Contain membrane-bound organelles
Larger in size (10-100 µm)
Unicellular or multicellular
Prokaryotic Cells (Bacteria & Archaea)
No nucleus, DNA in nucleoid region
No membrane-bound organelles
Cell wall: Bacteria (peptidoglycan), Archaea (branched lipids)
Both Eurkaryotic and Prokaryotic
Ribosomes
Cell Wall (plants, fungi, and bacteria)
Cytoplasm
Plasma Membrane
Origin of Cells (Chemical Evolution & Prokaryotic Cells)
Early Earth Conditions
Formation of First Prokaryotic Cells
Self-Replicating RNA (RNA World Hypothesis)
Oparin’s Bubble Hypothesis
Miller-Urey Experiment
Cell Junctions (Plant vs. Animal Cells)
Plasmodesmata – Allows material exchange between plant cells (Plants)
Tight Junctions – Seals neighboring cells to prevent leakage (Animals - epithelial cells)
Desmosomes – Anchors cells together using keratin (Animals - skin, heart tissue)
Gap Junctions – Channels for direct cell communication (Animals - heart, neurons)
Cytoskeleton & Cell Motility
Microtubules – Transport, cell division, structure (mitotic spindle, cilia, flagella)
Microfilaments – Shape, movement, muscle contraction (actin, myosin)
Intermediate Filaments – Mechanical support (keratin, nuclear lamina)
Chemical Bonds
Intramolecular
Covalent Bond
Polar
Nonpolar
Glycosidic Bonds
Peptide Bonds
Ionic Bond
Charges (+/-)
H+
Hydrogen Ions
pH
> 7
Acidic
= 7
Neutral
< 7
Basic
OH-
Hydroxide Ions
pOH
Intermolecular
Hydrogen Bond
Ion-Dipole
Hyrdrophobic Interactiosn
Van der Waals
Phosphodiester
Ester
Biological Molecules
Carbohydrates
Monosaccarides
Isomers
Cis Isomer
Trans Isomers
Glycosidic Bonds
Energy storage
Structure
Proteins
Amino Acids
Peptide Bonds
Enzymes
Structure
Lipids
Fatty Acids and Glycerol
Ester Bonds
Membrane
Energy
Nucleic Acids
Nucleotides
DNA
RNA
Phosphodiester Bond
Water
Properties
Cohesive Behavior
High Specific Heat
High Heat of Vaporization
Expansion upon Freezing
Denser as Liquid than Solid
Universal Solvent
Membranes
Structure of Membranes
Phosplipid Bilayer
Phospholipids
Hydrophobic Tails (fatty acids)
Maintains Flexibility
Glycoproteins
Cell-cell recognition & signal reception
Glycolipids
Cell recognition, stability & protection
Functions of membranes
Selective Permeability
Signal Transduction
Factors Affecting Fluidity
Cholesterol (maintains fluidity at various temperatures)
Temperature (higher = more fluid)
Fatty Acid Composition (unsaturated vs saturated)
Cell Signaling
GCPR receptor
Pathway
Ligand binds to GCPR receptor
GPT --> GTP and activates G protein
Activated G protein activates adenylyl cyclase
Adynylyl cyclase converts ATP --> cAMP
cAMP activates first kinase
Tyrosine Kinase receptor pathway
Ligand binds to dimer
activates kinase --> autophosphorylation of tyrosine
Phosphorylated tyrosines --> signaling proteins
activated signaling proteins --> cascades --> gene expression
ATP production in aerobic respiration
Glycolysis
ATP generation: 2 ATP made thourgh substrate level phosphorylation
ATP usage: 2 ATP consumed in first 5 steps of glycolysis
Citric acid cycle
ATP generation: 2 ATP made through substrate level phosphorylation
ETC
NADH and FADH2 made from glycolysis and citirc acid cycle, give e- to ETC
e- go through protein complexes
H+ pumped into intermembrane space, creates proton gradient
O2 combines with e- and protons to form water
Chemiosmosis
proton gradient drives ATP synthase, ADP + Pi --> ATP
Lots of ATP produced
ETC
location: inner membrane space
ATP production: chemiosmosis through ATP synthase
e-: from NADH and FADH2, gives to O2
Light reactions in photosynthesis
location: thylakoid membrane of chloroplast
e-: from H20, gives to NADP+
ATP production: chemiosmosis (protons pumped across thylakoid membrane, create sproteon gradient, drives ATP synthase)