Unit 1: Cell Biology Flashcards
Cell Theory
- Most basic form of life
- Make up all living things
- Cells must come from preexisting cells
Macromolecules
- Polysaccharides (sugars) (polymers)
- Lipids (not true polymers but can be large molecules)
- Nucleic acids (DNA, RNA) - polymers
- Proteins - polymers
Polymer
A long molecule consisting of many similar or identical building blocks known as monomers
How do polymers grow and disassemble
- Grow by dehydration synthesis
- Disassemble by hydrolysis
Polysaccharides
- Macromolecules, consisting of a few hundred or thousand monosaccharides joined by glycosidic linkages
- Serve as fuel and as building material, based on the monomer of glucose
Disaccharide
Consists of two monosaccharides joined by a glycosidic linkage (by losing water)
Storage polysaccharides
- Animals store sugars in the form of glycogen, most in the muscles, gets assembled from glucose monomers in the liver
- Plants store sugars in the form of starch
Types of starch
- amylopectin (somewhat branched)
- amylose (unbranched)
Structural polysaccharides
- Cellulose in plants
- Chitin in exoskeletons of arthropods
Lipids
- A diverse group of hydrophobic molecule
- Components of cell membranes
- Lipids are fats , phospholipids and steroids
Fatty acid
- Has a long carbon skeleton, usually 16 or 18 carbon atoms in length
- Carbon at one end in part of a carboxyl group (acid), the rest of the skeleton consists of a hydrocarbon chain
Triglycerides
Three fatty acid molecules joined to a glycerol with an ester linkage
Phospholipids
- Two fatty acids attached to a glycerol
- The third hydroxyl group of the glycerol is joined to a phosphate groups
- Some are kinked some are not, based on the double bond
- Heads are hydrophilic, tails are hydrophobic
- Extra molecules in the phospholipid head, length and saturation of fatty acid tails can change
Steroids
Lipids characterized by a carbon skeleton consisting of four fused rings
Proteins
- Polymers of amino acids
- A wide range of structures, resulting in a wide range of functions
- Everything in a cell is mediated by proteins
- Account for more than 50% of the cell’s dry mass
Purposes of Proteins (8)
- Enzymatic proteins accelerate specific chemical reactions
- Antibodies are proteins that protect against disease
- Storage proteins serve as a source of amino acids (ex. Casein, milk protein)
- Proteins mediate the selective transport of substances (ex. Hemoglobin transports oxygen from lungs to other body parts)
- Hormonal proteins coordinate an organisms’ activities (ex. insulin)
- Receptor proteins are responsible for the response of the cell to chemical stimuli
- Contractile and motor proteins are responsible for movement
- Structural proteins offer support (keratin)
Amino acid
- An organic molecule with both an amino group and a carboxyl group
- 20 amino acids, all with different physical and chemical properties
- The covalent bond between two amino acids in called a peptide bonds
Protein Structure
- Primary structure: The sequence of amino acids
- Secondary structure: The regions stabilized by hydrogen bonds between atoms of a polypeptide backbone (alpha helix or beta pleated sheets)
- Tertiary structure: The overall shape of a polypeptide resulting from interactions between the various amino acids
- Quaternary structure: Refers to protein complexes, where two or more polypeptides chains (subunits) aggregate into one functional macromolecule. It describes the way in which these polypeptide chains aggregate.
Heme
An iron containing molecule bound to hemoglobin and some other biological molecules
Nucleic acids
- Store, transmit and help express hereditary information
- DNA and RNA
- Polymers are called polynucleotides, monomers are called nucleotides
Nucleotide
- Monomer of a polynucleotides
- Composed of 3 parts: nitrogenous base, a five carbon sugar, and one phosphate group
DNA vs RNA
- DNA: Deoxyribose sugar (lacks an oxygen on the second carbon), Thymine
- RNA: Ribose sugar, Uracil replaces Thymine
Nitrogenous bases
- Pyrimidines: (Cytosine, Thymine, Uracil)
- Purines: (Guanine, Adenine)
- Guanine binds with Cytosine, Adenine binds with Thymine)
DNA molecule structure
- DNA molecules have two polynucleotides, or “strands” that wind around an imaginary axis, forming a double helix.
- The two phosphate backbones run in opposite 5’-3’ directions from each other (antiparallel)
RNA molecule structure
- RNA molecules exist as single strands
- Complementary base pairing occurs between two stretches of nucleotides in the same RNA molecule
What contains DNA? (eukaryotes)
The nucleus, the mitochondria, and the chloroplast
Prokaryote vs Eukaryote
- Eukaryotic cells have internal membranes that compartmentalize their functions, have a nucleus that contains DNA
- A prokaryotic cell lacks a true nucleus and the other membrane-enclosed organelles
Parts of a prokaryotic cell (7)
- Fimbriae: Attachment structures on the surface of some prokaryotes
- Nucleoid: region where the cell’s DNA is located (not enclosed by a membrane)
- Ribosomes: Complexes that synthesize proteins
- Plasma membrane: membrane enclosing cytoplasm
- Cell wall: Rigid structure outside the plasma membrane
- Glycocalyx: Outer coating of many prokaryotes, consisting of a capsule or a slime layer
- Flagella: Locomotion organelles of some prokaryotes
Fluid Mosaic Model
The membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids
Nuclear pores
Nuclear pores made by the nuclear pore complex regulate the entry and exit of proteins and RNAs, as well as large complexes of macromolecules
Nucleolus
- The nucleolus is where a type of RNA called ribosomal RNA (rRNA) is synthesized
Ribosomes
Complexes made of ribosomal RNAs and proteins that carry out protein synthesis
Free Ribosomes vs Bound Ribosomes
Ribosomes build proteins in two cytoplasmic locales:
1. Free ribosomes are suspended in the cytosol (most proteins made by free ribosomes function within the cytosol)
2. Bound ribosomes are attached to the outside of the endoplasmic reticulum or nuclear envelope (most proteins made by bound ribosomes are membrane proteins and secreted proteins)
Mitochondria and Chloroplast Parts (6)
- Outer membrane
- Intermembrane space
- Inner membrane
- Cristae
- Matrix
- DNA (in mitochondria only)
Chloroplasts also have a third internal membrane called the thylakoid membrane with a thylakoid space in the lumen
Plastids
- The chloroplast is a specialized member of a family of closely related plant organelles called plastids
- The amyloplast is a colorless organelle that stores starch
- The chromoplast stores pigments
Peroxisomes
- Peroxisomes have a single membrane and contain enzymes that produce hydrogen peroxide H2O2
- Peroxisomes use oxygen to break fatty acids down into similar molecules
Endomembrane System (6)
- Composed of the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles and vacuoles, and the plasma membrane
- The endomembrane are related through direct physical continuity or by the transfer of membrane segments as tiny vesicles (sacs made of membrane)
Endoplasmic Reticulum
- The endoplasmic reticulum consists of a network of membranous tubules and sacs called cisternae
- There are two distinct, though connected, regions of the ER that differ in structure and function: smooth ER and rough ER
Smooth ER
- The outer surface lacks ribosomes (doesn’t make proteins)
- Functions in diverse metabolic processes, which vary with cell type. These processes include synthesis of lipids, metabolism or carbs, detoxification of drugs and poisons, and storage of calcium ions
Rough ER and Glycoproteins
- Studded with ribosomes on the outer surface of the membrane (makes proteins)
- Makes membrane proteins and proteins to be secreted
- The proteins made by the RER are fed into the lumen of the ER
- Secretory proteins depart from the ER wrapped in the membranes of the vesicles called transport vesicles
- Most secretory proteins are glycoproteins, proteins with carbohydrates covalently bonded to them
- The carbs are attached to the proteins in the ER lumen by enzymes
- In addition to making secretory proteins, the rough ER is a membrane factory for the cell
Golgi Apparatus
- The Golgi apparatus consists of flattened membranous sacs - cisternae - looking like a stack of pita bread
- Secretory proteins depart from the ER wrapped around in the membranes of vesicles called transport vesicles
- The Golgi manufactures and refines its products in stages, with different cisternae containing unique teams of enzymes
- The cisternae of the Golgi progress forward from the cis to the trans face, carrying and modifying their cargo as they move
- The Golgi stack dispatches its products by budding vesicles from the trans face, it sorts these products and targets them for various parts of the cell
- Molecular identification tags, such as phosphate groups added to the Golgi products, aid in sorting by acting like postal codes on mailing labels
- Transport vesicles budded from the Golgi may have external molecules on their membranes that recognize “docking sites” on the plasma membrane, thus targeting the vesicles
Lysosomes
- A lysosome is a membrane sac of hydrolytic enzymes that many eukaryotic cells use to digest (hydrolyze) macromolecules
- Lysosomal enzymes work bests in the acidic environment found in the lysosomes
- Unicellular eukaryotes eat by engulfing smaller organisms or food particles, a process called phagocytosis
- The food vacuole formed in this way then fuses with a lysosome, whose enzymes digest the food
Autophagy
- Lysosomes use their hydrolytic enzymes to recycle the cell’s own organic material
- During autophagy, a damaged organelle becomes surrounded by a double membrane, and a lysosome fuses with the outer membrane of this vesicle
- The resulting small organic compounds are released to the cytosol for reuse
Vacuoles
- Vacuoles are large vesicles derived from the endoplasmic reticulum and Golgi apparatus
- Contractile vacuoles pump excess water out of the cell, thereby maintaining a suitable concentration of ions and molecules inside the cell
- Mature plant cells generally contain a large central vacuole, the plant cell’s main repository of inorganic ions
Cytoskeleton
- A network of fibers that organizes structures and activities in the cell
- Gives mechanical support to the cell and maintains its shape
- Dynamic. It can be quickly dismantled in one part of the cell and reassembled in a new location, changing the shape of the cell
- Bacterial cells also have fibers that form a type of cytoskeleton although with different proteins
Cell Motility
- Includes both changes in cell location and movement of cell parts, and generally requires interaction of the cytoskeleton with motor proteins
Motor Proteins
Motor proteins that attach to receptors on vesicles can “walk” the vesicles along microtubules or, in some cases, microfilaments
Types of filaments
- Microtubules (the thickest)
- Intermediate filaments (fibers with diameters in the middle range)
- Microfilaments (Also called actin filaments) (the thinnest)
Tubulin
- Microtubules are big hollow rods constructed from a globular protein called tubulin
- each tubulin protein is a dimer, a molecules made up of two subunits
- A tubulin dimer consists of two slightly different polypeptides, alpha-tubulin and beta-tubulin
- Minus end (alpha-tubulin exposed), and plus end (beta-tubulin exposed)
Microtubules
- Microtubules shape and support the cell and also serve as tracks along which organelles equipped with motor proteins can can move
- Microtubules grow out from the centrosome, a region that is often located near the nucleus. These microtubules function as compression-resisting girders of the cytoskeleton
Flagella vs Cilia
- A flagellum has an undulating motion like the tail of a fish
- Cilia work more like oars, with alternating power and recovery strokes, much like the oars of a racing crew boat
- Both are made of microtubules
Kinesins
Motor proteins that move vesicles and organelles along microtubules
Microfilaments
- Thin solid rods
- A twisted double chain of actin subunits
- Also called actin filaments because they are built from molecules of actin, a globular protein
Myosin
- A microfilament motor protein
- The sliding of myosin over actin drives muscle contraction
Intermediate filaments
- A diverse class of cytoskeletal elements, the most common of which is keratin
- Unlike microtubules and microfilaments, which are found in all eukaryotic cells, intermediate filaments are only found in some animals, including vertebrates but not insects
ECM
- Although animal cells lack cell walls they do have an elaborate extracellular matrix (ECM). The main ingredients of the ECM are glycoproteins and other carbohydrate-containing molecules secreted by the cells.
- Integrins connect the ECM to the cell
Collagen
The most abundant glycoprotein in the ECM of most animal cells is collagen, which forms strong fibers outside the cells
Cell junctions
Three main types
1. Tight junctions: prevent fluid from moving across a layer of cells (waterproof)
2. Desmosomes: strong connections between cells. Cells are fastened together
3. Gap junctions: provide cytoplasmic communicating channels
ATP
- Powers cellular work by coupling exergonic reactions to endergonic reactions
- ATP contains sugar ribose, with the nitrogenous base adenine and a chain of 3 phosphate groups (triphosphate) bonded to it
- The bonds between the phosphate groups and of ATP can be broken by hydrolysis. The reaction is exergonic and releases energy (ATP to ADP)
- The cell’s proteins harness the energy released by this reaction in several ways to perform the 3 types of cellular work: Chemical, transport, and mechanical
- ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP. The free energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) in the cell
ATP activating proteins
- ATP hydrolysis causes changes in the shapes and binding affinities of proteins
Enzymes
- Enzymes speed up metabolic reactions by lowering energy barriers
- The reactant an enzyme acts on is referred to as the enzyme’s substrate
- Only a restricted region of the enzyme molecule actually binds to the substrate. this region is called the active site
Catalyst
A chemical agent that speeds up a reaction without being consumed by the reaction
Activation Energy
The initial investment of energy for starting a reaction - the energy required to contort the reactant molecules so the bonds can break
Catabolic Pathways
- Yield energy by oxidizing organic fuels
- Metabolic pathways that release stored energy by breaking down complex molecules are called catabolic pathways
Redox Reaction
In a redox reaction, the loss of electrons from one substance is called oxidation, and the addition of electrons to another substance is known as reduction
Glycolysis
- Glycolysis harvests chemical energy by oxidizing glucose to pyruvate
- Occurs in the cytosol
- Begins the degradation process by breaking glucose into two molecules of a compound called pyruvate
- In eukaryotes, pyruvate enters the mitochondrion and is oxidized to a compound called acetyl-coA which enters the citric acid cycle.
Citric Acid Cycle
- Also called the tricarboxylic acid cycle or the Krebs cycle
- After pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation of organic molecules
- The hydrogen atoms are not transferred directly to oxygen, but instead are usually passed first to an electron carrier, a coenzyme called NAD+
ETC
- The ETC is a series of proteins that pass electrons from NADH to oxygen, while accumulating protons (H+ ions) across a membrane
- The end result of the ETC is the accumulation of protons in between the two membranes of the mitochondria
- ATP synthase uses the energy of the existing ion gradient to power ATP synthesis
- The power source for the ATP synthase is a difference in the concentration of H+ on the opposite sides of the inner mitochondrial membrane
DNA packaging
- Chromatin refers to a mixture of DNA and proteins that form the chromosomes found in the cells of humans and other higher organisms
- A nucleosome is the basic repeating subunit of chromatin packaged inside the cell’s nucleus
- DNA molecules are packaged into structures called chromosomes
- Each duplicated chromosome consists of two sister chromatids, which are joined copies of the original chromosome
- Each chromatid has a centromere, a region in the chromosomal DNA where the chromatids are attached most closely
Cell Cycle
- Before the cell can divide to form genetically identical daughter cells, all of its DNA must be copied, or replicated
- A cell cycle is a series of events that takes place in a cell as it grows and divides
- G1 (gap 1): Cell increases in size
- S (synthesis) phase: DNA is duplicated (in the form of chromatin)
- G2 (gap 2): cell prepares to divide
- G1, S, and G2 make up interphase, which accounts for the time between cell divisions
- during interphase, microtubules extend from the centrosomes
- Mitosis: Prophase, prometaphase, Metaphase, Anaphase, Telophase
Mitosis
Prophase:
- The chromosomes condense from chromatin into x shaped structures
- Each chromosome is composed of two sister chromatids, containing identical genetic information
- The chromosomes pair up so that both copies of chromosome 1 are together and so on
- At the end the membrane around the nucleus in the cell dissolves away releasing the chromosomes
- The mitotic spindle, consisting of the microtubules and other proteins, extends across the cell between the centrioles as they move to opposite poles of the cell
Metaphase:
- The chromosomes line up neatly end-to-end along the center (equator) of the cell
- The centrioles are now at opposite poles of the cell with the mitotic spindle fibers extending from them
- The mitotic spindle fibers attach to each of the sister chromatids
Anaphase:
- The sister chromatids are then pulled apart by the mitotic spindle which pulls one chromatid to one pole and the other chromatid to the opposite pole
Telophase:
- At each pole of the cell a full set of chromosomes gather together
- A membrane forms around each set of chromosomes to create two new nuclei
Kinetochore
Each of the two sister chromatids of a duplicated chromosome has a kinetochore, a structure made up of proteins that have assembled on a specific section of DNA at each centromere
Cytokinesis
- The physical process of cell division, which divides the cytoplasm of a parental cell into two daughter cells
- The place where cytokinesis occurs is called the cleavage furrow
- On the cytoplasmic side of of the furrow is a contractile ring of actin microfilaments associated with molecules of the protein myosin
Cell Cycle Regulation
- The frequency of cell division varies with the type of cell
- The eukaryotic cell cycle is regulated by a molecular control system composed of cyclins and cyclin-dependent kinases
- phosphorylation of various proteins of the nuclear lamina promotes fragmentation of the nuclear envelope during prometaphase of mitosis
- Cells have stop signals that halt the cell cycle at checkpoints until overridden by go-ahead signals
- Cancer cells do not need the normal signals to regulate the cell cycle so they do not stop dividing
Kinase
- A kinase is an enzyme that adds phosphate groups to other molecules and modulates protein functions
- To be active, cyclin dependent kinases (Cdks) must be attached to a cyclin, a protein that gets its name from its cyclically fluctuating concentration in the cell
- The activity of a Cdk rises and falls with changes in the concentration of its cyclin partner
Quorum Signaling
- Bacterial cells secrete molecules that can be detected by other bacterial cells. Sensing the concentration of such signaling molecules allows bacteria to monitor the local density of cells, a phenomenon called quorum sensing
Local signaling
Cells in a multicellular organism usually communicate via signaling molecules targeted for cells that may or may not be immediately adjacent
Types: Direct contact, cell junctions, cell-cell recognition, paracrine signaling, synaptic signaling, long-distance signaling
Direct Contact Signaling
Communication by direct contact between cells is a type of local signaling
Cell Junction Signaling
Both animals and plants have cell junctions that allow molecules to pass readily between adjacent cells without crossing plasma membranes
Cell-Cell Recognition
Two cells in an animal may communicate by interaction between molecules protruding from their surfaces
Paracrine Signaling
Paracrine signaling is another type of local signaling, in which molecules are secreted by the signaling cell and these molecules travel only short distances
Synaptic Signaling
- A more specialized type of local signaling called synaptic signaling occurs in the animal nervous system
- Muscle contractions involve synaptic signaling between a neuron and a muscle
A ligand-gated (ligand= neurotransmitters) ion channel is a type of membrane channel receptor containing a region that can act as a “gate” opening or closing the channel when the receptor changes shape.
Long Distance Signaling
Both animals and plants use chemicals called hormones for long-distance signaling
Three Stages of Signaling
- Signal reception:
- A signaling molecule binds to a receptor protein, causing it to change shape
- Receptor Tyrosine Kinases (RTKs) belong to a major class of plasma membrane receptors characterized by having enzymatic activity
- A kinase is any enzyme that catalyzes the transfer of phosphate groups. Phosphorylation is a widespread mechanism for regulating protein activity
Phosphorylation can activate or inactivate proteins
- Intracellular receptor proteins are found in either the cytoplasm or nucleus of target cells
- Steroid hormones have intracellular receptors - Signal transduction:
- Cascades of molecular interactions relay the signal from receptors to target molecules in the cell
- In a phosphorylation cascade, a series of different proteins in a pathway are phosphorylated in turn, each protein adding a phosphate group to the next one in line
- Small molecules and ions can also act as Second Messengers (ex. Cyclic adenosine monophosphate (cAMP), calcium ions and inositol triphosphate)
- Enzyme cascades amplify the cell’s response to a signal - Cellular response:
- A signaling leads to a regulation of transcription or cytoplasmic activities
- Many signaling pathways ultimately regulate protein synthesis, usually by turning specific genes on or off in the nucleus
Example: expression of antimicrobial peptides
- A signaling pathway may regulate the activity of proteins
