Cell Biology Review Flashcards
What are the 3 main types of RNA?
Messenger, mRNA
Ribosomal, rRNA
Transfer, tRNA
______ are triplets of nucleotides in the mRNA
Codons
mRNA is termed the _____ strand
sense
What tells which triplets to use to make sense?
The reading frame
What can cause a shift in the reading frame?
Insertions or deletions
What is the dense, inactive (not being transcribed) form of the chromosome called?
Heterochromatin
What is the disperse and active form of the chromosome called?
Euchromatin
What are enhancers and silencers and where are they found?
Regulatory DNA segments upstream of the promoter or downstream of the gene
List the two types of transcription factors (proteins)
Activators
Repressors
What is the function of activators?
Bind to enhancers increasing transcription
What is the function of repressors?
Bind to silencers decreasing transcription
What is the promoter?
Region of DNA that initiates transcription of a particular gene
Describe the parts of the promoter
Distal- upstream of the proximal promoter
Proximal
Core- has binding sites for transcription factors (i.e. TATA box), binding site for RNA polymerase and the transcription start site (TSS)
What is the function of the 5’ cap?
Protects the nascent mRNA from degradation and assists in ribosome binding
What is the function of 5’ UTR?
(leader sequence) - helps in regulation of translation
Describe the protein coding region
-Introns are spliced out (RNA processing) in the nucleus
-Exons are variably retained (alternative splicing) allowing for multiple proteins (isoforms) to be made from the same gene
What is the function of the 3’ UTR?
Determines termination and regulation of translation
What is the function of the poly A tail?
(Multiple adenine residues) which prevents degradation of the mRNA. Can also influence localization of the transcript and translation
It is estimated that >94% of the DNA that is transcribed is not translated into protein, rather it is used to __________
regulate transcription
Describe functional, non-protein coding DNA
-Structural DNA involved in cell function (telomeres, centromeres)
-Structural DNA involved in gene regulation (histone binding sites, promoters/enhancers, mobile genetic elements - transposons)
-Most is transcribed into non-coding regulatory RNAs
List the Housekeeping RNAs
Transfer RNA
Ribosomal RNA
List the regulatory RNA
-Long non-coding RNA (lncRNA - linear or circular)
-Small non-coding RNA (sncRNA): microRNA (miRNA) and small interfering RNA (siRNA)
Describe the features of Micro-RNAs (miRNAs)
- 20-30 bp
- ~6,000 miRNA genes, each regulating multiple protein-coding genes
-Trimmed by enzyme Dicer
-Associate with RNA-induced silencing complex (RISC) to bind to mRNA
-Leads to posttranslational silencing of genes (most of the time)
Describe the features of small interfering RNA (siRNA)
- dsRNA (20-24bp) designed to interfere with translation of a specific mRNA
-Very useful in research: can create synthetically and use to decrease expression (i.e. knockdown) of a gene and study the effect of that gene
Describe the features of long noncoding RNA (lncRNA)
- > 200bp
-Many more of these than coding mRNA
-Multiple ways of modifying gene expression:
1. Interact with transcription factors to activate or suppress
2. May alter acetylation or methylation of DNA or histones
3. Stabilize secondary or tertiary structure of protein complexes that influence chromatin architecture or gene activity
What is the clinical relevance of long noncoding RNA (lncRNA)?
We proved that a multitude of them play a pivotal role in the different processes involved in the progression of the disease. lncRNAs could become unique and valuable biomarkers or future targets for personalized medicine
Where do single nucleotide polymorphisms (SNPs) occur?
Across the whole genome
What happens when single nucleotide polymorphisms (SNPs) occur in non-coding regions?
Can affect regulatory regions –> altered gene expression
Describe the interaction between single nucleotide polymorphisms (SNPs) and disease
-Effect on disease susceptibility is weak
-If co-inherited with a disease-associated gene, it can be a useful marker for that disease
What is copy number variation?
-A type of genetic variation
- 1000-millions of base pairs of repeated segments of DNA
-Responsible for a significant portion of variation between people
What is CRISPRs?
-Clustered regularly interspaced short palindromic repeats (CRISPRs)
-Gene editing
-Allows inserting specific genes into cells, which may allow “correction” of genes associated with disease
-Human trials are promising
What is the purpose of membrane-bound organelles?
Allows cell functions to be compartmentalized without damaging the cell
What is the function of the rough endoplasmic reticulum (RER)?
Synthesis and folding of plasma membrane proteins and secreted proteins
(factory builders)
What is the function of the smooth endoplasmic reticulum (SER)?
-Lipid synthesis-membranes
-Specialized features based on cell type: liver (drug detoxification), ovaries/testes/adrenals (steroid hormone synthesis), muscle (calcium regulation)
-Protein transport
(factory builders)
What is the function of the golgi apparatus?
-Modifies, packages, transports proteins/lipids
-Glycosulation (adding sugar resides) helps target where proteins will go and determine protein interactions with cell matrix
(packaging plant)
What is the function of the proteasome?
Degrades denatured or other cytosolic proteins that are “tagged” (with ubiquitin) for destruction
(demolition crew)
What is the function of the lysosome?
Digests (acid hydrolases) many macromolecules (protein, lipid, nucleic acid), damaged organelles and microbes
(demolition crew)
What is the function of peroxisome?
Breaks down long chain fatty acids to make H2O2; catalase breaks down the H2O2 to water
(Demolition crew)
In which organelle is DNA virtually entirely maternally inherited?
Mitochondria
What is the function of mitochondria?
-Central roll in regulation of programmed cell death (apoptosis) and necrosis
-Makes ATP but can shift intermediates away from energy production to building lipids, nucleic acid and some proteins. This is based on cellular signals, nutrients, and O2 availability
What does the plasma membrane contain?
A heterogeneous collection of different phospholipids, which are distributed asymmetrically
What is the function of the plasma membrane?
-Cell-cell interactions: inflammation, sperm/egg
-Cell-matrix interactions: structural scaffold, can initiate intracellular second signals
In regards to the protein component of the membrane, most are ___________ with _______ charged cytoplasmic domains that anchor to negatively charged membrane phospholipids
transmembrane (integral); positively
T/F: Additional proteins can attach on the inside or outside of the cell membrane which anchors them to the cell
TRUE
The extracellular face of the membrane and associated proteins are studded with carbohydrates to form ______ and ______ which together form the glycocalyxl.
glycolipids; glycoproteins
What is the function of the glycocalyx?
-Chemical and mechanical barrier
-Helps in cell-cell and cell-matrix interactions
In passive diffusion, what molecules are let through?
O2, CO2, small polar molecules, hydrophobic molecules
What is the transporter for passive diffusion?
-Channel proteins - hydrophilic pores for rapid solute movement (passive transport)
-Solute concentration and/or electrochemical gradient moves solutes across membranes
What is the membrane impermeable to?
Charged molecules
What type of transporters do charged molecules use to get across the membrane?
Carrier proteins - bind solute –> conformational change –> transfers solute across (active transport- required ATP)
In general, what is the typical state of a cell in terms of charge?
The inside of the cell is negatively charged and the outside is positively charged
What maintains the cell gradient?
Na+ ATPases actively pump ions out of the cell to maintain this gradient and to prevent osmotic swelling
What is the function of the cytoskeleton?
-Maintains shape, polarity, and organization of cellular components and creates a scaffold for proteins within the cell
-Like the highway connecting everything together
Describe the actin microfilaments?
-Part of the cytoskeleton
- G-actin is most abundant cytosolic protein
- F-actin combine into fibrils that control cell shape and movement
Describe the intermediate filaments
Fibrils giving tensile strength; many are cell specific
-Lamins (nuclear lamina)
-Vimentin (mesenchymal cells)
-Desmin (muscle cells)
-Neurofilaments (axons of neurons)
-Cytokeratins (epithelial cells)
What are microtubules?
-Part of cytoskeleton
-Large fibrils allow movements of vesicles and organelles around cell
-Made of tubulin dimers
-Support for chromatid separation during mitosis
-Is the core of cilia and flagella
Describe microtubule movement
-Negative end near the nucleus embedded in the centrosome paired with centrioles
-Positive end elongates or recedes outward into the cytosol
How do two chemotherapy drugs, Taxol and Vincristine, work?
By stopping microtubule function so mitosis stops –> kills the cell.
What is the function of occluding junctions (tight jxns)?
-Seals together as a barrier to prevent movement of molecules between cells
-Maintains cell polarity (apical and basal ends)
What is the function of anchoring junctions (desmosomes)?
-Mechanically attach cells and their cytoskeletons (intermediate or microfilaments) to:
1. other cells (using cadherins)
2. the extracellular matrix - hemidesmosomes at the basal part of the cell are made of integrins that connect to basement membrane
-Distributes force through multiple cells and can influence cell shape and motility
What is the function of communicating junctions (gap junctions)?
-Mediate passage of chemical or electrical signals between cells through pores made of connexin proteins
-Many small molecules pass through (ions, nucleotides, sugars, aa, vitamins, etc)
-Permeability reduced by lowered pH or increased intracellular calcium
-In cardiac muscle Ca2+ flows through gap junctions so cells contract as a unit
What is the function of the extracellular matrix (ECM)?
-Mechanical support for cell anchorage and migration
-Control of cell proliferation and is thus a scaffold for tissue renewal- binds growth factor, water and minerals
-Created microenvironments (basement membrane is a boundy between epithelium and connective tissue)
What is the extracellular matrix (ECM) comprised of?
-Interstitial matrix (made by mesenchymal cells)
-Basement membrane (made by mesenchymal and epithelial cells)
What are the components of the ECM?
-Fibrous structural proteins (collagen and elastin) give tensile strength and recoil
-Water-hydrated gels (proteoglycans an hyaluronan) proivde resiliance, compressibility and lubrication
-Adhesive glycoproteins connect the matrix together
Describe the adhesive glycoproteins and their function
-Fibronectin: bind ECM components to each other and to cells. In plasma, binds to fibrin within a blood clot
-Laminin: attaches cells to basement membrane and can alter growth and motility
-Integrins: transmembrane glycoproteins - cellular receptors for ECM components
What must cells respond to in order to develop and adapt to their environment?
Extracellular signals
What can loss of cellular communication lead to?
unregulated growth (cancer)
What is paracrine signaling?
affects adjacent cells
What is autocrine signaling?
cells signaling itself
What is synaptic signaling?
neurons
What is endocrine signaling?
hormones released into bloodstream to act on distant target cells
What are the intracellular receptors?
Are activated by lipid soluble ligands that easily transit plasma membranes (vitamin D, steroid hormones)
What are the cell surface receptors?
Generally transmembrane proteins. Ligand binding may:
-open ion channels
-activate G proteins
-activate an endogenous or associated enzyme
-trigger proteolysis or change protein binding to activate a latent transcription factor
List the cell surface receptors
-Receptors associated with kinase activity
-Non-receptor tyrosine kinase
-G protein coupled receptors
Describe the receptors associated with kinase activity
Add charged phosphate residues to target molecules (part of the receptor)
Describe the non-receptor tyrosine kinase
Ligand binding recruits a tyrosine kinase molecules
Describe the G protein coupled receptors
-Ligand binding –> binding of G protein exchanges GDP for GTP (active) –> other protein activation downstream
-Key pathways stimulated:
1. cAMP - 2nd messenger stimulates multiple effects
2. Inositol 3-phosphate (IP3) –> Ca2+ release
T/F: Most signaling effects multiple pathways to induce multiple complementary effects (like a computer network)
TRUE
Most pathways ultimately affect cell function by ____________ through transcriptions factors
changing gene transcription
-Signaling causes these proteins to undergo conformational changes (often due to phosphorylation), allows translocation to the nucleus, binding to DNA and alteration in transcription of genes
