Bio

• Nucleus


  Membrane-bound organelle that contains the genetic material (DNA) of a eukaryotic cell
• Mitochondria


  Organelles that produce energy for the cell through cellular respiration
• Eukaryotic cells


  • Have a true nucleus
  • Have membrane-bound organelles
  • Contain multiple linear chromosomes
  • Reproduce via mitosis
• Nucleus


  • Has a double membrane with nuclear pores for selective passage of molecules
  • Contains nucleoli which are sites of ribosome assembly
  • Genetic information is stored as chromatin and chromosomes
• Cytoplasm


  • Everything in the cell other than the nucleus and cell membrane
  • Contains cytoskeletal fibers and cytosol (gel-like fluid)
  • Site of cellular metabolism
• Mitochondria


  • Are the "powerhouses" of the cell, producing ATP through the citric acid cycle and oxidative phosphorylation
  • Originated from a bacterium engulfed by another cell (endosymbiotic theory)
  • Have their own DNA and can self-replicate
  • Mitochondrial DNA is maternally inherited

  
• Mitochondrial structure


  • Have an outer and inner membrane with an intermembrane space
  • Matrix is the site of the Krebs cycle
  • Inner membrane houses the electron transport chain complexes and ATP synthase for oxidative phosphorylation
  • Cristae increase the surface area of the inner membrane
  • Intermembrane space is critical for the proton gradient that facilitates ATP synthesis
• Endoplasmic reticulum (ER)


  • A continuous, net-like organelle connected to the nuclear membrane
  • Has invaginations (cisternae) that increase its surface area
  • Two types: rough ER and smooth ER
• Rough ER


  • Has ribosomes on its surface that synthesize proteins
  • Newly synthesized proteins can undergo folding, modification, and targeting in the ER
• Smooth ER


  • Lacks ribosomes on its surface
  • Involved in lipid and steroid hormone synthesis
  • Extensive in liver cells due to detoxification function
  • Participates in phospholipid production for cellular membranes
  • In muscle cells, specialized to store calcium for muscle contraction
• Golgi apparatus


  • Stacks of membrane-bound compartments (cisternae)
  • Receives protein-packed vesicles from the ER, modifies them, and packages them into vesicles that bud off from the trans face
  • Vesicles are usually for secretion out of the cell
• Lysosomes


  • The "garbage disposal" of the cell, fusing with vesicles containing extracellular material or intracellular waste for degradation
  • Contain hydrolytic enzymes and maintain an acidic interior (pH 4.5-5) for optimal enzyme function
  • Originate from the Golgi apparatus
• Peroxisomes


  • Accumulate and neutralize peroxides, protecting the cell from oxidative stress
  • Involved in the degradation of very long-chain fatty acids and detoxification of harmful substances
• Cytoskeleton


  • Skeletal network in the cell that provides structure and enables movement
  • Comprises microfilaments, microtubules, and intermediate filaments
• Microfilaments


  • The smallest unit of the cytoskeleton, composed of actin polymers
  • Involved in cell motility, phagocytosis, cell division, muscle contraction, and endocytosis/exocytosis
• Microtubules


  • Wider than microfilaments, composed of alpha-tubulin and beta-tubulin protein dimers
  • Maintain cell structure and serve as "highways" for motor proteins like kinesin and dynein
  • Form the mitotic spindle during cell division
  • Part of the 9+2 structure of eukaryotic flagella and cilia
• Kinesin and dynein


  • Motor proteins that "walk" along microtubules
  • Kinesin moves from the cell center towards the cell edge (anterograde), e.g. delivering neurotransmitters in neurons
  • Dynein moves from the cell edge towards the center (retrograde), involved in the movement of endocytosed materials
• Centrosomes and centrioles


  • Centrosomes are the main microtubule organizing centers in the cell
  • Centrioles form part of the centrosome and play a key role in cell division
• Eukaryotic flagella and cilia

  • Composed of microtubules and generate motion
  • Flagella are long and thin, propelling the cell forward (e.g. in sperm cells)
  • Cilia are short, moving substances along the cell surface (e.g. in respiratory tract or fallopian tubes)
• Polarity in microfilaments and microtubules

  • One end is labeled "plus" and the other "minus"
  • They grow at the plus end and shrink at the minus end, a phenomenon known as treadmilling
  • Capping proteins can halt polymerization by stabilizing either end
• Intermediate filaments


  • Sized between microfilaments and microtubules
  • Composed of different protein polymers, providing structural support and cell-to-cell adhesion
  • Include lamin (supports the nucleus) and keratin (makes up hair and nails)
• Nucleic Acids


  DNA and RNA
• DNA


  Deoxyribonucleic acid, encodes genetic information
• RNA


  Ribonucleic acid, involved in protein synthesis
• DNA Structure


  • Double helix secondary structure with two strands
  • Backbone: alternating sugar (deoxyribose) and phosphate groups
  • Nitrogenous bases: Adenine (A), Thymine (T), Guanine (G), Cytosine (C)
  • Base pairing: A-T and G-C via hydrogen bonds
  • Chargaff's rule: Amounts of A=T and G=C in double-stranded DNA
• RNA Structure


  • Usually single-stranded
  • Backbone: alternating sugar (ribose) and phosphate groups
  • Nitrogenous bases: Adenine (A), Uracil (U), Guanine (G), Cytosine (C)
  • Can form some secondary structures (e.g., hairpin loops)

  
• Nucleotides


  • Composed of a nitrogenous base, a pentose sugar, and phosphate(s)
  • Building blocks of nucleic acids
  • Connected by phosphodiester bonds: 3' carbon of one sugar to 5' carbon of the next
• Nitrogenous Bases


  • Purines: Adenine (A) and Guanine (G), two-ring structures
  • Pyrimidines: Cytosine (C), Thymine (T, in DNA only), Uracil (U, in RNA only), single-ring structures
  • A-T/U form two hydrogen bonds, G-C form three hydrogen bonds
• Denaturation and Annealing


  1. Denaturation: separation of DNA strands by breaking hydrogen bonds (e.g., via heat)

  2. Melting temperature (Tm): temp. at which 50% of DNA strands dissociate

  3. Annealing: reassociation of complementary DNA strands
• DNA and RNA Differences

  • DNA: stable, long-term storage of genetic info, lacks OH group at carbon 2
  • RNA: less stable, more reactive due to OH group at carbon 2, involved in protein synthesis

  
• Central Dogma of Molecular Biology

  • DNA → RNA → Protein
  • Fundamental principle: Genetic information flows from DNA to RNA to protein

  
• Exceptions: RNA viruses employ reverse transcriptase
• Hershey-Chase Experiment - 1950s


  • Established DNA as heritable genetic material
  • Used radioactive labeling to distinguish protein from DNA
  • Phage viruses with radioactive phosphorus showed DNA transferred into bacteria, but not protein

  
• DNA and RNA


  • DNA: Deoxyribonucleic acid, stores and transmits genetic information
  • RNA: Ribonucleic acid, transcribed from DNA, has multiple forms

  
• RNA Varieties and Roles

  • mRNA: Messenger from DNA to ribosomes; carries code for proteins
  • hnRNA: Precursor to mRNA, gets processed into mature mRNA
  • tRNA: Transfer RNA with cloverleaf structure; carries amino acids for protein assembly
  • rRNA: Ribosomal RNA, part of ribosome structure; facilitates protein formation
  • Ribozymes: RNA with catalytic activity, e.g., rRNA
  • siRNA/miRNA: RNA molecules that can downregulate gene expression

  
• Exceptions to Central Dogma

  • Reverse transcriptase: RNA → DNA
  • Non-coding RNA: Not all RNA is translated into protein

  
• Translation and the Genetic Code

  • Ribosomes read mRNA in codons (3-nucleotide sequences)
  • 64 possible codons from 4 bases in groups of 3
  • The genetic code is degenerate: multiple codons exist for some amino acids

  
• Start and Stop Codons

  • AUG: Start codon, codes for methionine
  • Stop codons: UAA, UAG, UGA; signal end of translation
• Wobble Hypothesis


  • Flexibility in the 3rd base of the codon
  • Reflects less strict base pairing, allows for degeneracy of the code
  • The first two bases are more likely conserved
• DNA Replication


  • Fundamental process for genetic inheritance
  • Occurs via a semi-conservative mechanism