Quiz 1 Flashcards
Histology
- Microscopic anatomy linked to functions – cell biology, physiology, genetics, biochemistry, etc.
2.Study of tissues of the body
Structure, Arrangement,
How structure and arrangement optimize functions specific to each organ
whole mounts
entire organism/structure is placed directly onto a microscope slide;
preserves structural relationships
squash preparations
where cells are intentionally squashed/crushed onto a slide
to reveal their contents; allows counting of cell numbers and individual cell details
smears
cells suspended in a fluid=
(blood, semen, cerebro-spinal fluid);individual cells scraped, brushed or aspirated
from a surface or from within an organ (exfoliative cytology).
“Pap test”
allows counting of cell numbers and individual cell detail
Sections
slices are cut from specimens, mounted on slides, and stained
preserves structural relationships
Axial vs Appendicular
Axial – head, vertebrae, ribs, sternum
Appendicular – everything else (arms, legs)
Planes and directions
Median, sagittal (parallel to it), transverse (axial), oblique, coronal (anterior separate posterior),medial (toward median), lateral (away from median), proximal, distal, anterior (ventral), posterior (dorsal) superior (cranial or rostral ), inferior (caudal), longitudinal (parallel to long axis), horizontal, vertical, peripheral, superficial, deep, external, internal, apical, basal, frontal, basilar
A-P (anterior – posterior) can also refer to superior/inferior direction depending on context
Thoracic skeletal elements
Manubrium, body, xiphoid process [ these 3 make up the sternum] ribs (true (1-7),false (8-10) floating(11-12)) costal cartilage, vertebral body, intervertebral discs
Shoulder Osteology
Clavicle, scapula, coracoid process, superior angle, inferior angle, lateral angle, scapular spine, infraspinous fossa, medial border, supraspinous fossa, acromion
pelvic osteology
Os Coxae (hip bone) – 3 bones, fuse to form the pelvis Intervertebral disc, pubis, ischium, ilium, pubic symphysis, sacrum (fused vertebrae), coccyx
Joint types
Synarthroses (immovable joints) ex. suture (skull only; fibrous tissue is continuous with periosteum) or gomphoses (teeth; ligament is periodontal ligament)
Diarthroses (freely movable; all synovial)
movement at joints has limits due to bones, muscles, ligaments, other tissues
Muscles
smooth, cardiac, skeletal
Connective tissue around muscles
Connective tissue surrounds fibers, bundles, muscles, muscle groups, neurovascular bundles
Connective tissue partitions the body – implications for muscle function, infections, surgery
Endomysium (surround individual fibers), perimysium (surrounds fiber bundles, or fasiculi), epimysium (surrounds entire muscle)
Superficial back muscles
trapezius, levator scapulae, rhomboid major, rhomboid minor, latissimus dorsi; together with serratus posterior these are NOT innervated by dorsal rami, are innervated by ventral rami (part of branchial plexus) except trapezius which is done by cranial nerve
Trapezius
Innervated by spinal accessory nerve; 3 different fiber angles (different movements); elevation, inward rotation of scapula, tilts head towards and rotates head away from unilateral contraction
Levator Scapulae
innervated by dorsal scapular nerve (C5), elevates scapula; unilateral contraction- tilts neck to same side
Rhomboid major/minor
innervated by dorsal scapular nerve (C5); retracts/ adducts scapula (closer to midline/central point)
Latissimus dorsi
innervated by thoracodorsal nerve (C6-8); adduction, medial rotation of shoulder
Deep Back muscles (paraspinal, intrinsic, epaxial)
All innervated by dorsal rami of spinal nerves;
Function: postural support, extension of spine/trunk/neck, unilateral contraction (bending and some rotation)
Splenius, erector spinae, transversospinalis, suboccipital groups
Splenius
superficial deep back muscles; splenius capitus, splenius cervicis
Erector spinae
Iliocostalis, longissimus, spinalis (I Love Sluts)
Transversospinalis
semispinalis, rotatores, multifidus
Suboccipital
Under semispinalis (part of transversospinalis group) rectus capitis posterior minor, rectus capitis posterior major,[ medial] obliquus capitis inferior, obliquus capitis superior [lateral]
suboccipital nerve (C1- dorsal ramus); bilateral (extends head/neck), unilateral (rotates head to same side), EXCEPT OCSM (tilts head to same side, rotates to opposite; cute dog tilting head)
Shoulder muscles
Innervated by brachial plexus; ex. deltoid (innervated by upper and lower subscapular nerve C5-6) subscapularis (inner surface), while these are outer surface (suprascapular nerve; C4-6): infraspinatus, supraspinatus
thorax, deep back muscles (segmental body plan make innervation easy)
Arms, shoulders, superficial back (not segmented)
Brachial plexus
(C5-T1) Ventral rami, Trunks (axons mix, no longer separated by level), divisions (no nerves emerge here), cords (2 anterior [lateral and medial] and 1 posterior)
Dorsal Scapular Nerve
C5; levator scapulae, rhomboid major, rhomboid minor
Long thoracic nerve
C5-7; serratus anterior
Subclavius nerve
C5-6; subclavius muscle
Suprascapularis nerve
C4-C6; supraspinatus, infraspinatus
Thoracodorsal Nerve
C6-8 innervates latissimus dorsi
Upper and Lower Subscapular Nerve
C5-6; innervates subscapularis, teres major
Epithelial Tissue
Aggregated Polyhedral cells that are strongly attached to one another, small amount of ECM; Protective lining, glandular secretions, and transport
Primary functions:
- Covering, lining, and protective surfaces (ex. epidermis)
- Absorption (ex. intestinal lining)
- Secretion (ex. Parenchymal cells of the gut) from inside to outside
formation of cell sheets that coat outer surface of body (GI) and line various organ surfaces, form glands and other secretory tissues and linings, undergo mitosis and is typically avascular (relies on the diffusion from blood vessels in adjacent CT) and is a POLAR tissue (apical pole that faces lumen/space and basal pole which faces CT)
Connective Tissue
All sorts of different cell types. Some fixed, some forever voyaging. Generally quite a bit of ECM. Functions: Support and protect body structures ex. tends to attach epithelial tissues etc. Ex. blood
Cells are generally separated by ECM, generally not linked together. It is generally holding some other tissue in place and not at a free surface (outside)
Consists of cells, ECM fibers (collagen), and ECM ground substance
Derived from mesoderm (primarily), contains multipotent mesenchymal progenitor cells
Function:
- Mechanical/protective support of other tissues. Often found as stroma in organs, surrounds blood vessels, lymphatics, and nerves
- Stores interstitial fluid, water, electrolytes
- involved in early repair of damaged organs, if repairs not complete, can lead to permanent scar formation/ fibrosis (big injury, pump collagen in a non ordered way)
- contains immune system cells and presents a physical barrier so provides defense and protection
Muscle
Contractile tissue. A muscle contains CT, but muscle tissue is distinct. Has a moderate amount of ECM
Nervous
Conducts nerve impulses. Very little ECM.
Relationship between Epithelial and CT
Epithelium lines various surfaces and generally anchored by underlying CT; tissues often joined by a basement membrane which is a thin sheet of ECM anchoring the epithelium to underlying CT. Both epithelium and CT contribute to it; Sometimes called the basal lamina (electron microscopy)/ structure seen by light microscopy is basement membrane
Basement Membrane
ECM sheet attaching epithelium to CT; Cells anchored to basement membrane via HEMIDESMOSOMES; 50-100 nm thick with 3 zones: lamina lucida (has hemidesmosomes, laminin, entactin, integrins), lamina densa (Collagen IV), lamina fibroreticularis (Col III)
Simple squamous
Lining blood/lymph vessels, kidney glomeruli, lung alveoli, or any surface that has a lot of diffusion happening
Simple cuboidal
Secretory cells lining glands and ducts, kidney tubules. Anywhere secretion of proteins is actively happening
Simple Columnar
Mucus secreting absorptive surfaces, notably much of the GI tract (stomach to anus), can be ciliated as in bronchi of lungs and uterine tubes
Pseudostratified ciliated columnar
Mucosal surfaces, where they secrete mucus. Ciliated to push mucus along, as in various sperm carrying ducts and ducts of large glands. Also lining the trachea and upper respiratory tract
stratisfied squamous
Keratinized: skin and attached gingiva
Non Keratinized: lining mucosa of mouth, esophagus, and vagina.
Anything that might encounter abrasive forces on a regular basis
Urothelium
Bladder lining. Stretchy and irregular
Stratisfied cuboidal
Somewhat rare. Ducts of large sweat glands, salivary glands, and mammary glands
Stratisfied columnar
Fairly rare; found in the male urethra and associated with salivary glands. Sometimes transitional between simply columar and stratisfied squamous. Looks a bit like cuboidal cells with columnar cells stacked atop
Microfilaments
Cytoskeletal component; made of actin, 6-8nm diameter, structural function, microvilli, filopodia, gives shape to the cells, forms tracks for myosin, giving contractibility
Intermediate filaments
Cytoskeletal component; different in various tissues (vimentin, cytokeratin); around 10nm diameter, anchors, structural, non contractile
Microtubules
Cytoskeletal component; made of tubulin, around 25nm diameter, monorail system (kinesins, motor protein complex), cilia and flagella (dynein)
Tight Junctions (Zonula Occludins)
Cell attachment type; homotypical interactions between transmembrane proteins (proteins that are identical and stick tightly together); very narrow gaps between cells, control movement of stuff between cells, maintains cell polarization, bind to ACTIN MICROFILAMENTS (inside of cell), claudins, occludins, JAM, roles in various cell signaling pathways
Cell to cell Adhesive Junctions (Zonula Adherins)
Cell attachment type; Hold cells together,cadherins (outside; Ca2+ dependent) and catinins (inside) complexes, Nectin-Afadin complexes, vinculin and actinin attachments to ACTIN FILAMENTS, gaps of 20 nm so small stuff can get through
Focal Adhesion Junction
Cell attachments type; hold cells to ECM, similar to cell to cell adhesion, integrins replace cadherins as transmembrane component and they interact with many ECM proteins ex. collagen, fibronectin; integrin receptors (role in cell signaling); vinculin, actinin, and talin attachments to ACTIN FILAMENTS
Desmosomes
Cell attachment type; more cell to cell adhesion, cadherins (outsides) are called desmogleins and desmocollin; catinins (inside) are called desmoplakin, plakoglobin, and plakophilin; form lines externally, and plaques internally visible as dark bands (electron dense); attach to INTERMEDIATE FILAMENTS; Heterotypical interaction of desmoglein and desmocollin; gaps of 25 nm, help resist shearing forces- flat force across the surface
Hemidesmosomes
Cell attachment type; more cell- matrix adhesion, similar appearance to desmosomes (intracellular plaque visible), attach to INTERMEDIATE FILAMENTS; integrin transmembrane protein, tightly attach to basal lamina by integrin-laminin and collagen XVII; resist shear
Gap Junctions
Cell attachment type; cell to cell aqueous pores; 6x connexins= 1x connexon; forms a 2nm pore, 2-3 nms between cells; ions and small water soluble molecules may pass; nucleic acids, sugars, and proteins are too large; propagation of electrical signal
Cell attachments
All types of cell attachments function together to provide both cell to cell adhesion and anchoring, forming tissues;
Junctional Complex (tight junctions, zonula adherins, desmosomes, and gap junctions)
Terminal bar (group of junctional complexes which attach cells on their lateral surfaces. appear as a sort of band under a light microscope
Epithelial turnover and maintenance
Epithelial cells turnover, from several days to months, and are replaced by the divisions of progenitor cells (adult stem cells), which are pluripotent
Ex. small intestine; in epithelia, mitosis occurs on basal lamina, so stem cells and transit amplifying cells are normally in basal layer; stem cells in “niche” division rates and developmental choices are influenced by cytokines
Epithelial Function: Protection
Provides a physical barrier due to junctions; augmented by various secretions: mucus + cilia to trap and move things along, defensins in some cases ; provides a zone for antigen detection;
Ex. of primary protective epithelia: skin, upper respiratory tract, oral mucosa, gut, urinary system
Epithelial Function: Transport
Epithelium controls the passage of selective stuff; active or passive transport, can secrete (mucus or fluid) and can absorb (GI tract); blood gases passively diffuse across an epithelial barrier, most interactions with the outside world occur across an epithelial barrier
CT Cell Types
Permanent: Fibroblasts, adipocytes, macrophages, mast cells
Transient: Plasma cells, lymphocytes, neutrophils, eosinophils
Fibroblasts
Main cell of CT, highly motile, involved in ECM production and therefore tissue repair and renew; rarely have cell to cell connections (exception: perio ligaments); often have cytoskeletal (actin) connections from integrin to fibronectin in the ECM (fibronexus); many subtypes in many different tissues(pulp, PDL, oral mucosa); fibroblasts age- slower healing with age; incredible diversity of secretory products
Collagen
triple helical structure, most abundant protein in the body (28 types), major synthetic product of cells derived from the mesenchyme; rich in proline and lysine (H bond allows triple helical assembly), fibrillar collagen and many other types, dentine (mostly type I, some III) pulp (mixture of type I and III) cartilage (Type II) basement membrane ( Type IV chicken wire meshwork)
5 ‘microfibrils’ with a 1/4 stagger (overlap) align in a parallel fashion; banded structure of fibrils, stagger in microfibrils; bone/dentin (mineral deposition in gap regions) ; many diseases result from malformation of collagen (OI, epidermolysis bullosa) s
Scurvy (vitamin C deficiency; prolyhydroxylase and lysyl hydroxylase- assembly of collagen much less stable)
Elastin
Fibroblast product, assembled into sheets or fibers, glycoproteins fibrillin 1 and 2 (and others) form a microfibril scaffold onto which elastin fibers accumulate; final result is a fiber with an elastin core, supported by a glycoprotein scaffold
Marfan’s syndrome- fibrillin 1 mutation
Adipocytes and adipose tissue
Adipocytes are single lipid droplet with thin rim of cytoplasm; flattened nucleus, each adipocyte is surrounded by basal lamina
Adipose tissue function: store lipid (energy), insulate, cushion, make hormones
CT ground substance
made up of all sorts of things, mainly proteoglycans and glycoproteins; it is the non fibrillar stuff that makes up CT ECM (fills in the left spaces by the fibrils), gel like (highly hydrated), sequesters fluid, gives compressive strength to tissue (cartilage), keeps what should be squidgy, squidgy
Proteoglycan
main component of ground substance made by fibroblasts; they are protein core with glycosaminoglycan chains (GAGs- aggregation and fluid sequestration ex. hyaluronic acid, chondroitin sulfate, keratin sulfate etc.) [carb with protein backbone that will sequester water and give it is squidginess] Ex. versican, perlecan, syndecan, and many others; have relatively strong negative charge and are hydrophilic; Non aggregating proteoglycans (many; perlecan, found in basal laminae, syndecan); CAN SERVE TO SEQUESTER GROWTH FACTORS IN ECM AND CAN HELP ACTIVATE GF RECEPTORS
Glycoprotein
Proteins with carbohydrate side chains attached; found everywhere but also in ground substance; huge category but notable examples (fibronectin (cell migration/wound healing), tenascin (directs migration), thrombospondin (attachment, migration, collagen alignment)
Difference between glycoproteins and proteoglycans (proteoglycans are specialized glycoproteins and have a larger carbohydrate component than protein)
Growth factors
Many; these can be secreted by a wide array of cells for immediate use (development) or can be sequestered into the ECM for later use (repair)
Matrix digestion
Extracellular vs Intracellular; MMPs (matrix metallo proteases) are very significant in operative dentistry; kept tightly controlled in ECM because it can break it down; implications for tissue remodeling and disease states
Loose CT
Most abundant type of CT; more cells and ground substance; fewer fibers, most cell types are present; location (underlies epithelia, forms stroma, fills spaces between tissues and organs, sheathes lymphatic and blood vessels); provides support and form, but not as much structure as dense CT
Dense Irregular CT
more fibers, fewer cells, little ground substance; fibers arranged randomly, location (deeper dermis, organ capsules, submucosa of intestine) provide multidirectional structure
Dense regular CT
Fibers arranged in same direction; few cells, mostly fibroblasts; location: tendons and ligaments, provides directional structure
Skin
Epidermis (keratinized stratisfied squamous)
Dermis (loose CT) –> dense irregular CT
Lipids and Fatty Acids Function **
store energy (Triglycerides especially), form membranes, carry info and signal (inflammation), perform diverse additional services ( vitamins, enzyme cofactors, colorants [absorb light at different wavelengths]) surfactants (like a detergent)
Fatty Acids **
carboxylic acid with a long hydrocarbon chain
ex. saturated, unsaturated (cis vs trans), polyunsaturated
Fatty acid nomenclature
18:1 (Δ9) cis- 9 octadecenoic acid; 18 C, 1 double bond at 9 , cis, 18 long chain
omega 3 FA- omega is carbon at tail end so omega 3 has a double bond off the 3rd C
Fatty acid physical characteristics **
A mixture of saturated and unsaturated FA makes a membrane more mobile than just saturated FA; as the number of C increases, melting point increases; saturated FA have a higher melting point (from solid –> liquid)
lipids **
one or more FA connected to a linker molecule
Common linkers: glycerol, sphingosine, glycerophosphate
Ex. triglycerides
Storage Lipids (Triacylglycerides)**
Contain a glycerol linker with 3 FA; saturated, unsaturated, polyunsaturated; nonpolar, stable and relatively inert in aqueous solutions, not found in biological membranes, energy dense (have highly reduced long chains of carbon), primary storage molecules, primary source of energy for many organ systems
Lipids are key metabolic constituents **
movement of energy through body; Organism metabolism (anabolism/catabolism[break down and release energy to do work/make more complex structures])
Dietary Sources of lipids and FA
Dietary sources form triglycerides (fats, carbs, proteins)
Albumin (protein) transfers bloodstream free FA
Lipoproteins transfer triglycerides from adipose tissue to other cells
Dietary sources are ingested–> gallbladder–> bile emulsifies dietary fats in small intestine, forming mixed micelles–> interact with ApoC-11–> form chylomicron (lipoprotein)–> go into vasculature and lipoprotein lipase breaks it and releases lipids and deliver lipids to different cells and storage
Lipids form membranes
Form micelles (individual lipid is wedge shaped; one tail) , vesicles, bilayer (individual lipid is cylindrical; 2 tails) because entropy is increased; allows water to be more disordered by causing lipid to be ordered
Plasma membrane lipids and FA
3 major lipids: phospholipids, sphingolipids, and glycolipids; sterols (FA, cholestrol; sit in bilayer and change fluidity in membrane)
Membrane Lipids: Phospholipids **
phosphate group, glycerol or sphingosine linker, FA, major constituent of most animal plasma membranes
Membrane Lipids: Sphingolipids **
one shingosine, one FA, phosphate, glucose or polysaccharide head group components; membrane components, direct signaling activity
Membrane Lipids: Glycolipids **
Anchor proteins to membrane, involved in cellular identification, tied to many diseases ex. lipopolysaccharides to tell if its a bacteria; Ceramide, sphingosine, FA
Membrane FA: Sterols **
major membrane components, increases membrane rigidity, reduces membrane permeability, lipid raft constituent, needed for endocytosis ex. Cholestrol
Lipids carry info and signal
Hormones, cell surface markers, inflammatory mediators (drive it and also resolution of it)
Lipid Signaling Drives and Resolves Inflammation **
Injury and infection drive the release of inflammatory lipids (vasodilators, increase temp of region, increase rate of metabolism, sensitize nerve cells that innervate these periphery cells)
Ex. prostaglandins, thromboxanes, and leukotrienes
The enzymes cyclooxygenase 1 and 2 (COX 1/2) produce prostaglandins and thromboxanes from arachidonic acid
Non-steroidal anti- inflammatory drugs (NSAIDs) block COX 1/2 function (Aspirin, Ibuprofen, Naproxen)
Lipids and FA perform diverse functions
Cell surface markers (blood type, cellular identity), antibiotics, vitamins and cofactors (compulsory, biochemically relevant)
Essential FA
Essential- the human body requires but can’t produce the FA so must be obtained through the diet ex. Linoleic acid and alpha linolenic acid
Nucleotide**
A molecule with a pentose (5 C ring), phosphate (1-3; if none= nucleoside), purine or pyrimidine base; foundational molecule of all life
Nucleic acid**
Nucleotides connected by phosphodiester bonds;
Importance of Nucleotides and Nucleic acids **
Information transfer (DNA [genetic], RNA [proteomic])
Energy transfer (ATP, GTP, NAD/NADH)
Signal transduction (cAMP, cGMP)
Nucleic acids regulate cellular function **
DNA–>RNA–> Protein
Replication, Transcription, Translation
plus RNA replication and reverse transcription
basis for the cell hypothesis- cell is a recurrent organism; has blueprint of its function
Purine**
A (Adenine) G (Guanine)
2 rings
Pyrimidines**
C (Cytosine) U (uracil) T (thymine)
1 ring
DNA vs RNA **
DNA (Deoxyribonucleotide polymer)
RNA (ribonucleotide polymer)
Key differences: 2’ ribonucleotide oxidation, reactivity, Thymidine vs Uridine, DNA confined to nucleus, RNA found throughout the cell
Nucleic Acids form complex structures
Primary (nucleic acid chain), secondary (anti- parallel chains that bind to one another- H bond between bases), tertiary ( 3D right hand alpha helix)
quaternary (DNA bound on histone–> nucleosome–> chromosome)
DNA Primary Structure
Phosphodiester bonds form nucleic acids
RNA is less stable (2’ OH can attack chain and break it)
Read DNA 5’–> 3’
DNA Secondary Structure
Base H bonding forms strand (purine to pyrimidine)
Adenine- Thymine (Uracil)
Guanine to Cytosine
Antiparallel; stable in aqueous environments
Base bonding is not uniform- palindrome (sequence if separates from adjacent strand, can bind to itself creating cruciform structures or hairpins - form physical structures in which different proteins can target and bind to
DNA Tertiary Structure
Strands form double helix; taking sheets of DNA, put in aqueous solution and forms a rightward helix
Different compressions: A form (more compressed), B form (regular), Z form (least compressed)
DNA Quaternary Structure
Strands and Proteins create complex structures;
DNA–> Nucleosome (DNA wraps around histones)–> chromosome (copied, pulled apart for translation and replication)
RNA is functionally Diverse
- Messenger RNA (mRNA)- DNA transcript that encodes proteins for production
- Transfer RNA (tRNA)- RNA adapter molecule tethered to amino aicds that interact with mRNA and form polypeptide chains
- Ribosomal RNA (rRNA)- RNA that forms the structural and functional backbone of ribosomes
Regulatory RNAs (aRNA, shRNA, siRNA)- a large class of RNA that regulates translation, signal transduction, and prevent infection by viruses
RNA Primary Structure
Single stranded (mostly), formed from DNA transcription by RNA polymerase, mirror of the DNA template sequence; DNA is read 3–> 5 (template) and made 5–>3 (identical to nontemplate)
Nucleotides are energy substrates and coenzymes
Electron rich, phosphate groups high in free energy, phosphate hydrolysis moves electrons to perform work, ATP is the primary euk energy currency; ex. Coenzyme A –> Acetyl CoA; NAD+
Nucleotides are signaling molecules
(cyclic) cAMP; cGMP,
Electronegativity
measure of the tendency of an atom to attract a bonding pair of electrons
F is the most electronegative element and Cs and Fr are the least;
Interatomic bonding
Ionic (metallic with non metallic; NaCl) transfer of electrons (cation-anion) STRONGEST
Molecular or Covalent (non-metals, SO2, H20, C2H4O2) sharing of electrons
Atomic or Metallic (metals Cu2) electrons surrounding the element (cation) WEAKEST
Intermolecular Interactions
Ion dipole, H bond, dipole- dipole, ion-induced dipole, dipole-induced dipole, dispersion (weakest)
Van der Waals Forces: random variations in the positions of electrons around one nucleus may create a transient electric dipole, which induces a transient opposite electric dipole in the nearby atom
Noncovalent (weak) interactions among biomolecules in aqueous solvent
H bonds (between neutral groups or peptide bonds), Ionic interactions (attraction/ repulsion), hydrophobic interactions, Van der Waals interactions (any 2 atoms in close proximity)
between OH and F, N, O bonded to H
Structure of a water molecule
Repulsion of H but O is attracting electrons forming a partial neg. and pos.; water molecules can combine with up to 4 other molecules
Water has a high specific heat (Amount of heat required to raise the temperature of 1 gr of substance by 1 degree Celsius) because of the H bonds
H bonding in ice
In ice a single molecule of water binds to 4 molecules of water to yield a regular lattice structure while in liquid only 3.4; As water is cooled down, however, the molecules have less energy and hydrogen bonding takes over. The molecules form an ordered crystal through hydrogen bonding that spaces the molecules farther apart than when they were in a liquid. This makes ice less dense than water allowing it to float.
H bonds in biological systems
Between the OH of an alcohol and water; between the carbonyl group of a ketone and water, between peptide groups in polypeptides, between complementary bases of DNA
Directionality of H bonds
strong H bond when bonded molecules are oriented to maximize electrostatic interaction (straight line)
All proteins can perform their functions better if they have a certain direction
Water as a solvent
Entropy=ΔS=(degree of molecular disorder)
Enthalpy= ΔH
free energy= ΔG = ΔH- TΔS (where ΔG is negative, ΔH has a small positive value and TΔS is positive) spontaneous (lower the free energy of a system) ex. water interacts electrostatically with CHARGED solutes
Amphipathic compounds in aqueous solutions
highly ordered water molecules
ΔG = ΔH- TΔS (where ΔG and ΔH are positive and TΔS is negative)non- spontaneous
ex. water interacts unfavorably with non polar compounds ; interfere with the H bonding among water molecules [decrease in entropy]
ex. lipids in water (soaps work by emulsifies the grease (lipids) binds to internal part of micelles and they transport it) ; ex. drug delivery; liposome, lipid bilayer; all minimize the number of ordered water molecules required to surround hydrophobic portion of the solute molecules
Release of ordered water favors formation of enzyme substrate complex
Ordered water interacting with S and E–> disordered water displaced by E-S interaction (stabilized by H bonding, ionic, and hydrophobic interactions)
Solutes affect colligative properties of a solution
Adding salt- boiling point elevation;
Pressure boiling point melting point and osmotic pressure, water as a conductor; The presence of a solute lowers the freezing point of a solution relative to that of the pure solvent
Extracellular osmolarity on water movement
Aquaporins
Isotonic- no net water movement
Hypertonic- water moves out of cell and cell shrinks
Hypotonic-water moves in creating outward pressure, cell swells and may eventually burst
Proton Hopping
water can be an acid or base; hydronium
Pure water is slightly ionized
not likely to dissociate
Keq= [products]/[reactants]
Kw= 1E-14
pH Scale
pH= -log [H] concentration= E^-# gives you a pH
Acidic-7; strong acids completely dissociate in water while weak acids only partially do
Henderson Hasselback
weak acids
pH= pKa+ log [A-]/[HA]
Ka is the equilibrium of dissociation constant or ionization constant
pKa is analogous to pH the stronger the tendency to lose its proton the stronger is the acid and the lower PkA
Conjugated bases
consist of a proton donor and a proton acceptor
ex. carbonic acid/ bicarbonate is the most important physiological buffer in body (ex. pH of saliva)
HCO3- (bicarbonate) H+–> H2CO3 (carbonic acid)–> CO2(d) (aqueous phase in blood in capillaries)–> Co2(g) (gas phase in lung air space)
The titration curve of acetic acid
pka= pH when acid and base have equal concentrations
buffer- maintains pH
ex. acetic acid (CH3COOH); Acetate (CH3COO-)
pH of ammonium is higher than that of acetic acid but can still act as an acid
optimal pH in enzymes
pH is critical for digestion, etc. each enzyme we have has an optimal pH (where they can optimally function)
Saliva
Salivary flow rate, buffering capacity, pH, electrolytes, organic components, proteins
flow rate and buffer capacity are clinically useful diagnostic indicators; no evidence that other biological characteristics of saliva are useful in predicting an increased risk of caries
pH of body is controlled by 3 systems
- The chemical acid-base buffering by the body fluids that immediately combine with acids or base to prevent excessive changes in pH ex. buffers in blood, urine, etc.
- The respiratory center which regulates removal of volatile CO2 as a gas in the expired air from the plasma and therefore also regulates bicarbonate from the body fluids via the pulmonary circulation. (occurs in min)
- The kidneys which can excrete either acid or alkaline urine, thereby adjusting the pH of the blood. This response takes place over hours or even days, but represent a more powerful regulatory system.
Metabolic alkalosis
Abnormal loss of acid (as in vomiting gastric HCl) or addition of a weak base can lead to this. Increases pH above 7.4
Metabolic acidosis
abnormal removal of HCO3- or another alkali or addition of acids other than CO2 or H2CO3 (renal failure) can lead to this. decrease pH below 7.4
Since the pH of a Co2/ HCO3- solution depends on the ratio of these 2, and becuase lungs control CO2, but kidney controls HCO3, the overall description of this= pH= K+ kidney/lung
Respiratory acidosis
the inability of the lungs to eliminate CO2 efficiently so equilibrium shifts toward increased H+ and HCO3= and pH decreases
Normally, 1.2 M/L of CO2 is dissolved in plasma, which is a partial pressure or pCO2 of 40 mmHg.
Respiratory alkalosis
Excessive loss of CO2 through ventilation driving the equilibrium to the left, away from H+ and increasing H+ and increasing pH
Normally, 1.2 M/L of CO2 is dissolved in plasma, which is a partial pressure or pCO2 of 40 mmHg.
Modern Cell Theory
- Cells are the most fundamental unit of life
- All living organisms are composed of 1 or more cells
- Cells give rise to organ systems that coordinate function in a complex organism
- All cells within a given species have the same general structure and chemical composition
- Cells are formed by the division of pre-existing cells
- Hereditary info is encoded by DNA and is passed along (or recombined) as cells divide
- Metabolism (energy processing; anabolism and catabolism) occurs within cells
Domains of life
Bacteria, Archae, Eurkarya
Use to be 5 kingdoms: animalia, plantae, protista, fungi, bacteria and later archae
The constant transition of energy maintains life
2 real sources of energy on earth: light [phototrophs] and chemical [chemotrophs] (we depend on chemical)
Proks vs Euk
Proks: 1-5µm scale, cell wall,no membrane bound organelles, cytoplasmic DNA, No cytoskeleton, 70S ribosome, replicate through binary fission, genetic diversity via mutation
Euks: 10-500µm, no cell wall, membrane bound organelles, nuclear DNA, cytoskeleton, 80S ribosome, replicate through mitosis, genetic diversity via meiosis/recombination
Both have plasma membrane
Prok cells
gram positive (large peptidoglycan layer) and negative (LPS, sugar that sits on outside of cells targeted by our immune system) are different in their membranes; treated in different ways
Cell envelope differs, ribosome is smaller, nucleoid has one or several long circular DNA molecules, pili provide points of adhesion to surface of other cells, flagella propel cell through its surroundings
Euk cell components **
Peroxisome (catabolism of lipids and fatty acids), cytoskeleton (structure, actin, IF, microtubules), lysosome (breaks down membrane associated organelles, proteins, fats), transport vesicle, golgi complex (structure that organizes movement of materials in membrane or material to be released or going to other organelles), smooth ER (lipid synthesis), nucleus (double membrane attachment to ER, nuclear membrane is continuous with it), nucleolus (make ribosome parts), rough ER (ribosomes embedded make proteins in cytoplasm), mitochondria (powerhouse of the cell), plasma membrane, nuclear membrane (outer and inner)
Membrane segregate environments and function
Segregation is critical for biochemical reactions; can not have concentration gradients without it
Endosynic pathway
The plasma membrane- boundary, interface, and information regulator
Fluid mosaic model (plasma membrane components move fluidly within the lipid bilayer)
Dynamic interface, heterogenous (different from one side to another), discrete domains (lipid rafts)
Too fluid; loss of barrier function
too rigid: restricted cell shape and transport capacity
Lipid Rafts
Discrete plasma membrane domains; cholesterol and sphingolipid rich, limited fluidity, regulate signal transduction and endocytosis
Endocytosis- Internalizing the external environment **
Internalization of the plasma membrane;
Phagocytosis, Macropinocytosis, Clathrin dependent, Caveolin dependent, Clathrin and caveolin independent
Functions: remodel the plasma membrane, alter the extracellular environments (ex. macrophages), provide necessary nutrients, regulate signal transduction, bring things in
occurs in all membrane domains
Clathrin Mediated Endocytosis
Need dyamin to be present for this to occur
Recruitment of AP2 to attach to transmembrane proteins with ligand bound–> allows clathrin to interact–> dyamin fuses membrane–> clathrin coated vesicle into cell
Lattice- cause invagination of plasma membrane as lattice form
The Endocytic pathway sorts internalized vesicles **
Vesicular fusion and excision, transport can occur between every compartment, Rab GTPase proteins critical; tells it which path to take (drives formation/fusion of vesicles), pH decreases along pathway; dissociation of binding of proteins together
Golgi Network
Organizing import and export (from ER to outer)
cis–> trans side psorting[
Cytoskeleton
Morphology (cellular form and shape), structure (backbone) and transport (movement of intracellular cargo)
Microfilaments (Actin- monomeric), microtubules (tubulin- dimer), Intermediate filaments (vary)
Molecular motors
Transporting intracellular content along the cytoskeleton; directed process
vesicles tethered to Dynein or Kinesins
ex. Dynein (retrograde movement- toward nucleus)
ex. Kinesin (anterograde movement- away from nucleus to outside)
Mitochondria
Cellular energy production; multifolded cisternae, inner membrane forms matrix, mitochondria is all throughout cell, glycolysis (cytoplasm) Krebs cycle (in matrix of mitochondria) and ETC (intermembrane space; formation of ATP)
Nucleus
Director of Cellular function and hereditary transmission; where DNA resides, relaxed/spread out most of time but condenses toward nucleolus sometimes; accessible to transcription factors leads to the transcription for the production of RNA (template for protein production)
Transcription**
DNA–> RNA; RNA polymerase reads 3–> 5 and RNA is produced 5–>3; RNA actively exported through nuclear pore complexes; requires ATP
Ribosomes
80S; Polypeptide Chain production from mRNA; codons encode for specific amino acids–> put together in a chain; complex made of rRNA (structural role), appropriate tRNA (associated with codon of mRNA) will be recruited, bind, and peptides bind to each other and form polypeptide chain
Translation
(from nucleus–> rER–>) RNA–> protein [proteins associated with membrane [bound polyribosome] or vesicular space [free in cytosol–> free polyribosome] that can be released to exterior]
(rER–> cis golgi–> trans–> lysosome, transport vesicle or secretory granule)
Activation of aa –>Initiation–> Elongation–> termination–> protein folding
Cell Cycle**
INTERPHASE
G0= cell cycle arrest (no active division, chromatin dispersed throughout the nucleus)
G1 phase=Gap phase 1 (cellular contents are duplicated, chromosome not)
S= synthesis (chromosomal material duplicated)
G2 phase= Gap phase 2 (chromosomes cohere and proper duplication checked)
MITOSIS (cell division- replication of genetic material)
PMAT= prophase, metaphase, anaphase, telophase
Euk cells divide by mitosis and meiosis **
Mitosis: Interphase–> PMAT–> cytokinesis (diploid cells with 46 chromosomes)
Meiosis: Interphase –> meiosis 1 (PMAT 1–> cytokinesis)–> meiosis 2 (PMAT 2–> cytokinesis) (haploid cells with 23 chromosomes ex. gametes)
