cell bio

cell

fundamental unit of life and central to biology

E.B Wilson

An early American cell biologist who emphasized that biological problems can ultimately be understood by studying the cell

All cells share six core characteristics

• Store heredity information in DNA

• Replicate DNA via a conserved, template-based polymerization mechanism.

• Express genetic information (gene expression) by transcription of DNA into RNA and translation of RNA into protein

• Encode functional proteins or catalytic/structural RNAs within discrete segments of DNA called genes^[1][5].

• Require energy to power cellular processes, utilizing free-energy carriers like adenosine triphosphate (ATP).

• Are enclosed by a plasma membrane that functions as a selective barrier

heredity

the passing on of characteristics from one generation to the next

• language established by the monomers that make up dna

Information is expressed in two main steps (central dogma)

• transcription (DNA → RNA) produces single-stranded RNA (which uses ribose instead of deoxyribose and replaces thymine with uracil)

• Translation (RNA → proteins) then reads nucleotide triplets called codons to synthesize proteins from 20 amino acids

template based copying mechanism

polymerization is the linkage of monomers into a polymer occurring but using a preexisting template strand

ATP

ATP stores transferable chemical energy in its phosphate bonds. When the bond between the second and third phosphate group is hydrolyzed, energy is released to power energetically unfavorable cellular processes such as replication, transcription, and translation

RNA differs from DNA in:

• (1) the sugar: uses ribose instead of

deoxyribose

• (2) the bases: uses C, G, and A, but

replaces T with U (uracil)

• (3) the ‘strandedness’: RNA is

primarily single-stranded

codons

nucleotide triplets that specify amino acids

• start codon:

• stop codon:

gene

the segment of dna sequence corresponding to a single protein, set of protein variants, or a single catalytic, regulatory, or structural RNA

cellular membranes are composed of ___ molecules

amphiphilic

• hydrophobic : water insoluble

• hydrophilic: water loving

  • In an aqueous environment, these molecules spontaneously orient their hydrophobic tails inward away from water to form a phospholipid bilayer

  • phospholipid monolayer at an oil-water interface

three domains of life

bacteria, archaea, and eukaryotes

genetic innovation occurs thru ___

mutation : A change in genetic material that can create a new gene variant.

• intragenic mutation: A change within a gene that creates a new variant.

• What is gene duplication? → A gene is copied, creating two related copies that can later diverge.

• What is horizontal gene transfer? → Genetic material is transferred from one organism to another.

• What is DNA segment shuffling?→ DNA segments are rearranged or combined to create new gene combinations.

plasma membrane

The membrane surrounding the cell that acts as a selective barrier

transporters

membrane proteins that help substances move into and out of cells.

homologous genes and its types

homologous genes: genes related by decent

• orthologs: genes in two separate species that derived from the same ancestral gene

• paralogs: related genes in the same genome that resulted from gene duplication

eukaryotes vs prokaryotes

eukaryotes: have a membrane enclosed nucleus that houses DNA

• nucleus

• single or multi celled

• larger genomes (also more noncoding DNA)

• complex internal organization and compartmentalization

prokaryotes: have no distinct nucleus (bacteria and archaea)

• no nucleus

• simple genomes

• little internal compartmentalization

What are the common parts of a typical eukaryotic cell?

• nucleus

• mitochondria: energy hub

• lysosome: degradation center

• endoplasmic reticulum, chloroplast (in plant cells)

• actin filaments

• specialized membrane-bound organelles

• plasma membrane

• nuclear envelope: surrounds envelope

phagocytosis

how mitochondria and cholorplasts (perform photosynthesis) came about.

• a cell engulfs and internalizes an extremal particle

What are common experimental model organisms, and what are they commonly used to study?

• E. coli: Prokaryote used for studying basic biochemical processes like DNA replication and protein synthesis

• S. cerevisiae & S. pombe: Single-celled eukaryotic yeasts used for simple mutant analysis and cell cycle regulation

• Arabidopsis: Plant model used to study multicellular plant development^[8].

• C. elegans & Drosophila: Invertebrates used to study multicellular animal development and model human diseases

• Zebrafish, humans, mice, frog: vertebrates used to study multicellular animal development and model human diseases

What is CDK, and why is it important

An S. pombe cell lacking CDK (essential cell division cycle regulator) becomes

long. Cell division and propagation can be rescued by expressing human CDK

carbon

predominant molecule of life; able to build complex molecules

organic chemistry

the study of carbon compounds

cytosol

the aqueous component of the cellular cytoplasm in which organelles and particles are suspended. (70%)

• cellular life originated at deep sea hydrothermal vents

covalent bonds

strong molecular bond in which electrons are shared between atoms

• polar covalent: unequal sharing of electrons

• nonpolar covalent bonds: have a more equal distribution of electrons

noncovalent bond

weaker bonds in which electrons are not shared

• hydrogen bonds: attraction when a hydrogen atom is sandwiched between two electron attracting atoms

• ionic/electrostatic bonds: attraction between charges

• van der Waals: distance dependent weak attraction due to fluctuating electrical charges

• hydrophobic forces: attraction of hydrophobic groups due to their repulsion by water (minimize distortion of a hydrogen bonded water network)

can also define conformational shapes of molecules

bond strength

the amount of energy it takes to break a bond

• covalent > ionic > hydrogen > van der waals

4 families of small organic molecules

• sugar : soluble carbohydrates that consist of carbon, hydrogen, and oxygen

  • form polysaccarides

• amino acids: carbon atom attached to a carboxyl group, amino group, side group, a hydrogen

  • form proteins

• fatty acids: hydrocarbon chain + carboxylic group

• nucleotides: sugar phosphate + chemical bases

  • nucleic acids

macromolecules

polymers made by covalently linking organic molecules into long chains

• the most abundant carbon containing molecules

• formed by condensation reaction

2nd law of thermodynamics

disorder (entropy) has the natural tendency ti increase in an isolated system

catabolic reaction

break down food stuff into smaller molecules, generating energy and new molecular building blocks

anabolic reaction

biosynthetic using energy and small molecules provided by catabolism to build macromolecules

free energy

energy available to do work

enzyme

specialized protein catalyst that reduces the activation energy of a reaction

• ribosomes : rna catalyst

• enzymes → bind substrate → via active site.

  • they speed up reactions but cannot force energetically unfavorable ones

• substrate: molecule an enzyme binds and acts on.

• Product: molecule formed from the enzyme-catalyzed reaction.

  • E + S → ES → EP → E + P

coupling

Pairing an energetically unfavorable reaction with a favorable reaction so the overall reaction can proceed. (- ∆G)

activated carrier molecules

store energy created by the breakdown of food molecules for use elsewhere

• ATP (most versatile)

head polymerization

• proteins

• the reactive bond required for the condensation reaction is carried on the end of growing polymer, and must be regenerated each time a monomer is added

tail polymerization

• nucleic acids and polysaccharides

• the reactive bond required for the condensation reaction is carried by each monomer and used immediately for its own addition

condensation and hydrolysis reactions

• hydrolysis : Breaks molecules apart by adding water.

• condensation: Joins subunits together while losing one water molecule for each subunit added.

high energy intermediate

A temporary, energy-rich molecule produced during coupling that can help drive an unfavorable reaction forward.

How can cells create order without violating the second law?

→ Cells use energy to create internal order but release heat into their surroundings, increasing

external disorder.

• Heat

→ Energy in a highly disordered form that cells release into their environment.

Energetically favorable reaction vs Energetically unfavorable reaction

• Energetically favorable reaction → A downhill reaction with a net decrease in free energy; can occur spontaneously.

  • hydrolysis

• Energetically unfavorable reaction → An uphill reaction that requires an input of energy.

  • condensation

Reactive bond

A high-energy bond used to help drive the condensation/addition of a monomer.

terminology relevant to proteins

• Protein — a molecule made of amino acids linked together by peptide bonds.

• Amino acid — protein building block with an amino group, carboxyl group, hydrogen, and side chain.

  • Peptide bond — covalent bond that holds amino acids together.

  • Amino group — one of the main groups attached to an amino acid’s central carbon.

  • Carboxyl group — another main group attached to an amino acid’s central carbon.

  • Side chain / R group — unique part of an amino acid that gives it its chemicalnproperties.

  • Polypeptide backbone — repeating sequence of atoms at the core of a polypeptide chain.

  • N-terminus — amino end of a polypeptide.

  • C-terminus — carboxyl end of a polypeptide.

    • Polypeptides are written — N → C

amino acid classification

• hydrophobic/ nonpolar: A,G,V,L,I,P,F,M,W,C

• polar/ basic: R,H,K (positive)

• polar/acidic: D,E (negative)

• polar: N,Q,S,T,Y

  • hydrophilic

molecular chaperones

help folding to proceed along the most energetically favorable pathway and mask transiently exposed hydrophobic regions to prevent protein aggregation

common folding patterns

• α-helix: single peptide that twists around itself with a hydrogen bond btw every 4th amino acid

• ß sheet: flat sheets that form from hydrogen bonding btw adjacent segments of the polypeptide

  • antiparallel: run in opposite direction (favored, symmetrical)

  • parallel: run in the same direction

4 levels of protein organization

• primary: the sequence of amino acids

• secondaries: formation of the α-helix and ß sheet

• tertiary: 3D organization of a polypeptide chain

• quartenary: a complex formation btw other than polypeptides

hemoglobin

iron containing protein that carries oxygen in red blood cells

• 2 alpha, 2 beta

protein domain

substructure of a polypeptide that can often fold independently and exert a unique function

ligand

molecule that binds to a protein at a specific binding site.

• proteins bind ligands via specific binding sites

other ways proteins can bind

• surface: string interactions: an extended loop (string) of one polypeptide contacts a rigid surface on anoher

  • eg: antigen recognition by the hypervariable loop of an anitbody

• helix - helix: α helices wrap around each other to form a stable coiled-coil (typically hydrophobic residues on one side)

• surface- surface interactions: two complementary rigid surfaces fit tg, most common, and very strong and specific due to many weak bonds in sum

enzyme kinetics

• Vmax: maximum rate of a reaction, when the enzyme is saturated with substrate

• Km: the substrate concentration at which the reaction proceeds at half its maximum rate

  • lower Km: reaches maximum at a lower substrate concentrations; tighter bonding

  • higher Km: reaches its maximum at a higher substrate concentration; weaker binding

multienzyme complex

bring tg enzymes in the same pathway such that diffusion is not limiting

segregation of enzymes and substrates into cellular compartments

can locally increase concentrations many fold, tho absolute cellular levels of a substrate do not change

feedback loop

later steps/products in a pathway affect earlier steps.

• negative regulation: a regulatory molecule prevents an enzyme from working

  • feedback inhibition (a late product opposes an enzymes activity)

• positive regulation: a regulatory molecule further stimulates an enzymes activity

scaffold

a structure that helps keep interacting proteins together.

allosteric regulations

a molecule that binds to a site other than ab enzymes active (catalytic site, and thereby regulates the enzymes activity

• Allosteric site : regulatory binding site separate from the active site.

allosteric control is due to chemical principle known as____

linkage

• negative linkage: binding of one prevents the other

• positive linkage: binding of one helps the other

kinase

enzyme that adds a phosphate

phosphatase

enzyme that removed a phosphate

GTP binding proteins

active when bound to a GTP aka GTPase bc catalyze the hydrolysis of GTP themselves

• activation is due to a conformational change

• like the ON button

GAP (GTPase activating protein)

activates the GTPase function (GTP → GDP), inactivating the protein

GEF ( guanine nucleotide exchange factor)

cause GDP to be released, allowing GTP to be reloaded, and protein function to be restored

ubiquitin

an abundant small portion with multiple functions depending on how its attached

• monoubiiquitination- histone regulation

• multiubiiquitination- endocytosis/trafficking

• polyubiiquitination:

  • Lys48: degradation

  • Lys63: DNA repair

ubiquitin cascade

• E1: activating enzyme

• E2: conjugating enzyme

• E3: ligase

• DUB: deubiiquitinating enzyme

1st experimental demonstration ***

• In the 1940s, experiments demonstrated that heat-killed pathogenic S strain (smooth pathogenic bacterium causes pneumonia) bacteria could undergo transformation to convert nonpathogenic R strain cells into live S strain cells. Chemical fractionation of cell extracts into classes of molecules showed that only purified DNA transformed R strain cells

polarity

directionality

• 5’: the phosphate group

• 3’: hydroxyl group from the deoxyribose sugar

• 5’ → 3’

dna groves

• Minor groove — the smaller/narrower groove formed by the DNA double helix.

• Major groove — the larger/wider groove of the DNA double helix; many DNA-binding proteins recognize DNA sequences here.

chromosomes

single, linear, enormous molecules of DNA and proteins, that carries genes

• humans have 22 pair of autosomes (non sex) and 1 pair of sex chromosome

• homologous chromosomes: two copies if each autosome (or the X chromosome), one from mother and one from father

  • sex chromosome in males is non-homologous

• DNA + protein

  • chromatin: the nuclear DNA with its associated protiens → histones

genome

organisms complete set of DNA

exon vs introns

exons: actual coding sequences that will be spliced together in mRNA

introns: intervening/noncoding sequences

promoters

sequences to which RNA polymerase bonds for transcription

interphase vs M phase

interphase

• longest phase

• chromosomes are replicated into sister chromatids

  • sister chromatid: one of the two identical copies of a replicated chromosome.

• geners are expressed → less condensed state

M phase

• expression is turned off → more condenstated state

• condensed chromosomes segregate to opposite daughters

3 parts of a chromosome allow for faithful replication and segregation

• replication origins: sites where DNA duplication begins in interphase (multiple origins per eukaryotic chromosomes)

• centromere: region of chromosome where microtubules of the spindle attach, via the kinetochore, during M phase (one per eukaryotic chromosome)

  • kinetochore: made up of proteins that specifically attach to the spindle microtubules

  • Spindle: structure made mainly of microtubules that moves and separates

• telomere: end of chromosome that contains repeated sequences which form a special “cap” that protects the chromosomes (2 per eukaryotic chromosome; one on each end)

30 nm fiber

a more condensed level of chromatin formed when nucleosomes stack together, possibly in a zigzag arrangement.

• Lampbrush chromosome: highly extended chromosome containing large DNA/chromatin loops. Highly expressed genes are often found in the loops.

Histones

proteins associated with DNA that help package DNA into chromatin; they form the protein “beads” of nucleosomes.

• allow formation of nucleosome (the most basic level of chromosome packing)

Linker DNA

DNA located between neighboring nucleosomes.

histone octamer

forms the protein core of each nucleosome: 2 molecules each of H2A, H2B, H3, H4

different chromosome packing

euchromatin: less condensed; active genes

• acetylation: regions with high transcriptional activity are loosely packed heterochromatin: tingly condensed; centromeres, telomeres, inactive genes

  • loosens chromatin by negating the modified lysines positive charge, thereby reducing histone tail interactions

• methylation: regions with low or no transcriptional activity are densely packed

  • condenses chromatin by creating a binding site for HP1, a heterochromatin- promoting factor

• found around the nuclear periphery

• can self propagate

position effect

spreading of heterochromatin into the previous euchromatic regions, saying these genes to be silenced, however, there ate barriers to this spread

• barrier sequences block the spread of heterochromatin

variegation

spreading can occur over different distances in different cells

epigenetic inheritance

once the new chromatin state is changed, it cab be inherited and passed on to new cells

N terminal sistine tails have multiple sites that can be covalently modified

• histone acetylene transferase: adds an acetyl group

• histone deacetylase complex: removes an acetylene group

• histone methyltransferase: adds a methyl group

• histone demethylase: removes a methyl group

HP1 (Heterochromatin Protein 1)

protein that binds certain methylated histones and promotes heterochromatin formation and spreading.

Reader-writer complexes

protein complexes that help spread and maintain a chromatin state. The “reader” recognizes an existing histone modification, while the “writer” places the same type of modification on nearby histones.

Think: READ what is already there → WRITE it onto the neighbor → spread the chromatin state.

semiconservative

each of the two daughters inherits a new DNA double helix containing one original and one old strand

gene expression

using the information in a gene to make a functional product, usually RNA or protein.

RNA polymerase

enzyme that catalyzes covalent linkage of RNA monomers

transcription units

each transcribed section

steps of transcription

1. transcription initiation: RNA core polymerase pairs with sigma factor (to form holoenzyme) and slides on DNA until it recognizes a promoter (starting point fo RNA synthesis)

• sigma factor: protein that binds RNA core polymerase and helps it recognize promoters

• transcription bubble: region of unpaired DNA)

• holoenzyme: RNA core polymerase + sigma factor; the complete complex that recognizes the promoter and begins transcription.

2. abortive transcription: initial, inefficient synthesis of short ttabscrips that are often released

3. promoter clearance and elongation: the holoenzyme produced >10 nt and “breaks free” from the promoter, discarding sigma factor and moving down the dna

4. hairpin formation and transcription termination: a terminator sequence in the RNA folds into a conformation that disengages the transcript from RNA polymerase

5. reassociation of the holoenzyme: the cycle can begin again

Promoter

DNA sequence marking the starting point for transcription where RNA polymerase binds.

consensus sequence

an “average” or commonly occurring nucleotide sequence\ recognized by a DNA-binding protein.

• Your lecture uses the −35 and −10 promoter regions as examples.

5′ to 3′

direction in which RNA is synthesized. New RNA nucleotides are added to the 3′ end, so the transcript grows 5′ → 3′

Types of RNA

• mRNA (messenger RNA) — RNA that carries the protein-coding message from DNA to the ribosome.

• rRNA (ribosomal RNA) — RNA that forms part of the ribosome and helps it function during protein synthesis.

• tRNA (transfer RNA) — RNA that carries amino acids to the ribosome and matches its anticodon to mRNA codons.

• snRNA (small nuclear RNA) — small RNA involved mainly in RNA splicing as part of the spliceosome.

Eukaryotic RNA processing

• 5′ cap — modified nucleotide structure added to the 5′ end of eukaryotic RNA. protects the RNA and also helps with translation.

• Guanyl transferase — enzyme that adds a GMP nucleotide to the 5′ end during formation of the 5′ cap.

• Poly-A tail — long stretch of adenine nucleotides added to the 3′ end of mRNA; helps protect and stabilize the RNA.

• Poly-A polymerase — enzyme that adds the poly-A tail to the 3′ end of an RNA.

• Exon — sequence that is retained in the mature mRNA and joined to other exons.

• Intron — intervening RNA sequence that is removed during splicing.

• Mature mRNA — fully processed mRNA containing joined exons plus its 5′ cap and 3′ poly-A tail, ready for translation.

RNA splicing

• 5′ splice site — beginning boundary of an intron where the first cut occurs during splicing.

• Branch site — region inside the intron containing an important adenine nucleotide used to form the lariat.

• 3′ splice site — end boundary of the intron where the second cut occurs.

• Spliceosome — large RNA-protein complex that removes introns and joins exons together.

• snRNP — “small nuclear ribonucleoprotein”; complex of snRNA + proteins that forms part of the spliceosome.

  • U1 snRNP — snRNP that recognizes/binds the 5′ splice site.

  • U2 snRNP — snRNP that recognizes/binds the branch site.

Genetic code

• Codon — sequence of 3 nucleotides on mRNA that codes for an amino acid or signals stop.

• Degenerate code — genetic code is redundant because more than one codon can code for the same amino acid.

• Reading frame — way an mRNA sequence is divided into groups of three nucleotides. The correct reading frame is established by the start codon.

  • Start codon — AUG; establishes the reading frame and usually codes for methionine.

  • Stop codon — codon that ends translation. The three stop codons are UAA, UAG, and UGA.

tRNA and codon recognition

• tRNA — adaptor RNA that connects an mRNA codon with its correct amino acid.

• Anticodon — group of 3 nucleotides on a tRNA that base-pairs with a complementary codon on mRNA.

• Wobble — flexible base pairing at the third nucleotide of a codon, allowing one tRNA to recognize more than one codon for the same amino acid.

• Aminoacyl-tRNA synthetase — enzyme that attaches the correct amino acid to its corresponding tRNA. Your lecture notes one type for each amino acid, so about 20 total.

Ribosome

• Ribosome — RNA-protein complex that reads mRNA and builds a protein. It contains rRNA and proteins and has a large and small subunit.

  • Ribosomal large subunit — portion of the ribosome that catalyzes peptide-bond formation.

  • Ribosomal small subunit — portion that matches tRNA anticodons with mRNA codons.