Final

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Mutation

Translation

Protein Transport

Final

Cell Signaling

Light reactions in photosynthesis

ATP production: chemiosmosis (protons pumped across thylakoid membrane, create sproteon gradient, drives ATP synthase)

e-: from H20, gives to NADP+

location: thylakoid membrane of chloroplast

e-: from NADH and FADH2, gives to O2

ATP production: chemiosmosis through ATP synthase

location: inner membrane space

ATP production in aerobic respiration

Chemiosmosis

Lots of ATP produced

proton gradient drives ATP synthase, ADP + Pi --> ATP

ETC

O2 combines with e- and protons to form water

H+ pumped into intermembrane space, creates proton gradient

e- go through protein complexes

NADH and FADH2 made from glycolysis and citirc acid cycle, give e- to ETC

Citric acid cycle

ATP generation: 2 ATP made through substrate level phosphorylation

Glycolysis

ATP usage: 2 ATP consumed in first 5 steps of glycolysis

ATP generation: 2 ATP made thourgh substrate level phosphorylation

Tyrosine Kinase receptor pathway

activated signaling proteins --> cascades --> gene expression

Phosphorylated tyrosines --> signaling proteins

activates kinase --> autophosphorylation of tyrosine

Ligand binds to dimer

GCPR receptor

Pathway

cAMP activates first kinase

Adynylyl cyclase converts ATP --> cAMP

Activated G protein activates adenylyl cyclase

GPT --> GTP and activates G protein

Ligand binds to GCPR receptor

Membranes

Factors Affecting Fluidity

Fatty Acid Composition (unsaturated vs saturated)

Temperature (higher = more fluid)

Cholesterol (maintains fluidity at various temperatures)

Functions of membranes

Signal Transduction

Selective Permeability

Structure of Membranes

Glycolipids

Cell recognition, stability & protection

Glycoproteins

Cell-cell recognition & signal reception

Phosplipid Bilayer

Maintains Flexibility

Phospholipids

Hydrophobic Tails (fatty acids)

Water

Properties

Universal Solvent

Denser as Liquid than Solid

Expansion upon Freezing

High Heat of Vaporization

High Specific Heat

Cohesive Behavior

Biological Molecules

Nucleic Acids

Phosphodiester Bond

RNA

DNA

Nucleotides

Lipids

Energy

Membrane

Ester Bonds

Fatty Acids and Glycerol

Proteins

Enzymes

Amino Acids

Carbohydrates

Structure

Energy storage

Monosaccarides

Isomers

Trans Isomers

Cis Isomer

Chemical Bonds

Intermolecular

Ester

Phosphodiester

Van der Waals

Hyrdrophobic Interactiosn

Ion-Dipole

Hydrogen Bond

Intramolecular

Ionic Bond

Charges (+/-)

OH-

pOH

Hydroxide Ions

H+

pH

> 7

= 7

< 7

Basic

Neutral

Acidic

Hydrogen Ions

Covalent Bond

Peptide Bonds

Glycosidic Bonds

Nonpolar

Polar

Cell Structure

Cytoskeleton & Cell Motility

Intermediate Filaments – Mechanical support (keratin, nuclear lamina)

Microfilaments – Shape, movement, muscle contraction (actin, myosin)

Microtubules – Transport, cell division, structure (mitotic spindle, cilia, flagella)

Cell Junctions (Plant vs. Animal Cells)

Gap Junctions – Channels for direct cell communication (Animals - heart, neurons)

Desmosomes – Anchors cells together using keratin (Animals - skin, heart tissue)

Tight Junctions – Seals neighboring cells to prevent leakage (Animals - epithelial cells)

Plasmodesmata – Allows material exchange between plant cells (Plants)

Origin of Cells (Chemical Evolution & Prokaryotic Cells)

Miller-Urey Experiment

Oparin’s Bubble Hypothesis

Self-Replicating RNA (RNA World Hypothesis)

Formation of First Prokaryotic Cells

Early Earth Conditions

Prokaryotic vs. Eukaryotic Cells

Both Eurkaryotic and Prokaryotic

Cytoplasm

Cell Wall (plants, fungi, and bacteria)

Ribosomes

Prokaryotic Cells (Bacteria & Archaea)

Cell wall: Bacteria (peptidoglycan), Archaea (branched lipids)

No membrane-bound organelles

No nucleus, DNA in nucleoid region

Eukaryotic Cells (Plants, Animals, Fungi, Protists)

Unicellular or multicellular

Larger in size (10-100 µm)

Contain membrane-bound organelles

Have nucleus (DNA enclosed in membrane)

Eukaryotic Organelles & Functions

Cytoskeleton – Provides structure & facilitates cell movement (microtubules, microfilaments, intermediate filaments)

Vacuoles – Storage & water balance (large in plants, small in animals)

Chloroplasts (plants only) – Photosynthesis (light energy to chemical energy)

Peroxisomes Breaks down fatty acids & detoxifies harmful substances

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Peroxisomes – Breaks down fatty acids & detoxifies harmful substances

Lysosomes – Digest macromolecules & waste (contains hydrolytic enzymes)

Golgi Apparatus – Modifies, sorts, & packages proteins for secretion

Smooth Endoplasmic Reticulum (SER) – Synthesizes lipids, detoxifies drugs, stores calcium

Rough Endoplasmic Reticulum (RER) – Modifies & folds proteins, has ribosomes

Ribosomes – Protein synthesis (free ribosomes → cytoplasmic proteins; rough ER ribosomes → secreted/membrane proteins)

Nucleus – Stores DNA, controls gene expression

Cell Energy

Cellular Respiration: ATP Production

ATP: The Energy Currency

ATP used in:

Chemical Work (Biosynthesis)

Transport Work (Active Transport)

Mechanical Work (Motor Proteins)

ATP Synthesis: ADP + Pᵢ → ATP (Requires energy)

ATP Hydrolysis: ATP → ADP + Pᵢ (Releases energy)

Photosynthesis: ATP & Energy Transfer

Comparison to Cellular Respiration

ATP is generated using a proton gradient in both mitochondria and chloroplasts.

Both processes use electron transport chains.

Calvin Cycle (Stroma)

ATP & NADPH used to fix CO₂ into glucose.

Light-Dependent Reactions (Thylakoid Membrane)

Electron transport & proton pumping to create ATP and NADPH.

Electron Transport Chain (ETC) & Chemiosmosis

ATP is generated by oxidative phosphorylation.

Proton (H⁺) gradient in the intermembrane space drives ATP Synthase.

Stages of Cellular Respiration

Oxidative Phosphorylation (ETC + Chemiosmosis) (Inner Mitochondrial Membrane)

Outputs: ATP (32-34), H₂O

Inputs: NADH, FADH₂, O₂

Citric Acid Cycle (Krebs Cycle) (Mitochondrial Matrix)

Outputs: ATP, NADH, FADH₂, CO₂

Inputs: Acetyl-CoA, NAD+, FAD

Pyruvate Oxidation (Mitochondrial Matrix)

Inputs: Pyruvate, NAD+

Outputs: Acetyl-CoA, NADH, CO₂

Glycolysis (Cytoplasm)

Inputs: Glucose, ATP, NAD+

Outputs: Pyruvate, ATP (net 2), NADH

Energy Transfer in Cells

Types of Metabolic Pathways

Anabolic Pathways ( Photosynthesis: synthesis of glucose using light energy)

Catabolic Pathways (Cellular Respiration: breakdown of glucose for ATP)

Laws of Thermodynamics

2nd Law: Energy transfer increases entropy.

1st Law: Energy is transferred and transformed, not created or destroyed.

Translation & Protein Trafficking

Two types of Ribosomes

Bound Ribosomes

Free Ribsomes

Permanent change in DNA sequence

Types of Mutations

Frameshift Mutations

Reading frame shift

Deletion

Insertion

Point Mutations

Nonsense

Creates premature stop codon

Missense

Changes one amino acid

Silent

No change in amino acid

Secretory Pathway

Final vesicle sends protein to:

Cel Membrane

Lysosome

Plasma Membrane

Golgi further modifies, sorts, packages.

Travels to Golgi Apparatus in vesicles.

Protein enters ER lumen ).

Signal peptide directs ribosome to ER membrane.

Steps of Translation

3. Termination

Ribosomal subunits separate.

Release factor binds

Ribosome reaches a stop codon (UAA, UAG, UGA).

2. Elongation

Amino acids are joined by peptide bonds

Matching tRNAs bring amino acids.

Ribosome moves along mRNA, reading codons.

1. Initiation

Large ribosomal subunit joins to form complete ribosome.

tRNA carries methionine to start codon

Small ribosomal subunits bind to mRNA at start codon (AUG)

mRNA -> Protein

Prokaryotes

No mRNA processing

smaller ribosomes

Eukaryotes

larger ribosomes

mRNA Processing: Capped, spliced, poly-A-Tail

DNA Structure & Replication

DNA as Genetic Material

Chargaff's rule (A = T, C = G)

DNA vs. protein as genetic material

Hershey & Chase bacteriophage experiment

Griffith's transformation experiment

DNA Replication

Features of Replication

Polymerases need a primer to begin synthesis

Requires dNTPs as substrates

High fidelity (1 error per 10⁶ bases, proofreading)

High speed (E. coli: 2000 nt/sec)

Leading vs Lagging Strand

Directionality matters: DNA pol adds only to 3′ end

Okazaki fragments

Lagging strand synthesized discontinuously

Leading strand synthesized continuously

Overview

Replication bubble

Bidirectional replication

Replication fork

Replication origin (ORI)

Meselson-Stahl experiment (14N vs. 15N labeling)

Semiconservative replication model

Enzymes in DNA Replication

Ligase – seals nicks between Okazaki fragments

DNA Polymerase I – removes RNA primers & fills gaps

Sliding clamp – increases DNA pol processivity

DNA Polymerase III – synthesizes new strand (5′→3′)

Primase – adds RNA primers

Single-Stranded Binding Proteins (SSBPs) – stabilize separated strands

Topoisomerase – relieves tension ahead of fork

Helicase – unwinds DNA

DNA Structure

Hydrogen bonds (between bases)

Phosphodiester bonds (covalent, between nucleotides)

Complementary base pairing: A–T (2 H-bonds), G–C (3 H-bonds)

Nitrogenous bases: purines (A, G) vs pyrimidines (T, C)

Sugar-phosphate backbone

Antiparallel strands (5′→3′ / 3′→5′)

Double helix model (Watson & Crick)

Transcription & RNA Processing

Transcription

Eukaryotes

RNA polymerase detaches

Cleavage factors cut RNA transcript

RNA polymerase reads termination factor

U --> T in RNA

RNA polymerase reads 5' --> 3'

synthesizes complementary RNA 3' --> 5'

Initiation

forms transcription bubble

Transcription factors bind to promotor sequnce

recruits RNA Polymerase II to bind to promotor

Promotor region

Enhancer sequences

Promotor = TATA box

Location

goes to cytoplasm for translation

Nucleus

Prokaryotes

Termination

Newly synthesized mRNA released

Termination factor reached

Elongation

RNA synthesis in the 5' --> 3' direction

RNA polymerase adds complementary nucleotides

C-G

A-U

Initiaton

Topoisomerase keeps it from rewinding and relieves stress

Helicase unwinds DNA at promotor

Unwinds DNA

Forms transcription bubble

RNA polymerase binds to promotor

promotor = specific sequece on DNA

Location

Cytoplasm

Transcription and Translation coupled here

RNA processing

Splicing

Alternative splicing

makes many proteins from one gene

Splicesome

snRNA + proteins

Joins exons

Removes introns

3' Poly-A tail

Poly-A Polymerase adds A LOT of A's to 3' end

~100-300

Cut RNA downstream

Cleavage factor binds

5' Cap

Protects mRNA

Happens as RNA is synthesized

Eukaryotes only