BIO 130 term 1

Cell theory(week 1: section 1)

• cell is the basic organizational unit of life
• all organisms are comprised of 1 or more cells
• cells arise from pre-existing cells

Prokaryotic cells(week 1: section 1)

• no nuclei
• single-celled
• no membrane-bound organelles
• DNA bound by nucleoid(not membrane)
• smaller than eukaryotes
• less DNA than eukaryotes
• Bacteria and Archaea

Cell theory(week 1: section 1)

• cell is the basic organizational unit of life
• all organisms are comprised of 1 or more cells
• cells arise from pre-existing cells

Prokaryotic cells(week 1: section 1)

• no nuclei
• single-celled
• no membrane-bound organelles
• DNA bound by nucleoid(not membrane)
• smaller than eukaryotes
• less DNA than eukaryotes
• Bacteria and Archaea

Eukaryotic cells(week 1: section 1)

• nuclei
• single-celled/multicellular
• several membrane bound organelles
• plants, fungi, animals, humans

Differences between animal and plant eukaryotic cells(week 1: section 1)

• plants are larger and more complex
• plants: cell wall, chloroplasts, large vacuole

Origins of mitochondria(week 1: section 1)

• aerobic bacterium engulfed by anaerobic eukaryotic cell
• aerobic bacterium loss plasma membrane and split into mitochondria w/ double membrane
• becomes early aerobic eukaryotic cell

origins of chloroplasts(week 1: section 1)

• early aerobic eukaryotic cell engulfs photosynthetic bacterium
• photosynthetic bacterium loses membrane and splits into chloroplasts
• becomes photosynthetic eukaryotic cell

Endosymbiont hypothesis(week 1: section 1)

• organelles in eukaryotic cells were once prokaryotic microbes that entered eukaryotic cells living together
• shown w/ origins of mitochondria + chloroplasts

Evidence for endosymbiont hypothesis(week 1: section 1)

1. remnants of mitochondria + chloroplasts’s genomes + genetic systems resemble that of modern day prokaryotes
2. their own protein + DNA synthesis components resemble prokaryotes too

General attributes of model organisms(week 1: section 2)

• rapid development w/ short life cycles
• small adult(reproductive) size
• readily available(collections or widespread)
• tractability (ease of manipulation or modification)
• understandable genetics

Examples of model organisms(week 1: section 2)

• E. coli
• Brewer’s yeast
• Arabidopsis thaliana (wall cress)
• Drosophila melanogaster (fruit fly)
• Caenorhabditis elegans (nematode worm)
• Zebrafish
• mice

E. coli as a model organism(week 1: section 2)

• prokaryote
• bacteria
• helps show fundamental mechanisms of life (ex: how cells replicate)

Brewer's yeast as a model organism(week 1: section 2)

• eukaryote
• single celled fungus similar to plant cells (has cell wall, immobile, no chloroplasts)
• simple eukaryote to help study more complex ones

Arabidopsis thaliana(wall cress) as a model organism(week 1: section 2)

• eukaryote
• weed plant
• helps give insight into development + physiology of crop plants, as well as other plant species

Drosophila melanogaster(fruit fly) as a model organism(week 1: section 2)

• eukaryote
• fly (insect)
• helps to understand how all animals develop

Caenorhabditis elegans(nematode worm) as a model organism(week 1: section 2)

• eukaryote
• relative of eel worms
• hermaphrodite
• complete genome (959 body cells)
• share genes w/ humans, so helps to see how humans develop

zebra fish as a model organism(week 1: section 2)

• eukaryote
• transparent first 2 weeks of life
• helps to see how cells behave during development of a living animal

mice as a model organism(week 1: section 2)

• eukaryote
• used to study mammalian genetics, development, immunology + cell bio.

Model organisms + humans(week 1: section 2)

• study of model organisms helps us to understand humans bc:

• humans can also be studied using:

  1. clinical studies
  2. cell cultures
  3. organoids

information flow in the cell(week 1: section 3)

Refined central dogma(week 1: section 3)

Elaborated central dogma(week 1: section 3)

Information flow in prokaryote + eukaryote cells(week 1: section 3)

• DNA, RNA + proteins synthesized as ==linear chains of info w/ a definite polarity==
• info in RNA sequence is translated into amino acid sequence via ==genetic code==(universal among all species)

Nucleic acids(week 1: section 4)

• genetic material in a cell(organism’s blueprints)
• DNA = deoxyribonucleic acid
• RNA = ribonucleic acid

Parts of a nucleotide(week 1: section 4)

1. pentose sugar(foundation for base)
2. nitrogenous base(A, T, C, G, U)
3. phosphate group(backbone, 1-3 P’s)

Bases(week 1: section 4)

• nitrogen containing ring compounds
• single ring = pyrimidine (U, T, C)
• double ring = purine (A, G)

Differences between RNA and DNA(week 1: section 4)

RNA:

• ribose sugar
• G, C, A, U

DNA:

• deoxyribose sugar(missing oxygen)
• G, C, A, T

Nucleic acid nomenclature(week 1: section 4)

• base + sugar = nucleoside
• base + sugar + phosphate = nucleotide
• 1 phosphate = mono, 2 = di, 3 = tri

Bases and their nucleoside naming(week 1: section 4)

Nucleic acid chains(week 1: section 4)

• DNA synthesized from deoxyribonucleoside triphosphates(dNTPs)
• RNA synthesized from ribonucleoside triphosphates(NTPs)
• nucleotides are linked by ==phosphodiester bonds==

Molecular interactions(week 1: section 5)

• interactions btwn individual molecules usually mediated by noncovalent attractions
• individually very weak, but can add up to make strong binding btwn molecules

Types of molecular interactions(week 1: section 5)

1. electrostatic attractions
2. hydrogen bonds
3. van der waals attractions
4. hydrophobic force

electrostatic attractions(week 1: section 5)

• noncovalent force of attraction between 2 oppositely charged molecules
• similar idea to attractions btwn ions or polar molecules
• in bio. can be seen with regions of positive/negative charges on large molecules

Hydrogen bond(week 1: section 5)

• weaker than covalent bonds
• between hydrogen and really electronegative atom(O, N, F)
• allows for special properties of water

van der Waals attraction(week 1: section 5)

• weakest force of attraction
• nonspecific interaction, can happen in all types of molecules

Hydrophobic force(week 1: section 5)

• similar types of forces interacting w/ e/o(hydrophobic w/ hydrophobic)
• helps to promote molecular interactions
• important for building cell membrane

Base pairing(week 1: section 5)

• holds DNA double helix shape together
• A - T has 2 hydrogen bonds
• G - C has 3 hydrogen bonds

Forces that keep DNA strands together(week 1: section 5)

1. hydrogen bonds
2. hydrophobic interactions
3. van der Waals attractions

Advantages of DNA structure(week 1: section 5)

• energetically favourable conformation
• proteins can recognize + make contact w/ specific DNA sequences in major + minor grooves

DNA strands(week 1: section 5)

• 2 strands are complementary
• can be unzipped
• antiparallel (one strand is 5’→3’, other is 3’→5’)
• end of 5’ made of phosphate group(PO4)
• end of 3’ made of hydroxyl group(OH)
• can be separated by proteins in cell + heat

Advantages of separating DNA strands(week 1: section 5)

important for:

• DNA replication
• RNA synthesis

Flow chart of protein structure(week 2: section 2)

Amino acids(week 2: section 3)

• subunits of proteins
• Types of amino acids:

1. acidic (important for enzymes)
2. basic (important for enzymes)
3. uncharged polar (h-bonds in water)
4. nonpolar (insides of proteins, may be present in lipid bilayers)

Structure of amino acids(week 2: section 3)

• alpha carbon
• carboxyl group
• amino group
• R group(what decides amino acid)

Cysteine’s uniqueness(week 2: section 3)

• has disulfide bonds
• non polar amino acid

Peptide bonds(week 2: section 4)

• forms btwn carboxyl group + amino group of diff. amino acids
• R groups r not involved
• causes polypeptide chain to have amino end(N terminus) + carbonyl end(C terminus)
• water as product(condensation reaction)

Alpha helix(week 2: section 5)

• has N-terminal + C-terminal
• R groups r not involved
• hydrogen bonds btwn every 4 amino acids(residue)

Beta sheet(week 2:

• R groups are not involved (but alternately project up + down)
• usually contains 4-5 beta strands, but can have 10+
• H-bonding btwn carbonyl oxygen (C=O) + amine hydrogen (N-H) of 2 diff. amino acids in neighbouring strands

Types of Beta sheets(week 2: section 6)

• anti-parallel
• parallel

H-Bonding in secondary structures(week 2: section 6)

• atoms in bonding: carbonyl oxygen + amine hydrogen in peptide backbone
• Alpha helices: h-bonding every 4 AA’s apart within polypeptide chain
• Beta sheet: btwn AA’s in diff. segments/strands of polypeptide chain

Coiled coils(week 2: section 6)

• multiple alpha helices tied together
• amphipathic (has both hydrophilic + hydrophobic parts)
• found in alpha-keratin of skin, hair + myosin motor proteins

Tertiary structure(week 2: section 6)

• overall 3D structure of a protein

• proteins fold into conformation that is ==most energetically favourable==

• protein ==shape dictated by amino acid sequence== aided by chaperone proteins

• held together by:

  1. hydrophobic interactions
  2. non-covalent bonds
  3. covalent disulfide bonds

Chaperone proteins(week 2: section 6)

• helps the process of protein folding more efficient + reliable

Diff. models of tertiary structures(week 2: section 6)

1. backbone model: shows overall organization of polypeptide chain
2. ribbon model: shows folding patterns
3. wire model: shows R groups’ positions
4. space filling model: shows protein surface

Protein domains(week 2: section 6)

• regions of polypeptide chain that are able to independently fold into tertiary structure
• domains specialized for diff functions
• important for evolution of proteins

Protein families(week 2: section 6)

• common evolutionary origin
• have similar aa sequences + tertiary structures
• members evolved to have diff functions
• most proteins belong to families w/ similar structural domains

Quaternary structure: hemoglobin(week 2: section 6)

• hemoglobin protein formed from separate subunits: 2 α, 2 β

• ==each subunit = separate polypeptide chain==

• sickle cell anemia caused by mutation in

  β subunit

Multiprotein complexes + molecular machines(week 2: section 6)

Can be:

• many identical subunits(proteins)
• mixtures of diff proteins + DNA/RNA (more diverse in function w/ diff protein subunits)
• dynamic assemblies of proteins to form molecular machines

Studying proteins(week 2: section 7)

1. purify protein(s) of interest using electrophoresis/chromatography
2. determine amino acid sequence (using mass spectrometry)
3. discover precise 3D structure

• Proteomics(large scale study of proteins)

Genomes(week 3: section 1)

• can come in all sizes(size not always correlated w/ # of genes/organism complexity)
• includes all DNA including non-coding regions

Elements of human genome(week 3: section 1)

Repeated sequences(~50%):

• simple repeats

• segment duplications

• mobile genetic elements:

  1. LINEs
  2. SINEs
  3. retrotransposon
  4. DNA-only transposon

Unique sequences(~50%):

• nonrepetitive DNA(neither introns/exons)
• introns (transcribed, not translated)
• exons (codes for proteins) (~1.5% of genome)

Packing of DNA in the cell(week 3: section 2)

• DNA condensed through folding + twisting, complexed w/ proteins (genome very big w/o packing)
• forms the prokaryotic nucleoid

Eukaryotic genome packing in cells(week 3: section 3)

Challenge:

• human genome very very big(no personality, smh)

Solution:

• packing DNA into chromosomes

Fluorescence In Situ Hybridization(FISH)(week 3: section 3)

• uses idea of complementary strands + able to unzip strands

• looks for particular sequence in chromosome(DNA probe hybridizes with chromosome DNA)

Chromosomes(week 3: section 3)

• 23 pairs in humans(last pair for sex of human)
• made of chromatin
• replicated in interphase + M phase
• held together at centromere
• ends are called telomeres

Chromatin(week 3: section 3)

• single, long, linear DNA molecule + associated proteins
• tightly packaged but remains assessible for transcription, replication, + repair
• is DYNAMIC(on how tightly packed it is)
• made of 8 different nucleosomes

Cell cycle: chromosome replication(week 3: section 3)

2 phases:

• interphase
• M phase(mitosis)

Interphase:

• gene expression + chromosome duplication

M phase:

• mitosis
• chromosome separated

Structure of a nucleosome(week 3: section 4)

• made of DNA wrapped around histones
• ~6 packed histones make 1 nucleosome

Histones(week 3: section 4)

• small proteins rich in lysine + arginine

• positive charge able to neutralize negative charge of DNA

• 4 core histone proteins:

  1. H2A
  2. H2B
  3. H3
  4. H4

• pair of each in octamer core

• 1 linker histone(H1)

Packing of nucleosomes(week 3: section 4)

• non-histone clamp proteins involved in forming chromatin loops

Chromatin packing + re-modeling(week 3: section 5)

performed by:

• chromatin remodeling complexes
• histone modifying enzymes

Can cause:

• heterochromatin
• euchromatin

Heterochromatin(week 3: section 5)

• Highly condensed chromatin
• areas where gene expression is suppressed

examples:

• meiotic + mitotic chromosomes
• centromeres + telomeres
• one X chromosome in females(Barr body)

Euchromatin(week 3: section 5)

• relatively non-condensed chromatin
• areas where genes tend to be expressed

Conservatism of DNA replication(week 3: section 6)

• DNA synthesis is semiconservative(only one seen in nature so far)

Directionality of DNA replication(week 3: section 6)

• Always occurs from 3’ end to 5’ end(DNA polymerase stitching)
• Growth occurs from 5’ end to 3’ end

3 possible models:

1. unidirectional growth of single strands from 2 starting points
2. unidirectional growth of 2 strands from 1 starting point
3. bidirectional growth from 1 starting point

Replication origin(week 3: section 6)

• Where DNA replication begins

Characteristics:

• easy to open, rich in A-T bonds(less h-bonds)
• recognized by and binding of initiator proteins occurs

# of origins of replications:

• 1 in bacteria
• multiple in Eukaryotes

DNA replication in bacteria(week 3: section 6)

• bidirectional growth from 1 starting point
• this style of replication only applies to circular genomes

Replication forks(week 3: section 6)

• is asymmetrical

Causes:

• 2 strands

  1. lagging strand: replicated discontinuously(causes Okazaki fragments)
  2. leading strand: replicated continuously

Initiator proteins for replication(week 4: section 1:

1. binds to origin
2. helps helicase bind
3. requires ATP

Unwinding DNA(week 4: section 1)

Performed by:

• 2 types of helicases
• predominant one moves along ==lagging strand== template(5’→3’)

Requires:

• a lot of ATP

Single strand binding proteins(week 4: section 1)

• binds single stranded DNA(ssDNA) to separate strands
• prevents strands from H-bonding, reannealing, hair pins, and loops until replication occurs

Primase(week 4: section 1)

• synthesize RNA primers needed for DNA polymerase to bind
• proceeds(reads) in 3’→5’ along template strand

DNA polymerase(week 4: section 1)

• reads 3’→5’ along parent strand
• creates DNA in 5’→3’ direction
• removes 2 phosphates from nucleoside triphosphate to add onto growing strand

Sliding clamp(week 4: section 1)

• holds polymerase onto DNA

DNA ligase(week 4: section 1)

• seals nick(gap) caused by removal of RNA primers

Primosome (week 4: section 1)

• helicase + primase

Unwinding problem(week 4: section 2)

Problem:

• as helicase unwinds DNA, supercoiling + torsional strain increases
• problem in circular chromosomes + large linear eukaryotic chromosomes

Solution:

• solved by DNA topoisomerase (breaks phosphodiester bond and reseals it)

Loss of DNA problem(week 4: section 2)

Problem:

• major problem for lagging strand
• loss of sequence information on 5’ end on daughter strand

Solution:

• repetitive sequence added to the 3’ end of parent strand determined by RNA template in telomerase

Telomere replication(week 4: section 2)

• RNA template
• resembles reverse transcriptase
• generates G-rich ends
• adds nucleotides to 3’ ends to parental strand template

Telomeres and cancer(week 4: section 2)

• telomerase are abundant in stem and germ-line cells, but not in somatic cells
• loss of telomeres during DNA replication, limits # of time cell can divide
• Most cancer cells produce high level of telomerase

Issues in DNA replication(week 4: section 2)

• if mistake during replication not repaired, mutation occurs and stays in new generations

High fidelity of DNA replication(week 4: section 2)

RNA polymerases:

• has error rate ~1 in 1000

DNA polymerases:

• has error rate ~1 in 1000000000

• human genome(3 bill. bp) only changes ~3 nucleotides every time a cell divides

DNA proofreading + repair: 3’ to 5’ exonuclease(week 4: section 2)

Function:

• removes misincorporated nucleotide
• performed by DNA polymerase(polymerizing section(P) + editing section(E)
• DNA pol. detects helix distortion and moves back 1 space to remove nucleotide

DNA proofreading + repair: strand-directed mismatch repair(week 4: section 2)

• error repair process(when proofreading fails)
• initiated by direction of distortion in geometry of double helix generated by mismatched base pairs

DNA damage(week 4: section 2)

• even after synthesis, DNA can get damaged + need repair

• defects in repair mechs., linked w/ variety of human diseases

Types of damage:

1. oxidation
2. radiation
3. heat
4. chemicals

• and other cell stressors

Spontaneous damage to DNA(week 4: section 2)

Depurination:

• loss of purines(A,G) in nucleotide
• causes deletion mutation

Deamination:

• loss of amine(NH2) group on cytosine(C)
• converts C to U
• improper base pairing mutation

DNA repair mechanisms(week 4: section 2)

1. base excision repair: fixes smaller problems(1 base removed)
2. nucleotide excision repair: removes multiple nucleotides(ex: dimers)

DNA repair of double-stranded breaks(week 4: section 2)

Two situations:

1. nonhomologous end joining: results in ==some== ==loss of nucleotides at repair site==
2. homologous end joining: results in ==no loss of nucleotides at repair site==

Molecular definition of a gene(week 5: section 1)

• Segments of DNA that are transcribed into RNA

• Types of genes when transcribed:

  1. RNA that encodes for a protein(mRNA)
  2. RNA that functions as RNA and may not be translated into protein(tRNA + rRNA)

Generation of RNA transcript(week 5: section 2)

• RNA nucleotides added in 5’→3’ (anti-parallel)
• uses ssDNA as template(other ssDNA is coding strand)
• RNA nucleotides linked by phosphodiester bonds
• DNA-RNA helix held by base pairing

Schematic of RNA polymerase(week 5: section 2)

• no need for primers
• just needs the temple
• less accurate than DNA pol.(more mistakes)