The Cell Flashcards
What are the three major classes of lipids that make up the plasma membrane?
Phospholipids, cholesterol, and glycolipids.
What are the two major classes of proteins that make up the plasma membrane?
Integral-embedded in or pass through the lipid bilayer
Peripheral-associate noncovalently with the membrane proteins. Basically just chill on the surface of the bilayer.
What does cholesterol do in the plasma membrane?
Intercalates (gets between} phospholipids in order to reduce membrane fluidity.
Glycolipids
Contain sugar. Found exclusively in the outer monolayer and help with cell recognition, self v non self, etc.
What are the 6 general categories of integral membrane proteins?
1) Pumps/carriers/transporters (transport ions or metabolic precursors)
2) Channels (passive defusion, etc)
3) Receptors
4) Linkers (anchor proteins)
5) Enzymes
6) Structural proteins (hold cells together)
What are the three types of endocytosis?
Receptor medicated, pinocytosis, and phagocytosis.
Regulated vs. constitutive exocytosis
Regulated is in response to a stimulus and constitutive is a substance that is continuously delivered to the plasma membrane for export.
Receptor Mediated Endocytosis
Selective uptake of large molecules, depends on Cathrin to make a Cathrin coated pit which drives the vehicle formations. Then dynamin causes the visible to pinch off from the plasma membrane.
Endosomes
Membrane enclosed structure associated with the Endocytosic pathway
Early endosome
Functions to sort and recycle proteins
Late endosome
Receives proteins for degradation and matures into a lysosome with help from the Golgi (Golgi gives it lysosomal enzymes).
Pinocytosis
Cell drinking, non specific ingestion of small vesicles. Constitutive, clathrin independent, found a lot in smooth muscle.
Phagocytosis
Ingestion of large particles, generally performed by specialized phagocytes, dependent on action and independent of clathrin.
Glycocalyx
Carbohydrate rich zone on the cell surface (sugar coating) that helps to establish the micro environment of the cell surface. It provides protection from mechanical and chemical damage, cell recognition, and cell to cell interactions. Made up of glycolipids attached to a glycoprotein.
Neoplasm
New growth, usually a tumor, abnormal mass of cells
What are some characteristics of malignant neoplasms?
Grow rapidly and may invade invade other areas, ignore restraints on cell division, unregulated growth
How are malignant neoplasms classified?
Based on the cell type from which they originate, usually the epithelium or connective tissue
Carcinoma
Malignant tumor of the epithelium
Sarcoma
Malignant tumor growing from connective tissue
Leukemia
Cancer of the blood/bone marrow
Sarcoma
Naming used for connective tissue tumors
Metastasis
When tumors are invasive and can spread into other tissues
Why are carcinomas so prevalent?
The epithelial tissue covers a lot of area and is constantly reproducing so there is greater chance of it mutating. It is also frequently exposed to physical and chemical damage.
Clonal Evolution theory
idea that tumors develop through repeated rounds of mutation and proliferation and eventually take over neighbor cells
Stem Cell Theory
Tumors contain their own set of stem cells so they can reproduce indefinitely and can’t truly be killed
karyotype
Chart showing the organization of chromosomes according to size, shape, and fluorescent colors
Necrosis
Cell death is a pathological and chaotic way in which the cell swells, bursts, and spills its member and everywhere
Apoptosis
Programmed cell death, orderly, normal, cells shrinks and maintains membrane
What is the central dogma of molecular biology?
DNA–>RNA–>Protein
What are the monomeric units that make up the DNA polymer?
Nitrogenous base, pentose sugar, and phosphoric acid group
Ribose
Hydroxyl group attached to the 2’ carbon
Deoxyribose
The hydroxyl group attached to the 2’ carbon in ribose is replaced by a hydrogen group
Nucleosides
Nitrogenous base and a ribose or deoxyribose sugar
Nucleotides
Nitrogenous base, sugar, and a phosphate group
Phosphodiester Bond
Bond between the 3’ OH group of the sugar and the 5’ phosphate on the nucleoside triphosphate
How many bonds are between C and G?
3
B-DNA
Basis of Watson and Crock model. Right hand helix
Z-DNA
Left hand helix, found in sequences where pyrimidines and purines alternate
A-DNA
Right hand sequence of dehydrated DNA, very compact
Primary Structure
Sequence of nucleotides (AGTACA)
Secondary Structure
3-D structure-double helix of DNA
Tertiary Structure
Supercoiling of secondary structure
Quarternary Structure
Interaction of nucleic acids with proteins (DNA wrapped around a histone)
mRNA
Single stranded, carries codon information for translation
tRNA
Folded stem loop system that carries amino acid to ribosome
rRNA
Linear, single stranded, folded molecule, helps form ribosome
snRNA
Small nuclear RNA that is involved in generation of mature mRNA transcripts and are an essential part of splicing
miRNA
Micro RNA is responsible for the regulation of gene expression and can either silence of express mRNAs
Negative Supercoiling
Promotes strand separation (good for DNA Replication) . Introduced behind the protein.
Positive Supercoiling
Unwanted side effect of negative super coiling and must be corrected so DNA can be separated. Introduced ahead of the protein.
What is the function of topoisomerase I?
Forms a single covalent bong with DNA, breaking phosphodiester bonds, allowing the DNA to rotate and relieve stress from supercoiling
What is the function of topoisomerase II?
Topoisomerase II (DNA grade in bacteria) is activated when two double helices cross over each other. It bonds to both ends of the strand, breaking the backbone, and allowing the second DNA helix is pass through the first. Requires ATP
Chromatin
Complex of DNA and chromosomal proteins
What are the 5 major types of histones?
H1, H2A, H2B, H3, and H4
Nucleosome Structure
Core of histones (2 molecules of each type) around which DNA is wrapped, and linker DNA
Euchromatin
Decondensed and transcriptionally active
heterochromatin
Condensed and transcriptionally inactive
How does chromatin form?
DNA methylation occurs which tags a region of the genome for his tone modification that causes the formation of heterochromatin (by deacetlyting) The acetylation removes the positive charge and reduces the affinity between histones and DNA which increases transcription.
What is the central dogma of molecular biology?
DNA–>RNA–>Protein
What are the monomeric units that make up the DNA polymer?
Nitrogenous base, pentose sugar, and phosphoric acid group
Ribose
Hydroxyl group attached to the 2’ carbon
Deoxyribose
The hydroxyl group attached to the 2’ carbon in ribose is replaced by a hydrogen group
Nucleosides
Nitrogenous base and a ribose or deoxyribose sugar
Nucleotides
Nitrogenous base, sugar, and a phosphate group
Phosphodiester Bond
Bond between the 3’ OH group of the sugar and the 5’ phosphate on the nucleoside triphosphate
How many bonds are between C and G?
3
B-DNA
Basis of Watson and Crock model. Right hand helix
Z-DNA
Left hand helix, found in sequences where pyrimidines and purines alternate
A-DNA
Right hand sequence of dehydrated DNA, very compact
Primary Structure
Sequence of nucleotides (AGTACA)
Secondary Structure
3-D structure-double helix of DNA
Tertiary Structure
Supercoiling of secondary structure
Quarternary Structure
Interaction of nucleic acids with proteins (DNA wrapped around a histone)
mRNA
Single stranded, carries codon information for translation
tRNA
Folded stem loop system that carries amino acid to ribosome
rRNA
Linear, single stranded, folded molecule, helps form ribosome
snRNA
Small nuclear RNA that is involved in generation of mature mRNA transcripts and are an essential part of splicing
miRNA
Micro RNA is responsible for the regulation of gene expression and can either silence of express mRNAs
Negative Supercoiling
Promotes strand separation (good for DNA Replication) . Introduced behind the protein.
Positive Supercoiling
Unwanted side effect of negative super coiling and must be corrected so DNA can be separated. Introduced ahead of the protein.
What is the function of topoisomerase I?
Forms a single covalent bong with DNA, breaking phosphodiester bonds, allowing the DNA to rotate and relieve stress from supercoiling
What is the function of topoisomerase II?
Topoisomerase II (DNA grade in bacteria) is activated when two double helices cross over each other. It bonds to both ends of the strand, breaking the backbone, and allowing the second DNA helix is pass through the first. Requires ATP
Chromatin
Complex of DNA and chromosomal proteins
What are the 5 major types of histones?
H1, H2A, H2B, H3, and H4
Nucleosome Structure
Core of histones (2 molecules of each type) around which DNA is wrapped, and linker DNA
Euchromatin
Decondensed and transcriptionally active
heterochromatin
Condensed and transcriptionally inactive
How does chromatin form?
DNA methylation occurs which tags a region of the genome for his tone modification that causes the formation of heterochromatin (by deacetlyting) The acetylation removes the positive charge and reduces the affinity between histones and DNA which increases transcription.
DNA A Proteins
Binds to the origins of replication and breaks hydrogen bones between bases
DNA B
Helicase , opens and binds primase
Single copy genes
unique sequences in the genome that code for a proteins
Multigene Families
Genes with similar functions that have arisen by gene duplication
Classic gene families
Multicopy genes that show a high degree of homologous (HOX, globin, etc)
Gene super families
Not so closely related as classic gene families, but have similar function.
Extragenic DNA
Mostly transcriptionally inactive, might regulate gene expression
Tandem DNA
Tandem repeats of DNA sequences that are non coding and are inherited in a co-dominant fashion
SNP
Single nucleotide polymorphism where there is a single base pair change in individuals. Fairly common!
SSR
Simple Sequence repeat. Most simple of the repetitive sequences and most polymorphic. repeats of 2-4 base pairs.
VNTR
Variable and tandem repeats- longer than the SSR (5-100 bp) repeating many times
LINE
Long intersperses nuclear elements-make RNA and include genes that encode reverse transcriptase and integrates LINE into genome
SINES
Short interspersed nuclear elements. Short RNAs that were converted to DNA by reverse transcriptase that they stole from a LINE. Most common is the Alu sequence
Rare variants
Not usually found, but thought to contribute to human disease more than SNP.
Pseudogenes
Look like real genes, but don’t code for a product (gene that used to allow us to make vitamin C, but is now inactive)
When is the chromosome maximally condensed?
At metaphase (this is when karyotyping occurs)
Metacentric chromosome
Centromere in the middle
Submetacentric Chromosome
Centromere closer to the top (p arm shorter than q arm)
Acrocentric Chromosome
Centromere very close to the top and p arm contains little genetic information. Involved in robertsonion translocation.
Uniparental Disomy
When both the chromosomes are derived from the same parent
Lyonization
X-inactivation. One of the X chromosomes is condensed into the Barr body and is inactive. Random event-either X from mom or dad could be inactivated. regulated by X-inactivation center that has the XIST gene.
Asymmetric X inactivation
When more than 50% of the cells from either the father or mother is active
How does XIST work?
Produces an RNA that coats the X chromosome, causing it to condense into heterochromatin. Methylation of cytosine bases and histone deacteylation results in transcriptional repression.
What is the Huntington gene locus?
4p
In which direction is protein written?
N-terminus to C-terminus
What is the start codon?
AUG
How many reading frames are there per RNA?
3
What frame shift mutation does CF have?
F508
P site
Holds the tRNA that carries the growing polypeptide chain
A site
Holds the tRNA that carries the next amino acid to be added to the chain
E site
Exit site, where discharged tRNAs leave the ribosome
where on the tRNA do amino acids attach?
The 3’ end
What is the wobble baby hypothesis?
Base pairing is less strict for the third base, allowing tRNA to read more than one codon.
how is tRNA activated?
Amino acid is bound by amino acid adenylate, forming aminoacyl-tRNA. This requires the hydrolysis of pyrophosphate.
N-formylmethionine:
First amino acid that is recognized. By the ribosome allowing initiation. Usually two tRNAs, one which recognized fMET and other recognized AUG. Not formylated in eukaryotes.
In eukaryotes, where does the small ribosome bind? In prokaryotes?
Close to the 5’ cap (scans until it finds a start codon) and at the Shine Dalgarno sequence.
Chaperones
Help to regulate the number of folds in a newly synthesized protein.
Differences between prokaryotic and eukaryotic translation:
In eukaryotes: first MET is not formylate, monocistroni, start at first AUG (don’t internally pick), transcription and translation occur in different membranes.
Diphtheria toxin
Inactivation of EF-2 by ADP ribosylation
Streptomycin (aminoglycoside)
Binds to 30s and prevents assembly of ribosome
Tetracycline
Four ring structure that blocks elongation by reverting aminoacytRNA-access to A site
Erythromycin
Binds to the 50s subunit of the complete ribosome and blocks translocation
Chloramphenicol
Inhibits peptidyl transferase activity in prokaryotes and may inhibit mitochondrial translation
cycoheximide
Inhibits eukaryotic peptidyl transferase activity
Puromycin
Causes premature termination of translation in both prokaryotes and eukaryotes
EF-g
Prokaryotic protein, EF-2 in eukaryotes.
Zymogen Activation
Zymogen (pro enzyme) is an inactive enzyme precursor that can be activated by enzymatic cleavage of peptide bonds. Can lead to active apoptosis, blood coagulation, digestion of proteins.
Protein phosphorylation by a kinase
Phosphate is transferred from ATP to a protein on a SER/THR residue of a protein
Insulin Receptor
Tyrosine kinase that transfers a phosphate from ATP to a protein on a Tyr residue of a protein
O-linked glycosylation
Glycosylation on the OH group of the SER/THR. Often found as extra cellular proteins or as membrane bound proteins.
N-linked glycosylation
On the Asn residue. Can be high mannose or complex.
Lipid anchoring
Adding a farnesyl (15 carbon isoprenoid) group to the cysteine to anchor amino acid into the membrane. Anchors Ras to inner leaflet.
Totipotent
Give rise to all tissues in the body. Both embryonic and extra embryonic.
Pluripotent
Ability to develop into all cells and tissues
Multipotent
Develop into a small number of cell types
Unipotent
Develop into one cell type
Morula
Totipotent
Blastocyst
Inner cell mass that is pluripotent and gives rise to all derivative of the 3 primary germ layers
What are the three primary germ layers?
Ectoderm, endoderm, and mesoderm
Mesoderm
Gives rise to muscles and lining of organs
Endoderm
Gives rise to the epithelia
Ectoderm
Skin
Hematopoietic
RBCs and immune cells
Mesenchymal
Bone marrow stromal cells. Create bone cells, cartilage cells, fat cells, and other CT cells
Neural
Nerve and glial cells
Epithelial
Lining of the digestive tract
Skin
Basal layer of the epidermis, keratinocytes, hair follicles
Stem Cell Plasticity
Ability of adult stem cells to form specialized cell types of other tissues
Asymmetric Cell division
Mechanism to maintain the stem cell population while generating differentiated cells. 2 daughter cells and 2 distinct cell fates
Stem Cell Niche
Microenvironment that regulates the self-renewal and maintenance of stem cells
Extrinsic Signaling
External cues that control the proliferation of stem cells. Cell to cell interactions (Cadherins) and cell to EC matrix (integrins), and growth factors.
Intrinsic Mechanism
Preferential serration of molecules prior to cell division. Maintain one daughter cell as a stem cell and other daughter cell differentiates.
Transcription Factors
Proteins that work together to activate pathways needed for stem cell identity. Include Oct4, Sox2, and Nanog.
Epigenetic Modification of DNA
Chromatin structure of stem cells is very different compared to differentiated cells. More relaxed and ready for transcription.
Polycomb proteins
Family of proteins that function to modify chromatin structure. May function to silence genes associated with stem cells.
Progenitor Cell
Intermediate between stem cells and differentiated cells
SCNT
Somatic Cell Nuclear Transfer. Creating a cloned embryo with a donor nucleus. Can be reproductive or therapeutic.
Therapeutic Cloning
Used to make new embryonic stem cells which can generate an organ and have the same genetic markers as the patient.
Induced Pluripotent Stem cells
Adult stem cells that are reprogrammed into a pulripotent state. Requires vectors and can lead to tumors.
Cloudy Swelling
First sign of cell injury. Organelles swell and give off a cloudy appearance when stained.
Hydropoic Degeneration
Continued swelling of the organelles, vacuoles appear in the cytoplasm.
Steatosis
Fatty acid change in response to cell injury. The cytoplasm gains lipid dots. Frequently seen in the liver.
Atrophy
Decrease in cell size. Reduction in functional cell mass. Reversible. Caused by decreased functional demand or blood supply. Also caused by loss of stimulation and aging. Commonly affects the testis in elderly, skeletal muscle, and the brain.
Hypertrophy
Increase in cell size resulting in increased organ size. Reversible. No change in cell number. Caused by increased functional demand or hormone stimulation. Seen frequently in cardiac muscle, skeletal muscle, and uterus.
Hyperplasia
Increase in cell number. Reversible. Caused by increased function demand or hormone stimulation. Commonly affects the endometrium, prostrate gland, RBC s, glandular epithelium of the breast, and uterine enlargement (pregnancy).
Metaplasia
Change in differentiation (change in cell type). Reversible, seen in reprogrammed stem cells and other cells. It is an adaptive response to environmental stimuli (cigarette smoke, acid reflux). Typically affects the epithelium of the respiratory tract, cervix, and esophagus. Puts you at increased risk for dysphasia and neoplasia.
Involution
When the cell turns in on itself and shrinks.
Kidney Atrophy
Caused by decreased blood flow to kidney from the narrowing of the renal artery. Often due to atherosclerosis.
Dysplasia
Failure of differentiation and maturation. Persistently atypical cells. Caused by rapid multiplication of cells. Affects the cervix and skin. Increased risk of neoplasia.
Neoplasia
Cellular growth and proliferation in absence of external stimulus. Can be benign or malignant.
Cloudy Swelling
First sign of cell injury. Organelles swell and give off a cloudy appearance when stained.
Hydropoic Degeneration
Continued swelling of the organelles, vacuoles appear in the cytoplasm.
Steatosis
Fatty acid change in response to cell injury. The cytoplasm gains lipid dots. Frequently seen in the liver.
Atrophy
Decrease in cell size. Reduction in functional cell mass. Reversible. Caused by decreased functional demand or blood supply. Also caused by loss of stimulation and aging. Commonly affects the testis in elderly, skeletal muscle, and the brain.
Hypertrophy
Increase in cell size resulting in increased organ size. Reversible. No change in cell number. Caused by increased functional demand or hormone stimulation. Seen frequently in cardiac muscle, skeletal muscle, and uterus.
Hyperplasia
Increase in cell number. Reversible. Caused by increased function demand or hormone stimulation. Commonly affects the endometrium, prostrate gland, RBC s, glandular epithelium of the breast, and uterine enlargement (pregnancy).
Metaplasia
Change in differentiation (change in cell type). Reversible, seen in reprogrammed stem cells and other cells. It is an adaptive response to environmental stimuli (cigarette smoke, acid reflux). Typically affects the epithelium of the respiratory tract, cervix, and esophagus. Puts you at increased risk for dysphasia and neoplasia.
Involution
When the cell turns in on itself and shrinks.
Kidney Atrophy
Caused by decreased blood flow to kidney from the narrowing of the renal artery. Often due to atherosclerosis.
Dysplasia
Failure of differentiation and maturation. Persistently atypical cells. Caused by rapid multiplication of cells. Affects the cervix and skin. Increased risk of neoplasia.
Neoplasia
Cellular growth and proliferation in absence of external stimulus. Can be benign or malignant.
