Chapters 1-5 Flashcards
Characteristics of life:
Movement, metabolism, reproduction, response to stimuli
Cell theory:
All organisms are composed or one or more cells.
The cell is the structural and functional unit of life.
All cells arise from other cells. (Omnis cellula e cellula.)
Who came up with which parts of cell theory:
First two - Schleiden and Schwann. Last one - Virchow.
Requirements for the formation of the first cell:
Organic molecules (from inorganic molecules), molecules for catalysis of chemical reactions and self-replication, and a barrier between internal and external cell environments.
RNA as catalytic molecule:
The only molecule capable of both catalyzing chemical reactions (ribozyme) and self-replicating.
What was the first genetic material the precursor to the first cell?
RNA! Special because it can be a catalyst!
Present-day prokaryotes:
Archaebacteria, eubacteria, cyanobacteria
__bacteria are the most common form of bacteria.
Eu
__bacteria are often extremophiles.
Archae
The cytoskeleton is not solely structural…
It can also have functions in mobility. Ex: sperm.
Function of peroxisomes:
Perform various oxidative reactions
Function of ER:
Processing/transporting proteins; lipid synthesis.
Function of golgi apparatus:
Sorts and transports proteins destined for secretion; lipid synthesis.
In plant cells: cell wall polysaccharide synthesis
Yeast:
Saccharomyces cerevisiae. Unicellular with intercellular communication.
Volvox:
Colonial unicellular alga.
Main tissue systems of plants:
Ground, dermal, vascular.
Main tissue systems of animals:
Epithelial, connective, nervous, muscle, blood.
Epithelial cells:
Specialized for protection, secretion, absorption. Skin and lining of internal organs.
Connective tissues:
Bone, cartilage, adipose.
Fibroblasts: cells that fill the spaces between organs and body tissue.
Different kinds of erythrocytes:
Granulocytes (feathery purple thing with no envelope), monocytes (blobby middle bit), macrophages, lymphocytes (round middle bit).
What do different muscles look like?
Skeletal - super ordered.
Cardiac - striated, a little more random.
Smooth - like frog eggs.
Model organism - e coli:
Divides every 20 minutes under ideal conditions. Small genome - 4.6 million bp, 4300 genes.
Model organism - yeast:
12 million bp. Divides every 2 hours.
Model organism - nematode:
Caenorhabditis elegans. 959 somatic cells. Entire cell lineage is known.
Model organism - fruit fly:
Drosophila melanogaster. Effects of every gene mutation known.
Model organism - xenopus laevis:
Eggs are large single cells. All stages of development can be studied in a lab.
Model organism - zebrafish:
Transparent embryos, amenable to mutation.
List of model organisms:
E coli, yeast, nematode, drosophila, xenopus, zebrafish, mouse.
Microscopy - bright field:
Thin slice. Stain. Requires fixing. Light passes directly through specimen.
Microscopy - phase contrast and differential interference-contrast:
Stain. Live cells. Converts variations in density or thickness into contrast.
Microscopy - fluorescence:
Fluorescent markers, dyes, and proteins. Ex: GFP. Living cells. Light does not pass through, just excites the dye.
Microscopy - TEM:
Slice. Electrons through specimen.
Microscopy - SEM:
Whole thing. Electrons bounce of metal coating.
Ultracentrifuge stats:
100 000 rpm. Forces 500 000 times greater than gravity.
Order that components of broken cell suspension sediment:
Nucleus. Mitochondria, lysosomes, peroxisomes. Plasma membrane and ER. Ribosomes. Cytosol remains.
Term - the stuff left over after something has been sedimented out:
Supernatant!
Nutrients in media for growing animal cells:
Serum, salts, glucose, amino acids, vitamins
Define - primary culture:
First culture established from a tissue. Limited number of divisions before death.
Define - permanent/immortal culture:
Embryonic stem cells or cancer cells. May proliferate indefinitely.
What percent of the wet weight of cells is water?
70%
Membrane solubility is dependent on ___.
Solubility in water.
80-90% of the dry weight of cells is composed of ___.
Macromolecular forms of proteins, lipids, nucleic acids, and carbs.
Cellular monosaccharides contain ___ carbons, with ___ being the most common.
3-7; 3, 5, 6
Major forms of polysacchs:
Glycogen, starch, cellulose
Shapes of glycogen, starch, cellulose:
Glycogen - branched alpha glucose polymer
Starch - un/branched alpha glucose polymer
Cellulose - unbranched beta glucose polymer
Saturated vs unsaturated fatty acids:
Saturated has only single bonds. Unsaturated has one or more double bonds.
Structures of different lipids:
Triacylglycerol - three fatty acids linked to a glycerol
Phospholipid - two fatty acids and a phosphate group bound to a glycerol (other things can be added to the phosphate)
New info about RNA:
Gene regulation, catalytic functions
Which nucleic acids are purines/pyrimidines?
Purines (big) - A, G
Pyrimidines (small) - C, T, U
Define nucleoside vs nucleotide:
Nucleoside - nitrogenous base linked to deoxy/ribose sugar
Nucleotide - includes the phosphate group
Which nucleic acid pairs form two/three hydrogen bonds?
AT form 2; CG form 3
Can RNA be double-stranded?
Not really, but it can form double-stranded secondary structures
Tendency of R groups in secondary structures:
In alpha helix and beta sheets, R groups tend to stick out.
Lipids constitute what percent of membrane mass?
50%
Water travelling across a membrane:
Simple diffusion but it needs a little help because it’s so polar.
Passive transport:
You know what it is. It uses a transport protein but doesn’t expend energy.
Define: -omics
Large-scale analysis of cell molecules
Define: proteome
All proteins expressed in a given cell
Define: interactomics
How proteins interact with each other
The reason we’re as complex as we are is that ___ are separate.
The processes of transcription and translation
Composition of nuclear envelope:
Two bilayer membranes, underlying nuclear lamina, nuclear pore complexes
Nuclear lamina:
Fibrous protein mesh that provides structural support. Composed of lamins (fibrous proteins) and other proteins.
Analogy: window screen holding up a blanket
Nuclear pore complexes are complicated because they have to get which huge molecule through?
Ribosomes
Which nuclear membrane is continuous with the ER?
Outer.
Function of the perinuclear space:
Functions like an ER, since it’s continuous with it
Define: phenotype
Basically any expressed trait.
TH Morgan’s work on drosophila:
Phenotypic traits are inherited together in linkage groups.
# of linkage groups = # of chromosomes.
Evidence that chromosomes are the heritable material.
Historically, scientists weren’t sure if __ or __ was the genetic material.
Proteins or DNA
Not all genes code for proteins. What do those genes code for?
Structural/regulatory RNAs that are never translated into a protein.
Basic unit of genetic code?
Codon.
General trend between complexity and genome size:
Increase in one increases the other. NOT LINEARLY THOUGH.
Define: gene
A segment of DNA within a chromosome that is expressed to yield a functional product.
Some numbers concerning the makeup of genes:
35% of human genome is introns
10% of the average gene sequence is exons
1% of human genome is exons that encode proteins
What’s the point of introns?
Info for regulatory RNA
Which organisms do we have complete genomes for?
E. coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Arabidopsis, and the mouse
Genome of mycoplasma genitalium:
Simplest present-day prokaryote. Second-smallest genome with 580k BPs / 470 genes. Likely represent the minimal gene set required to maintain a self-replicating organism.
The human genome: how many genes?
20-25000
The human genome: how come we’re so complicated with so few genes?
Spread over greater distances with more introns between, may be subject to more alternative splicing
The human genome: what’s the significance of sharing 40% of genome with lower eukaryotes?
It’s probably the minimum required proteins involved in basic cellular processes.
The human genome: what do the other 60% of unshared genes do?
Dedicated to making us more complex. Lots are only actives in embryonic development.
Define: chromatin
Eukaryotic chromosomal DNA complexed with proteins.
Ratio of proteins and DNA in chromatin:
Twice as much protein as DNA
Chromatin is super compressed. Here are some numbers.
Human DNA is 2 m long; chromatin is packed into 5-10 um nucleus.
Chromosome number and organism complexity:
UNRELATED!!!!!!
Nucleosomes:
The basic structural unit of chromatin. Composed of DNA and histones.
Histones:
Small proteins containing a high proportion of the basic amino acids (arg and lys). This facilitates binding to the negatively charged DNA sugar-phosphate backbone.
H1, H2a, H2b, H3, H4
Nucleosome core particles:
147 base pairs of DNA wrapped twice around an octamer consisting of two molecules of each histone except H1.
Chromatosome:
166 bp and histone H1.
Forms of chromatin in interphase cell:
Eu, hetero (constitutive or facultative)
Euchromatin:
Least condensed form. Transcriptionally active, usually as 10 and 30 nm fibres.
“Naked” DNA:
You never seen DNA without proteins.
Heterochromatin:
Highly condensed, transcriptionally inactive chromatin. Contains highly repetitive DNA sequences. Two types.
Constitutive heterochromatin:
Contains DNA that is not transcribed in any cell type. Ex: some DNA sequences at centromeres.
Facultative heterochromatin:
Contains DNA sequences that are not transcribed in the cell being examined but may be transcribed in other cell types. Ex: the chromosomal region containing some genes expressed only in developing red blood cells is packaged into facultative heterochromatin in all other cell types.
When are chromosomes most condensed?
During mitosis
What does DNA look like during metaphase?
Large loops attached to a protein scaffold. In 30 nm fibres.
Centromere:
A specialized region of the chromosome that plays a critical role in ensuring the correct distribution of duplicated chromosomes to daughter cells during mitosis
Kinetochore:
A protein structure associated with the centromere, to which microtubules bind. They act as a molecular motor during mitosis and meiosis. Not associated with centromere during interphase. Not present in normal growth.
Common thread in centromeres:
Contain a histone variant within the nucleosomes known as centromeric histone H3 (CenH3). Centromeric DNA sequence is not conserved across organisms.
Telomere:
Sequences at the ends of eukaryotic chromosomes. Critical role in maintaining stability of linear chromosomes. Repeated clusters of G residues. Exonuclease can’t attach here because it’s a loop.
Reasons DNA has to have high fidelity, reasons why not:
Cell reproduction has to be very accurate. However, genetic variation needs to be maintained.
DNA polymerases:
Enzymes that catalyze DNA synthesis.
DNA replication in prokaryotes vs eukaryotes:
Pretty much the same process, just with different players.
Two fundamental properties of all DNA polymerases:
Synthesize only in 5’-3’ - read template only in 3’-5’. Can only add to a free 3’ OH.
Replication fork:
The region of DNA synthesis where parental strands separate and daughter strands elongate. Contains the replication complex.
How long is an Okazaki fragment?
1000-3000 BPs
Primase:
Enzyme that synthesizes short fragments of RNA (3-10 nucleotides) complementary to the lagging strand at the replication fork.
Exonuclease:
Enzyme activity that hydrolyses DNA or RNA molecules from their ends.
RNase H:
Exonuclease that degrades the RNA stuck in RNA-DNA hybrids.
E coli’s special DNA polymerase I:
DNA polymerase I has RNase H-like exonuclease activity that can degrade RNA primers in 5’ to 3’ direction.
DNA ligase:
Seals breaks in DNA after RNase H does its job.
Is DNA polymerase the same across cells?
Different kinds of cells have different polymerases.
Accessory proteins: list
Clamp-loading proteins, sliding clamp proteins, helicases, single-stranded DNA-binding proteins
Clamp-loading proteins:
Loads clamp proteins onto the replication fork at the primer
Sliding clamp proteins:
Load and hold polymerase onto template
Helicase:
Catalyzes DNA unwinding (with ATP use)
Single-stranded DNA-binding proteins:
Stabilize the unwound single-stranded DNA
Topoisomerases:
Enzymes that catalyze the breakage and rejoining of the double helix ahead of the replication fork
How many oris does a human cell have?
Approximately 30,000 origins (every 50-300 kilobase pairs)
Theoretically, how many oris should there be?
Minimum one per chromosome or else it would take 5ever.
of oris vs how fast a cell replicates:
Fast-replicating cells have more oris, slow ones will have fewer.
First oris in eukaryotes were studied in:
Yeast!
Exons:
DNA segments that code proteins and 5’ and 3’ UTRs.
Autonomously replicating sequence (ARS):
Origin of replication in yeast. 100 bp with common 11 bp core. Origin recognition complex binds to it to initiate replication bubble.
Analog of ARS in bacteria:
Initiator
Telomerase:
Enzyme that maintains the ends of eukaryotic chromosomes. Possesses reverse transcriptase activity. Elongates 3’ end of lagging strand to allow one more Okazaki fragment to synthesize.
Reverse transcriptase:
A DNA polymerase that uses an RNA template.
How DNA replication fidelity arises:
Need less than 1/10^9 errors.
Simple free energy differences in correct vs incorrect hydrogen bonding; polymerase actively selecting the right base; proofreading by polymerase; DNA repair mechanisms.
The process of proofreading:
Polymerase chops off the incorrect base using 3-5 exonuclease, then regular synthesis proceeds.
