BIS2A Final

Cytoskeleton

A network of fibers that holds the cell together, helps the cell to keep its shape, aids in movement of cytoplasm and vessicles, and enables cell to move in response to stimuli

Microfilaments

Long, thin fibers that function in the movement and support of the cell. rate of monomer in + ATP hydrolysis; composed of actin subunits

Actin

proteins present as free monomer (G) or part of polymer microfilament (F); bound to ATP to assemble filament forms & maintain structural integrity; + end elongates filament & - end disassembles filament & controlled by ATP & ADP ratio; track for movement of motor proteins called myosins

intermediate filaments

Threadlike proteins in the cell's cytoskeleton that are roughly twice as thick as microfilaments; bears tension, maintains cell shape, anchors nucleus and other organelles in place (purely structural)

Microtubes

Spiral strands of protein molecules that form a tubelike structure; alpha & beta tubulin; rapidly elongating and elogating + and - ends; resists compression, provides tracks for motor proteins; composed of flagella, cilia, & centrioles

flagella

whiplike tails found in one-celled organisms to aid in movement

cilia

Hairlike projections that extend from the plasma membrane and are used for locomotion

Dyneins

In cilia and flagella, a large motor protein extending from one microtubule doublet to the adjacent doublet. ATP hydrolysis drives changes in dynein shape that lead to bending of cilia and flagella; + to - end

Kinesins

motor protein

associated with microtubules

important in vesicle transport

bring vesicles toward the positive end of the microtubule (periphery)

- to + end with ATP hydrolysis

Endocytosis

A process in which a cell engulfs extracellular material through an inward folding of its plasma membrane.

cellular structure of bacteria and archaea

unicellular, genetic material from nucleoid, smaller than eukaryotes, rigid cell walls, increases membrane SA with folds

how do cells get bigger

become independent of diffusion, increase volume, need for intracellular transport and compartmentalization

microbial mats

very thick biofilms

-built by phototrophic and/ or chemolithotrophic bacteria

Stromatolites

Oldest known fossils formed from many layers of bacteria and sediment.

Extremophiles

Organisms thriving in extreme environmental conditions.

endosymbiotic theory

theory that eukaryotic cells formed from a symbiosis among several different prokaryotic organisms; argardian archaea are ancestors of eukaryotes

Selective Filter

combo of all living and nonliving factors in an environment which influence how successful an organism can reproduce

selective pressures

forces in the environment that influence reproductive success in individuals

dna double helix

the two DNA strands run antiparallel and held together by hydrogen bonds; 5' to 3' ends; nitrogenous bases stack on top of each other via hydrophobic forces (A&T and G&C); redundant info

Higher M.T.? G&C or A&T

G&C bc more stable

conservative replication

the parental molecule serves as a template for the synthesis of an entirely new molecule

semi-conservative replication

in each new DNA double helix, one strand is from the original molecule, and one strand is new; most accepted

dispersive replication

replication results in both original and new DNA dispersed among the two daughter strands

DNA replication initiation

initiator protein recognizing a DNA sequence of origin of replication -> destabilizes double helix and recruits proteins like helicase -> helicase unwinds double helix

Helicase

An enzyme that untwists the double helix of DNA at the replication forks.

-malfunction: Unable to unwind DNA for replication to occur

DNA replication elongation

-primase creates 3'OH to initiate synthesis

-DNA polymerase III synthesize DNA from the primer and DNA polymerase I removes primer and synthesizes remaining DNA

-ligase: joins together Okazaki fragments

Primase

An enzyme that joins RNA nucleotides to make the primer.

-malfunction: Unable to attach new DNA nucleotides to existingnucleotide strands

DNA Polymerase III

adding bases to the new DNA chain; proofreading the chain for mistakes

-malfunction: Unable to replicate leading and lagging strands

DNA Polymerase I

removes the RNA primer and replaces it with DNA

-malfunction: Unable to remove RNA primers and replacethem with DNA

Ligase

An enzyme that connects two fragments of DNA to make a single fragment

-malfunction: Unable to connect Okazaki fragments

Topoisomerase

corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands

in prokaryotes, uses ATP to introduce negative supercoils to circular chromosomes

-malfunction: DNA would supercoil, which would prevent helicasefrom operating, which would stop replication.

telomere

repeating nucleotide at the ends of DNA molecules that do not form genes and help prevent the loss of genes

Telomerase

An enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells.

-malfunction: Unable to lengthen telomeres, which leads to faster degradation or cause cancer

DNA proofreading

During synthesis, DNA polymerase will proofread.

Can detect incorrectly paired H-bonds, and excises/ replaces with correct pair.

tradeoff: speed and accuracy

Damaged bases

UV light / radiation damages nucleotides, solved with BER & DCR & NER

Mutations

a random error in gene replication that leads to a change, structurally normal so cannot be recognized and easily fixed

Direct chemical reversal of damage

simplest and most energy effiecient method to fix damaged bases, doesn't require reference template, doesn't involve breaking phosphodiester backbone of DNA

basic excision repair (BER)

removes damaged base from DNA by glocosylase, followed by removal of region of DNA surrounding missing base and AP site by endonuclease, gap is repaired by DNA polymerase and ligase

nucleotide excision repair (NER)

a DNA repair system in which several nucleotides in the damaged strand are removed from the DNA and the undamaged strand is used as a template to resynthesize a normal strand by DNA polyemerase and sealed in by ligase; has thymine dimer

Mismatch Repair (MMR)

A type of repair that corrects mispaired bases, typically immediately following replication

thymine dimers

This is a type of damage often caused by ultraviolet radiation. directly effects DNA; then RNA and proteins, in NER

Central Dogma

DNA-transcription-RNA-translation-protein

Transcription

synthesis of an RNA molecule from a DNA template; synthesizes 5' to 3'

transcription initiation

sigma factor of RNA polyermase recognizes TATA box (TATAAT at -10 box) of promoter in prokaryotes but eukaryotes also has TATA box

promoter

specific region of a gene where RNA polymerase can bind and begin transcription

RNA polymerase

enzyme that links together the growing chain of RNA nucleotides during transcription using a DNA strand as a template; unwinds and rewinds DNA; doesn't proofread and correct mistakes

nontemplate strand

the strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA; coding strand

template strand

The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript.

upstream of DNA

toward the 5' end of the RNA molecule

downstream of DNA

toward the 3' end of the RNA molecule

transcription start site

The site at which the first RNA nucleotide is added; also known as the +1 site.

terminator

In prokaryotes, a special sequence of nucleotides in DNA that marks the end of a gene.

transcription termination site

DNA site of the last nucleotide incorporated into the transcribed RNA

transcription elongation

After binding, RNA polymerase unwinds the DNA

Transcription bubble produced

moves with the polymerase as it transcribes mRNA from template strand

within the bubble a temporary RNA:DNA hybrid is formed

Transcription Termination

When RNA polymerase reaches terminator, transcription stops & RNA chain is released

mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome

Cistron

a section of a DNA or RNA molecule that codes for a specific polypeptide in protein synthesis -> monocistronic mRNA -> single protein; in prokaryotes

operon

group of genes operating together under the control of a single promoter -> polycistronic mRNA -> several different proteins; in prokaryotes and rarely in eukaryotes

Splicing

the process of removing introns and reconnecting exons in a pre-mRNA; allows cells to mix &match which exons are incorporated into final mRNA product; removes non-coding sequences

spliceosome

complex of enzymes that serves to splice out the introns of a pre-mRNA transcript

rho dependent termination

a mechanism of transcription termination in prokaryotes, reliant on the rho protein that binds to the RNA and helps release the transcript from the RNA polymerase.

rho independent termination

a mechanism of transcription termination in prokaryotes that does not rely on the rho protein, characterized by the formation of a hairpin structure in the RNA transcript.

5’ cap

is a modified guanine nucleotide added to the 5' end of eukaryotic mRNA transcripts. It protects the mRNA from degradation and helps in ribosome binding during translation.

3’ Poly A tail

is a string of adenine nucleotides added to the 3' end of eukaryotic mRNA. It enhances the stability of the mRNA and facilitates export from the nucleus.

intron

a non-coding sequence in a gene that is transcribed into precursor mRNA but is removed during RNA splicing before translation.

extron

a coding sequence in a gene that is transcribed into mRNA and retained after RNA splicing for translation into protein.

direction of DNA replication and RNA synthesis and DNA reading

replication and synthesis: 5’ to 3’

reading: 3’ to 5’

direction of protein synthesis

NH2-COOH

translation

the process of synthesizing proteins from mRNA, energy from GTP hydrolysis

ribosomes

macromolecular machines that facilitate translation by decoding mRNA into polypeptide chains, made of rRNA and proteins (ribonucleoproteins: RNP)

translation start site

the specific nucleotide sequence on mRNA where translation begins, commonly recognized by ribosomes, AUG

translation termination site

the specific nucleotide sequence on mRNA where translation ends, typically recognized by release factors and signals the disassembly of the ribosome, UAA, UGA, UAG

tRNA

a type of RNA that carries amino acids to the ribosome during translation, pairing with the corresponding codon on mRNA to ensure accurate protein synthesis, anticodon allows ribosome to read and translate mRNA

aminoacyl-tRNA

a charged tRNA molecule that has an amino acid covalently bonded to it, delivering the specific amino acid to the growing polypeptide chain during translation, 20 different types

amino-acyl tRNA synthesases

enzymes that attach amino acids to their corresponding tRNA molecules, essential for accurate translation and protein synthesis, requires ATP to make charged tRNA, releases AMP and Pi

ribosome large subunit

the larger component of the ribosome that facilitates peptide bond formation and the assembly of amino acids into a polypeptide chain during translation.

ribosome small subunit

the smaller component of the ribosome that binds to the mRNA and ensures the correct pairing of tRNA anticodons with mRNA codons during translation.

aminoacyl site (A site)

The site on the ribosome where incoming aminoacyl-tRNA binds during the translation process, playing a crucial role in the elongation of the polypeptide chain.

Peptidyl site (P site)

The site on the ribosome that holds the tRNA carrying the growing polypeptide chain, facilitating peptide bond formation during translation.

Exit site (E site)

The site on the ribosome where uncharged tRNAs exit after delivering their amino acids, allowing for the recycling of tRNAs during translation.

rRNA

A type of RNA that is a fundamental component of the ribosome, playing a crucial role in protein synthesis by facilitating the binding of tRNAs and the formation of peptide bonds, a ribozyme that catalyzes peptidyl transfer (peptide bonds)

ribozyme

RNA molecules that catalyzes biochemical reactions, including RNA splicing and peptide bond formation, rRNA

translation initiation

is the process by which ribosomes assemble around the start codon of an mRNA strand, recruiting & binding tRNA to start codon with assistance from initiation factor and initiates protein synthesis, 5’ cap required for eukaryotes

translation elongation

is the phase of translation where the ribosome moves along the mRNA, facilitating the sequential addition of amino acids to the growing polypeptide chain through tRNA binding and peptide bond formation.

peptide bond

a covalent bond formed between the carboxyl group of one amino acid and the amino group of another, releasing a molecule of water (condensation)

translation termination

is the final phase of translation where the ribosome reaches a stop codon on the mRNA, leading to the release of the newly synthesized polypeptide chain and disassembly of the ribosomal complex.

protein sorting

protein tagged for destination with short string of amino acids called the signal peptide that encodes info for where protein should end up

bacteria protein signaling

proteins identify signal proteins during translation, binds, and direct synthesis of protein to plasma membrane

eukaryote protein signaling

signal recognition, protein modification, and trafficking of vesicles between organelles or membrane

initated in endoplasmic reticulum and refined in golgi apparatus where proteins are modified and packaged into vesicles bound for various parts of cell

intracellular proteins: cytoplasm

membrane associated or excreted proteins: translated in rough ER

rough endoplasmic reticulum

translates membrane associated or excreted proteins

diploid

in eukaryotes, 3 pairs of homologous chromosomes

haploid

in prokaryotes and eukaryotes, one set of chromosomes

genome

contains all genetic information regarding structure and function and reproduction

genome sequence

list of position and order of every base pair and all genetic information

protein-coding sequences (CDS)

open reading frames with AUG, evolutionary conservation of protein domains (DNA polymerase), splice junctions in eukaryotes

open reading frames (ORF)

AUG, region of DNA that has potential to be transcribed and translated into proteins

non-coding DNA

DNA that doesn’t code into proteins, essential for gene expression by regulating transcription, also essential for genome integrity and transmission

retrotranspoons

“repeating” genes, consists of 50% genes, uses reverse transcriptases to copy and paste, randomly inserting gives rise to new gene regulatory elements like enhancers

C-value paradox

no strong correlation between size of genome and complexity of organism (neither does gene number)

mutations

error or physical damage in DNA sequencing