Feralis Bio Flashcards
Atom
made up of neutrons, electrons, and protons
Molecules
group of 2 or more atoms held together by a chemical bond
chemical bonds
due to electron interactions
Electronegativity
the ability of an atom to attract electrons
Ionic Bonds
transfer of electrons from one atom to another (different electronegativities)
Covalent Bonds
electrons are shared between atoms (similar electronegativity)
-can be single, double, or triple bonds
Nonpolar covalent bonds
equal sharing of electrons
-identical electronegativity
Polar Cavalent bonds
unequal sharing of electrons
-different electronegativity and formation of a dipole
Hydrogen bonds
weak bond between molecules with a hydrogen attached to a highly electronegative atom and attracted to a negative charge on another molecule (has to be N, O , or F)
Properties of water
- excellent solvent: dipoles of H2O break up charged ionic molecules
- High Heat capacity: the temp of large water body are very stable in response to temperature changes of surrounding fair; must add large amount of energy to warm up water. High heat of vaporization as well
- ICE FLOATS: water expands as it freezes, becomes less dense the its liquid form (H-bonds become rigid and form a crystal that keeps molecules separated)
- COHESION/SURFACE TENSION: attraction between like substance due to H-bonds: the strong cohesion between molecules produces a high surface tension
- ADHESION: attraction of UNLIKE substances (wet finger and flip pages); capillary action of liquid to flow without external forces (against gravity)
Functional Group
a particular cluster of atoms
-give molecules unique properties
Hydroxyl
properties
(-OH)
- polar
- hydrophilic
Carboxyl properties
- COOH
- polar
- hydrophilic
- weak acid
Amino properties
NH2
- polar
- hydrophilic
- weak base
Phosphate properties
PO3
- polar
- hydrophilic
- acid
Carbonyl properties
(C=O)
- polar and hydrophobic
- aldehyde
- ketone
Methyl
CH3
- nonpolar
- hydrophobic
Monosaccharide
-Type of Carbohydrate
-single sugar molecule (ex: glucose and fructose)
-alpha or beta based on position of H and OH on first carbon
(down=alpha, up=beta)
Disaccharide
-type of carbohydrate
-two sugar molecules joined by a glycosidic linkage (joined by dehydration)
-Ex: Sucrose (glucose + fructose)
or Lactose (glucose + galactose) + Maltose (glucose + glucose)
Polysaccharide
- type of carbohydrate
- series of connected monosaccharides
- polymer
- bond via dehydration syntehsis
- breakdown via hydrolysis
Starch
a polymer of alpha-glucose molecules
-stores energy in plant cells
Glycogen
- a polymer of alpha-glucose molecules
- store energy in animal cells
- differ in polymer branching
Cellulose
- a polymer of Beta-glucose
- structural molecules for walls of plant cells and wood
Chitin
- polymer similar to cellulose, but each Beta glucose has a nitrogen-containing group attached to ring
- structural molecule in fungal cell walls (also exoskeleton of insects etc.)
Lipids
- hydrophobic molecules
- functions: insulation, energy storage, structural (cholesterol and phospholipids in membrane), endocrine
Triglycerides
- type of lipid
- three fatty acid chains attach to a glycerol backbone
Saturated Triglyceride
no double bonds
- bad for health
- saturated= straight chain= stack densely and form fat plaque
Unsaturated Triglyceride
double bonds
- better for health
- unsaturated=double bonds cause branching= stack less dense
Phospholipid
- type of lipid
- two fatty acids and a phosphate group (+R) attached to glycerol backbone
- AMPHIPATHIC
Amphipathic
both hydrophobic and hydrophilic properties
Steroids
three 6 membered rings and one 5 membered ring
-hormones and cholesterol(membrane component)
Wax
- lipid derivative
- esters of fatty acids and monohydroxylic alcohols
- use as protective coating or exoskeleton
Carotenoids
- lipid derivative
- fatty acid carbon chains with conjugated double bonds and six membered C-rings at each end
- pigments which produce colors in plants and animals– carotenes and xanthophylls (subgroups)
Porphyrins
- lipid derivatives
- tetrapyrroles
- 4 joined pyrrole rings
- often complex with metal
Adipocytes
- specialized fat cells
- white fat cells contain a large lipid droplet composed primarily of triglycerides with a small layer of cytoplasm around it
- Brown fat cells have considerable cytoplasm, lipid droplets scattered throughout, and lost of mitochondria
Glycolipids
-are like phospohlipids but with carb group instead of phosphorus group.
How are lipids transported in the blood?
lipids are insoluble thus they are transported via lipoproteins (lipid core surrounded by phospholipids and apolipoproteins)
Storage Protein
- casein in milk
- ovalbumin in egg whites
- zein in corn seeds
Transport Proteins
Hemoglobin carries oxygen
cytochromes carry electrons
Enzymes
- amylase catalyzes the reaction that breaks the alpha-glycosidic bonds in starch
- catalyzes a reaction in both forward and reverse directions based on substrate
- -efficiency is determined by temp and pH
- cannot change spontaneity of a reaction
- ALWAYS CONSIDERED TO BE PROTEINS, but sometimes RNA can act as an enzyme Ribozyme
Cofactor
nonprotein molecules that assist in enzymes.
- can be organic (called coenzymes ex: vitamin) or inorganic (metal ions Fe2+ and Mg2+)
- if cofactor strongly covalently bonds to enzymes its called a prosthetic group
Globular Proteins
- somewhat water soluble
- many functions: enzymes, hormones, inter and intracellular storage and transport, osmotic regulation, immune response etc.
- mostly dominated by tertiary structure
Fibrous/structural proteins
not water soluble
- made from long polymers
- maintain and add strength to cellular and matrix structure
- mostly dominated by secondary structure
Membrane Proteins
membrane pumps/channels/ receptors
Protein Denaturation
The secondary and tertiary structure of the protein is basically removed, but not necessarily means that the protein is broken down into individual amino acids
-usually irreversible
nucleoside
sugar + Base
Nucleotide
nitrogen base, five carbon sugar deoxyribose, phosphate group
Purines
- 2 rings
- adenine and guanine
- 2 Hydrogen bonds
Pyrimidines
- 1 ring
- Thymine, cytosine
- 3 hydrogen bonds
Cell doctrine/theory
- all living organisms are composed of one or more cells
- the cell is the basic unit of structure, function, and organization in all organisms
- all cells come from preexisting, living cells
- cells carry hereditary information in the form of DNA
RNA world hypothesis
proposes that self-replicating ribonucleic acid (RNA) molecule were precursors to current life (based on deoxyribonucleic acid (DNA), RNA and proteins).
- RNA stores genetic information like DNA and catalyzes chemical reactions like an enzyme protein
- may have played a major step in the evolution of cellular life
- RNA is unstable compared to DNA, so more likely to participate in chemical reactions (due to its extra hydroxyl group)
Central Dogma of Genetics
biological information cannot be transferred back from protein to either protein or nucleic acid
DNA-> RNA-> Proteins
Stereomicroscope
visible light for surface of sample
-can look at living samples, but low resolution versus compound light microscope
Compound Microscope
- visible light for thin section of sample
- can look at SOME icing samples (single cell layer)
- may require staining for good visibility
Phase contrast
- uses light phases and contrast
- allows for detailed observations of living organisms (including internal structures) if thin
- Good resolution/contrast, but not good for thick samples and produces “halo effect” around perimeter of samples
Confocal Laser scanning and fluorescense
- can look at thin slices while keeping sample intact.
- can look at specific parts of the cell via fluorescent tagging
- can look at living cells, but only fluorescently tagged parts
- Fluorescence can cause artifacts
- -used to observe chromosomes during mitosis
**confocal laser scanning microscope can be w/out fluorescence as well. Uses laser light to scan dyed specimen, then displays the image digitally
Scanning Electron Microscope
- looks at the surface of (3D) objects with high resolution
- can’t use on living
- preparation is extensive (sample needs to be dried and coated)
- costly
CryoSEM
Like scanning electron microscope (SEM) but no dehydration/drying so you can look at samples in more “natural” form
- can’t use on living
- samples frozen for prep, which causes aritifacts
Transmission Electron Microscope
looks at very thin cross-sections in high detail
- can look at internal structures
- very high resolution
- cant be used on living things
- preparation is extensive
- costly
Electron Tomography
3D model buildup using TEM data
- can look at objects in 3D and see objects relative to one another
- Can’t be used on living things
Centrifugation
- spins and separates liquified cell homogenates
- seperate into layers based on density
Catalysts
lower activation energy, accelerating the rate of the reaction
Metabolsim
catabolism+ anabolism + energy transfer
Characteristics of chemical reactions
- concentration of reactants and products determine which way a reaction will go.
- Enzymes are globular proteins that act as catalysts. –Substrate specific, unchanged during a reaction, catalyzes in both the forward and reverse direction, temperature and pH affect enzyme function, active site and induced fit is how enzymes bind
- Cofactors are nonprotein molecules that assist enzymes usually by donating or accepting some component of a reaction like electrons
- ATP is the common source of activation energy. New ATP IS formed via phosphorylation
Allosteric enzymes
have both an active site for substrate binding and an allosteric site for binding of an allosteric effector (activator, inhibitor)
Competitive inhibition
substance that mimics the substrate inhibits the enzyme by binding to the active site.
- Can be overcome by increasing substrate concentration
- Km changed (raised) but Vmaxx is not
Noncompetitive inhibition
substance inhibits enzyme by binding elsewhere than active site, substrate still binds but reaction is prevent from completing.
-Km unchanged but Vmax is NOT
Uncompetitive/anti-competitive inhibition
enzyme inhibitor binds only to the formed E-S complex preventing formation of product (Vmax is lowered)
Cooperativity
enzyme becomes more receptive to additional substrate molecules after one substrate molecule attaches to an active site
Km
is the Michaelis constant
- it represents the substrate concentration at which the rate is half of Vmax
- it is indirectly represents binding affinity in a way, Inversely
- small Km indicates that the enzyme requires only a small amount of substrate to become saturated
- Large Km indicates the need for high substrate concentration to achieve maximum reaction velocity
THUS a raise Km=substrate binding worse, lowered Km=substrate binding better
Types of Membrane Proteins
Peripheral-loosely attached to one side surface
integral-imbeds inside the membrane
transmembrane-all the way through, both sides of the membrane
Phopholipid membrane Permeability
- small uncharged, non polar molecules and hydrophobic molecules can freely pass across the membrane. Polar molecules can only pass through if they are small and uncharged
- everything else requires transporter (large, polar, charged molecules)
Peripheral membrane proteins
- hydrophilic
- held in place by Hydrogen bonding and electrostatic interaction
- Disrupt/detach by changing salt concentration or pH to disrupt these interactions
Integral Proteins
- hydrophobic
- use detergent to destroy membrane and expose these proteins
Channel Proteins
provide passageway through membrane for hydrophilic (water soluble) substances
-polar and charged substances?
Recognition proteins
- such as major histocompatibility complex on macrophage to distinguish between self and foreign
- they are glycoproteins due to oligosaccharides attached
Ion Channels
passage of ions across membrane
-called gated channels in nerve and muscle cells, respond to stimuli
-these can be:
1) voltage gated- respond to difference in membrane potential
2)ligand gates- chemical binds and opens channel
3) mechanically gated- respond to pressure, vibration, temperature, etc.
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Porins
allow passage of certain ions and small polar molecules
- aquaporins increase the rate of H2O passing (kidney an plant root cells)
- these tend not to be specific, they’re just large passages, if you can fit you’d go through
Carrier Proteins
-bind to specific molecules, protein changes changes shape, molecule passed across
EX: glucose into cell (this is a type of transport protein)
-Carrier proteins seem to be specific to movement across membrane via integral membrane protein
Transport Proteins
- can use ATP to transport materials across (NOT ALL TRANSPORT USE ATP)
- Active Transport: EX: Na+, K+ pump to maintain gradients
- Facilitate diffusion as well
- Transport protein is a broad category
** CHAD”s quiz says transport use ATP sources but other sources contradict: transport can be facilitate diffusion
Adhesion Proteins
- attach cells to neighboring cells
- provide anchors for internal filaments and tubules (stability)
Receptor Proteins
binding site for hormones and other trigger molecules
Cholesterol
adds rigidity to membrane of animal cells under normal conditions, but at norma temperature it maintains its fluidity
- STEROLs provide similar function in plant cells
- prokaryotes DO NOT HAVE cholesterol in their membranes instead they use hopanoids
Glycocalyx
a carbohydrate coat that covers outer face of cell wall of some bacteria and outer face of plasma membrane in some animal cells
- it consists of glycolipids (attached to plasma membrane) and glycoproteins (such as recognition proteins)
- it may provide adhesive capabilities, a barrier to infection, or markers for cell-cell recognition
Nucleus
- where DNA is located
- the nucleus is bound by double layer nuclear envelope with nuclear pores for transport (mRNA, ribosome subunits, dNTPs, proteins like RNA polymerase and histones, etc.)
-there is no cytoplasm inside the nucleus there is a nucleoplasm!
nucleolus
inside the nucleus are the marker of ribosomes (rRNA)
-rRNA are synthesized inside the nucleolus and ribosomal proteins are imported from cytoplasm which results in the formation of ribosomal subunits
Chromatin
is the general packaging structure of DNA around proteins in eukaryotes, the tightness of the packaging varies depending on cell stage
Chromosomes
is tightly condensed chromatin when the cell is ready to divide
Histones
serve to organize DNA which DNA coils around histones to form nucleosomes
Nuclear Lamina
dense fibrillar network inside nucleus of eukaryotic cells
- intermediate filaments and membrane associated proteins
- provides mechanical support
- helps regulate DNA replication, cell division, and chromatin organization
Nucleoid
irregular shaped region within the cell of prokaryote that contains all/most genetic material
Cytoplasm
THIS IS AN AREA NOT A STRUCTURE
- metabolic activity and transport occurs here
- cyclosis is streaming movement within the cell
- doesn’t include nucleus, but does include cytosol, organelles, everything suspended within cytosol BUT NOT THE NUCLEUS
Cytosol
- also known as the cytoplasmic matrix
- cytosol doesn’t include the stuff suspended within the gel-like substance it is just the GEL LIKE STUFF
Ribosomes
- 60s + 40s=80s, eukaryotic
- 50s+ 30s= 70s, prokaryotic
- the two subunits produced inside the nucleolus is moved into the cytoplasm where it is where it assembles into a single 80s ribosome/70s ribosome.
- larger s value indicates heavier molecule
- made of RNA and protein
- function to make proteins
Endoplasmic Reticulum
- Rough ER: with ribosomes, creates glycoproteins by attaching polysaccharides to polypeptides as they are assembled by ribosomes. In eukaryotes the rough ER is continuous with the outer nuclear membrane.
- Smooth ER- no ribosomes, synthesizes lipids and steroid hormones for export. In liver cells, smooth ER has functions in breakdown drugs, and toxic-by products from cellular reactions.
Smooth striated muscle have smooth ER’s called SARCOPLASMIC RETICULUMS that store and release ions ex: Ca2+
Lysosomes
- vesicles produces from golgi that contain digestive enzymes (low pH for function), breakdown nutrients/bacteria/cell debris
- Any enzyme that escapes from the lysosome remains inactive in neutral pH of cytosol (other sources says autolysis)
- lysosomes in plant cells, BUT GENERALLY TAUGHT AS NONE
- functions in apoptosis- which releases contents into cell
Golgi Apparatus
- transport various substances in vesicles
- cis face for incoming vesicles
- trans face for secretory vesicles
- has flattened sacs known as cisternae
Peroxisomes
break downs substances, fatty acid, and amino acids
- common in liver and kidney where they break down toxic substances
- in plant cells, peroxisomes modify by-products of photorespiration
- in germinating seeds it is called glyoxysosomes- breaks down stored fatty acids to help generate energy for growth
- Peroxisome produces H2O2 which they then use to oxidize substrates, they can also breakdown H2O2 if necessary
Microtubules
- made up of protein tubulin
- provide support and motility for cellular activities
- spindle apparatus which guide chromosomes during division
- in flagella and cilia (9+2 array, 9 pairs and 2 singlets in center) in all animal cells and lower plants (mosses and ferns)
Intermediate Filaments
provide support for maintaining cell shape
Ex: keratin
Microfilament
made up of actin and involved in cell motility
-skeletal muscle, amoeba pseudopod, cleavage furrow
Microtubules Organizing Centers (MTOCs)
include centrioles and basal bodies- are at the base of each flagellum and organize their development
- 9x3 array
- plant cells lack centrioles and its division by cell plate instead of cleavage furrow therefore they do not have MTOC’s
Transport Vacuoles
-temporary receptacles of nutrients
0merge with lysosomes which break down food
Central Vacuoles
- large, occupy most of plant cell interior
- exert turgor when fully filled to maintain rigidity
- nutrients, cary out functions performed by lysosomes in animal cells
- has a specialized membrane called a TONOPLAST
Storage vacuole
plants store starch, pigments, and toxic substance (nicotine)
Contractile Vacuole
in single celled organisms that collect and pump excess water of the cells (prevents bursting)
- active transport
- found in protista like amoeba and paramecia, organisms that live in hypotonic environment
Cell walls
found in plants, fungi, protists, and bacteria
- provides support
- somtimes a secondary cell wall develops beneath the primary one
What is the cell wall in plants made of?
celluose
what is the cell wall in fungi made of?
chitin
What is the cell wall in bacteria made of?
peptidoglycans
What is the cell wall in archea made of?
polysaharrides
Extracellular matrix
- found in animals
- area between adjacent cells (beyond plasma membrane and glycocalyx)
- occupied by fibrous structural proteins, adhesion proteins, and polysaccharides secreted by cells
- provde mechanical support and helps bind adjacent cells (collagen is most common)
how do cells adhere to the extracellular matrix
- focal adhesions- connection of extracellular matrix to actin fibronetin
- hemidesmosomes- connection of extracellular matrix to intermediate filaments (ex: keratin)
Plastids
found in plants cells
- chloroplasts (site of photosynthesis)
- leucoplasts (can specialize to store starch/lipid/protein as amyloplsats/elaioplasts/proteinplasts or serve general biosynthetic functions
-chromoplasts-store carotenoids
Mitochondria
- make ATP
- fatty acid catabolism (beta-oxidation)
- have their own circular DNA and ribosomes ( gives rise to endosymbiotic theory)
- have a double layered membrane
Cytoskeleton
- microtubules (flagella and cilia), microfilaments, intermediate filaments
- in eukaryotic cells it aids in cell division, cell crawling, and the movement of cytoplasm and organelles
In plant cell the cytockeleton in a hypnotic solution
- their normal state
- vacuole swells- TURGID
In plant cel the cytoskeleton in a isotonic solution
-plant cell is flaccid
in plant cell the cytoskeleton in a hypertonic solution
the cell is plasmolyzed- cytoplasm is pulled away from the cell wall
Endomembrane system
in the network of organelles and structures, either directly or indirectly connected, that function in the transport of proteins and other macromolecules into or out of the cell
-includes the plasma membrane, endoplasmic reticulum, golgi apparatus, nuclear envelope, lysosome, vacuoles, vesicles, endosomes, BUT NOT THE MITOCHONDRIA or CHLOROPLASTS
Brownian Movement
- intracellular movement
- particle move due to kinetic energy, spreads small suspended particle throughout the cytoplasm
Cyclosis/streaming
- intracellular movement
- circular motion of cytoplasm around cell transport molecules
Diffusion
- Extracellular movement
- if cells in close contact with external environment, this can suffice for food and respiration needs
- used for transport of materials between cells and interstitial fluid around cells in more complex animals
Circulatory System
- extracellular movement
- complex animals with cell to far from external environment require one.
- uses vessels
Eukaryotes
include all organisms except for bacteria, cyanobacteria, and arachaebacteria
Prokaryotes
-have a plasma membrane, DNA molecule, ribosomes, cytoplasm, and cell wall
-NO NUCLEUS
- single (circular) naked dsDNA NO CHROMATIN
-50s+30s=70s ribosome
-cells walls=peptidoglycan
archea=polysachardes
many have sticky capsules on wall
-flagella are constructed from flagellin not microtubules
Bulk Flow
collection of movement of substance in the same direction in response to a force or pressure
-EX: blood
types of Passive Transport
- simple diffusion
- osmosis
- dialysis
- plasmolysis
- facilitated diffusion
- countercurrent exchange
dialysis
diffusion of different solutes across a selectively permeable membrane
Plasmolysis
movement of water out of a cell that results in its collapse
countercurrent exchange
diffusion by bulk flow in opposite directions
-ex: blood and water in fish gills
Active Transport
- movement of transports against their concentration gradients requiring energy
- usually solutes like small ions, amino acids, monosacchariedes
Endocytosis
- uses ATP (active process)
- invaginates material from the outside of the cell
Exocytosis
- uses ATP (active process)
- secretes vesicles outside the cell
Phagocytosis
undissolved material (solid) enters cell
- EX: white blood cell engulfs
- plasma membrane wraps outward around material
Pinocytosis
- dissolved material (liquid)
- plasma membrane invaginates
Receptor Mediated
- a form of pinocytosis
- specific molecules (ligand) bind to receptors
- proteins that transport cholesterol in blood (LDL) and hormones target specific cells by this
Anchoring Junctions
- desmosome- keratin filaments inside attach to adhesion plaques which bind adjacent cells together via connecting adhesion proteins, provides mechanical stability and hold cellular structures together
- in animals cells
- present in tissues with mechanism stress: skin, epithelium, cervix/uterus
Tight Junctions
Completely encircles each cell, producing a seal that prevents the passage of materials between cells
- characteristic of cells lining the digestive tract where materials are required to pass through cells into blood
- They prevent passage of molecules and ions through the space between cells so materials must actually enter the cells by diffusion or active transport in over to pass through the tissue
-in animal cells
Gap junction
- narrow tunnels between animal cells (connexins)
- prevents cytoplasm of each cell from mixing, but allows passage of ions and small molecules
- essentially channel proteins of two adjacent cells that are closely aligned (smooth muscle single of spreading action potential)
- in animal cells
- tissue like heart have these to pass electrical pulses
Plasmodesmata
- narrow tunnels between plant cells
- narrow tube of endoplasmic reticulum-DESMOTUBULE
- exchanges material through cytoplasms surrounding the desmotubule
