BZ110 exam 3

Cell structure & function: 10/24

• Biological levels of organization: atoms → molecules → organelles → cells → tissues → organs & organ systems → organisms, populations, communities → ecosystems → biosphere

• Prokaryotes vs eukaryotes: 

  • Prokaryote: bacteria & archaea; lack a nucleus, DNA is just contained in a single chromosome in their cytoplasm; can be multi or unicellular

  • Eukaryote: animals are eukaryotes; have organelles & nucleus; can be multi or unicellular

  • Key difference: the presence of a nucleus & mitochondria (only in eukaryotes); membrane structure, ribosome structure, how transcription & translation work, presence/ absence of specific genes & other organelles

• Organelles of the cell: 

  • Fluid mosaic model: phospholipid bilayer is dynamic

    • Fluid: membrane is not static, lipids & proteins are constantly in motion in the membrane. Mosaic: the membrane is a larger complex whole made up of multiple smaller parts

  • Plasma membrane: boundary of cells; regulates what moves in & out of the cell (semi- permeable)

  • Cytoskeleton: maintains cell shape, provides anchor points, and makes up the ‘roads’ for movement around the cell; changes support ‘ameboid movement’ of macrophages

  • Flagella & cilia: movement; cilia - for a cell to move (especially in single celled euk.)

  • Nucleus: store chromatin (DNA); manufacture ribosomes in nucleolus

  • Ribosomes: translate mRNA into polypeptide sequences; made of both rDNA & proteins

  • Endoplasmic reticulum: ER surrounds the nucleus

    • Rough ER: protein synthesis & processing

    • Smooth ER: lipid synthesis, sugar synthesis, steroid synthesis & detox

  • Golgi apparatus: processing, tagging, organizing transport of cell components; (‘post office’ of the cell)

  • Mitochondria: cell respiration, making ATP

    • Endosymbiotic origin: mitochondria was a bacteria that was engulfed by early archaea & instead of digesting it, it turned bacteria into organelle (mito)

  • Lysosomes, peroxisomes, vesicles: lysosomes = break things down; peroxisomes = detox; vesicles = move things around

• Tissues & how cells stick together: 

  • Extracellular matrix: consists of a network of proteins & carbohydrates

  • Tight junctions: form watertight connections between adjacent animal cells; proteins create tight junction adherence

  • Desmosome: forms a very strong spot weld between cells; it is created by the linkage of cadherins & intermediate filaments

  • Gap junction: protein-lined pore that allows water & small molecules to pass between adjacent animal cells

DNA, & gene expression: 10/29

DNA: primary info storage molecule for all cellular life

• In humans: ~6B base-pairs per cell; ~20k protein coding genes. Across animals, number of chromosomes, base-pairs, and genes varies a lot → genome size & number of genes is generally not associated with perceived organismal complexity

• Nucleotide structure & bases: c & t are pyrimidines; g & a are purines

• Both strands together: a-t & c-g; strands run in opposite directions (antiparallel). Linked via phosphodiester bond → phosphate group linked to 5’ end, carbon linked to 3’

• Packaging DNA: chromosome > rosettes of chromatin loops > chromatin loop . solenoid > DNA double helix (duplex) > nucleosome

• Genomic equivalence & gene regulation: DNA contains info a cell needs to function

  • Every cell in your body has the same DNA (genomic equivalence)

  • DNA template strand → transcription → mRNA → translation on ribosomes → proteins

RNA vs DNA: 

• RNA: 1 strand; uracil bonds with thymine; ribose has an oxygen on the 2’ carbon; hydroxyl group & uracil has a hydrogen; dozens to thousands of nucleotides

• DNA: 2 strands; has a hydrogen, thymine has a methyl group; mil-bil of nucleotides

Eukaryotic transcription initiation: 

• DNA is unzipped 5’ to 3’ and is read in this way on the DNA template strand. RNA polymerase reads this

• Regulatory sequences upstream of the transcribed part of the gene (promotor) or elsewhere (enhancers) are recognized by a variety of proteins that ‘turn on’ or ‘turn off’ the gene

• Gene is ‘turned on’ when RNA polymerase is recruited to transcribe the transcribable of the gene

• Genes may be differentially turned on or off in response to cell communication, the environment, development, location of cell in body, etc

• Transcription termination: RNA polymerase will continue transcribing a gene until it reaches the ‘transcription termination signal’ at the end of the gene. This leads to RNA polymerase letting go of the DNA and releasing the mRNA

RNA processing: occurs during transcription

• A 5’ cap is added (untranslated), then it’s spliced (to get rid of the introns), and the poly-A is at the tail (just a long strand of As) → this makes up the structure of mature RNA

• Introns (parts of the genome that need to be spliced out, will not leave the DNA overall) & extrons (parts of the DNA that will stay – exons spliced together)

Anatomy of a mature eukaryotic mRNA: UTR = untranslated region; CDS = coding sequence, translated, begins with start codon & ends with stop codon

Eukaryote translation initiation:

• Small subunit of ribosome binds to 5’ cap along with initiation factors and first tRNA

• Then these scan along the mRNA until the start codon is found (always aug)

• Then large subunit attaches, with tRNA in P site (tRNA binding), and peptide bond forms

• In A site, translocation happens (it shifts over) – and this process can then start again

• Translation termination: 

  • Release factors: recognize stop codons, fit in A site because they mimic a tRNA; terminate the protein chain and cause it to release from the ribosome

The genetic code is: 

• In a linear form, using ribonucleotide (mRNA)

• Unambiguous & degenerate: 3 triplet of letters = one codon = one amino acid; multiple codons lead to same amino acid. They’re nonoverlapping, so codons don’t overlap

• Contains start & stop signals

• Commaless: no breaks between the codes

• Nearly universal: can be translated using a single coding dictionary 

Mitosis & meiosis: 10/31

• Why do cells divide?

  • Unicellular: reproduction

  • Multicellular: growth, development, healing/repair, organ structure/maintenance, repro

• Cell division stages: 

• G1 phase: cell is getting ready to divide – copying organelles

and most cellular contents are duplicated (excluding chromosomes)

• S phase: each of the 46 chromosomes is duplicated by the cell

• G2 phase: the cell ‘double checks’ the duplicated chromosomes

for error, making any needed repairs

• Semiconservative model of DNA replication: DNA is double stranded so when replicating they unzip and they form the template for a new strand and it forms a new DNA sequence → makes an antiparallel copy

Mitosis – asexual cell division: ends with 2 diploid cells

• Prophase: chromosomes condense & become visible; spindle fibers become visible; nuclear envelope breaks down; centrosomes move toward opposite poles

• Prometaphase: chromosomes continue to condense; kinetochores appear at the centromeres mitotic spindle microtubules attach to kinetochores

• Metaphase: chromosomes are lined up at the metaphase/middle plate; each sister chromatid is attached to a spindle fiber originating from opposite poles

• Anaphase: centromeres split in 2; sister chromatids (not called chromosomes) are pulled towards opposite poles; certain spindle fibers begin to elongate the cell

• Telophase: chromosomes arrive at opposite poles & begin to condense; nuclear envelope material surrounds each set of chromosomes; mitotic spindle breaks down; spindle fibers continue to push the poles apart

• Cytokinesis: 

  • Animal cells: a cleavage furrow that separates the daughter cells

  • Plant cells: a cell plate, the precursor to a new cell wall, separated the daughter cells

Meiosis – cell division to make gametes: 

• 2 rounds of cell division coupled together; end with 4 haploid cells

• Meiosis 1 starts with 1 diploid cell where each chromo has 2 chromatids →

ends with 4 haploid cells (each chromo has 2 chromatids still)

• Meiosis 2 then separates the 2 chromatids. In the end there are (up to) 4

Haploid cells, each with 1 chromatid per chromosome

• Stages: 

  • Interphase → prophase 1 (homo chromo line up single file & pair up)

  • Meiosis 1: prometaphase 1, metaphase 1, anaphase 1, telophase 1

  • Then telophase → cytokinesis to separate the homo chromo; they are

now haploid cells with replicated cells

• Meiosis 2: prophase 2, prometaphase 2, metaphase 2, anaphase 2, 

Telophase 2 → cytokinesis (to separate from 2 → 4 cells)

Genetic inheritance: 11/5

• Independent assortment: 

  • Alleles on the chromosomes can line up wherever so the resulting gametes are different

• Crossing over/ recombination: during prophase 1; results in completely different exchange of chromosomes post recombination

• Random fertilization: random sperm fertilize eggs… so adding in recombination basically makes the number of different possible offspring for 2 individuals infinite

Mendelian genetics: 

• Allows us to predict what the offspring of individuals with known genotypes will look like

• When combined with modern understanding of meiosis, Mendelian genetics is a great entry point toward understanding patterns of inheritance

• Genetics terminology: 

  • Allele: alternate forms of a gene that occurs at the same locus of a chromosome

  • Dominant allele: an allele that masks one or more alleles of the same gene

  • Recessive allele: expression is masked by a dominant allele of the same gene

  • Genotype: the specific gene combinations that characterize a cell or an individual

  • Phenotype: the physical/B characteristics of an organism arising from the interaction of its genotype and environment

  • Homozygote: an individual with 2 identical copies of a gene at a particular locus

  • Heterozygote: an individual with 2 different copies of a gene at a particular locus

• Mendelian assumptions: 

  • Traits are determined by a single gene (one gene = one trait)

  • Typically, a gene has 2 alleles – one is dom and the other is recessive

  • If examining multiple traits (and multiple genes), their genes are on separate chromosomes and assort independently

Beyond mendelian genetics: 

• Incomplete dominance: red-white flowers = 2 pink flowers & 1 red & 1 white… intermediate phenotype between the 2 initial ones

• Co-dominance: both alleles of hetero produce approx. equal amounts of enzymes & products; phenotype would be intermediate or show products of both alleles

  • ABO blood types

  • ‘Dominant’ lethal allele: presence of one copy of allele results in death – mutation behaves as dominant lethal allele; example is Huntington disease. Onset of disease in heterozygotes (Hh) is delayed → late onset around age 40 (postreproductive)

• Sex-linked traits: gene for trait is on a sex chromosome; trait appears at different rates in M&F

• Epistasis: 2+ genes affect a single trait; the effect of one gene masks or modifies the effect of the other (example: bald)

• Discrete vs continuous variation: 

  • Discrete: variation in a qualitative trait that falls into distinct categories (is this or that)... mendelian genetics & simple modifications to it can easily explain discrete traits

  • Continuous: variation in a quantitative trait that falls along a numerical continuum (range of values… straight → curly hair, skin color)

• Additive genetics: if many genes are involved in generating a phenotype, each contributing a small portion, then the cumulative effect of many genes can explain a continuous distribution of the trait

  • One phenotype is affected by many genes… EDS, mental illness… that shit