Section 1 (Ch. 1-6), Exam 2 info, BioL 202 Exam 3 (16, 17, 14, 18, 20) Card 24

Rb is an important protein for controlling cell proliferation by blocking entry into S phase. How does it exert its effect?

Rb blocks the passage from G1 into S phase by inactivating transcription factors required for the expression of genes that allow entry into S phase. Mitogen signaling can activate Cdks to phosphorylate and inactivate Rb, thus lifting the restriction on S-phase entry.

Notch receptor signaling

Receptors Activate a Fast Track to the Nucleus itself is a transcription regulator. Controls nerve-cell production in the fruit fly Drosophila. -Direct pathway to nucleus. +activated--part of receptor migrates from PM to nucleus.--that regulates transcription of specific genes. -Unspecified epithelial cells --[cell specialization and lateral inhibition]--> Nerve cell developing from epithelial cell with membrane-bound inhibitory signal protein (Delta) + receptor (notch) + inhibited epithelial cell.

Protein Kinase

Receptors acting on two protein kinases activating or inhibiting leading to cell growth. Enzyme that catalyze the transfer of a phosphate group from ATP to a specific amino acid side chain on a target protein.

Receptors

Recognize and respond specifically to the signal molecule. Each receptor is selective and usually activated by one type of signal.

Oxidation and Reduction

Redox reactions: Reduction = gain of electrons (or hydrogen atoms (e- + H+) Oxidation = loss of electrons (or hydrogen atoms (e- + H+)

Redox reactions

Reduction = gain of electrons (or hydrogen atoms (e- + H+) Oxidation = loss of electrons (or hydrogen atoms (e- + H+)

Centromere

Region of a chromosome where the two sister chromatids attach

Alpha helix

Regular folding patterns in many diff. proteins. -Found in protein alpha-keratin (abundant in skin & its derivatives, i.e. hair, nails, and horn). The N-H of every peptide bond is hydrogen-bonded to C=O of neighboring peptide bond located 4 amino acids away in same chain.

M cyclin

Regulatory protein that binds to mitotic Cdk to form M-Cdk, the protein complex that triggers the M phase of the cell cycle.

Cdk inhibitor protein

Regulatory protein that blocks the assembly or activity of cyclin-Cdk complexes, delaying progression primarily through the G1 and S phases of cell cycle.

G1 cyclin

Regulatory protein that helps drive a cell through the first gap phase of the cell cycle and towards S phase.

G1/S cyclin

Regulatory protein that helps to launch the S phase of cell cycle.

S cyclin

Regulatory protein that helps to launch the S phase of the cell cycle.

Cyclin

Regulatory protein whose concentration rises and falls at specific times during the euk. Cell cycle. Cyclins help control progression from one stage of the cell cycle to the next by binding to cyclin-dependent protein kinasas (Cdks).

Bcl2 Family

Related group of intracellular proteins that regulates apoptosis; some family members promote cell death, others inhibit it. - intracellular proteins that regulate activation of caspases Bax and Bak - two important members of family •Activated in response to DNA damage or other insults •Induce release of cytochrome c from mitochondria to promote cell death

Nanog regulatory sequence

Relative nucleotide preference in one strand.

trimeric GTP-binding proteins (G proteins intra signaling)

Relay messages from G-protein-coupled receptors (GPCR) Stimulation of GPCRs Activates G-Protein Subunits activate this membrane-bound - then activate (or inhibit) an enzyme or an ion channel in the PM, initiating an intracellular signaling cascade. Once binds its extra. sig. molecule, the activated receptor signals to a trimeric G protein on the cytosolic side of PM, then turns on (or off) an enzyme (or ion channel) in the same membrane. i.e. Inc. cytosolic concentration of cyclic AMP. Largest family of cell surface receptors 700 GPCRs in humans Diverse signal molecules bind GCPRs e.g. proteins, fatty acids, amino acids. All GPCRs possess a similar structure single protein 7 transmembrane segments. Stimulation of GPCRs Activates G-Protein Subunits: -G protein: 3 subunits (each is a protein) 2 are membrane-bound contain lipid tail ~20 different types of G proteins. -GDP-bound = inactive -GTP-bound = active two active parts alpha beta-gamma that bind target proteins activity persists while bound. -Some Bacterial Toxins Cause Disease by Altering the Activity of G Proteins Cholera and whooping cough (cholera toxin and pertussis toxin). 1. Inactive receptor protein embedded activated by signal molecule and binds to inactive G protein (in cytosol). 2. Activated receptor causes dissociation of GDP from G protein complex. Forming GTP which activated G protein. 3. Activated α subunit and beta-Y complex from exchange from GDP for GTP resultings in Effector activation.

Paracrine signals

Released by cells into the extracellular fluid in their neighborhood and act locally. -Diffuse locally through the extracellular fluid, remaining in the neighborhood of the cell that secretes them. Act as local mediators on nearby cells. Equiv. of posting a flyer on selected notice boards near the arena. -Signal diffuses locally within a multicellular organism e.g. inflammation at site of infection or that controls cell proliferation in a healing wound function in this way.

Mechanism of DNA Repair

Repair of DNA damage on single-strand of DNA: 1.Recognition and removal of damaged DNA •Typically involves nucleases that cleave covalent bonds at damaged nucleotides and leave small gap on one strand 2.Repair DNA Polymerase binds to 3' hydroxyl end of cut DNA strand •Different from replication DNA polymerases, still have proofreading capability Nick left after repair sealed by DNA Ligase

Telomeres

Repeated DNA sequences at the ends of eukaryotic chromosomes.

transcription regulators

Repressors: Turn Genes Off Activators: Turn Them On

RNA polymerase anatomy**

Requires RNA polymerase; main transcription enzyme. can simultaneously transcribe the same gene. (dark circles outside of organelle). crucial because it carries out transcription, the process of copying DNA (deoxyribonucleic acid, the genetic material) into RNA (ribonucleic acid, a similar but more short-lived molecule). Transcription begins when RNA polymerase binds to a promoter sequence near the beginning of a gene (directly or through helper proteins). RNA polymerase uses one of the DNA strands (the template strand) as a template to make a new, complementary RNA molecule. Transcription ends in a process called termination. Termination depends on sequences in the RNA, which signal that the transcript is finished. -Intergenic region: joining the two organelles. Short end on left forms secondary structures and then right end the gene continues increasing in length.

Voltage-gated ion channels

Respond to the membrane potential.

Cell Can Change the Expression of Its Genes

Response to External Signals

Intracellular signaling molecules

Response to signals also depends on intracellular signaling molecules and the activity of effector proteins. The same signal molecule can induce different responses in different target cells. i.e. Response to signaling molecule (acetylcholine). (A) Heart pacemaker cell require acetylcholine to bind to receptor protein --> decreased rate of firing. (B) Salivary gland cells require acetylcholine to bind to receptor protein --> secretion. (C) Skeletal muscle cell requires 2 acetylcholine --> contraction. (D) Acetylcholine (signaling molecule)

Tight junctions

Restrict membrane proteins to particular domains of the plasma membrane of gut epithelial cells.

Cancer and genomic instability

Results in cancer cells having highly abnormal chromosomes due to genomic instability. +An increased rate of mutation often caused by defects in the systems that govern the accurate replication and maintenance of the genome; the resulting mutations sometimes drive the evolution of cancer. i.e. genes can be broken up (translocated) or regulators not near so apoptosis can't occur. OR -Accumulation of mutations that can also lead to genomic instability. -Image: The karyotype on the right is most likely from an advanced tumor. Note the significant evidence of genetic instability. Cancer cells often have highly abnormal chromosomes, reflecting genetic instability.

Rod photoreceptor cell from retina (sensitive to life).

Rhodopsin (outer segment) Inner segment Nucleus Synaptic region (absorbs light) production altered neurotransmitter release.

Specific Codons in an mRNA Signal

Ribosome Where to Start and to Stop Protein Synthesis.

Activity: RNA splicing

Ribozymes: Small nuclear RNAs (snRNAs), self-splicing RNAs.

X-ray Diffraction of DNA

Rosalind Franklin studied the structure of DNA using X-rays •Found that concentrated, viscous solution of DNA can be separated into fibers yielding diffraction pattern. •Under the right condition, fibers can produce an X-ray diffraction pattern •Produced X-ray diffraction photographs •Provided evidence that DNA •Is a helix •Some portion of the helix is repeated •Shows 3-D structure of molecule. •Wilkins, a colleague of Franklin, showed the image to James Watson that lead to present day DNA sequence.

Amino acid sequence

Rules by which the base sequence of a DNA gene is translated into protein structures

Local mediator

Secreted signal molecule. Acts at a short range on adjacent cells.

Secretory pathways 3

Secretory Proteins Are Released from the Cell by Exocytosis. Constitutive exocytosis pathway of vesicle transport does not require additional signals for vesicles to move from the trans Golgi to the plasma membrane. Specialized secretory cells: Constitutive and regulated exocytosis pathways diverge in the trans Golgi network.

Electron-transport chain

Series of membrane embedded electron carrier molecules. Facilitate movement of electrons from a higher energy to lower energy level. i.e. Oxidative phosphorylation , Photosynthesis. Water provides a large reservoir of mobile protons, which would tend to bond with any atom in the electron transport chain that becomes reduced. +So placement of an electron acceptor on the inside of the inner mitochondrial membrane and an electron donor on the outside could move a co-transported proton to the outside.

MAP-kinase signaling module

Set of 3 functionally interlinked protein kinases - allows cells to respond to extracellular signal molecules that stimulate proliferation; Includes a mitogen-activated protein kinase (MAP kinase), a MAP kinase kinase, and a MAP kinase kinase kinase.

respiratory enzyme complexes

Set of proteins in the inner mitochondrial membrane that facilitates the transfer of high-energy electrons from NADH to water while pumping protons into the intermembrane space.

epithelial tissue

Sheets of tightly packed cells that line organs and body cavities. •Forms continuous layer over body surfaces •Lines body cavities •Forms glands May be connected by: •Tight junctions •Adhesion junctions •Gap junctions Functions include •Protection •Secretion •Absorption •Excretion Filtration

Muscle contraction

Shortening of all sarcomeres actin filaments sliding past myosin filaments

Side chain

Side chain is another name for an R group, and is a group of atoms attached to the main part of a molecule and having a ring or chain structure.

Factors Positively Influencing Cell Survival

Signals that positively influence cell survival, cell growth, and cell division 1.Survival factors - suppress apoptosis to promote survival 2.Mitogens - stimulate cell division 3.Growth factors - stimulate cell growth (increase in cell size and mass)

Phospholipids

Similar structure to triglycerides •Consists of one glycerol molecule linked to two fatty acids and a modified phosphate group •The fatty acids (tails) are nonpolar and hydrophobic •The modified phosphate group (head) is polar and hydrophilic

Myosin-I

Simplest type of myosin, present in all cells; consists of a single actin-binding head and a tail that can attach to other molecules or organelles. -Acts as monomer. -Head bind actin filament and hydrolyzes ATP Tail binds cargo.

Rise in intracellular cyclic AMP can activate gene transcription

Slow response to increase in cAMP within minutes to hours. Response occurs after change in gene expression that is elicited by signal. - Rise in cyclic AMP activates protein kinase A (PKA) activates transcriptional regulators (phosphorylated) binds to activated target gene (DNA) expression --> transcription of target gene.

Phospholipase C

Small Messenger Molecules. Activated GPCR--> Response to activation the C cleaves a inositol phospholipid to produce inositol 1,4,5 triphosphate (IP3) --> diacyglycerol (DAG) (In plasma membrane) AND migrates through binds to Ca2+ channel (ER lumen) --> Ca2+ and diacyglycerol binds and activates PKC. The Inositol Phospholipid Pathway Triggers a Rise in Intracellular Ca2+ activates two signaling pathways

Okazaki fragment

Small fragments of DNA produced on the lagging strand (3')during DNA replication, joined later by DNA ligase to form a complete strand. Leading 5'

Cyclic AMP (cAMP)**

Small intracellular signaling molecule formed from ATP in response to hormonal stimulation of cell-surface receptors. Pathway: Receptor binds w signal molecule. Activated G protein binds with adenylyl cyclase. Phosphorylation occurs making second messenger and finally protein kinase A.

Inositol 1,4,5-trisphosphate (IP3)

Small intracellular signaling molecule. Triggers the release of Ca2+ from the endoplasmic reticulum into the cytosol; produced when a signal molecule activates a membrane-bound protein called phospholipase C. Promotes accumulation of cytosolic Ca2+

Diacylglycerol (DAG)***

Small messanger molecule produced via cleavage of membrane inositol phospholipids in response to extracellular signals. Helps activate protein kinase C.

Monomer

Small molecule

Intracellular receptors

Small, hydrophobic, extracellular signal molecules pass via target cell's PM and bind to intracellular receptors — in the cytosol or nucleus. Can then regulate gene transcription or other functions.

Quinone

Small, lipid-soluble, mobile electron carrier molecule. Functions in the respiratory & photosynthetic electron-transport chains. (Fig 14-21)*

Monomeric GTPases

Small, single-subunit GTP-binding protein. Proteins of this family, such as Ras and Rho, are part of many different signaling pathways. -Controlled by 2 types of regulatory proteins. Molecular switch. 1. Guanine nucleotide exchange factors (GEFs) promote the exchange of GDP for GTP, active monomeric GTPase protein. 2. GTPase-activating proteins (GAPs) stimulate the hydrolysis of GTP to GDP, inactive monomeric GTPase protein. 3. Activation of Rho-family GTPases can have a dramatic effect on the organization of AF in fibroblasts.

Chromosomal Translocation

Some inherited disorders and certain cancers have chromosomal abnormalities

Molecular switches*

Some intra. sig. proteins behave as molecular switches: receipt of a signal causes them to toggle from an inactive —> active state. Once activated, these proteins can stimulate— or in some cases suppress—other proteins in the signaling pathway. They then persist in an active state until some other process switches them off again. -Switching-off: *A signaling pathway is to recover after transmitting a signal & make itself ready to transmit another, every activated protein in the pathway must be reset to its original, unstimulated state. Thus, for every activation step along the pathway, there is an inactivation mechanism. Both are crucial for a signaling pathway to be useful. -Some Intracellular Signaling Proteins Act as Molecular Switches "on and off" switches Turning off response to a signal is important for restoring the cell/tissue/organism to the pre-signal state 2 main classes of molecular switch proteins: --Fall into one of two classes. 1st: phosphorylation: Phosphoproteins *By far the largest— consists of proteins that are activated or inactivated via ; chemical modification. 2nd: GTP-binding proteins: *Trimeric GTP binding proteins (G proteins) Monomeric GTPases -Deactivated then activated once signal comes in

alternative RNA splicing **

Some pre-mRNAs produce different mRNAs and proteins from the same gene.

Endosome

Sorting of endocytosed material. 1% of total cell

pre-mRNA transcript

Special nucleotide sequences that signal the beginning and the end of an intron. pre-mRNA and has to go through some processing steps to become a mature messenger RNA (mRNA) that can be translated into a protein. protect the transcript and help it get exported from the nucleus and translated on the ribosomes (protein-making "machines") found in the cytosol. polyadenylation signal - RNA forms 3' end. This sequence shows up in an RNA molecule during transcription, an enzyme chops the RNA in two at that site.

desmosome

Specialize cell-cell junction. Typically found b/w 2 epithelial cells--serves to connect the ropelike keratin filaments of the adjoining cells, providing tensile strength

Desmosomes

Specialized cell-cell junction, usually formed between two epithelial cells, that serves to connect the ropelike keratin filaments of the adjoining cells, providing tensile strength. Bundles of intermediate filaments allow for cell-cell junctions that are Anchored at plasma membrane. link the keratin intermediate filaments of one epithelial cell to those of another.

Chloroplast

Specialized organelle in algae & plants that contains chlorophyll. Serves as a site of photosynthesis. organelle found in cells of plants and some other organisms that captures the energy from sunlight and converts it into chemical energy

Cell Junctions in Epithelia

Specialized region of connection b/w 2 cells or a cell and extracellular matrix.

Meiosis

Specialized type of cell division by which eggs and sperm cells are made. Two successive nuclear divisions w only one round of DNA replication generate 4 genetically distinct haploid cells from an initial diploid cell. Maternal and paternal homologs are parceled out to gametes such that each gamete receives one copy of each chromosome. Because the segregation of these homologs occurs randomly, and crossing-over occurs b/w them, many genetically diff. Gametes can be produced from a single individual. In addition to enhancing genetic mixing, crossing-over helps ensure the proper segregation of chromosomes during. Explains both Mendel's laws.

Amino Acid Sequence

Specifies Protein Shape •Amino acids are linked by peptide bonds •Proteins = polypeptides or polypeptide chains •Amino acid sequence - unique order of amino acids in a particular protein •Polypeptide backbone - formed from repeating sequence of core atoms of amino acids •Directionality of peptide chain •N-terminus - end with amino group •C-terminus - end with carboxyl group

INTERMEDIATE FILAMENTS

Stable, ropelike polymers fibers w ~10nm diameter; Others extend across the cytoplasm, giving cells... *mechanical strength. *Distributing the mechanical stresses in epithelial tissue by spanning the cytoplasm from one cell-cell junction to another. -Flexible and have great tensile strength. -Deform under stress but doesn't rupture. -Form a strong, durable network in the cytoplasm of the cell. Helps cells resist tension applied from outside. -Strongest cytoskeleton filaments (survive salt and detergent treatments other filaments do not) strong but flexible -Surround nucleus and create cytoplasmic network Anchored at plasma membrane at cell-cell junctions (desmosomes) -4 major classes: **Intermediate filaments —cytoplasmic—> 1. Keratin filaments—epithelial cells. 2. Vimentin & vimentin-related " " —connective tissue, muscle, and glial cells. 3. Neurofilaments —nerve cells. **Intermediate filaments —nuclear—> 4. nuclear lamins— all animal cells.

Stages of ATP Formation via Membrane

Stage 1 •high energy electrons transferred along series of electron carriers (electron-transport chain) embedded in membrane. -Complexes that pumps H+ ions against concentration gradient. Facilitated via high E electrons being transfered. •Electron transfer release energy that is used to pump protons across the membrane •Generating an electrochemical gradient - form of stored energy. Stage 2 •Protons flow back down electrochemical gradient via ATP synthase. (now has proton gradient across membrane) Become more equilized. ATP synthases - uses E from flow of ions (electrical signal). Driving ADP to ATP that translocates out for other biosynthesis processes. i.e. mitochondria (E formation) and chloroplast (how it uses proton gradient.) •Catalyzes energy-requiring synthesis of ATP from ADP and Pi

Light reactions

Stage 1 of photosynthesis, the set of reactions that converts the E of sunlight → chemical energy in the form of ATP and NADPH.

Photosynthesis Overview

Stage 1: Light reactions. Photosynthesis is a process that takes place in chloroplasts and uses light energy to generate high-energy electrons, which are passed along an electron-transport chain. With proteins of the electron-transport chain located in thylakoid membrane of chloroplasts. -Utilizes solar E. and when dark; ATP + NADPH leaves thylakoid membrane to be used in carbon-fixation cycle. Stage 2: Light-independent reactions "dark reactions"--reduction of CO2 to produce organic compounds i.e. sucrose. +NADPH --Cofactor that is the electron donor for carbon fixation.

2. Prometaphase

Stage of mitosis when the nuclear envelope breaks down Duplicated chromosomes are captured by the spindle microtubules via their kinetochores and undergo active movement Precede metaphase.

Mitogens

Stimulate cell division. Extracellular signal molecule that stimulates cell proliferation. -Animals cells proliferate only if stumuated via extracellular mitogens produced by other cells. -Release the normal intracellular brakes blocking progession from G1 or G0 --> S phase.

Epinephrine in skeletal muscle cells

Stimulates glycogen breakdown. Rapid response to increase in cAMP within seconds All components of response are present when signal is received PKA and its targets, including effectors. Activated GPCR --> Activated denylyl cyclase --> Activated alpha subunit G protein --> phosphorylation signals cyclic AMP then one signal molecule activated PKA --> goes through further phosphorylation --> glycogen breakdown.

Disulfide bond

Strong chemical side bond that joins the sulfur atoms of two neighboring cysteine amino acids to create one cystine, which joins together two polypeptide strands like rungs on a ladder.

Bivalent

Structure formed when a duplicated chromosome pairs w its homolog at beginning of meiosis. Contains 4 sister chromatids.

Contractile ring

Structure made of actin and myosin filaments. Forms a belt around a dividing cell, pinching it in two.

Genetics

Study of genes, heredity, and the variation that gives rise to differences b/w one living organism and another.

Metabolism

Sum of all the chemical reactions that occur in a cell Catabolism: Metabolic process that breaks down large molecules into smaller ones into useful energy for cells due to lost of heat. Used to drive synthesis Anabolism: Chemical reaction in which smaller molecules (monomers) are combined to form larger molecules (polymers)

Embryonic stem cells

(ES cells)- undifferentiated cell type derived from inner cell mass of early mammalian embryo and capable of giving rise to any specialized cell type in the adult. -Come from inner cell mass of early embryo. Pluripotent. 1. Early embryo (blastocyst) - Creates pool of inner cell mass. *Researchers can take out inner cell mass and culture them to in specific factors inducing rise to any type of cell or tissue.

Protein kinase networks

(How integration works) and cell response.

Small Molecules Add Extra Functions

(Left image) Retinal changes shape when it absorbs light, and the rhodopsin visual protein to which it is bound senses this change and starts a series of biochemical reactions. The heme group of hemoglobin binds to oxygen, thereby allowing blood cells to transport oxygen. Also transports electrons Other molecules bound to polypeptides: sugars, lipids, metal ions

stop codons

(UAA, UAG, UGA).

ATP

(adenosine triphosphate) main energy source that cells use for most of their work

Enzyme coupled receptors (receptor tyrosine kinases (RTKs))

(e.g. when a receptor cannot dimerize, etc.) Yield activation of downstreem intracellular signaling pathways.

Action potential

*depolarizing stimulus" only causes a small change in membrane potential. Depolarization - makes the cell less polar (membrane potential gets smaller as ions quickly begin to equalize the concentration gradients) . Voltage-gated sodium channels at the part of the axon closest to the cell body activate, thanks to the recently depolarized cell body. voltage-gated triggers and open.

Cell-surface receptors

+Activates one or more intra. signal. path, each mediated by a series of ISM, then can be proteins or small messenger molecules. Cells reacts to a signal depending on the set of intracellular signaling molecules each receptor produces & how they alter the activity of effector proteins - that have direct effect on behavior of target cell. Intracellular relay system and the intracellular effector proteins acts independent per type of specialized cell to another. Cells respond to the same signal in diff. ways. Most extracellular signal molecules are large & hydrophilic. Unable to cross PM directly; so bind to cell-surface receptors yield in generating one or more intracellular signaling molecules in target cell. -Require extra. sig. molecule bound to cell-surface receptor protein that converts to intra. sig. molecule across PM. -3 main classes: 1. Ion-channel-coupled receptors. 2. G-protein-coupled receptors. 3. Enzyme-coupled receptors

Plasmodesmata (singular plasmodesma)

- Cell-cell junction-connections between plant cells that pass through the cell wall •contains strand of cytoplasm •Consists of a channel of cytoplasm lined by membrane-allows passage of material between cells

Specific Codons in an mRNA Signal the Ribosome Where to Start protein synthesis

- Cells decode mRNAs by reading their nucleotides in groups of three letter genetic code (non overlapping). +Most codons specify an amino acid are read during translation, beginning with a start codon and continuing until a stop codon is reached. mRNA codons are read from 5' to 3' , and they specify the order of amino acids in a protein from N-terminus (methionine) to C-terminus. -Three "stop" codons mark the end of a protein UAA, UGA, UAG. -One "start" codon, AUG, marks the beginning of a protein and also encodes the amino acid methionine. -tRNA - adapters b/w mRNA and proteins. -Reading frame - each potential starting point for interpreting the 3 letter code.Translation of correct message requires selection of the correct frame. -DNA - only 4 bases (A, T, G, C), and must code for 20 amino acids.

actin-bind proteins

- Controls whether monomer versus filament. i.e. nucleating protein (i.e. formin, ARP complex)

RNA transcript and RNA polymerase *polarity of template strand

- Enzyme that transcribes DNA to RNA. -Many molecules of enzyme can simultaneously transcribe same gene. Transcription is the process in which a gene's DNA sequence is copied (transcribed) to make an RNA molecule. When an RNA transcript is first made in a eukaryotic cell, it is considered a pre-mRNA and must be processed into a messenger RNA (mRNA). A 5' cap is added to the beginning of the RNA transcript, and a 3' poly-A tail is added to the end. In splicing, some sections of the RNA transcript (introns) are removed, and the remaining sections (exons) are stuck back together.

DNA TO RNA

- Eukaryotes, Protein-Coding Genes Are Interrupted by Noncoding Sequences Called Introns

RNA molecules

- Fold into specific structures. -Held via hydrogen bonds b/w different base pairs.

Cyclin-Cdk Specificity

- G1 --> S Active S-Cdk and S cyclin complex. -G2 --> M Active M-Cdk and M cyclin complex.

Ion channel

- K+ leak channel; PM most animal cells. Maintenance of resting membrane potential. Voltage-gated Na+; PM nerve cell axon. Generates action potential. Voltage-gated K+; PM nerve cell axon. Return of membrane to resting pot. after initiation of an action pot. Voltage-gated Ca2+; PM nerve terminal. Stimulation of neurotransmitter release.

Membrane phospholipids move within the lipid bilayer.

- Lateral diffusion: -Flexion: -Rotation: -Flip-flop (rare):

Endoplasmic Reticulum (ER)

- Lipid bilayer Membrane Assembly Begins. -Phospholipids are randomly distributed. 1. Newly synthesized phospholipids are added to the cytosolic side. 2. redistributed by transporters that transfer them from one half of the lipid bilayer to the other. -Some new membrane stays in ER; the rest is used to supply other organelles

Translation

- Mature Eukaryotic mRNAs are exported from the Nucleus. -mRNA Molecules Are Eventually Degraded in the Cytosol.

•Cell wall

- Mechanically strong fibrous layer deposited outside the PM of some cells. Prominent in most plants, bacteria, algae, and fungi, NOT in animal calls. boxlike structure that encloses, protects, immobilizes, and shapes each cell - type of extracellular matrix. -Each cell surrounds itself w extracellular matrix forming wall- made of cellulose and other polysaccharides.

Electrochemical H+ Gradients

Symport Drive the Transport of Solutes in Plants, Fungi, and Bacteria. Instead of Na+ pumps (animal cells only). Create proton gradient for symporters to transport sugars and amino acids into cell Create acidic environment outside cell. Also used in organelle membranes to acidify interior of organelle (e.g. lysosome)

Eukaryotic mRNAs

- Processed in the Nucleus. -modified by capping and polyadenylation.

TFIIB

- Promotors located @ -35

The proton gradient that drives ATP synthesis during photosynthesis is generated by which of the following?

- Stage 1 of photosynthesis, electron carrier that pumps protons out of the stroma into the thylakoid space--ATP is synthesized. (concentrated in thylakoid space) Cytochrome b6-f complex is the sole proton pump in the photosynthetic electron-transport chain; it uses energy from the transfer of electrons released by photosystem II to pump H+ into the thylakoid space.

•Hemidesmosome

- Structure that anchors (connect) epithelial cells (intermediate filaments) to basal lamina beneath them. Epithelial cells are attached to the basal lamina by hemidesmosomes. The interaction is mediated by integrins in the basal plasma membrane of the epithelial cell binding to laminins in the basal lamina. -Attach basal face of epithelial cell to basal lamina, a specialized sheet of extra. matrix. +Attachment is mediated by transmembrane integrin proteins liked to intra. keratin filaments. Tight Junction.

Signals in DNA tell RNA polymerase

- Where to start and stop transcription. RNA synthesis begins is formed —> Sigma factor is released —> polymerase clamps firmly down on DNA; RNA synthesis continues —> RNA transcript grows; termination and release of both polymerase & completed RNA transcript —> Release of Terminator sequence and rebinding of sigma factor.

Buffer

- a chemical or combination of chemicals that keeps pH within normal limits. Health of organisms requires maintaining the pH of body fluids within narrow limits. Human blood is normally pH 7.4 (slightly basic). If blood pH drops below 7.0, acidosis. If blood pH rises above 7.8, alkalosis. Both are life-threatening situations. The body has built-in mechanisms to prevent pH changes.

Tissue

- collection of specialized cells of the same or similar type that perform a common function in the body. -Cooperative assembly of cells and extracellular matrix woven together- form a distinctive multicellular fabric w specific function. Four Main Types: Connective, epithelial, muscle, and nervous.

•Desmosome

- different cadherins that connect to keratin filaments to those in a neighbor(specialized intermediate filaments in epithelial cells. Tight Junction.

•Adherens junctions

- hold epithelial cells together via cadherins (epithelium) tethered with linker proteins to actin filaments . Joins actin bundle in one cell to a similar bundle in a neighboring (epithelial) cell. epithelium: actin filaments inside the cell attach to its cytoplasmic face. Cell adhesion proteins of cadherin family span the epithelial cell PM & bind to identical cadherins in adjacent epithelial cells. -During development, actin bundles at adherens junctions connect cells in an epithelial sheet can contract-helping epithelium to bend & pinch off-forming epithelial tube or vesicle. Tight Junction

•Primary cell wall

- initial cell wall of newly formed cells, expands slowly during growth •Turgor pressure - result of osmotic imbalance between interior of plant cell and surroundings - lettuce leaf

ATP synthase

- large, multi-subunit protein embedded in the inner mitochondrial membrane. Large protein that uses energy from H+ ions to bind ADP and a phosphate group together to produce ATP •Movement of protons through the ATP synthase is thought to produce mechanical motion of the stalk. Somehow, this motion drives the synthesis of ATP in the head. If the proton gradient is small enough, the ATP synthase functions instead in reverse - as an ATPase which pumps protons to the intermembrane space. (ATP hydrolysis occurs) Potential E drives synthesis of ATP. Not energetically favorable. E comes from gradient. 1. ATP synthesis: 2.ATP hydrolysis:

ATP Synthase

- large, multi-subunit protein embedded in the inner mitochondrial membrane. •Movement of protons through the ATP synthase is thought to produce mechanical motion of the stalk. Somehow, this motion drives the synthesis of ATP in the head. If the proton gradient is small enough (F1 ATPase), the ATP synthase functions instead in reverse - as an ATPase which pumps protons to the intermembrane space. Electron transport complexes and ATP synthases/proton pumps are found in the plasma membranes of modern bacteria; these ATPases generate proton gradients used for transport of molecules across the membranes.

Stratified Epithelia

- layers of cells

Cellulose Microfibrils

- main long, thin polysaccharide fibers, and unbranched chains of glucose. Helps strengthen plants cells. Tend to ring plant cells like a series of belts. +Each glucose subunit is inverted w respect to its neighbors and joined via beta1,4-linkage. +~16 cellulose molecules held via hydrogen bonds in single cellulose microfibril. •Resists both compression (stretching) and tension, turgor pressure pushes cells to grow out either end of the belt loops. Plant cell elongate perpendicular to the orientation of the cellulose microfibrils.

•Secondary cell wall

- more rigid wall that develops after growth ceases

Endosymbiosis

- one organism lives inside another organism Mitochondria and chloroplasts share many similarities with bacteria: •Reproduce in a manner similar to prokaryotes •Harbor bacterial-like machinery for making RNA and proteins •Possess DNA-based genomes. -Retain own genome and divides similar to bacterial cell division.

Gap Junctions

- plasma membrane channels are joined (allows communication) •Important in heart muscle and smooth muscle. Animal tissues, specialized connection b/w juxtaposed cells through which ions & small molecules can pass from one cell to the other. - Form channels allowing the direct passage of inorganic ions & small, intracellular water-soluble hydrophilic molecules, inorganic molecules and metabolites from cell-cell.

Apoptosis

- programmed cell death. A tightly controlled form of cell suicide that allows cells that are unneeded or unwanted to be eliminated from an adult or developing organism. Major form of apoptosis. •Normal process that occurs throughout the life of an organism - including during development. •During digit formation in organisms with independent digits (e.g. mouse and human) •During metamorphosis of tadpoles into frogs - loss of tail from tadpole

Simple Epithelia

- single layer of cells •Classified according to cell type +Squamous epithelium - flattened cells +Cuboidal epithelium - cube-shaped cells +Columnar epithelium - cells that resemble columns

Plasma MEMBRANE PROTEin

-50% of mass of membrane. -Lipid molecules in membrane are 50x more abundant than protein molecules. -Has a variety of functions: Transports & channels, anchors, receptors, and enzymes. -Some properties need to be separated from membrane & analyzed on their own via solubilized in detergents.

Redox reaction

-A reaction in which electrons are transferred from one chemical species to another. An oxidation-reduction reaction. +Reduction = gain of electrons (or hydrogen atoms (e- + H+) +Oxidation = loss of electrons (or hydrogen atoms (e- + H+) Respiratory enzyme complex Set of proteins in the inner mitochondrial membrane. Facilitates the transfer of high-energy electrons from NADH to H2O while pumping protons into the intermembrane space.

Cholesterol

-A sterol. -tends to stiffen cell membranes. -Hydrophilic heads. -OH. *movie 11.3 & 11.4 properties of membrane lipids and their effects on membrane fluidity

Acetylcholine and Glutamate receptor

-Acetylcholine-gated cation channel. PM of muscle cell @ neuromuscular junction. Excitatory synaptic signaling. -Glutamate-gated cation channel. PM of many neurons @ synapses. Excitatory synaptic signaling.

Receptor Tyrosine Kinases (RTKs)

-Activated RTKs Recruit a Complex of Intracellular Signaling Proteins. +can have a dramatic effect on the organization of actin filaments in fibroblasts. -Enzyme-coupled receptor where the intracellular domain has tyrosine kinase activity activated by ligand binding to the receptor extracellular domain. -Phosphorylate themselves and selected intra. sig. proteins on tyrosines. -Phosphotyrosine on RTKs--serve as docking sites for various intra. sig. proteins. -Inactive catalytic domain (RTK) binds to dimer and stimulated kinase activity across PM. -Active RTK serves as docking site and activates intracellular signaling proteins. (activation of downstream intra. sign. pathways)

Acetyl CoA

-Activated carrier: acetyl group

Rise in cytosolic Ca2+

-Activates troponin and tropomyosin complexes troponin is a Ca2+ sensitive protein --> changes shape when Ca2+ level rises this causes tropomyosin movement on actin filament, allowing myosin to bind actin. -T tubules and the sarcoplasmic reticulum surround each myofibril. +T tubules are inward projects of the plasma membrane (channels). +Skeletal muscle contraction is triggered by the release of Ca2+ from the sarcoplasmic reticulum to the cytosol.

Cyclin-Cdk Activity Regulation - inactive p27-cyclin-Cdk complex

-Active cyclin-Cdk complex --> inhibited by p27 --> p27-cyclin-Cdk complex (inactivated)

Actin-specific drug

-Affect cellular movements, which rely on assembly and disassembly of actin filaments: -Phalloidin-- binds & stabilizes filaments. -Cytochalasin--caps filaments plus ends, preventing polymerization there. -Latrunculin--binds actin monomers & prevents their polymerization.

mRNA processing events

-After termination, transcription is finished. An RNA transcript that is ready to be used in translation. -In bacteria, RNA transcripts are ready to be translated right after transcription.

Development from a single cell

-All multicellular organisms arise from a single fertizlised egg. -All cells of an individual contain the same genome, but each cell type expresses diff. Set of genes/proteins. -Differentiation and specialization forming tissues/organs required once development begins..

Intermediate Filaments Are Strong and Ropelike

-All protein-protein interactions are non-covalent. -Central rod domains: similar among different filament types. Pack together into similar structures. -Terminal head and tail domains: vary from one filament type to another. Interact with specific partner proteins. -Dimers face opposite direction —> therefore the ends of the tetramer are the same (N termini of filament proteins). 1. Alpha-helical region of monomer (NH2 --COOH) 2. Coiled-coil dimer ( 2 alpha-helical); staggered antiparallel tetramer of 2 coiled-coils. 3. Lateral association (8 tetramer) 4. Addition of 8 tetramers to growing plus end.

Transcription switches

-Allow Cells to Respond to Changes in Their Environment.

The cell-cycle control system uses Cdk inhibitory proteins to

-Arrest the cell cycle @ specific transition points. -Some Cdk inhibitor proteins, for example, keep Cdks in an inactive state during the G1 phase of the cycle, thus delaying progression into S phase.

Mitotic Spindle Composition

-Astral MT; spindle pole. -Kinetochore MT; duplicated chromosomes (sister chromatids). When nuclear envelope breaks down, spindle MT capture duplicated chromo. at the equator of metaphase spindle. -Interpolar MT; Kinetochore.

Extracellular signal molecules

-Bind either to cell-surface receptors or to intracellular receptors. -Any molecule present outside cell that can elicit a response inside cell once bound to a receptor. 1. Hundreds of signals at any given time in a multicellular organism. Two major classes, depending type of receptor. 1st largest class: Large and/or hydrophilic - can't cross PM of target cell. *Via cell-surface 2nd class: small and hydrophobic enough to pass PM and into cytosol of target cell. *Via intracellular receptors. Alone isn't the message: the information conveyed by the signal depends on how target cell receives and interprets the signal. 2. Each cell responds selectively to signals it encounters receptors needed for response: -each cell expresses a particular set of receptors 1. cell surface receptors (focus of chapter) 2. intracellular receptors

Transcription Regulators*Concept

-Bind to Regulatory DNA Sequences. typically bind in the major groove of DNA at specific sequences. bind to DNA as dimers. base pairing in double helix not disrupted

calmodulin

-Ca2+ then acts as 2nd messenger--altering activity of Ca2+ responsive proteins. -Small Ca2+-binding protein. Modifies activity of many target proteins due to changes in Ca2+ concentration. i.e. calmodulin-dependent protein kinases (CaM-kinases). +Enzyme that phosphorylates target proteins due to increase in Ca2+ ion concentration through its interactions w Ca2+-binding protein calmodulin.

A small, bipolar myosin-II filament

-Can slide two actin filaments of opposite orientation past each other. (contraction) -Head of a myosin-II molecule walks along an actin filament through an ATP-dependent cycle of conformational changes.

Triton X-100

-Can solubilized membrane proteins. -Mild detergent.

messenger RNAs (mRNAs)

-Carry instructions for making proteins. -Sequence is decoded in sets of 3 nucleotides. -During RNA to protein; mRNA message is decoded on ribosomes. -Located on outer surface of rough ER. RNA molecules need to go through special processing steps before translation. That means translation can't start until transcription and RNA processing are fully finished. Pre-mRNA and has to go through some processing steps to become a mature messenger RNA (mRNA) that can be translated into a protein. Addition of a 5' cap to the beginning of the RNA. [Cap]. +Added to the first nucleotide in the transcript during transcription. The cap is a modified guanine (G) nucleotide, and it protects the transcript from being broken down. It also helps the ribosome attach to the mRNA and start reading it to make a protein. Addition of a poly-A tail (tail of A nucleotides) to the end of the RNA. [Tail] +Nucleotides to the cut end, forming a poly-A tail. The tail makes the transcript more stable and helps it get exported from the nucleus to the cytosol. Chopping out of introns, or "junk" sequences, and pasting together the remaining, good sequences (exons) then RNA yields mature mRNA. It can travel out of the nucleus and be used to make a protein.

Cyclin-Cdk Activity Regulation - active M-Cdk

-Cdks can be inactivated by phosphorylation. Mitotic Cdk binds to M cyclin --[inhibitory kinase]--> inactive M-Cdk (inhibitory phosphates ) --[dephosphorylation]--> activates phosphatase (Cdc25) --> active M-Cdk

Flippases

-Certain Phospholipids Are Confined to One Side of the Membrane. -Help to establish and maintain the asymmetric distribution of phospholipids start in Golgi is a characteristic of animal cell membranes. help to establish and maintain the asymmetric distribution of phospholipids characteristic of animal cell membranes. asymmetric distribution of phospholipids starts in the Golgi. move lipids to cytosolic face

Cilia and Flagella

-Contain Stable Microtubules Moved by Dynein. -Many hairlike cilia project from the surface of the epithelial cells that line the human respiratory tract A cilium beats by performing a repetitive cycle of movements, consisting of a power stroke followed by a recovery stroke. Flagella propel a cell through fluid using repetitive wavelike motion. Rhythmic beating cause by bending MT--driven via ciliary dynein motor protein.

Eukaryotic promoters

-Contain sequences that promote the binding of the general transcription factors.

Eukaryotic Transcription Regulators

-Control Gene Expression from a Distance.

ribosomal RNA (rRNAs)

-Crucial to forming the core of the ribosome's structure. -Catalyze protein synthesis.

Epidermis cross section

-Dead cells on surface. -Langerhans cell (involved in immune response) -Melanocyte - producing pigment granules. -Keratinocytess

Cell Crawling

-Depends on Cortical Actin (= associated with cortex). -Amoeba crawling, Axon development, Neutrophil migration.

Differentiated cells

-Different Cell Types of a Multicellular Organism Contain the Same DNA. -contain all the genetic instructions needed to direct the formation of a complete organism.

Cell Size Varies Across Tissues and Organs

-Different cell types within the same animal can vary greatly in size. i.e. Neuron and liver cell. -Adult animal: +Most tissues are maintained and renewed by the same basic cell processes that generated them in the embryo: cell proliferation, movement, differentiation, and death. +In embryo- processes are controlled via intra. communication, selective cell-cell adhesion, and cell memory.

Electron-Transport Chain

-Electrons are donated to the first carrier by a high energy carrier like NADH. -Each complex contains multiple proteins that extract the energy of the electrons to pump protons from the matrix to the intermembrane space. -Electrons are carried between complexes by mobile electron carriers.

tRNA binding at ribosomal A, P, & E sites --P site occupied; question about A site.

-Elongation occurs when initiator tRNA (in P site) 1. Positioning the correct aminoacyl-tRNA (A site). 2. Forms a peptide bond. 3. Shifting mRNA by one codon [translocation]. +Ribosome must align 2 charged tRNA so anticodons interact w correct mRNA codon. -5' anticodon - has some flexibility in base pairing. -3' codon.

Fat molecules

-Entirely hydrophobic

Producing mRNA molecules

-Euk: More complex. -Prokar: simple.

Dense connective tissue of dermis

-Fibroblast - -Elastic fiber - -Collagen fibers -

Some Extracellular Signal Molecules Cross the Plasma Membrane and Bind to Intracellular Receptors

-Fig. 16-40: small, hydrophobic hormones bind to intracellular receptors that act as transcription regulators. -Fig. 16-41: Cortisol activates a transcription regulator yielding in transcription of target gene.

G-protein-coupled receptors (GPCRs)

-Form the largest family of cell-surface receptors. -More than 700 GPCRs (humans), and ~1000 involved in only the sense of smell (mice). -Mediate responses to a diversity of extracellular sig. molecules, including hormones, local mediators, and neurotransmitters. -Signal molecules that bind GPCRs are varied in structure as they are in function: can be proteins, small peptides, or derivatives of amino acids or fatty acids, and for each one there is a diff. receptor or set of. -Due to involvement in such large variety of cell processes, they are an attractive target for development of drugs to treat many disorders. -All GPCRs have similar structure: made of a single polypeptide chain that threads back and forth across lipid bilayer 7 times. -Rhodopsin (light-activated photoreceptor protein in the vertebrate eye): GPCR super family, the olfactory (smell) receptors in the vertebrate nose, and those involved in mating rituals of sing-celled yeast. -Ancient: even prokaryotes posses similar membrane proteins. i.e. bacteriorhodopsin: functions as a light-driven H+ pump. Resemble euk. GPCRs, but don't act through G proteins, but are coupled to other signal transduction systems. -Stimulate ion channels and regulate membrane-bound enzymes; that control the concentrations of small intra. messenger molecules, including cyclic AMP and Ca2+, that control the activity of important intracellular signaling proteins. --found in eukaryotes from yeast to mammals. In animals GPCRs are used in endocrine, paracrine, and neuronal signaling. -Repond to extra. signals by activating one or more intra. signaling pathways--that activate effector proteins that alter behavior.

Small subunit of complete eukaryotic ribosome

-Formed from ~33 ribosomal proteins + 1 rRNA molecules. -MW = 1,400,000

Large subunit of complete eukaryotic ribosome

-Formed from ~49 ribosomal proteins + 3 rRNA molecules. -MW = 2,800,000

Lipid Bilayer Is a Flexible Two-dimensional Fluid

-Free movement of molecules within the plane of the bilayer (2 dimensional fluid, Movie 11.1) -Bilayer is bendable, but to a limit: smallest vesicles are 25 nm in diameter. Pure phospholipids can form closed, spherical liposomes.

Dominant mutation

-Gain of function. -Proto (initial) - oncogene (cancer promoter) -Start out normal until disruption to cell that triggers to cancer cell (oncogene). -Normal cell (proto-oncogene) —-[mutation in one copy of proto-oncogene] —> Hyperactive oncogene —> excessive cell survival, proliferation, or both. -Itself can drive proliferation when mutated. -One recent promising approach uses drugs that lead to ubiquitination and proteasomal degradation of the target protein. Which of the following mutated proteins are good candidates for this approach? A: are normal cellular genes that contribute to cell proliferation in a regulated, controlled fashion. A gain-of-function mutation in a proto-oncogene converts it into an oncogene that causes unregulated cell proliferation and contributes to cancer. These oncogenes need to be inhibited, either through the binding of inhibitory molecules (via drugs such as Gleevec) or by tagging for destruction. A recent exciting approach to eliminating oncogenes is tagging them with ubiquitin, leading to proteasome destruction

GPCR Signaling Pathway

-Generates a Dissolved Gas That Carries a Signal to Adjacent Cells. -Endothelial cell --> Acetycholine --> IP3 -> Ca2+ -> Nitric oxide (NO) [Locally acting gaseous signal molecule that diffuses across cell membranes] to affect activity of intracellular proteins.--> GTP -> cyclic GMP t[riggers smooth muscle relaxation in a blood-vessel wall]. -All GPCRs possess a similar structure. -The polypeptide chain traverses the membrane as seven alpha helices. The cytoplasmic portions of the receptor bind to a G protein inside cell. -Receptors that recognize small signal molecules, i.e. acetylcholine or epinephrine, the ligand usually binds deep w/i the plane of the membrane to a pocket that is formed by amino acids from several transmembrane segments. -Receptors that recognize signal molecules that are protein usually have a large, extracellular domain that, together w some of the transmembrane segments, binds to protein ligand. -Extra. sig. mole. binds to a GPCR, the receptor protein undergoes a conformational change, enabling the activation of G protein on other side of PM.

Galactocerebroside

-Glycolipid. -Hydrophilic heads. Gal and OH.

Bacterial promoters and terminators

-Have specific nucleotide seq. recognized by RNA polymerase.

Actin filaments (microfilaments; MF)

-Helical polymers of globular actin (protein) monomers. -More flexible that MT structures w diameter ~7 nm. -Organized into a variety of linear bundles, 2-D networks, and 3-D gels. -a major constituent of all eukaryotic cells, this cytoskeletal element is essential for cell movement and for the contraction of muscle cells. -Polarized--a fast-growing plus end and slow-growing minus end.--assembly & disassembly controlled via hydrolysis of ATP tightly bound to each actin monomer & by various actin-binding proteins. -Dispersed throughout cell, but are most concentrated in cortex: layer of cytoplasm beneath PM. Usually in bundles or networks (not single filaments) shorter than microtubules but far more numerous Actin represents ~5% of a cell's total protein content! Essential for many cellular movements and many stable cell structures -Extra. signals change conformation of AF. i.e. microvilli, small contractile bundles, dynamic protrusions, and contractile ring.

Controlled Protein Breakdown

-Helps Regulate the Amount of Each Protein in a Cell.

Cells receive signals, From the environment From other cells = Cell signaling, (focus of chapter)

-I.e. via receptors that recognize, and respond specifically to the signal molecule.

Plant cells

-In constant communication w one another via cell-cell interactions: Allowing them to coordinate what happens in its roots, stems, and leaves.

Light induced signaling cascade

-In rod photoreceptor cells greatly amplifies the light signal.

transcription and cell fate determination

-In transcription, the DNA sequence of a gene is "rewritten" in RNA. -In eukaryotes, the RNA must go through additional processing steps to become a messenger RNA, or mRNA.

Polymer

Synthesis Requires Energy Input

Endoplasmic Reticulum (ER)

Synthesis of most lipids; proteins for distribution to many organelles and to PM. 12% of total cell

Cytoskeleton

-Intricate network of protein filaments that extend throughout cytoplasm. +Filamentous structure helps to support the large volume of cytoplasm, a function that is particularly important in Animal cells, have no cell walls. Highly dynamic structure that is continuously reorganized as a cell changes shape, divides, and responds to its environment. Also directly responsible for large-scale movements, incl crawling of cells along cell-surface. -Gives a cell its shape and allows it to organize its internal components & move. IMG: Microtubules (green) and Actin filaments (red). Overlap of the two (yellow). Nucleus (blue). Eukaryotic cells: Most prominent and provides it to organize the variety of components in their interior, adopt variety of shapes, interact mechanically w environment, and carry out coordinated movements. -Provides structural support for large volume in eukaryotic cells. - Maintains cell integrity during mechanical stress. -Confers shape to cells Over all is highly organized, dynamic—changing and reorganizing itself, generates cell movements-- crawling on a surface, muscle contraction, cell shape changes, and cell division.

Reading frame

-Know the concept and how it Affect translation prdt.

Translation**

-Know the order of tRNAs binding to ribosome E, P, and A sites during elongation -What is bound to tRNAs in those sites. -gene that's transcribed encodes a protein (which many genes do), the RNA molecule will be read to make a protein

Cancer characteristics

-Lack differentiation: 1. Cells are non-specialized. 2. Cells are immortal (enters cell cycle repeatedly) -Abnormal nuclei: 1. May be enlarged. 2. Have abnormal number of chromosomes. 3. Often have extra copies of genes. -Doesn't undergo apoptosis: 1. Normally, damaged DNA undergoes apoptosis. 2. Immune system can also recognize abnormal cells and trigger apoptosis. 3. Cancer cells are abnormal but fail to undergo apoptosis producing large mass of cells. -Also caused by alterations in cell proliferation, DNA damage response, cell growth, and cell survival. -Pathway: 1. One mutation (w/i epithelial cell of basal lamina) 2. Proliferation** 3. Cancer usually begins after 3rd mutation which increases the advantage further and makes the cell invasive.

Complete Eukaryotic ribosome

-Large & small subunit w ~82 different proteins + 4 different rRNA molecules. -MW = 4,200,000 -catalyzes peptide bond formation. Move 5' → 3' along mRNA. Composed of both rRNA and protein (small [30s] and large subunit [50s]. -Accessory protein factors - assist ribosome. -mRNA - carries info. -Charged tRNA molecules - carries activated AA. -Peptide growth - N to C direction.

Photosystem

-Large multiprotein complex containing chlorophyll. Carries light E & converts it into chemical bond E. Consists of a set of antenna complexes & a reaction center. ETCs associated with--to transfer electrons from water to NADP+ → NADPH + O2 (by-product). During photosynthesis in chloroplast & photosynthetic bacteria--E of sunlight captured by chlorophyll molecules embedded in these large protein complexes. In plants, located in thylakoid membranes of chloroplasts in leaf cells.

Properties of phospholipids affecting their movement (fluidity)

-Length of hydrocarbon tails (14 - 24 Carbons) -Number of double bonds in hydrocarbon tails. 1. none on one hydrocarbon chain (saturated) 2. 1 or more on the other hydrocarbon chain (unsaturated) -looser packing of adjacent hydrocarbon chains. -unsaturated hydrocarbon chains --> more fluidity. i.e. Phosphatidylcholine is the most common phospholipid in cell membranes

RNA AND THE ORIGINS OF LIFE

-Life Requires Autocatalysis. -Can Store Information and Catalyze Chemical Reactions. -Thought to Predate DNA in Evolution. 1. Original RNA sequence serves as template to produce complementary RNA sequence. 2. complementary RNA sequence serves as template to produce original sequence.

Recessive mutation**

-Loss of function. -Keeps genes in check. -Relieved of inhibition to drive proliferation when mutated.

Loose connective tissue of dermis

-Macrophage - -Collagen fiber - -Fibroblast - can attach indirectly to collagen via which type of extracellular matrix protein (fibronectin) -Endothelial cell forming capillary - -Lymphocyte. -

mRNA molecules**

Synthesis of protein in... -Eukaryotes - More complex. -Prokaryotes -

Intracellular signaling proteins

-Many extracellular signals activate intracellular signaling pathways to change the behavior of the target cell. -can relay, amplify, integrate, distribute, and modulate via feedback an incoming signal. 1st: Primary transduction: A receptor protein on the cell surface transduces an extra. cellular sig. —> intracell. sig, which initiates one or more intracell. signaling proteins that can function in various ways. i.e. Integrate signals from other intracellular signaling pathways. Many of the steps in the process can modulate via feedback by other molecules or events in the cell. *Some proteins in the pathway may be held in close proximity by a scaffold proteins, that allows them to be activated @ a specific location in the cell and w greater speed, efficiency, and selectivity. Production and function of small intracellular messenger molecules. Primary transduction:

Mitochondria Structure

-Matrix: Contains high concentration of enzymes. i.e. those req. for oxidative of pyruvate and fatty acids, and citric acid cycle. -Inner membrane--encloses mitochondrial matrix, the citric acid cycle produces a lot of NADH and FADH2 via oxidation of acetyl CoA from sugars & fatty acids. Folded into numerous critse- contains proteins carrying out phosphorylation i.e. ETC, ATP synthase (makes ATP), and transport proteins that move selected molecules in & out of matrix. +A lot of the E released via electron transfers along electron-transport chain (ETC)-- is harnessed to pump protons (H+) out of matrix, creating an electrochemical proton gradient. +Embedded are 3 large respiratory enzyme complexes--carries out proton pump. -Outer layer: Contains large channel-forming proteins (porin), permeable to molecules (<5000 Da) -Intermembrane space: Contains several enzymes; using ATP going out of matric to phosphorylate other nucleotides. & proteins that release during apoptosis. -Animal cells, produce most ATP--using E from oxidation of -

Following vesicle docking, SNARE proteins can catalyze the fusion of the vesicle and target membranes.

-Membrane fusion is energetically unfavorable. water needs to be displaced from hydrophilic surfaces. membranes do not fuse randomly (which is a good thing for the cell). -For vesicle fusion, SNARE proteins catalyze process. v-SNAREs and t-SNAREs wrap around each other and pull membrane to within 1.5 nm. close proximity allows lipids to intermix and membranes to fuse

Mitochondria Localization

-Mitochondria can change their shape, location and number to suit a cell's need. i.e. 1. Cardiac muscle: Mitochondria and myofibril of contractile apparatus. -Where ATP hydrolysis gives energy for contraction. 2. Sperm Tail: Mitochondria and flagellar core. -Needs ATP to move.

Feedback regulation

-Modulate response to the signal by regulating the activity of components upstream in sig. pathway Important feature of cell signaling. Occur anywhere in the signaling pathway. Either boost or weaken response to the signal. Common in biological systems and can lead to sophisticated responses: Pos. feedback; generate all-or-none, switch-like responses. Neg. feedback; generate responses that oscillate on & off as activities or concentrations of inhibitory components rise & fall. 1. Relay signal onward to assist spreading it through the cell via scaffold. 2. Transduce and amplify the signal received, making it stronger, so few extra. sig. molecules are enough to evoke a large intra. response. +Forms small intracellular messenger molecules. 3. Detect signals from more than one intra. sig. pathway and integrate them before relaying a signal onward or reused. 4. Distribute signal to more than one effector protein, creating branches in the information flow diagram; evoking a complex response. 5. Modulate response to the signal by regulating the activity of components upstream in sig. pathway, Aka FEEDBACK. 6. Final product after distribution; altered metabolism, cell shape or movement, and gene expression.

Na+ pump (Na+-K+ ATPase)

-Most Animal Cells Uses Energy Supplied by ATP hydrolysis to export 3 Na+ and import 2 K+ of PM. - also keeps Cl- outside of cell indirectly (Cl- partially balances Na+ outside cell).

Kinesins and cytoplasmic dyneins

-Motor proteins that drive Intracellular Transport: Both move in opposite directions along MT--carry specific organelles, vesicles, and other types of cargo to certain locations in cell. Two globular heads at one end, which bind and hydrolyze ATP and interact with MT Single tail at the other end, which interacts with cargo. Both proteins have tail + globular head: Cytoplasmic dynein binds to adaptor protein + cargo (i.e. vesicle) migrates towards minus end Kinesin (binds to a variety of cargo) + adaptor protein then migrates towards plus end . Different motor proteins transport different types of cargo along MT

Signaling pathways and stem cells (renewal)

-Needed in gut; proliferation activator. Wnt pathway (active): -Below crypt containing stem cells. -Wnt, ligand, and proteins turn on triggering cell division of stem cell. (proliferation begins) -Ligand that binds to receptor triggering intracellular signaling. (overall triggering cellular proliferation) Wnt pathway (inactive): -Cells migration through crypt and lose contact w Wnt. -Proliferation stops.

Voltage-gated Ca2+ Channels in Nerve Terminals Convert an Electrical Signal into a Chemical Signal

-Neurons -Electrical signal --> secreted chemical signal @ nerve terminal.

Lamins

-Nuclear intermediate filament proteins.

A cell can express different genes

-Occur at different rates depending on gene being coded from DNA to RNA.

cap binding protein

-Occurs @ 5' cap.

"capping proteins" Ch. 17

-Only some proteins that bind plus-ends of microtubule (MT) are "capping proteins", stabilize the MT; other such proteins could be destabilizing. Fast-growing plus ends maintain the presence of GTP-bound tubulin dimers.

Eukaryotic Cell Cycle

-Orderly set of stages from the first division of a eukaryotic cell to the next time the resulting daughter cells divide. -Related group of intracellular proteins that regulates apoptosis. -Some family members promote cell death, others inhibit it. Just prior to division: 1)Cell grows larger. 2)Number of organelles doubles. 3)DNA is replicated. -Two major stages: Interphase--cells grow and nuclear DNA is replicated. Mitotic stages (mitosis and cytokinesis)--Nucleus divides (mitosis) followed by the cytoplasm (cytokinesis).

Cancer-critical genes

-P53: Triggers apoptosis. Once mutated can't undergo apoptosis. - APC (component of Wnt signaling pathways) Normally degrades beta-catenin. Once no longer regulating beta-catenin then proliferation proceeds. promote the proliferation of the stem cells and precursor cells at the base of each intestinal crypt. Changes in Wnt signaling can lead to a failure of intestinal development or to the formation of intestinal tumors.

Actin-specific drugs

-Phalloidin: Binds and stabilizes filaments. -Cytochalasin: Caps filament plus ends, preventing polymerization there. -Latrunculin: Binds actin monomers and prevents their polymerization. These drugs affect cellular movements, which rely on assembly and disassembly of actin filaments

Phosphatidylserine*General features not atomic details. Know name.

-Phospholipid. -Hydrophilic heads. Serine (NH3+) and phosphate group (PO3-)

Osmotic swelling pressure

-Plant cells: keep plant tissue turgid.

Actin and Tubulin

-Polymerize by Similar Mechanisms: Treadmilling: -Minus end release (actin w bound ADP) --> out ADP and in ATP (actin monomer w bound ATP) adds to plus end and becomes phosphorylated -Grow at plus and minus end, but plus end growth faster Filaments are unstable(disassemble from both ends) Free monomers bind ATP --> hydrolyze to ADP after incorporation into filament ADP-bound monomers bind less strongly to each other --> disassemble.

Membrane proteins

-Proteins constitute 50% of mass of membrane. (embedded in lipid bilayer) -Lipid molecules in membrane are 50x more abundant than protein molecules.

Coronavirus has a RNA genome

-RNA Is Thought to Predate DNA in Evolution. Replicates its genome via a complementary RNA strand intermediate.

termination

-RNA polymerase will keep transcribing until it gets signals to stop. The process of ending transcription.

5. Telophase - Nuclear Envelope Reforms

-Reforms around the two sets of segregated chromosomes forming 2 new nuclei, then completing mitosis. -Nuclear envelope reassembles around each set, completeing formation of 2 nuclei and marking end of mitosis. Division of cytoplasm begins w assembly of the contractile ring. Interphase nucleus--[phosphorylation of nuclear pore and lamins]--> prometaphase --[dephosphorylation of nuclear pore and lamins] --> telophase --[continued fusion of nuclear envelope vesicles]--> interphase nucleus Final stage of mitosis when two sets of separated chromosomes decondense and become enclosed by a nuclear envelope.

GTP-binding protein

-Regulation by GTP Hydrolysis. -GTP (guanosine triphosphate) is a regulator that binds "GTP-binding-proteins" (G protein) to activate them. •activation of these proteins is regulated by the binding of another protein to the G protein •this protein speeds the release of GDP, so that GTP can bind again. •The G protein eventually inactivates itself by hydrolyzing the bound GTP. •GTP-binding proteins bind GTP - they do not phosphorylate GDP to produce GTP

Stem cells

-Relatively undifferentiated, self-renewing cells that produce daughter cells that either differentiate --> specialized cells OR remain as a stem cell (self-renewal). -Specialized cells (receives signal to begin) --> Proliferating precursor cells --> 2 terminally differentiated daughter cells (terminal differentiation)

Intracellular signaling proteins*

-Relay, amplify, integrate, distribute, and modulate via feedback an incoming signal. 1. Feedback regulation yields in: (signaling pathway 1) positive feedback and (signaling pathway 2) negative feedback. 2. Molecular switches: "on and off" -Switches Turning off response to a signal is important for restoring the cell/tissue/organism to the pre-signal state 2 main classes of molecular switch proteins: -Signaling by protein phosphorylation -->[phosphoproteins] -Signaling by GTP-binding proteins --> [trimeric GTP binding proteins (G proteins)] [monomeric GTPases]

Cell Cortex

-Rich in Actin Filaments Underlies the Plasma Membrane of Most Eukaryotic Cells. Specialized layer of cytoplasm on the inner face of the plasma membrane. In animal cells, it is rich in the actin filaments that govern cell shape and drive cell movement. -made largely of spectringives human red blood cells their characteristic shape. a form of anemia results in humans with certain spectrum mutant forms -Bulk of cortex--concentrated network of AF below PM--Responsible for shape & movement of the cell surface, including how cells crawl along a surface. Most other animal cells have a cortex containing actin and myosin proteins better for facilitating shape changes, movement, and other processes

Cells respond to signals

-Signal transduction leads to an output Examples: change in gene expression release of secretory vesicle contents -Response to signal

Intestinal and Skin tissue renewal

-Similar: cell division/renewal occurs in discrete locations. Areas of differentiated cells that don't divide.

Autocrin signaling

-Some cases, cells can respond to the local mediators that they themselves produce. -Cancer cells sometimes promote their own survival and proliferation in this way. -A form of paracrine communication. A reminder you add to your own personal calendar. -Autocrine signaling signal acts on signaling cell itself. -Signaling cell with local mediator (inside cell) is excreted into cytosol signaling to target cells by binding to receptors.

Stages of ATP formation via

-Stage 1: •high energy electrons transferred along series of electron carriers (electron-transport chain) embedded in membrane •Electron transfer release energy that is used to pump protons across the membrane •Generating an electrochemical gradient - form of stored energy -Stage 2: •Protons flow back down electrochemical gradient via ATP synthase •Catalyzes energy-requiring synthesis of ATP from ADP and Pi

Cholesterol

-Stiffen cell membranes. - Polar head, cholesterol stiffened region, and more fluid region. Membrane fluidity is important for several cellular processes.

Growth factors

-Stimulate cell growth (increase in cell size and mass) Extracellular signal molecule that stimulates a cell to increase in size and mass. I.e. epidermal growth factor (EGF) and platelet-derived growth factor (PDGF).

Skin tissue renewal

-Stratified epithelium Ascending order: -Dermis (connective tissue; bottom layer) -Basal layer (below basal layer; basal lamina and dividing basal cell. Cells are born that migrate apically through epidermis (epithelium) --> surface (scales) -Scales: Dead, flattened cells packed w keratin filaments. and shed.

SDS *

-Strong detergent

4. Anaphase

-Sudden synchronously separation of sister chromatids allows the chromosomes to be pulled to opposite poles; movement is driven via depolymerization of spindle MT and microtubule-associated motor proteins. Kinetochore MT gets shorter, spindle poles move apart; both contribute to chromosome segregation.

Polynucleotide

-Synthesis is Multistep •Specific example of using ATP hydrolysis indirectly to generate a polynucleotide •Also, uses an alternative route of ATP hydrolysis because the reaction requires more energy than that contained in single phosphate bond of ATP

Ribozyme

-The mRNA Message Is Decoded on Ribosomes. -The Ribosome

Shown here is the mechanism believed to be used for pumping protons by cytochrome c oxidase across the inner mitochondrial membrane. One of the steps shown is unidirectional because it is driven by the energy of electron transport. Why must this step be performed only in one direction?

-The protons could be also captured from the intermembrane space and released back into the matrix. The H+ transport complexes in the electron-transport chain have a conformation that, when open to the mitochondrial matrix, displays a high affinity binding site for H+. The transporter, with H+ bound, then switches conformation to open to the intermembrane space using energy from electron transport. This conformational change with the bound H+ is thought to be irreversible so that H+ cannot be released into the matrix.

Aminoacyl-tRNA synthetases **Function

-Their specificity is through recognition of anticodon loop. Specific Enzymes Couple tRNAs to the Correct Amino Acid —-> linkage of amino acid to tRNA; ATP to AMP + 2 phosphate (via high-energy bond) —> anticodon in tRNA binds to its codon in mRNA —> amino acid is selected by its codon in an mRNA. Complex with amino acid, tRNA, and aminoacyl-tRNA synthetase

What is true of the organelles that produce ATP in eukaryotic animal cells?

-They evolved from bacteria engulfed by ancestral cells billions of years ago. Mitochondria reproduce in a manner similar to most prokaryotes, harbor bacterial-like biosynthetic machinery for making RNA and proteins, and retain their own genomes. Such facts are considered evidence of their bacterial ancestry.

Tissue renewal 7:05

-Tissues are organized intricate mixture of cell types that must coexist while remaining distinct from each other. -All adult tissues undergo cycles of dying and renewal by 4 main factors: 1. Cell communication. -Signaling (i.e. secreted molecule that binds to receptors). -Contact mediated cell mechanism. 2. Selective cell adhesion. -Cells selectively adhere via tight junction, gap junction, ECM) 3. Cell memory. -Stem cells and what they need to become. -Diff. Tissues new @ diff. Rates: +Skin: +bone - (connective tissue made up of ECM components in b/w cells; make up structure and rigidity. i.e. give body stability to stand up right) Renews at slower rate. +blood: -Layers of tissue: 1. Epidermis - epithelium. -Held via tight junctions. Prevents passing of fluids. 2. Dermis - loose connective tissue. 3. Dermis- dense connective tissue. +Blood vessel and sensory nerves travel through. 4. Hypodermis - fatty connective tissue. -Has hemidesmosomes connecting bottom layer to ECM.

Membrane proteins can associate with the lipid bilayer in different ways

-Transmembrane: -Monolayer-associated: -Lipid-linked: -Protein-attached:

GTP-binding proteins

-Two main type participate in intra. signaling. 1. Large, trimeric GTP-binding proteins (G proteins) -Relay messages from G-protein-coupled receptors. 2. Small, monomeric GTPases. -Cell-surface receptors rely on. -Help relay their signals. -Generally aided by 2 sets of regulatory proteins helping bind and hydrolyze GTP: Guanine nucleotide exchange factors (GEFs)

RNA to protein

-Undergo translation.

Plasma Membrane Is Reinforced by

-Underlying Cell Cortex.

The Nernst equation

-Used to calculate the contribution of each ion to the resting potential of the membrane.

Polypeptide Chain

-Usually Crosses the Lipid Bilayer as an alpha Helix. -hydrophobic side chains (light green) of the amino acids forming the α helix contact the hydrophobic hydrocarbon tails of the phospholipid molecules, while the hydrophilic parts of the polypeptide backbone form hydrogen bonds with one another

Cell's response to a signals --> altered cell behavior

-Vary greatly, depending on what needs to happen once the message is received. 1. Fast response: -Signal affects the activity of proteins already present in the target cell. -Changes in cell movement, secretion, or metabolism; doesn't involve changes in gene expression yielding faster response. Signal affects the activity of proteins already present in the target cell. i.e. Acetylcholine; stimulate a skeletal muscle cell to contract w/i milliseconds. Or Salivary gland cell secrete w/i a min. Is possible b/c each case, the signal affects the activity of proteins already present w/i target cell, awaiting their next orders. 2. Slow response: -Signal results in gene expression changes to show effect. *Cell differentiation or inc. growth & cell division, once triggered by the appropriate signal molecule, can take hours to execute. Due to response to extracellular signals requires changes in gene expression and production of new proteins. Signal results in gene expression changes to show effect.

Electrochemical gradient

-Voltage & concentration gradients work in the same direction. Ions outside migrate inside of cell. -Voltage & concentration gradients work in opposite directions. Ions inside migrate out of cell.

Transcription

-an essential step in using the information from genes in our DNA to make proteins. Proteins are the key molecules that give cells structure and keep them running. Blocking transcription with mushroom toxin causes liver failure and death, because no new RNAs—and thus, no new proteins—can be made. the first step of gene expression. During this process, the DNA sequence of a gene is copied into RNA. Before transcription can take place, the DNA double helix must unwind near the gene that is getting transcribed. The region of opened-up DNA is called a transcription bubble -Produces RNA complementary [nontemplate (or coding) strand] to and is almost identical to one strand of DNA [template strand]. -Newly made RNA - T replaces U nucleotide.

TBP (TATA Binding Protein) **Mov. 7.4

-binds to the TATA box & bends DNA double helix. -Promotor located @ -30 -Subunit of TFIID

Most protein-coding human genes

-broken into multiple exons and introns.

differences in ribosomes and protein synthesis between eukaryotes and prokaryotes

-can be exploited to fight against bacteria.

DNA methylation patterns

-can be faithfully inherited when a cell divides -enzyme called a maintenance methyltransferase guarantees that once a pattern of DNA methylation has been established, it is inherited by newly made DNA. newly synthesized strand is not methylated at first

transmembrane hydrophilic pore

-can be formed by multiple amphipathic α helices. -hydrophobic amino acid side chains on one side of each helix (green) come in contact with the hydrophobic lipid tails of the lipid bilayer, while the hydrophilic side chains on the opposite side of the helices (red ) form a water-filled pore.

Porin proteins

-form water-filled channels in the outer membrane of a bacterium. -A transmembrane protein w beta barrel conformation.

Cancer

-have an abnormal metabolism that fuels their excessive growth and proliferation. They do not ingest neighboring cells as a source of nutrients.

glycoprotein synthesis

-involves the formation of O-glycosidic linkages by sequential addition of monosaccharides directly to OH− groups of serine or threonine residues in the protein. -occurs in two organelles in sequence such as endoplasmic reticulum and the Golgi apparatus. -The ribosome bearing the mRNA which codes for the proteins attaches to the endoplasmic reticulum. The newly synthesized protein enters the lumen of the endoplasmic reticulum where the addition of the glycan moiety takes place by the action of glycosyl transferase. The glycosylated proteins later enter the Golgi apparatus where trimming of the carbohydrate residues carried out by glycosidase and the final attachment of carbohydrates is done to produce matured glycoproteins which are ready to target their respective destinations.

Histone modifications

-may be inherited by daughter chromosomes. -The enzymes responsible for each type of modification bind to the specific modification they create, they can catalyze the "filling in" of this modification on the new histones, resulting in inheritance of the parental chromatin structure.

alternative splicing

-more than one mRNA can be made from the same gene.can sneakily encode more different proteins than we have genes in our DNA. -one pre-mRNA may be spliced in either of two (or sometimes many more than two!) different ways forming different mature mRNAs. each of which translates into a protein with a different structure.

Phosphatidylcholine

-most common phospholipid in cell membranes. - Unsaturated b/c of double bond causing kink in molecule.

Proto-oncogene —> oncogene pathway 31:05

-oncogene: +A gene that, when activated, can potentially make a cell cancerous. Typically a mutant form of a normal gene (proto-oncogene) involved in the control of cell growth or division. 1. mutation in coding sequence leads to the production of a hyperactive protein. 2. chromosomal rearrangement that leads to the production of a hyperactive protein 3. Gene amplification. 4. Chromosome rearrangement leads to the production of a hyperactive protein. Deletion of a proto-oncogene would decrease that gene's function. Proto-oncogenes are converted to cancer-promoting oncogenes by mutations that increase the gene's activity.

profilin& thymosin

-prevent monomers from forming filaments 50% of actin is free monomers

Mutations that prevent Bcl2 family proteins Bax and Bak from interacting with the outer mitochondrial membrane would have which effect?

-preventing the release of cytochrome c and inhibiting apoptosis -Bax and Bak trigger the release of cytochrome c and promote apoptosis; mutations that impair their ability to interact with the outer mitochondrial membrane would inhibit these actions.

Adenylyl cyclase

-produces cyclic AMP (cAMP). -cAMP is degraded by cyclic AMP phosphodiesterase. cAMP levels rise and fall rapidly upon signaling changes

Triggers muscle contraction

-sarcoplasmic Ca2+ channel is voltage-gated by association to the voltage-gated T-tubule Ca2+ channel. -Triggered by a Sudden Rise in Cytosolic Ca2+. -T tubules and the sarcoplasmic reticulum surround each myofibril. T tubules are inward projects of the plasma membrane (channels) -Skeletal muscle contraction is triggered by the release of Ca2+ from the sarcoplasmic reticulum into the cytosol.

DNA Mismatch Repair System

-system removes replication errors that escape proofreading. The problem: Neither the correct or incorrect nucleotide is damaged DNA, so how does the cell determine which to remove? -The solution: The mismatch system always removes the portion of the newly made DNA strand, which lacks a DNA modification contained by the old strand.

kinesin motor protein

-use the energy of ATP binding and hydrolysis to move in one direction. ATPase activity. Large family of motor proteins that uses E of ATP hydrolysis to move toward the plus end of a microtubule. Conformational change: swings one head forward Kinesins and cytoplasmic dyneins move in opposite directions along a microtubule using their globular heads. Two globular heads at one end, which bind and hydrolyze ATP and interact with microtubules. Single tail at the other end, which interacts with cargo. kinesin motor protein "walking" hand-over-hand. (1) One head of a two-headed kinesin molecule, initially with both heads in the ADP form, binds to a microtubule. (2) Release of ADP and binding of ATP results in a conformational change that locks the head to the microtubule and pulls the neck linker (orange) to the head domain, throwing the second domain toward the plus end of the microtubule. (3) ATP hydrolysis occurs while the second head interacts with the microtubule. (4) The exchange of ATP for ADP in the second head pulls the first head off the microtubule, releasing Pi and moving the first domain along the microtubule. (5) The cycle repeats, moving the kinesin dimer farther down the microtubule.

Tumor suppressor *

. genes encode proteins and RNAs that normally keep proliferation in check. Loss-of-function mutations in tumor suppressor genes contribute to cancer. Cancer treatments would want to re-introduce working copies of tumor suppressor genes, not cause degradation of tumor suppressor gene products.

transcription regulators Table: two bind same site

TR Dimer - dimerization doubles the number of protein-DNA contacts.

Two Process of Segregation

1. Anaphase A; chromosomes pulled poleward. 2. Anaphase B; Poles are pushed & pulled apart.

Examples of microtubules

1. Centrosome (nondividing cell). 2. Poles of mitotic spindle (dividing cell). 3. Ciliated cell (Cilium in basal body).

Cell-cycle Control Mechanisms - G2 --> M phase

1. Enter mitosis, all DNA is replicated and damages repaired. 2. Cdc25, inhibition of activating phosphatase blocks entry to mitosis. DNA damage or incomplete replication. - Cytokinesis is apart of M phase. Period of the euk. Cell cycle when the nucleus and cytoplasm divide.

3 main classes of cell-surfaced receptors*

1. Ion-Channel-Coupled Receptors: -A.k.a transmitter-gated ion channels. -Convert Chemical Signals into Electrical Ones. -Closed channel and open channels (Ions, signal molecule) -change permeability of PM to selected ions, altering the membrane potential, if conditions are right, producing an electrical current. -Important in nerve cells and other electrically excitable cells (muscle cells), G-protein-coupled receptors and enzyme-coupled receptors are important to practically every cell type in the body. 2. G-protein-coupled receptors: -Inactive receptor, G protein, and enzyme --Signal molecule--> Activated receptor binds to G protein and then crosses PM of target cell that activates both enzyme and G proteins bound together. -Activate membrane-bound, trimeric GTP-binding proteins (G proteins), which then activate (or inhibit) an enzyme or an ion channel in the PM, initiating an intracellular signaling cascade 3. Enzyme-coupled receptors. -Inactive catalytic domains binds to signal molecule (dimer) crosses PM of target cell -Either act as enzymes or associated w enzymes inside the cell; when stimulated, the enzymes can activate a variety of intracellular sig. pathways.

Types of DNA damage

1. Mutations (replacement of 1 base for another) 2. Thymine dimers - structural alteration in helix/distortion of helix

Elongation

1. P site; growing polypeptide chain & A site; newly bound charged tRNA. 2. A site now has growing polypeptide chain from P site. 3. Large subunit translocates, E site is gone, A site (i) is now P site, new A site is synthesized. 4. E site ejects tRNA, A site takes P sites spot, and New A site is formed. 5. Small subunit translocates, newly bound charged tRNA is formed.

Cell-cycle Control Mechanisms - M phase -->

1. Pull duplicated chromosomes apart. All chromosomes properly attached to mitotic spindle. 2. Inhibition of APC/C activation delays exit from mitosis. Chromosomes not properly attached to spindle. The shortening and thickening of chromosomes condensins assemble along the sister chromatids at the start of M phase, and help them coil up into a more compact form.

RNA polymerases (eukaryotic cells)

1. RNA polymerase I -Most rRNA genes. 2. RNA polymerase II -All protein-coding genes. 3. RNA polymerase III -tRNA genes. -Requires General Transcription Factors.

Stop Protein Synthesis

1. Ribosomal complex

plasma membrane is involved in

1. cell communication, 2. import and export of molecules. 3. cell growth and motility

Initiation factors for protein synthesis

1. mRNA binding- Small ribosomal subunit w translation initiation factors bound; translation initiation factors (E site), Initiator tRNA (P site) + RNA sequence start if AUG coding sequence. 2. Small ribosomal subunit w bound initiator tRNA, moves along mRNA searching or first AUG (start codon) 3. Translation initiation factos dissociate and large ribosomal subunit binds @ P site 3a. Charged tRNA binds @ A site. 3b. Initiator tRNA @ P site forms peptide bond w charged tRNA @ A site. -Ends in translation & degradation

3 degradation mechanisms

1. proteasomes (nucleus and cytosol) 2. lysosomes (plasma membrane and Golgi apparatus) 3. Soluble proteases (extracellular matrix, ECM)

DNA and RNA

1.) Sugar difference: [**position in structure] DNA (deoxyribose) | RNA (ribose; -OH) 2.) RNA (Uracil (U) - adenine (A) )via hydrogen bond. | DNA (T-A) 3.) Structural composition.

Signaling by protein phosphorylation (switch proteins involved)

1st: By far the largest— consists of proteins that are activated or inactivated via phosphorylation; chemical modification. i.e. Switch is thrown in one direction by a PROTEIN KINASE; that covalently attaches a phosphate group onto the switch protein, and in the opposite direction by a protein phosphatase; dephosphorylate again. Activity of any protein regulated depends —moment by moment—on the balance b/w the activities of the protein kinases that phosphorylate it and the protein phosphatases; dephosphorylate it. -Switch proteins controlled by phosphorylation are themselves protein kinases. -Organized into phosphorylation cascades: One protein kinase, activated via phosphorylation, phosphorylates the next kinase in the sequence, and so on, transmitting the signal onward and, in the process, amypllifying, distributing, and regulating.

In a classic experiment designed to study nuclear transport, investigators added a dye molecule to the subunits of a protein called nucleoplasmin, which is involved in chromatin assembly. They then injected the intact protein or combinations of its subunits into the cytosol of a frog oocyte or into its nucleus. The results of the experiment are shown in the diagram, where red indicates the location of the labeled protein. Based on these results, which part of the nucleoplasmin protein bears a nuclear localization signal?

Tail only.

GTP-proteins (intracellular signaling)

1st: The large, trimeric GTP-binding proteins (G proteins) —relay messages from G-proteins-coupled receptors. Includes both trimeric G proteins and monomeric GTPases, such as Ras. *Activated by GPCRs--acts as molecular switches, transmitting signal onward for a short time b/4 hydrolyzing their bound GTP to GDP. 2nd: Other cell-surface receptors rely on. The small, monomeric GTPases—help relay their signals. *These switch proteins are usually aided by 2 sets of regulatory proteins that help them bind & hydrolyze GTP: Guanine nucleotide exchange factors (GEFs) activate the switches by promoting GDP for GTP, and GTPase-activating proteins (GAPs) turn them off by promoting GTP hydrolysis. -Directly regulate ion channels or enzymes in PM. Some activate (or inactivate) enzyme adenylyl cyclase--increases (or decreases) the intracellular concentration of cyclic AMP (second messenger molecule). +Others activate enzyme phospholipase C--generates 2nd messenger inositol triphosphate (IP3) & diacylglycerol . -General structure - alpha, beta, and Y- +Inactivated state, alpha subunit bound GDP. Extra. sig. mole. binds to its receptor, the altered receptor activates a G proteion causing (alpha subunit) to decrease its affiniity for GDP, resulting in exchange for GTP. Some cases, this activation breaks up G-proteion subunits, so activated alpha, clutching its GTP, detaches from beta-Y complex, activating it. The longer target protein stays bound to alpha or beta-Y complex -- more prolonged the relayed signal is. GTPase activity hydrolyzes GTP to GDP, inactivated.

Human factor VIII gene

26 exons & 27 introns. 200,000 nucleotide pairs

Beta sheet

2nd folded structure. -Found in protein fibroin- major constituent of silk. -Several segments (strands) of an individual polypeptide chain- held together by hydrogen-bonding b/w peptide bonds in adjacent strands. -Adjacent chains run in opposite directions forming antiparallel beta sheet.

GTP binding proteins

2nd way to regulate protein activity by phosphate addition or removal. Functions as molecular switch. GTP-binding protein- Req. presence of active tightly bound GTP molecule. Deactivate via hydrolyzing GTp to GDp and inorganic phosphate (pi)

Human beta-globin gene

3 exons. 2000 Nucleotide pairs

Tertiary structure

3D conformation of a completely folded protein (polypeptide) 1. globular: not necessarily spheres. i.e. catalase, myoglobin, porin, lysozyme, aspartate transcarbamoylase. 2. fibrous- long rod-shaped proteins. Made from parallel cross-linked polypeptide chains. i.e. collagen.

Avogadro's number

6.02 x 10^23

Elements in Nature

92 elements are naturally occurring. 6 elements make up 95% of the body weight of organisms (acronym CHNOPS): •*Carbon •*Hydrogen •*Nitrogen •*Oxygen •Phosphorus Sulfur

Ribozymes

: Ribosomal RNA protein hydrolysis not catalyzed by ribozyme The 23S rRNA of the prokaryotic ribosome and the 28S rRNA of the eukaryotic ribosome catalyze the formation of peptide bonds. important in our understanding of the evolution of life on Earth capable via selection to evolve self-replication.

Muscle tissue

A body tissue that contracts or shortens, making body parts move.

Eukaryote

A cell that contains a nucleus and membrane bound organelles

Contact-dependent signaling

A cell-surface-bound signal molecules binds to a receptor protein on an adjacent cell. Same type of signaling molecules are used for endocrine, paracrine, and neuronal signaling. 4th style of signal-mediated cell-cell communication. Chemical nature is transmembrane protein Most intimate and short-range of all. Doesn't require the release of a secreted molecule, but make direct physical contact via signal molecules lodged in PM of the signaling cell and membrane-bound signal molecule receptor proteins embedded in PM of target cell. During embryonic development, such signaling allows adjacent cells initially similar to becoming specialized to form diff. cell types. Face to face conversation. -Signal sent to individual cells by direct physical contact "contact dependent signaling" e.g. cell specialization during development.

Ion

A charged atom

Covalent bond

A chemical bond that involves sharing a pair of electrons between atoms in a molecule

histone-modifying enzyme

A class of enzymes that covalently modify the N-terminal tails of histones.

Protein import into ER begins while the protein is being translated by a ribosome

A common pool of ribosomes is used to synthesize all the proteins encoded by the nuclear genome. Protein translation process provides energy for transport Since polysomes can form on a mRNA, multiple import events can occur together

DNA

A complex molecule containing the genetic information that makes up the chromosomes.

Positive feedback

A component that lies downstream in the pathways acts on an earlier component in the same pathway to enhance response to initial signal. And acts to inc. the activity of the protein that activated it. Can ignite explosive response, i.e. the activation of proteins that trigger cell division. IMG: (A)

Organelle

A discrete structure that carries out a specific function within the cell

Cancer

A disease in which some body cells grow and divide uncontrollably, damaging the parts of the body around them.

Karyotype

A display of the chromosome pairs of a cell arranged by size and shape.

Nuclear envelope

A double membrane that surrounds the nucleus in the cell.

Negative feedback

A downstream component; protein Y acts to inhibit an earlier component; protein T in the pathway to diminish response to initial signal. i.e. an inc. in prey (protein T) would promote expansion of predators (protein Y); as number of predators inc, the availability of prey will fall. Ultimately cause predator population to decline. As predators disappear, the prey populations will recover & multiply, providing food for more predators, and so on.

Homolog

A gene, chromosome, or any structure that has a close similarity to another due to common ancestry.

proteasomes

A giant protein complex that recognizes and destroys proteins tagged for elimination by the small protein ubiquitin. Made of core and caps, targeted proteins are unfolded by cap and degraded in the core

Genetic map

A graphic representation of the order of genes in chromosomes spaced according to the amount of recombination that occurs b/w them. 2 genes are close to each other on a chromosome, and tend to be inherited as a unit. 2 genes far apart, typically be separated by crossing-over. The frequency of the two genes during separation via crossing-over is used to construct a map to show the chromosome order.

Protein family

A group of polypeptides that shares a similar amino acid sequence or three-dimensional structure, reflecting a common evolutionary origin. Individual members often have related but distinct functions, such as kinases that phosphorylate different target proteins.

Cytoplasm

A jellylike fluid inside the cell in which the organelles are suspended

Nuclear pore complex

A large complex of dozens of proteins lining a nuclear pore, defining its shape and regulating transport through the pore.

Chaperone proteins

A large set of special proteins that assist protein folding in living cells Some bind to partly folded chains helping fold along most energetically favorable pathway. Require ATP binding and hydrolysis. Acts as isolation chamber to help polypeptide fold.

Electronegativity

A measure of the ability of an atom in a chemical compound to attract electrons

Redox potential

A measure of the tendency of a given redox pair to donate or accept electrons.

chromatin remodeling complex

A mechanism for epigenetic gene regulation by the alteration of chromatin structure.

Antiport

A membrane transport process that carries one substance in one direction and another in the opposite direction. Active transporters - coupled transport by gradient-driven pumps. Anti-transported ion moves out while transported molecule moves in.

Symport

A membrane transport process that carries two substances in the same direction across the membrane. Active transporters - coupled transport by gradient-driven pumps. Co-transported ion and transported molecule move into cell.

Nuclear lamina

A netlike array of protein filaments lining the inner surface of the nuclear envelope; it helps maintain the shape of the nucleus. And attachment sites for chromosomes. Breaks down and reforms in each daughter cell during mitosis cell division. Breakdown mediated by phosphorylation of lamins by kinases, weakens interactions b/w lamin tetramers yilending filaments to fall apart. Dephosphorylation by protein phosphatases at end of mitosis allows lamin reassembly. Support and strengthen the nuclear envelope. +Defects in a nuclear lamin--can cause a rare class of premature aging disorders called progeria but it is not clear how the defect results in the disease.

Base pair

A pair of complementary nitrogenous bases in a DNA molecule

Nucleus

A part of the cell containing DNA and RNA and responsible for growth and reproduction •Generally most prominent organelle •Enclosed within two concentric membranes = nuclear envelope •Contains DNA - visible as chromosomes during cell division Stores genetic information

Nucleus

A part of the cell containing DNA and RNA and responsible for growth and reproduction. -Processes Eukaryotic mRNAs. +RNAs - are synthesized & processed in factories (red) +DNA - replicated (green) in intracellular condensates that form discrete compartments w/i a mammalian nucleus. -Exports mature eukaryotic mRNAs that are degraded in cytosol.

Model organism

A particular species chosen for research into broad biological principles because it is representative of a larger group and usually easy to grow in a lab.

Fibrous protein

A protein that has only a secondary structure; generally insoluble; includes collagens, elastins, and keratins.

Motor protein

A protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell.

Antigen

A protein that, when introduced in the blood, triggers the production of an antibody

Gene

A segment of DNA on a chromosome that codes for a specific trait

Plasma membrane

A selectively-permeable phospholipid bilayer forming the boundary of the cells

Protein machine

A set of protein molecules that bind to each other in specific ways, so that concerted movements within the protein complex can carry out a sequence of reactions with unusual speed and effectiveness. A large number of the central reactions of the cell are catalyzed by such protein machines, with protein synthesis and DNA replication being particularly well understood examples.

Intracellular signaling pathways

A set of proteins and small molecule second messengers. Interact w each other to relay a signal from the cell membrane to its final destination in cytoplasm or nucleus. -Cell-Surface Receptors Relay Extracellular Signals -Receptor protein recognizes (binds) signal molecule generates an intracellular signal - generates a series of additional intracellular signals before, indirectly, generating a response "signaling cascade"

Activated carrier

A small molecule that stores energy or chemical groups in a form that can be donated to many different metabolic reactions. Examples include ATP, acetyl CoA, and NADH. - small molecule that stores energy of chemical groups in a form that can be donated to many different metabolic reactions

Terminator

A special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene. Begins once the polymerase transcribes a sequence of DNA

Substrate

A specific reactant acted upon by an enzyme

Endoplasmic reticulum

A system of membranes that is found in a cell's cytoplasm and that assists in the production, processing, and transport of proteins and in the production of lipids.

X-ray crystallography

A technique that depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule to study the three-dimensional structure of the molecule.

Chromatography

A technique that is used to separate the components of a mixture based on the tendency of each component to travel or be drawn across the surface of another material.

Nuclear magnetic resonance (NMR) spectroscopy

A technique that measures the alignment of magnetic moments from certain molecular nuclei with an external magnetic field; can be used to determine the connectivity and functional groups in a molecule.

aquaporins

A transport protein in the plasma membrane of a plant or animal cell that specifically facilitates the diffusion of water across the membrane. water channels, are channel proteins from a larger family of major intrinsic proteins that form pores in the membrane of biological cells, mainly facilitating transport of water between cells.

Hydrogen bond

A type of weak non covalent bond Slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule.

Macromolecule

A very large organic molecule composed of many smaller molecules Covalently linkage for proteins, nucleic acid, and polysaccharides

ADP and ATP

ADP -- Nucleoside diphosphate produced by hydrolysis of terminal phosphate of ATP. ATP -- Activated carrier that serves as E source

APC/C Triggers Separation

APC/C - Anaphase-promoting Complex/Cyclosome •Separase - protease that destroys cohesion linkage of sister chromatids •Securin - protease that holds separase in an inactive state APC/C targets securin for degradation and releases separase. Separase (inhibitory protein) + inactive proteolytic enzyme (separase) --[ubiquitylation of securin via Active APC/C]--> Activates separase that launches metaphase into anaphase. A protein complex that triggers the separation of sister chromatids. Orchestrates the carefully timed destruction of proteins that control progress through the cell cycle. The complex catalyzes the ubiquitylation of its targets. Tumor suppressor gene - inactivation of both copies of APC promotes excessive proliferation of cells in intestinal crypt

Additional Nucleotides

ATP (Adenosine TriphosPhate) is a nucleotide composed of adenine and ribose (adenosine) and three phosphates. ATP is a high-energy molecule due to the presence of the last two unstable phosphate bonds, which are easily broken. Additional triphosphates exist for each nitrogen base - GTP, TTP, CTP, and UTP

Mitochondrion

ATP synthesis by oxidative phosphorylation. 22% of total cell

The head of a myosin-II molecule walks along an actin filament through

ATP-dependent cycle of conformational changes

Start codon

AUG; encodes the amino acid methionine.

Apoptopic cell

Absence of proper signals yield in most animal cells programed to kill themselves.

ATP synthase:

Abundant membrane-associated enzyme complex that catalyzes formation of ATP from ADP and inorganic phosphate during oxidative phosphorylation and photosynthesis.

Microtubule-associated

Accessory protein that binds to microtubules; can stabilize microtubule filaments, link them to other cell structures, or transport various components along their length.

Foreign substances

Act on cell-surface receptors.

Both GPCRs and RTKs

Activate multiple intracellular signaling pathways.

PKA pathway

Activated GPCR (signal molecule) --> G protein --> adenylyl cyclase --> cyclic AMP --> PKA --> transcription regulator or many target proteins.

Intracellular relay system**

Activated by the diff. signals interact. So the presence of one signal will often modify the effects of another. One combination of signals might enable a cell to survive; another might drive it to differentiate in some specialized way; and another might cause it to divide. The absence of proper signals yield in most animal cells programed to kill themselves. [apoptotic cell]

Ras mutation**

Activates a MAP-kinase signaling module. -Stimulate cell proliferation by keeping Ras (and Ras-MAP kinase sig. path) constantly active. -Common feature of cancer.

Cells send signals, to other cells themselves

All rely on just a handful of basic styles of communications for getting the message across. i.e. proteins peptides amino acids nucleotides steroids fatty acids dissolved gases

Action Potentials

Allow Rapid Long Distance Communication Along Axons. Mediated by Voltage-gated Cation Channels

Action potential

Allow Rapid Long- Distance Communication Along Axons. Mediated by Voltage-gated Cation Channels. Triggered by a depolarization of a neurons PM. The initial "depolarization stimulus" has to lead to a large enough change in the membrane potential; (only causes a small change in membrane potential) (to the "threshold potential") for the depolarization to amplify into an action potential.

Vesicular transport

Allows materials to exit or enter the cell via exocytosis (secretory pathways) and endocytosis (Endocytic pathways) Starts by entry of a protein into ER lumen or ER membrane and creation of lipids within the ER membrane. carry proteins and membrane between compartments bud from one membrane and fuse with another.

Combinatorial Control

Also Generate Different Cell Types. Combinations of a few transcription regulators can generate many cell types during development.

Allele

Alternative form of a gene. For a given gene, many alleles may exist in the gene pool of the species.

Rough ER

That portion of the endoplasmic reticulum studded with ribosomes.

Larger uncharged polar molecules

Amino acids, glucose, and nucleosides

Replication fork

An Asymmetrical Y-shaped region on a replicating DNA molecule where new strands are growing. •The DNA strand growing in the 3' to 5' direction is discontinuously synthesized in small Okazaki fragments in the 5' to 3 ' direction. •Polymerase moves backward on this "lagging strand." •The fragments are later stitched together to make the lagging strand continuous. •Note that each strand is synthesized by both replication forks and had both leading and lagging strands

Protozoan

An animal-like protist

Telomerase

An enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells.

Primase

An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.

DNA helicase

An enzyme that unwinds the DNA double helix during DNA replication

Cytochromes

An heme/iron-containing protein that is a component of electron transport chains in the mitochondria and chloroplasts of eukaryotic cells and the plasma membranes of prokaryotic cells. during cellular respiration & photosynthesis.

Polarity

An inherent asymmetry that allows one end of an object to be distinguised from another; can refer to a molecule, a polymer (i.e. actin filament), or a cell (i.e. epithelial cell lining mammalian small intestine).

Microscope

An instrument that makes small objects look larger. •Robert Hooke - observed cork under a microscope and term the chambers cells - actually observed cell walls and empty spaces where cells used to be

Ionic Bonding

An ion is an atom that has lost or gained an electron. An ionic bond forms when electrons are transferred from one atom to another atom and the oppositely charged ions are attracted to each other. Example: formation of sodium chloride Salts are solid substances that usually separate and exist as individual ions in water.

spectrum mutant forms

Anemia due to low RBC and has a flattened conformation.

12.2 entire table

Animal and plant cells use a variety of transmembrane pumps to drive the active transport of solutes. -12.18 animal vs plant cell.

Active transport of solutes

Animal and plant cells use a variety of transmembrane pumps to drive the active transport. Animal cells: -Na+ pump; Na+ out, K+ in, ATP to ADP + P. -Na+ driven symport; Na+ and solute in. -H+ pump; H+ into lysosome and ATP to ADP + P. Plant cell: - 2 H+ pump; H+ (out of cell & in vacuole) and ATP to ADP + P. -H+-driven symport; H+ and solute into cell.

Somatic cell

Any cell that forms part of the body of a plant or animal that is not a germ cell or germ-line precursor.

Tight junction cross section

Apical surface in brown, basolateral in blue. Under normal conditions, a water-soluble tracer molecule added to the apical surface does not cross into the basolateral side. In the presence of pathogens that disrupt tight junctions, the tracer molecules would not remain in the lumen, but instead would cross into the basolateral area.

Intracellular Proteolytic Cascade

Apoptotic stimulus in mitochondria. Caspases - One of a family of proteases that, when activated, mediates the destruction of the cell via apoptosis. -Ensures that cells survive only when and where they are needed. •Two types •Initiator caspases - cleave and activate 1. Procaspases - inactive precursors of caspases Adaptor proteions (dimerization, activation and cleavage) Executioner caspases •Executioner caspases - dismember numerous key proteins in the cell. Cleave of multiple substrates --> apoptosis

Eukaryotic Genes

Are Controlled by Combinations of Transcription Regulators

Eukaryotic Genes

Are Controlled by Combinations of Transcription Regulators. **"How we know" section" gene regulation - the story of eve

Lipid Bilayers

Are Impermeable to Ions and Most Uncharged Polar Molecules.

Na+ pump undergoes a series of conformational changes

As it exchanges Na+ ions for K+. Generates a Steep Concentration Gradient of Na+ Across the Plasma Membrane high concentration of Na+ outside the cell is like water behind a high dam. [Na+] 10 - 30X higher outside vs inside [K+] 10 - 30X higher inside vs outside [Na+] difference plus resting potential (-20 to -200mV) —> Results in a large Na+ electrochemical gradient that is an energy store for operating other gradient-driven pumps

Microscopy Scales

Atoms (nm) [electron microscope] --> molecules (nm) [Super-resolution fluorescence microscope] --> Organelles (um) [light microscope]--> Cells (um) [unaided eye]

hydrophilic molecule

Attracted to water, will dissolve in water (Polar).

A hydrophobic molecule

Avoid water.

Resting membrane potential

B/w -20mV & -200mV. Interior of cell is slightly more neg. than exterior.

Representations of Protein Folding

Backbone model: what holds a protein together and gives it an overall shape (or tertiary structure). Compared to RNA and DNA backbone, protein backbone has a relatively simple chemical structure - a nitrogen atom, two carbon atoms, one or two oxygen atoms, and a few hydrogens. Wire model: -shows position of amino acid side chains (useful for showing which amino acids may be involved in protein activity) ribbon model. shows polypeptide backbone and emphasizes folds. space filling model. Ribbon model: -Containing protein or nucleic acid. -generated by interpolating a smooth curve through the polypeptide backbone. Space-filling model: -A representation of molecular structure in which atoms are shown as spheres whose diameters are proportional to their atomic radii.

Lateral plasma membrane

Basal plasma membrane

Nucleotides

Basic units of DNA molecule, composed of a sugar, a phosphate, and one of 4 DNA bases

The concentration of cyclic AMP rises rapidly in response to an extracellular signal

Becomes activated w/i 50 sec by adding serotonin. A nerve cell responds to the binding of the neurotransmitter serotonin to a GPCR by synthesizing cyclic AMP. Cell contains a fluorescent protein whose fluorescence changes when it binds cyclic AMP. Blue indicates a low level of cyclic AMP, yellow an intermediate level, and red a high level. (A) In the resting cell, the cyclic AMP concentration is about 5 × 10-8 M. (B) Fifty seconds after adding serotonin to the culture medium, the intracellular concentration of cyclic AMP has risen more than twentyfold (to >10-6 M)

Perinuclear space

Between the two layers of the nuclear envelope

RNA world

Big bang (14 billion years) —> solar system formed —> RNA world —> first cells w DNA —> First mammals —> present

Biological Order of Cells

Biological order is possible due to entropy; release of heat energy from cells

Chemical Bonds

Bonds between atoms in molecules contain energy. Bonds between atoms are caused by the interactions between electrons in outermost energy shells. The process of bond formation is called a chemical reaction.

For both clinical and cosmetic reasons, plastic surgeons inject substances into connective tissue underlying the skin epidermis. This plumps up areas deficient in soft tissue, and is used to reduce surgical scars or wrinkles, for example. Which normal connective tissue components are good candidates to be injected as fillers in this type of procedure?

Both collagen, a protein that provides tensile strength, and glycosaminoglycans, polysaccharides that resist compression, are components of the extracellular matrix and employed as fillers in soft tissue augmentation.

Oligosaccharide chains added in the ER can undergo further modification in which organelle(s)?

Both the cis and trans Golgi networks Many of the oligosaccharide chains that are added to proteins in the ER undergo further modifications in the Golgi apparatus. On some proteins, for example, more complex oligosaccharide chains are created by a highly ordered process in which sugars are added and removed by a series of enzymes that act in a rigidly determined sequence as the protein passes through the Golgi stack. As would be expected, the enzymes that act early in the chain of processing events are located in cisternae close to the cis face, while enzymes that act late are located in cisternae near the trans face.

Dendrites

Branchlike parts of a neuron that are specialized to receive information.

Hydrolysis

Breaking covalent bond b/w complex molecules by the chemical addition of water

Most protein-coding human genes

Broken into both exons & introns.

Formation of 5-methylcytosine

By methylation of a cytosine base in the DNA double helix.

Ca2+ Signal Triggers Many Biological Processes

Calmodulin

Expression of Different Genes

Can Be Coordinated by a Single Protein

Mutant organism

Can be generated by treating animals w mutagens, that damage DNA. Then screened to identify phenotypes of interest and, ultimately, to isolate the responsible genes.

Misfolded proteins

Can form amyloid structures that cause disease. 1. Protein undergoes rare conformational change producing abnormally folded prion form. 2. Abnormal form causes conversion of normal proteins to misfolded prion form. 3. Prions aggregate into amyloid fibrils- can disrupt brain-cell function causing neurodegenerative disorder. i.e. Alzheimers

Cancer cells often lack normal DNA damage response and cell-cycle control mechanisms. Why does this make them more susceptible to DNA-damaging chemotherapies?

Cancer cells might ignore the normal mechanisms that halt the cell cycle in response to damage, and subsequent division with damage leads to death. Normal cells halt the cell cycle in response to DNA damage to enlist repair mechanisms. Cancer cells often do not halt the cell cycle and will try to divide with damaged DNA, leading to catastrophic amounts of DNA damage and cell death.

Unipotent

Capable of giving rise to a particular cell type

Pluripotent

Capable of giving rise to any type of cell or tissue

Multipotent

Capable of giving rise to several cell types of a given lineage. Most adult stem cells - skin, intestine, blood. Give rise to a variety of diff. blood cell types. -Some stem cells that only give rise to 2 or 3 diff. cell types. -Variability but restricted linagely for what cells types are produced.

Calvin Cycle ("Dark" Reactions)

Carbon assimilation happens in the dark reactions that use both ATP and NADPH generated in the light reactions in the chloroplast stroma (appreciate their use, don't worry about the details of the biochemistry).

Fatty acid

Carboxylic acid attached to hydrocarbon chain tail -Starting point 4 synthesis phospholipids. -Major source of E in metabolism. often bonded to glycerol in a lipid.

Splicing

Carried out by snRNPs; a collection of RNA-protein complexes. +specific parts of the pre-mRNA, called introns are recognized and removed by a protein-and-RNA complex called the spliceosome. Introns can be viewed as "junk" sequences that must be cut out so the "good parts version" of the RNA molecule can be assembled. +The pieces of the RNA that are not chopped out are called exons. The exons are pasted together by the spliceosome to make the final, mature mRNA that is shipped out of the nucleus.

Each cell membrane has its own characteristic set of transporters.

Cell - Nucleotide, sugar, amino acid go into PM. Ions: Dependent on concentration gradient. In and out of PM. Lysosome (w/i cell) - H+ gradient. Mitochondrion - Pyruvate; flows in inner mitochondrial membrane. Release ATP into cytosol and transports ADP through inner mito. membrane.

Apoptosis vs Cell Necrosis

Cell necrosis - cell swells and bursts, releasing contents into extracellular space •Could trigger damaging inflammation Apoptosis - cell shrinks and condenses without damaging neighbors •Attracts phagocytic cells (typically macrophages) that engulf dying cell

Mitochondrion

Cell organelle that converts the chemical energy stored in food into compounds that are more convenient for the cell to use

differenciated cells

Cell that's undergone a coordinated change in gene expression- enabling it to perform a specialized function. -Stop receiving signals to divide. -Express same genome as initial stem cell. Maintainance of stem cell becomes inactivated.

Gamete

Cell type in a diploid organism that carries only one set of chromosomes and is specialized for sexual reproduction. A sperm or an egg; a.k.a germ cell. Meiosis, many genetically diff. gametes are produced from a single individual: maternal and paternal homologs are parceled out to gametes, so each gamete receives one copy of each chromosome. B/ the segregation of these homologs occurs randomly, and crossing-over occurs b/w them,

Tight Junctions

Cell-to-cell junctions that prevent the paracellular transport of materials; tight junctions form a collar around cells and link cells within a single layer - form impermeable barriers by connecting plasma membranes •Prevent fluid leakage between cells Cell-cell junction- seals adjacent epithelial cells together, preventing the passage of most dissolved molecules from one side of epithelial sheet to the other. (prevents leakage of extra. molecule b/w them; helps polarize cells) +Barring the diffusion of water-soluble molecules across epithelium. seal neighboring epithelial cells together. formed by proteins called claudins and occludins, form a tight seal between neighboring cells and prevent leakage of water-soluble molecules (and pathogens) across epithelia.

Transporters and Channels

Cells Contain Two Classes of Membrane Transport Proteins. Inorganic ions and small, polar organic molecules can cross a cell membrane through either a transporter or a channel.

During animal development

Cells in the embryo exchange signals to determine which specialized role each cell will adopt, what position it will occupy in the animal, and whether it will survive, divide, or die. Later in life, a large variety of signals coordinates the animal's growth and its day-to-day physiology and behavior.

In multicellular organism

Cells must interpret the multitude of signals received from other cells to help coordinate their behaviors.

Differenciate cells

Cells that have undergone coordinate gene expression changes to perform specialized functions.

Centrosome Duplication

CentroSome •Microtubule organizing center •Composed of Centrioles •Short, hollow cylinders •One pair of centrioles per animal cell •Oriented at right angles to each other •Separate during mitosis to determine the plane of division - nucleates into radial array called an aster •Organizes the mitotic Spindle •Duplication begins at same time as DNA replication. Duplicate during S phase and separate in G2. Some of the MT growing out of duplicated centrosomes interact forming mitotic spindle.

Spindle pole

Centrosome from which microtubules radiate to form mitotic spindles.

Evolution

Change in a kind of organism over time; process by which modern organisms have descended from ancient organisms.

Passive transport

Channel-mediated or transporter-mediated. Charged solutes are influenced by both the Concentration Gradient and Membrane Potential. Glucose - +Conformational changes in a transporter mediate the transportation in cell. +transports glucose out of cells when glucose concentration is higher in the cytosol.

Pedigree

Chart showing the line of descent, or ancestry, of an individual organism.

Noncovalent bond

Chemical association that does not involve the sharing of electrons; singly are relatively weak, but can sum together to produce strong, highly specific interactions between molecules. Examples are hydrogen bonds and van der Waals attractions.

Anabolism

Chemical reaction in which smaller molecules (monomers) are combined to form larger molecules (polymers)

Stable Microtubules

Cilia and Flagella moved by dynein. Many hairlike cilia project from the surface of the epithelial cells that line the human respiratory tract.

Clathrin

Clathrin molecules form basketlike cages that help shape membranes into vesicles. coated pit.

Dopamine

Closes Gap Junctions.

Chromatin

Clusters of DNA, RNA, and proteins in the nucleus of a cell

Exons (DNA)

Coding sequences occurs after promotor. In both bacterial and Eukaryotic genes.

Two-dimensional polyacrylamide-gel electrophoresis

Combination of 2 different separation methods. Protein separation due to isoelectric point (pH gradient)

Haplotype block

Combination of alleles or other DNA markers that has been inherited as a unit, undisturbed by genetic recombination, across many generations. Human genome consists of these large blocks--segments of DNA sequence that's passed down intact from ancestors and, in most individuals, have not yet been broken up by crossovers.

Chemical group

Combination of atoms, such as a hydroxyl group (-OH) or an amino group (-NH2), with distinct chemical and physical properties that influences the behavior of the molecule in which it resides.

Genome

Comparison of Genomes: •Even though organisms have very different physical appearances, the underlying genetics are highly conserved •Example: white patches in human and mouse both the result of a mutation in the same gene (Kit) required for skin pigment

Carbon Atoms Cycle

Complementary processes. through the process of photosynthesis and cell respiration - but are neither created nor destroyed

Extracellular matrix

Complex network of polysaccharides (i.e. glycosaminoglycans or cellulose) and proteins (collagen)- secreted by cells. A structural component of tissues that also influences their development and physiology. -Animals: tensile strength provided by fibrous collagen proteins.

Michaelis constant (KM)

Concentration of substrate at which an enzyme works at half its maximum velocity; serves as a measure of how tightly the substrate is bound.

Plectin pathway - linker proteins

Connect Cytoskeletal Filaments and Bridge the Nuclear Envelope.

Linker Proteins

Connect Cytoskeletal Filaments and Bridge through the Nuclear Envelope. -Nuclear and cytoplasmic cytoskeltonsare linked to each other. Plectin one of the proteins involved. -Plectin aids in the bundling of intermediate filaments and links these filaments to other cytoskeletal protein network. -Defects: Human disease caused by plectinmutation: multiple defects (skin, muscles, and nerves)

Cell membrane

Contain membrane transport proteins that selectively promote: Passive diffusion (blue) and Pumping (purple or green. contain specialized membrane transport proteins that facilitate the passage of selected small, water-soluble molecules. Cells need to exchange molecules w their environment.

Nucleus

Contains main genome; DNA and RNA synthesis. 6% of total cell

Cytosol

Contains many metabolic pathways. Protein synthesis. Cytoskeleton.

Cell surface carbohydrates

Contributes to cell function and identity. Most proteins on exterior of plasma membrane have sugars attached. Some lipids on exterior of plasma membrane have sugars attached. Oligosaccharides attached to form glycoproteins proteoglycans contain long polysaccharide chains

Gene Expression (euk. cells)

Controlled @ various steps.

Proteases

Controlled Protein Breakdown Helps Regulate the Amount of Each Protein in a Cell

Lac Operon**

Controlled by an Activator and a Repressor

Specific actin bind proteins

Controls properties of structures containing actin filaments. i.e. bundling protein (in filopodia), myosin motor protein, side-binding protein (tropomyosin), capping (Plus-end-blocking) protein, cross-linking (in cell cortex), severing protein. -Varied arrangements & functions of AF in cells from diversity of actin-binding proteins--control actin polymerization, cross-link AF into loose networks or stiff bundles--attach actin filaments to membranes, or move 2 adjacent filaments relative to each other. Forms bundling protein (in filopodia), myosin motor protein, side-binding protein (tropomyosin), Capping (plus-end blocking) protein, cross-linking protein (in cell cortex), and severing protein.

Nitrogen fixation

Conversion of N2(g) from atmosphere → nitrogen-containing molecules by soil bacteria and cyanobacteria. Requires a shit load of E.

Signal transduction

Conversion of an impulse or stimulus from one physical or chemical form to another. In cell biology, the process by which a cell responds to an extracellular signal. Begins when the receptor of target cell receives an incoming extracellular signal, and then converts to intracellular signaling molecules that alter cell behavior. -Majority are proteins, peptides, or small hydrophilic molecules; bind to cell-surface receptors spanning throughout PM.

Sister chromatid

Copy of a chromosome, produced by DNA replication, that remains bound to the other copy.

5 types of chemical bonds fold and stabilize 2, 3, and 4 structure

Covalent: Disulfide = strong and stable, rare Noncovalent: Hydrogen- ex: alpha helix and beta sheet Electrostatic- neutralize charged residues keeping interior hydrophobic Hydrophobic- occur in the interior protein leaving polar/ionic residues at surface to interact with water Van der Waals forces- only act at short distances

Membrane potential

Created by Differences in the Concentration of Inorganic Ions Across a Cell Membrane.

Solutes

Cross cell membranes by either passive or active transport.

Microtubule-associated proteins (MAPs)

Cross-linking proteins that stabilize bundles of permanent microtubules (e.g. the microtubules that run the length of nerve axons) by binding to the sides of the microtubules. also can transports cargo along microtubule

In most respects, cell division is similar between plant and animal cells. Which of the following events occurs by a different mechanism in animal and plant cells?`

Cytokinesis, the separation of the cell into two new daughter cells, occurs differently in plant and animal cells.

Ribosome

Cytoplasmic organelles at which proteins are synthesized.

There are five types of nitrogen bases found in nucleic acids.

DNA contains adenine (A), guanine (G), cytosine (C), and thymine (T). RNA contains adenine (A), guanine (G), cytosine (C), and uracil (U).

Polymorphism

DNA sequence for which 2 or more variants are present at high frequency in the general population. Also in some cases contribute to our individual phenotypes. Common polyM Including SNPs, indels, and CNVs--provide markers for genetic mapping. +Identical twins, no 2 human genomes are alike. Each of us carries a unique set of polymorphisms.

DNA replication

DNA unzips into two parts and splits with the cell. In it's new home each side of the DNA strand attack to matching nucleotides to create 2 exact copies. It is important in puberty and other times of growth as it is the reproducing of your cells.

mRNA Message

Decoded on Ribosomes.

Fluidity of a Lipid Bilayer

Depends on its composition. -Important for several cellular processes.

Diploid

Describes a cell or organism containing two sets of homologous chromosomes, one inherited from each parents.

Haploid

Describes a cell or organism w only one set of chromosomes, such as a sperm cell or a bacterium.

Apical

Describes the top or top of a cell, structure, or organ. - surface exposed to air or bodily fluid. In epithelial cell, this surface is opposite the base, or basal surface.

Transmembrane receptors

Detect a signal on the outside and relay the message, in a new form, across membrane into interior of cell. -Binds to intracellular receptor proteins. Producing only a limited set of receptors - a cell restricts the types of signals that can affect it. Changes behavior of a target cell in a large variety of ways: altering its shape, movement, metabolism, gene expression, or some combination.

Transcription of Notch-responsive genes

Developing nerve cell w Signal protein (Delta) binds to delta receptor (notch; embedded in PM (cytosol) of nucleus --> Notch tail cleaves and migrates to nucleus --> transcription of Notch-responsive genes.

Voltage

Difference across membrane (inside vs outside of cell)

Protein Assemblies

Dimer, helix, and ring

Zygote

Diploid cell produced by fusion of a male and female gamete. Fertilized egg.

Cellulose Orientation

Direct MT

Genetic information

Directs the synthesis of proteins.

Phospholipids and glycolipids

Distributed asymmetrically in lipid bilayer of animal cell plasma membrane.

M Phase (Mitosis) Entry

Division of the nucleus in euk cell. •M-Cdk (Cyclin B-Cdk1) - complex accumulates throughout G2, but not activated until Cdc25 removes inhibitory phosphates from M-cyclin (Cyclin E) •M-Cdk also inactivates Wee1 (inhibitory kinase) •M-Cdk also turns on APC/C which will actually direct destruction of M cyclin (with a delay)

Inorganic

Does not contain carbon

Nuclear envelope

Double inner and outer nuclear membrane perforated with pores that control the flow of materials in and out of the nucleus.

Most common human disorders

Due to many genes acting together; DNA sequencing studies are identifying mutations in these genes that increase the risk of developing these diseases.

Rare, inherited human diseases

Due to mutations in a single gene.

Actin Filaments Slide Against Myosin Filaments

During Muscle Contraction. A skeletal muscle cell is a large, multinucleated cell (fusion of smaller cells) Packed with myofibrils, containing a chain of contractile units called sarcomeres. -Myosins--motor proteins that use E of ATP hydrolysis to move along AF.

The Structure of Eukaryotic Chromosomes

The Basic Problem: •Each human cell contains about 2 meters of DNA, yet the cell nucleus is 5-8 micrometers (millionths of a meter) in diameter, so the chromosome structure needs to compact the DNA into nucleus efficiently. •The chromosome structure needs to allow the DNA to replicate and divide into two cells during cell division, without becoming a tangled mess. •Genes in the compacted DNA need to be accessible for transcription to make protein.

Interphase Chromosomes Occupy Distinct Regions

Each chromosome tends to occupy a particular region of the nucleus, as shown with fluorescent dyes that label particular chromosomes. Each chromosome occupy a particular region of nucleus and not spread out in nucleus. Homogolous chromosome: Two pairs of chromosomes aren't next to each other, but occupy discrete regions w/I nucleus.

Nucleotides

Each nucleotide is composed of three parts: A phosphate group A pentose sugar A nitrogen-containing (nitrogenous) base

Transport of Solutes in Plants, Fungi, and Bacteria

Electrochemical H+ Gradients Drive

The Complexity of Synaptic Signaling

Enables Us to Think, Act, Learn, and Remember

Internal Membrane Organelles (Euk)

Endoplasmic reticulum (ER) - network of interconnected spaces enclosed by a membrane and site of cell membrane component synthesis Golgi apparatus - stack of flattened membrane-enclosed sacs (look like flattened pancakes)

Which organelle is the major site of new membrane synthesis in a cell?

Endoplasmic reticulum, is the major site of synthesis of new membranes in the cell. New phospholipids are manufactured by enzymes bound to the cytosolic surface of the ER. These enzymes use free fatty acids as substrates and deposit the newly made phospholipids into the cytosolic half of the bilayer. Transporters called scramblases then ensure that these phospholipids are distributed evenly between each monolayer of the ER.

Activation energy

Energy can be acquired to get a chemical reaction started

Lipid

Energy-rich organic compounds, such as fats, oils, and waxes, that are made of carbon, hydrogen, and oxygen.

Proteins

Enter Peroxisomes from both the Cytosol and the Endoplasmic Reticulum. Enter the Endoplasmic Reticulum While Being Synthesized.

Phosphoinositide 3-kinase (PI 3-kinase)

Enzyme that phosphorylates inositol phospholipids in the PM, which generates docking sites for intracellular signaling proteins that promote cell growth and survival.

calmodulin-dependent protein kinases (CaM-kinases)

Enzyme that phosphorylates target proteins due to increase in Ca2+ ion concentration through its interactions w Ca2+-binding protein calmodulin. Activated GPCR (signal molecule) --> G protein --> phospholipase C --> IP3 --> Ca2+ --> Calmodulin --> CaM-kinase --> transcription regulator or target proteins.

Cyclic-AMP-dependent protein kinase (PKA)***

Enzyme that phosphorylates target proteins due to rise in intracellular cyclic AMP concentration can activate gene transcription

Protein kinase C (PKC)

Enzyme that phosphorylates target proteins in response to a rise in diacylglycerol and Ca2+ ions. Activated GPCR (signal molecule) --> G protein --> phospholipase C --> IP3 --> Ca2+ --> PKC --> Regulator or target proteins. OR Activated RTK --> phospholipase C --> diacylglycerol --> PKC

Cdk (cyclin-dependent protein kinase)

Enzyme that, when complexed w a regulatory cyclin protein. Can trigger various events in the cell-division cycle by phosphorylating specific target proteins.

serine/threonine kinases

Enzyme-coupled receptors *Most common. Phosphorylate proteins on serines or threonines.

Protein phosphatase

Enzymes that catalyze the removal of a phosphate group from a protein, often high specificity for phosphorylates site. Dephosphorylates

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed. more highly compacted chromatin and easily visible with light microscope •Concentrated in centromeres and telomeres. •Usually inactive due to high compact.

Histone modifications

Eukaryotic chromosome structure. 1st: double stranded DNA 2nd: double stranded DNA wrapped twice around each core nucleosome - Structure formed by long DNA molecule wrapped into multiple nucleosome sort of like beads on string called 10 nm filament. 3rd: using moderate extraction (detergent+ hi salt) core nucleosome + H1 H1 linker histone used Nucleosomes coiled together 4th: -30 nm filament attached to protein scaffold in long loops The basic form of most chromatin for most euchromatin during interphase Scaffold attachment regions (SARS) are linked to the scaffold my MARS Alternative extraction (dextran sulfate polysaccharide) histone removed scaffold stays. 5A: Heterochromatin are fully condensed and super packed throughout the entirety cell cycle Heterochromatin shows up as super dark stains Genome= heterochromatin + euchromatin Euchromatin is less dense and stains lighter or 5B: Chromatin loops condensed into short blobs during mitosis and form fully condensed chromosomes Very mild extraction- chromosomes released from cell with most protein still associates

Polysaccharides as Energy Storage

Examples of energy storage: •Starch - provides energy storage in plants •Glycogen - provides energy storage in animals

Polysaccharides as Structural Molecules

Examples of structural molecules: Cellulose •found in cell wall of plants •most abundant organic molecule on earth •Animals unable to digest cellulose Chitin •Found in cell walls of fungi and exoskeleton of some animals Peptidoglycan Found in cell walls of bacteria

Neurotransmitters Table 12-3 on effect of inhibitory signaling

Excitatory or Inhibitory

Intestinal tissue renewal

Exist in particular area of gut (crypt) -Crypt - Part of gut of microvilli that stick up increasing surface area. Get nutrients and waste products out into intestine. Villus (no cell division) -(embedded w/i crypt) Nondividing, terminally differentiated paneth cells divide below crypt and then migrates through crypt. --> precursor --> Become Nondividing, terminally differentiated cells.

Genetic screen

Experimental technique used to search through a collection of mutants for a particular phenotype. Mutant alleles can be dominant or recessive. If a single copy of the mutant alters the phenotype of an individual that also possesses a wild-type allele = dominant, and recessive if not.

Classical genetic approach

Experimental techniques used to isolate genes responsible for an interesting phenotype.

Gradient-driven pump

Exploit Solute Gradients to Mediate Active Transport. Can act as symports or antiports.

Hormone

Extracellular signal molecule that is secreted and transported via the bloodstream (in animals) or the sap (in plants) to target tissues on which it exerts a specific effect.

Survival factors

Extracellular signal molecule that must present to suppress apoptosis.

Cell responses mediated by cyclic AMP

Extracellular signal molecule | Target tissue | Major response: -Epinephrine; target heart tissue and inc. in HR and force of contraction. -Epinephrine; target skeletal muscle and yield glycogen breakdown. -Epinephrine, glucagon; target fat tissue and yield fat breakdown. -Adrenocorticotropic hormone (ACTH); adrenal gland responding in cortisol secretion. -Adrenaline stimulates glycogen breakdown in skeletal muscle cells by ultimately activating glycogen phosphorylase, the enzyme that breaks down glycogen

During oxidative phosphorylation, why does a single molecule of NADH result in the production of more ATP molecules than a single molecule of FADH2?

FADH2 and NADH feed their electrons to different carriers in the electron-transport chain. Feedback: FADH2 molecules bypass the first respiratory complex in the chain and pass their electrons to the carrier ubiquinone, ultimately resulting in the pumping of fewer protons across the inner mitochondrial membrane.

GPCR-Triggered Intracellular Signaling Cascades Exam info: Know steps that amplify vs not

Fast, Sensitive, and Adaptable via -Rod photoreceptor cell from retina (sensitive to life). - Light induced signaling cascade in rod photoreceptor cells greatly amplifies the light signal.

Amphipathic phospholipids

Form a bilayer in water.

Membrane Lipids in water

Form bilayers.

SNP (single-nucleotide polymorphism)

Form of genetic variation when one portion of the population differs from another in terms of which nucleotide is found at a particular position in the genome.

Flexibility 11.30

Formation of mouse-human hybrid cells shows that some plasma membrane proteins can move laterally in the lipid bilayer.

Contractile Structures

Formed by actin associating w myosin. -Myosin= motor protein like kinesins and dyneins uses ATP for energy move toward plus end of actin filament. A type of motor protein that associates into filaments that interact with actin filaments to cause cell contraction. -Myosin-I : simplest myosin. +A type of motor protein that associates into filaments that interact with actin filaments to cause cell contraction or vesicles along AF tracks. Several families (including Myosin-II) -Myosin-II: Protein associated with the fiber that makes muscle contractions. Made of 2 subunits of a head and 2 tails that twist together that form a dimer. Pulls the filament across themselves. Can cause adjacent actin filaments--slide past each other in contractile bundles. +Skeletal muscle cells--repeating arrays of overlapping filaments of actin & myosin II--form highly ordered myofibrils--contract as filaments slide past one another. -Acts as monomer: Head bind actin filament and hydrolyzes ATP Tail binds cargo

closed, Spherical liposomes.

Formed from pure phospholipids

Ionic bond

Formed when one or more electrons are transferred from one atom to another Forms electrically charge atoms

Intron (RNA)**

Forms a branched structure (lariat) during RNA splicing. Removed by Pre-mRNAs via RNA splicing. Due to special nucleotide sequences in Pre-mRNA transcript signal the beginning & end of intron. In a pre-mRNA molecule forms a branched structure during RNA splicing.

Dimers face opposite direction —>

Forms staggered antiparallel tetramer of two coiled-coil dimers. -Pathway: Alpha-helical region of monomer —> coiled-coil dimer —> tetramer. Ends of the tetramer are the same (N termini of filament proteins) -Dimers form via interactions between alpha helical regions of monomers.

A set of three transcription regulators

Forms the regulatory network that specifies an embryonic stem cell.

Glycolipids

Found exclusively in the noncytosolic face of a membrane.

Nucleolus

Found inside the nucleus and produces ribosomes.

Abnormally stretchy skin is part of a genetic syndrome that could result from which of the following?

From loss of proteinase that cleaves procollagen. A variety of defects in procollagen synthesis or processing can lead to disorders in which the skin is abnormally stretchy.

Triglycerides

Functions: long-term energy storage and insulation •Consist of one glycerol molecule linked to three fatty acids by condensation reactions •Fatty acids can be: •Saturated - no double bonds between carbons and tend to be solid at room temperature •Unsaturated - one or more double bonds between carbons and tend to be liquid at room temperature

G1 Phase - Mitogen Activation

G1-Cdk (Cyclin D-Cdk4/6) & G1/S-Cdk (Cyclin E-Cdk2) •Mitogen Activation --> intra. sig. pathway into nucleus --> Active Rb protein bound to transcription regulator (inactivated) --> G1-Cdk (Cyclin D-Cdk4/6) & G1/S-Cdk Phosphorylates Rb (retinoblastoma protein) --> inactivated Rb protein allowing active transcription regulator of gene launch into S phase. •Rb negatively controls the cell cycle •Phosphorylation of Rb relieves this inhibition. Gap 1 phase of the euk. Cell cycle. Falls b/w the end of cytokinesis and the start of DNA synthesis.

GABA and Glycine receptor

GABA & Glycine-gated Cl- channel ; PM many neurons @ synapses. Inhibitory synaptic signaling.

Plasmodesmata

Gap junction In Plants form a diff. type of channel - traverses cell walls, is lined by PM, and allows both small and large molecules to pass from cell-cell. Smooth ER connecting 2 dif. cells and desmotubule (b/w cell wall) a cell-to-cell junction in plants that connects the cytoplasm of adjacent cells

eukaryotic transcription regulators acting at a distance

Gdoc final 202

Combinatorial control **

Generate diff. cell types.

Individual chromosome

Genes are transcribed using one DNA strand as template, and others transcribed from other DNA strand.

Loss-of-function mutation

Genetic alteration that reduces or eliminates the activity of a gene. Such mutations are usually recessive: the organism can function normally as long as it retains at least one normal copy of the affected gene.

Gain-of-function mutation

Genetic change that increases the activity of a gene or makes it ative in inappropriate circumstances. Such mutations are usually dominant

Complementation test

Genetic experiment that determines if two mutations associated w the same phenotype lie in the same gene or in diff. genes.

Genotype

Genetic makeup of a cell or organism, including which alleles (gene variants) it carries.

Relative sizes

Give us clues to our evolutionary history, and help identify common disease-associated alleles.

Carbohydrate-rich layer

Glycocalyx

Which organelle receives proteins and lipids from the endoplasmic reticulum, modifies them, and then dispatches them to other destinations in the cell?

Golgi apparatus, is usually situated near the nucleus, receives proteins and lipids from the ER, modifies them, and then dispatches them to other destinations in the cell. Transport from the ER to the Golgi apparatus—and from the Golgi apparatus to other compartments of the endomembrane system—is carried out by the continual budding and fusion of transport vesicles. Proteins entering the Golgi can either move onward through the Golgi stack or, if they contain an ER retention signal, be returned to the ER; proteins exiting from the Golgi are sorted according to whether they are destined for lysosomes (via endosomes) or for the cell surface.

Membrane Potential

Governed by the Permeability of a Membrane to Specific Ions.

Gradients Across Inner Membrane

Gradient: 1. Electrical b/c protons have positive charge in intermembrane space and negative charge in matrix. Due to ions being on one side of membrane. The total "proton motive force" is the sum of the forces generated by the electrical and concentration gradients, which work in the same direction. -A lot of the E released via electron transfers along electron-transport chain (ETC)-- is harnessed to pump protons (H+) out of matrix, creating an electrochemical proton gradient. H+ - determines pH. i.e. More H+ - lower pH Acidic. -ETC across inner mitochondrial membrane--harnessed to make ATP when protons move back into matrix through ATP synthase located within. (cycling of protons) +Drives active transport of selected metabolites in and out of matrix. -Embedded are 3 large respiratory enzyme complexes--carries out proton pump.

Molecule

Groups of atoms joined by covalent bonds

Cell growth

Growth factor (dimer) activated RTK --> activated PI 3-kinase -> -> activated Akt -> -> -> activated Tor --> either inhibition of protein degradation or stimulation of protein synthesis (both lead to cell growth)

Active monomeric GTPase

Guanine nucleotide: *Inactive monomeric GTPase exchange factors (GEFs) promote exchange of GDP for GTP, switches protein on resulting in active monomeric GTPase.

MT Organize the Cell Interior

Guide the transport of organelles, vesicles, and macromolecules in both directions along a nerve cell axon. Backward transport (to cell body) Outward transport (to axon terminal) 1. Nondividing cell--centrosome. 2. Dividing cell--poles of mitotic spindle. 3. Ciliated cell-- cilium of basal body.

Ions

H+, Na+, K+, Ca2+, Cl_, Mg2+, and HCO3-

Small, uncharged polar molecules

H2O, ethanol, and glycerol

Carry phosphate and carboxyl group

HCO3-, Po4^3-, proteins, nucleic acids, metabolites.

Eukaryotic Transcription Regulators cont. **

Help Initiate Transcription by Recruiting Chromatin-Modifying Proteins

Stem cell potential- Hemopoiesis

Hematopoietic stem cell: -Adult stem cells: blood stem cells residing in marrow; produce a variety of cell types. Then again precursors will depend on signals of the precursor receive. Dictacts differentiated cells w/i blood. Hemopoietic stem cells produce all blood cell types: red and white blood cells, osteoclasts, and platelets.

Variability of Chromosome Condensation

Heterochromatin - more highly compacted chromatin and easily visible with light microscope •Concentrated in centromeres and telomeres. •Usually inactive due to high compact. Euchromatin - less condensed, typically region that is actively transcribed.

Chromosome

Highly Condensed. •The DNA of interphase chromosomes is 20X less condensed than that of of mitotic chromosomes but is still highly condensed to fit in nucleus. •The condensation has to be flexible (More/less condensed) and region-specific (e.g., genes need to be decondensed to be transcribed).

Microtubules

Hollow cylinders made of globular tubulin (protein) dimers w structurally distinct ends--polarized structures w slow-growing minus end & fast-growing plus end. Long and straight. All tubulin protein-protein interactions are non-covalent. Polarity: Beta end = plus end Alpha end = minus end Typically have one end attached to a single microtubule-organizing center: centrosome. Outer diameter of 25 nm. More rigid than actin or intermediate filaments. Rupture when stretched. Grow out from centrosome (organizing center)--where minus ends remains embedded. --Used by euk. To organize their cytoplasm and guide the intracellular transport of macromolecules and organelles. -Aster Star-shaped array of microtubules emanating from a centrosome or from a pole of a mitotic spindle.

Intracellular Signaling Pathways

How Cell-Surface Receptors Relay Extracellular Signals. Often generates a series of additional intracellular signals before, indirectly, generating a response "signaling cascade" Receptor protein recognizes (binds) signal molecule generates an intracellular signal. Many extracellular signals activate intracellular signaling pathways changing the behavior of target cell.

Ligand

How Proteins Work. How does protein structure relate to protein function? •Protein structure allows a protein to bind specifically with other molecules (ligands) •Key-in-lock fit or hand-in-glove fit

Feedback inhibition

How Proteins are Controlled. an enzyme working early in a pathway is inhibited (turned off) by a late product of the pathway. Metabolic pathways are typically interconnected and regulated by feedback inhibition at multiple points

Ion Channels***

How some G Proteins Directly Regulate channels in membrane. Some Bacterial Toxins Cause Disease by Altering the Activity of G Proteins. -(A) acetylcholine (signaling molecule, transmembrane), activated alpha subunit (GTP) -I.e. A Gi protein directly coupled receptor activation to the opening of K+ channels in the plasma membrane of heart pacemaker cells. *slows heart rate by dampening positive effect of Na+ inflow on membrane potential *outflow of K+ makes it harder for a depolarizing stimulus to have an effect. K+ outflow dampens positive effect of Na+ inflow on membrane potential

Cell-surface and intracellular receptors

Hundreds of signals at any given time in a multicellular organism some cannot cross the PM (large and/or hydrophilic) some can cross the plasma membrane (small and hydrophobic) Each cell responds selectively to signals it encounters receptors needed for response each cell expresses a particular set of receptors cell surface receptors (focus of chapter) intracellular receptors

Alpha and beta folding

Hydrogen bonds form b/w N-H and C=O groups in polypeptide backbone. B/c amino acid side chains don't have hydrogen bonds allows for generation of diff. amino acid sequences.

Steroid hormone

Hydrophobic signal molecule related to cholesterol. -Can pass through PM to interact w intracellular receptors that affect gene expression in the target cell. I.e. estrogen and testosterone.

often helices

Identical proteins with two different binding sites form chains

Coenzyme

If the cofactor is an organic molecule.

Membrane potential

If the membrane potential becomes more positive than it is at the resting potential, the membrane is said to be depolarized. If the membrane potential becomes more negative than it is at the resting potential, the membrane is said to be hyperpolarized. an electrical potential difference, or voltage, between the electrodes. This electrical potential difference is called the membrane potential.the gradient of potential energy that determines in which direction ions will flow.

Protein-free, artificial lipid bilayer (liposome)

Impermeable to most water-soluble molecules

Thylakoid

In a chloroplast, the flattened, disclike sac whose membranes contain the proteins and pigments that convert light energy → chemical-bond energy during photosynthesis. Photosynthetic ETC within also generates a proton gradient across the membrane--used by ATP synthase embedded in that membrane generating ATP.

phragomoplast

In a dividing plant cell, structure made of microtubules and membrane vesicles that guides the formation of a new cell wall.

Antenna complex:

In chloroplast and photosynthetic bacteria, part of the membrane bound photosystem that captures energy from sunlight; contains an array of proteins that bind hundreds of chlorophyll molecules and photosensitive pigments.

Metabolic processes

In eukaryotic cells, internal membranes create enclosed compartments that segregate different metabolic processes. cell from the lining of the intestine contains the basic set of membrane-enclosed organelles found in most animal cells.

Dynein produces MT sliding

In isolated doublet MT. Plus end and minus end + ATP

Pairing

In meiosis, process when a pair of duplicated homologous chromosomes attach to one another to form a structure containing 4 sister chromatids.

Cell-cycle

In most cells, interphase consists of an S phase when DNA is duplicated plus two hap phases: G1 and G2; that give proliferating cells more time to grow and prepare for S and M phases.

Dynein causes MT bending

In normal flagellum. Plus end, linking proteins, and minus end + ATP --> bending.

Protein unfold

In order to enter mitochondria & chloroplast.

Reaction center

In photosynthetic membranes, Complex of proteins associated with two special chlorophyll a molecules and a primary electron acceptor. Located centrally in a photosystem, this complex triggers the light reactions of photosynthesis. Excited by light energy, one of the chlorophylls donates an electron to the primary electron acceptor, for transport down the photosynthetic electron transport chain.

Epinephrine stimulates glycogen breakdown

In skeletal muscles.

Most RTKs Activate the Monomeric GTPase Ras**

In turn, activates a 3-protein MAP-kinase sig. module-- helps relay signal from PM to nucleus.

Promotion of cell survival by inhibition of apoptosis

Inactive Bcl2 + bad enzyme complex --> active AKT (survival signal) phosphorylation of Bad --> releases active Bcl2 + inactive Bad (phosphorylated) --> Promotes of cell survival by inhibition of apoptosis.

The G protein α subunit switches itself off by hydrolyzing its bound GTP to GDP****

Inactive G-protein and target protein: Inactive alpha-subunit reassembles w beta-Y complex.

Redox Potential

Increases Along ETC •The proteins of the respiratory chain guide the electrons to move sequentially from one enzyme complex to another in a series of oxidation-reduction reactions, with no short circuits. •Many of these proteins contain iron, whose affinity for electrons is "adjusted" by the protein. •The electrons pass from carriers that have a low affinity for electrons (high G, low redox potential) to carriers that have high affinity for electrons (low G and high redox potential) •ΔG is negative for overall pathway

ATP Hydrolysis Drives Unfavorable Reactions

Indirectly coupled ATP hydrolysis to drive reactions forward

Fibroblasts

Influence Collagen Alignment. In connective tissue, cells that secrete extracellular matrix of proteins and collagen fibers. Cell type that produces the collagen-rich extracellular matrix in connective tissues. i.e. skin and tendon. Proliferates readily in wounded tissue and in tissue culture. •Heart explants (chick) placed on collagen gel •Collagen between explants becomes aligned - influenced by fibroblasts in explants •Fibroblasts migrate out along collagen fibers •Likely similar in vivo to developing long-range order of ECM (e.g. tendons)

Actin-binding Proteins

Influenced by actin-binding proteins. Causes Protrusions Formed at the Leading Edge -Lamellipodium projection Actin assembly at leading edge disassembly further back. -ARPs= actin related proteins bind sides of filaments. nucleate formation of new filament a "branch" -Filopodium projection Formin Instead of ARP, promotes assembly at ends unbranched filaments. A web of polymerizing actin filaments pushes the leading edge of a lamellipodium forward.

G2 Arrest Triggered by Incomplete Replication

Inhibition of activating phosphatase (Cdc25) blocks entry to mitosis

Fluorescence microscope

Instrument used to visualize a specimen that has been labeled with a fluorescent dye; samples are illuminated with a wavelength of light that excites the dye, causing it to fluoresce.

Lipid-linked

Integral membrane protein.

monolayer-associated protein

Integral membrane protein.

Cytoplasmic network

Intermediate filaments form a strong, durable network in the cytoplasm of the cell Strongest cytoskeleton filaments (survive salt and detergent treatments other filaments do not) strong but flexible Surround nucleus and create cytoplasmic network Anchored at plasma membrane at cell-cell junctions (desmosomes) In these structures, cadherin molecules are linked to keratin filaments, a type of intermediate filament that extends throughout the cytoplasm.

Vimentin & vimentin-related filaments

Intermediate filaments —cytoplasmic-—> Connective tissue, muscle, and glial cells

Neurofilaments

Intermediate filaments —cytoplasmic-—> Nerve cells

Keratin filaments

Intermediate filaments —cytoplasmic-—> Epithelial cells. Intermediate Filaments Strengthen Cells Against Mechanical Stress. most diverse class different keratins present in different classes of epithelial cells specialized keratins : hair, feathers, claws, etc. Class of intermediate filaments abundant in epithelial cells, where it provides tensile strength. Main structural component of hair, feather, and claws. Epithelium: Ends of keratin filaments anchored in desmosomes -Example: Human disease: epidermolysis bullosa simplex -defect in formation of keratin filaments *predisposed to mechanical injury. *mutant form of keratin makes skin more prone to blistering (even with gentle pressure).

Nuclear lamins

Intermediate filaments —nuclear—> All animal cells. Formed meshwork from fibrous intermediate filament. Located beneath the inner nuclear membrane. -Nuclear intermediate filament proteins: lamins. -Breaks down and reforms every cell division -breakdown mediated by phosphorylation of lamins -dephosphorylation allows reassembly. -Supports & strengthens nuclear envelope. -Defects: can cause a rare class of premature aging disorders called progeria but it is not clear how the defect results in the disease

Ca2+

Intracellular concentration (mM): 10E-4 Extracellular concentration (mM): 1-2 Free ion. Most are bound to proteins and other organic molecules. Stored w/i various organelles.

K+

Intracellular concentration (mM): 140 Extracellular concentration (mM): 5

Cl-

Intracellular concentration (mM): 5-15 Extracellular concentration (mM): 110 Anion, Most cell constituents are negatively charged.

Na+

Intracellular concentration (mM): 5-15 Extracellular concentration (mM): 145

Lysosomes

Intracellular degradation. 1% of total cell

monomeric GTPases

Intracellular signaling pathways converge on Rho protein family members Activity controlled by regulatory proteins: -Guanine nucleotide exchange factors (GEFs): promote the exchange of GDP for GTP, thereby switching the protein on. -GTPase-activating proteins (GAPs): stimulate the hydrolysis of GTP to GDP, thereby switching the protein off.

Activation of Rho-family GTPases Know familiy members that promote structures

Intracellular signaling pathways converge on Rho protein family members = Monomeric GTPases Family of small, monomeric GTPases that controls the organization of the actin cytoskeleton. 1. Unspecified cell: 2. Rho activation (bundle): 3. Rac activation (lamellipodium): 4. Cdc42 activation (filopodia):

Signaling by GTP-binding protein (switch proteins involved)

Intracellular signaling protein whose activity is determined by its association w either GTP or GDP. Toggle b/w an activated (GTP binding) and an inactive state depending on if GTP or GDP bound to them. Once activated by GTP binding, many of these proteins have intrinsic GTP-hydrolyzing (GTPase) activity, and shuts off via hydrolyzing their bound GTP —> GDP. -2 main types: Includes both trimeric G proteins and monomeric GTPases, i.e. Ras.

Result of selective transport

Ion Concentrations Inside a Cell Are Very Different from Those Outside

Ion channels

Ion-selective and Gate has a selectivity filter that controls which inorganic ions it will allow to cross the membrane. typical ion channel fluctuates between closed and open conformations.

ION CHANNELS

Ion-selective and Gated

Cytochrome c and Heme

Iron atoms in heme groups bound to "cytochrome" proteins are electron carriers in the next two complexes (cytochrome reductase and cytochrome oxidase).

Mitochondrial inner membrane

It contains transporters for ATP molecules.

β-catenin

It is a proto-oncogene because mutations in β-catenin make the protein resistant to degradation, promoting cell proliferation. a proto-oncogene. Activating mutations in β-catenin make the protein resistant to degradation, promoting cell proliferation. After migrating from the cytoplasm into the nucleus, β-catenin binds to the TCF transcription regulator, creating a complex that activates transcription of various Wnt-responsive genes, including genes whose products stimulate cell proliferation.

Mitochondrial outer membrane

It is permeable to molecules with molecular mass as high as 5000 daltons

Ca2+ pump (Ca2+ ATPase)

Keep the Cytosolic Ca2+ Concentration Low In the sarcoplasmic reticulum was the first ATP-driven ion pump to have its three-dimensional structure determined by x-ray crystallography. Ca2+ pumps in plasma membrane and ER membrane both work to keep cytosolic [Ca2+ ] low. Does not bind and transport a second ion like the Na+ pump. PM of euk. cells; E from ATP hydrolysis, active export of Ca2+ Most animal cells; Active import into Sarcoplasmic reticulum membrane of muscle cells and endo. reticulum membrane.

Arrangement of Chromosomes into Looped Domains

Keeps Enhancers in Check

Kinetochore Attachment

Kinetochores - protein complexes on either side of centromere •Form at centroMere of chromosoMes •Attach chromosomes to mitotic spindle Bi-orientation - The symmetrical attachment of a sister chromatid pair on the mitotic spindle, such that one chromatid in the duplicated chromosome is attached to one spindle pole and the other is attached to the opposite pole. Protein complex that assembles on the centrosome of a condensed mitotic chromosome. Site that spindle microtubules attach.

GPCR-Triggered Intracellular Signaling Cascades: Fast, Sensitive, and Adaptable.

Know steps that amplify vs not. Rod photoreceptor cell vs light-induced signaling cascade.

Ras***

Large family of small GTP-binding proteins (monomeric GTPases) - helps relay signals from cell-surface receptors to the nucleus. Many human cancers contain an overactive mutant form of the protein. RTK ->-> activated Ras protein signals activated MAP kinase "" "" via ->-> Either signals changes in protein activity (protein) or gene expression (transcription regulator) Class proto-oncogene --> activating mutations in Ras is muted & render the Ras protein continuously active, promotes proliferation.

Matrix

Large internal compartment in mitochondria.

Cell body

Largest part of a typical neuron; contains the nucleus and much of the cytoplasm

Chlorophyll and Electron Transfer

Light energy is harvested by several different thylakoid chlorophyll molecules, which harvest light at different wavelengths and focus the absorbed energy into a reaction center.

Chlorophyll

Light-absorbing green pigment, and plays a central part in photosynthesis. Forms photosystem (antenna complexes)

TFIID

Located @ transcription start site & +30

Na+-H+ exchanger

Located PM of animal cells, E from Na+ gradient, Export of H+ ions, pH regulation.

basal surface

Located near base. Opposite of apical. surface attached to sheet of connective tissue called basal lamina

Myofibril

Long, cylindrical structure that forms the contractile element of a muscle cell; constructed of arrays of highly organized bundles of actin, myosin, and other accessory proteins.

filopodium

Long, thin, actin-containing extension on the surface of an animal cell. Sometimes has an exploratory function, as in a growth cone.

Proofreading

Looking for errors

Electron transfer (reaction center w chlorophyll special pair)

Lose electrons due to transfer of molecules. Replaced by H+ for photo system II. Electrons pass through system is to minimize E lost from heat.

Oxidation

Loss of electrons from a substance involved in a redox reaction.

Plant cell- Cellulose

MT cytoskeleton directs the orientation so cellulose is deposited in the cell wall. MT cytoskeleton confer tensile strength, while other cell-wall polysaccharides resist compression. Orientation that cellulose AF (actin filament) are deposited w/i wall controls orientation of growth.

Nerve cell axon

MT guide the transport of organelles, vesicles, and macromolecules in both directions along body. -In axon organelles can move rapidly and unidirectionally. "stop and go" reflecting motor protein movements on cytoskeletal filaments (kinesins and dyneins on microtubules in this figure, but also myosin motors on actin. "Saltatory" is a term for this "stop and go" movement.

"9 + 2" array

MT in cilium or flagellum arrangement. Dynein involved w central singlet MT and outer doublet MT (A MT and B MT)

Soluble Proteins

Made on the ER Are Released into the ER Lumen. Signal peptidase: cleaves off signal sequence.

Differentiated Cells

Maintain Their Identity. A positive feedback loop can generate cell memory. Protein A is a master transcription regulator that activates the transcription of its own gene—as well as other cell-type-specific genes (not shown). All of the descendants of the original cell will therefore "remember" that the progenitor cell had experienced a transient signal that initiated the production of protein A.

G1/S-Cdk

Major cyclins and Cdks of vertebrates. Protein complex whose activity triggers entry into S phase of the cell cycle. Consists of a G1/S cyclin plus a cyclin-dependent protein kinase (Cdk). Cyclin E + Cdk2

S-Cdk

Major cyclins and Cdks of vertebrates. Protein complex initiates DNA replication. Consists of an S cyclin plus a cyclin-dependent protein kinase (Cdk). Initiates DNA replication during S phase. Helps ensure that the genome is copied only once. The cell-cycle control system can delay cycle progression during G1 or S phase-- to prevent cells from replicated damaged DNA. Delay start of M phase--ensuring DNA replication is complete. Drive it into S phase. Cyclin A + Cdk2

M-Cdk

Major cyclins and Cdks of vertebrates. Protein complex that triggers the M phase of the cell cycle. Consists of an M cyclin plus a mitotic cyclin-dependent protein kinase (Cdk) Cyclin B + Cdk1

Membrane-bound Enzymes Exam info: know how cAMP created and degraded but not structure of cAMP (or ATP and AMP)***

Many G Proteins Activate these enzymes that produce Small Messenger Molecules: 1. Adenylyl cyclase (Enzyme that catalyzes formation of cyclic AMP (cAMP) from ATP. +Extra. sig. acting via GPCR affect activity of enzyme, altering the intra. concentration of the 2nd messenger molecule cyclic AMP. +Important component in some intracellular signaling pathways -cAMP exerts most of its effects by activating the enzyme cyclic-AMP-dependent protein kinsase (PKA) 2. Phospholipase C: (cleaves a inositol phospholipid to produce; small messenger molecules: 1. inositol 1,4,5 triphosphate (IP3) triggers a Rise in Intracellular Ca2+ into cytosol @ endoplasmic reticulum. +Ca2+ then acts as 2nd messenger--altering activity of Ca2+ responsive proteins. i.e. calmodulin-dependent protein kinases (CaM kinases). 2. diacyglycerol (DAG) in PM.

TATA box

Many eukaryotic have this sequence. promoter DNA sequence crucial in forming the transcription initiation complex.

Transcription regulators bind to regulatory DNA sequences

Many transcription regulators binds to DNA as dimers.

V max

Maximum rate of reaction

Ran GTPase

Mechanism powered by GTP hydrolysis, drives nuclear transport.

Chemiosmotic Coupling

Mechanism that uses the energy stored in a transmembrane proton gradient (electrochemical proton gradient) to drive energy-requiring processes (ATP synthesis or transport of a molecule across a membrane) -The overall relationship that links bond-forming reactions to membrane transport processes in the mitochondria. -Mitochondria, chloroplasts, and many prokaryotes generate energy

Chemiosmotic coupling:

Mechanism that uses the energy stored in a transmembrane proton gradient to drive an energy requiring process, i.e. synthesis of ATP by ATP synthase or molecules transport across membrane

Homologous recombination

Mechanism when double-strand breaks in DNA can be repaired flawlessly. Uses an undamaged, duplicated, or homologous chromosome to guide the repaid. During meiosis, the mechanism results in exchange of genetic information b/w maternal and paternal homologs.

Voltage-gated Cation Channels

Mediates action potential. Na+ channel; change conformation based on membrane potential. Change conformation during an action potential. K+ channel; responding to the depolarization created by the voltage-gated Na+ channels, open. K+ ions flow out of the cell through the open K+ channels, returning membrane potential to the resting state. After an action potential, when the membrane potential has been restored to resting state, Na+ pumps restore Na+ and K+ gradients to levels in resting cell (pump 3 Na+ out and 2 K+ in per cycle).

Oxidative phosphorylation

Membrane-based process in bacteria and mitochondria. Part of the electron transport chain. A process occurring in the mitochondria that results in the formation of ATP from the flow of electrons across the inner membrane to bind with oxygen.

G protein

Membrane-bound GTP-binding protein involved in intracellular signaling. Composed of 3 subunits, this intermediary is usually activated by binding of hormone or other ligand to a transmembrane receptor.

Mitochondrion

Membrane-enclosed organelle, about the size of a bacterium. Carries out oxidative phosphorylation. Produces most ATP in euk. Cells.

Catabolism

Metabolic process that breaks down large molecules into smaller ones into useful energy for cells due to lost of heat.

Non-homologous end joining (NHEJ)

Method for repairing double-strand breaks by joining nonhomologous DNA ends in a process that does not conserve the original sequence.

Centrosome

Microtubule-organizing center that sits near the nucleus in an animal cell. During cell cycle, this structure duplicates to form the two poles of the mitotic spindle. -Each gamma tubulin ring complex is a nucleation site for growth of one microtubule Growth is at plus end; minus end remains embedded in centrosome Centrosome matrix w nucleation site important for creation of tubular structure (y-tubulin ring complex) + pair of centrioles --> MT grows @ plus ends from y-tubulin ring complexes -Centrioles: paired and perpendicular to each others (gamma tubulin ring) role is not established = "basal bodies" of cilia and flagella

Inositol phospholipid

Minor lipid component of PM that plays a part in signal transduction in euk. Cells; cleavage yields 2 small messenger molecules, IP3 and diacylglycerol.

Antibiotics should inhibit bacterial cell growth without generating side effects in the human patient, but that is not always the case. Some antibiotics that inhibit bacterial protein synthesis by binding to bacterial ribosomes induce negative side effects in patients. What is the most likely cause of these side effects?

Mitochondria are of bacterial origin and contain ribosomes more similar to bacterial ribosomes than the ribosomes found in the eukaryotic cell cytoplasm. Antibiotics that target bacterial cell wall synthesis do not induce mitochondrial side effects.

MAP kinase

Mitogen-activated protein kinase. Signaling molecule that the final kinase in a 3-kinase sequence called the MAP-kinase signaling module. Activated RTK --> Ras-GEF --> Ras --> MAP kinase kinase kinase --> MAP kinase kinase --> MAP kinase --> trans. regulator or target proteins. Guanine nucleotide exchange factors (GEFs) promote the exchange of GDP for GTP, active monomeric GTPase protein.

Cytoskeleton and M Phase

Mitotic spindle (Of MT) --[progression through M phase]--> Contractile ring (actin and myosin filaments)

Asexual reproduction

Mode of reproduction in which offspring arise from a single parent, producing an individual genetically identical to that parent. Includes budding, binary fission, and parthenogenesis.

Sexual reproduction

Mode of reproduction when the genomes of 2 individuals are mixed to produce an individual that's genetically distinct from its parents. +Involves the cyclic alternation of diploid and haploid states: diploid germ-line divide by meiosis to form haploid gametes and the haploid gametes from two individuals fuse at fertilization to form a new diploid cell -- zygote.

Golgi apparatus

Modification, sorting, and packaging of proteins and lipids for either secretion or delivery to another organelle. 3% of total cell.

Proteoglycans

Molecules that consist of a small core protein with many carbohydrate chains (GAGS) covalently attached, weaving a network secreted by cells. They may be up to 95% carbohydrate., forms gels that regulate the passage of molecules through the extracellular matrix Molecule consisting of one or more glycosaminoglycan chains attached to a core protein. Aggregates can form gels that regulate the passage of molecules through extracellular medium & guide migration. core protein the GAGs bind to Additional ECM Proteins

Secretory pathways 1

Most Proteins Are Covalently Modified in the ER. -Many proteins are glycosylated on asparagines in the ER. -Common 14-sugar block transferred to all proteins with a glycosylation signal from dolichol (lipid in ER membrane). -Oligosaccharide processing; creates the variety of glycosylations seen in cells = subsequent trimming of and/or adding to common 14-sugar block Sugars in 14-sugar block; glucose, mannose, and N-acetylglucosamine.

Onward transmission of signal**

Most RTKs Activate the Monomeric GTPase Ras. Activated RTK binded to a docking site is (adaptor protein and Ras-GEF complex). Adaptor protein and Ras-GEF complex then signals dephosphorylation (GDP to GTP) activating Ras protein to proceed in onward transmission of signal.

Phosphatidylcholine

Most common phospholipid in cell membranes.

Myosin

Motor protein using ATP to drive movements along actin filaments. One subtype interacts w actin forming the thick contractile bundles of skeletal muscle.

Dynein

Motor protein using E of ATP hydrolysis to move toward minus end of a microtubule. One form of protein causes bending of cilia.

Passive Transporters

Move a Solute Along Its Electrochemical Gradient.

Diffusion

Movement of molecules from an area of higher concentration to an area of lower concentration.

Cells --> Tissues --> Organs

Multicellular organisms are built from organized collections of cells

Okazaki Fragments

Multiple RNA Primers Needed •leading strand synthesis only needs one primer •lagging strand synthesis needs an RNA primer for each Okazaki fragment. •RNA primer from previous Okazaki fragment is removed by a nuclease, DNA replacement is synthesized (proofread) and new fragment is ligated to the old.

An animal cell depends on multiple extracellular signals.

Multiple signals received by a target cell will be integrated to generate a variety of outcomes. Every cell type displays a set of receptor proteins that enables it to respond to a specific type of extracellular sig. molecule produced by other cells. These signals molecules work in combinations to regulate the behavior of the cell. i.e.: Blue arrow- require multiple signals --> survive. Red arrows- additional signals to grow and divide. Green arrow- other signals --> differentiate. If deprived of necessary survival signals, most cells undergo cell suicide a.k.a apoptosis.

DNA Proofreading

Must Be 5'à3'

Muscle Contraction

Myosin attaches to actin; ATP binding reduces the affinity of myosin for actin; myosin is "cocked" as its head is displaced along the actin filament; the power stroke puts myosin in a "rigor" configuration. -Skeletal muscle, smooth muscle, cardiac muscle. All use actin and myosin in a similar way to contract. -Initiated when sudden rise in cytosolic Ca2+--delivers signal to myofibrils via Ca2+-binding proteins associated w the AFs. -Myosin-II: small, bipolar filament can slide two actin filaments of opposite orientation past each other. acts as a dimer double head and single tail (like kinesins and dyneins) Clusters of dimers form filaments with two sets of myosins, with heads oriented away from the filament center. i.e. Skeletal muscle cells--repeating arrays of overlapping filaments of actin & myosin II--a large, multinucleated cell (fusion of smaller cells) packed with myofibrils, containing a chain of contractile units called sarcomeres.

Factors Negatively Influencing Cell Survival

Myostatin - secreted signal protein that normally inhibits growth and proliferation of myoblasts (precursors) that typically fuse to from skeletal muscle. •Mouse deletion mutant has muscle that grow to be several times larger than normal •Cattle breeds selected for large muscles have mutations in myostatin gene

Cell-Cycle Control System

Network of regulatory proteins that govern the orderly progression of euk. Cell through the stages of cell division. Coordinates events of the cell cycle by sequentially and cyclically switching on and off the appropriate parts of the cycles machinery. -Uses proteins complexes, i.e. APC/C--triggering destruction of specific cell-cycle regulators @ certain stages of cycle. -Halt cycle @ specific transition points to ensure that intracellular and extracellular conditions--are favorable and each step is completed before the next begins. Some of these mechanisms rely on CDK inhibitors that block activity of one or more cyclin-Cdk complexes. -Depends on on cyclin-dependent protein kinases (Cdks)--cyclically activated by the binding of cyclin proteins & phosphorylation and dephosphorylation--once activated, Cdks phosphorylate key proteins in the cell. •Cells must ensure each step of the cell cycle is complete before moving into the next phase. •Series of checkpoints that prevent the cell from proceeding if all requirements are not met for a given phase. •Series of molecular switches turned "on" and "off" at correct times. •Coordinates steps of cell cycle. •Molecular switches operate in a defined sequence. i.e. 1. G1 --> S phase, favorable environment? 2. G2 --> M phase, all DNA replicated and all damage repaired? 3. M phase (pull duplicated chromosomes apart), all chromosomes properly attached to mitotic spindle?

Neurotransmitters

Neuronal signaling converting electrical impulses to chemical: each impulse stimulates the nerve terminal to release a pulse of an extracellular signal molecule. Small signaling molecule secreted by a nerve cell at a synapse to transmit information to a postsynaptic cell. I.e. acetylcholine, glutamate, GABA, and glycine. Then diffusses across the narrow (<100 nm) gap that separates the membrane of axon terminal from that of the target cell, reaching its destination in < 1 msec.

GPCR Signaling Pathway Generates a Dissolved Gas That Carries a Signal to Adjacent Cells. Locally acting gaseous signal molecule that diffuses across cell membranes to affect the activity of intracellular proteins.

Nitric oxide (NO)

intron (DNA)

Noncoding sequence. Introns Are Removed from Pre-mRNAs by RNA Splicing. -In Eukaryotes, interrupts Protein-Coding Genes.

Receptors Activate a Fast Track to the Nucleus.

Notch receptor

Anaerobic archaeon to anaerobic eukaryotic cell

Nuclear membranes and the ER may have evolved through invagination of the plasma membrane. This process is thought to apply to other organelles of the "endomembrane system" (that is , all organelles except mitochondria & chloroplasts)

Nuclear import is driven by the hydrolysis of GTP, which is triggered by an accessory protein called Ran-GAP (GTPase-activating protein). Which is true of this process?

Nuclear receptors carry Ran-GTP from the nucleus to the cytosol. The import of nuclear proteins is powered by energy provided by the hydrolysis of GTP. This hydrolysis is mediated by a monomeric GTPase named Ran. Like other GTPases, Ran exists in two conformations: one bearing a molecule of GTP, the other GDP. The accessory protein that triggers GTP hydrolysis, called Ran-GAP (GTPase-activating protein), is found exclusively in the cytosol. When a nuclear receptor bearing Ran-GTP exits the nucleus, it encounters Ran-GAP, which activates Ran's GTPase activity, causing it to hydrolyze its bound GTP. Ran-GDP then dissociates from the nuclear import receptor to which it is bound, leaving the receptor free to pick up a protein that is destined for transport into the nucleus. At the same time, Ran-GDP is carried into the nucleus by its own import receptor. Inside the nucleus, there is an accessory protein that causes Ran-GDP to release its GDP and take up GTP, called Ran-GEF (guanine nucleotide exchange factor), which is found exclusively in the nucleus. The action of this protein guarantees that the concentration of Ran-GTP in the nucleus remains high. When the nuclear receptor bearing its nuclear protein enters the nucleus, it encounters Ran-GTP. Ran-GTP binds to the import receptor, displacing the nuclear protein and promoting its release into the nucleus. Having discharged its cargo in the nucleus, the receptor—still carrying Ran-GTP—is transported back through the pore to the cytosol, where it encounters Ran-GAP, causing Ran to hydrolyze its bound GTP. Ran-GDP falls off the import receptor, which is then free to bind another protein destined for the nucleus. And the cycle repeats. Fundamentally, it is the lopsided distribution of the accessory proteins Ran-GAP and Ran-GEF that allows Ran-GTP to accumulate in the nucleus, thus driving the nuclear import cycle in the desired direction.

Which of these organelles are surrounded by a double membrane?

Nucleus, chloroplast, and mitochondrion. The nuclear membranes most likely originated by invagination of the plasma membrane to form a two-layered envelope that surrounds the cell's DNA; mitochondria and chloroplasts evolved from bacteria that were engulfed by primitive eukaryotic cells

Electron Transport Chain Overview

O2 is the terminal electron acceptor. A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.

Small, nonpolar molecules

O2, CO2, Steroid hormones

protein glycosylation

Oligosaccharides are added by an enzyme that has its active site on the lumenal side of the ER membrane. In the ER, individual sugars are not added one by one to the protein to create an oligosaccharide side chain. Instead, a preformed, branched oligosaccharide containing a total of 14 sugars is attached en bloc to all proteins that carry the appropriate site for glycosylation. The oligosaccharide is originally attached to a specialized lipid, called dolichol, in the ER membrane; it is then transferred to the amino (NH2) group of an asparagine side chain on the protein, immediately after a target asparagine emerges in the ER lumen during protein translocation. The addition takes place in a single enzymatic step that is catalyzed by a membrane-bound enzyme (an oligosaccharyl transferase) that has its active site exposed on the lumenal side of the ER membrane—which explains why cytosolic proteins are not glycosylated in this way. A simple sequence of three amino acids, of which the target asparagine is one, defines which sites in a protein receive the oligosaccharide. Oligosaccharide side chains linked to an asparagine NH2 group in a protein are said to be N-linked, and this is by far the most common type of linkage found on glycoproteins.

Response to signal Yeast cells respond to mating factors

Once ready to mate, it secretes a small protein called MATING FACTOR. Yeast of the opposite "Sex" detect this chemical mating call and respond by halting their progress thru the cell-division cycle and reaching out toward the cell that emitted the signal. Budding yeast (Saccharomyces cerevisiae) cells are... (A) normally spherical. (B) Exposed to an appropriate mating factors produced by neighboring yeast cells, will extend a protrusion toward the source of the factor.

anticodon loop **

One of three loops on a tRNA which contains the 3 nucleotides that allow it to align specifically with mRNA. Contains the anticodon

Phosphorylation cascades

One protein kinases, activated by phosphorylation, phosphorylates the next protein kinase in the sequence, and transmits the signal onward resulting in amplifying, distributing, and regulating it.

Mechanically gated cation channel

Open; depolarized PM Closed; resting PM. allow us to hear. This is also referred to as stress-gated. In auditory hair cell in inner ear. underlie the leaf-closing response in the touch-sensitive plant Mimosa pudica.

Ligand-gated (extracellular ligand)

Open; resting PM. Closed; Depolarized PM.

Ligand-gated (intracellular ligand)

Open; resting PM. Closed; Depolarized PM.

Receptor Tyrosine Kinases (RTKs)

Operate in intracellular sig. pathways: *Phosphorylate proteins on tyrosines. Enzyme-coupled receptor in which the intracellular domain has a tyrosine kinase activity, which is activated by ligand binding to the receptor's extracellular domain.

Control of Cell Numbers and Cell Size

Organ and body size determined largely by three fundamental processes: 1.Cell Growth 2.Cell Division 3.Cell Death

Amino acid

Organic compound with an amino group on one end and a carboxyl group on the other end, monomer for protein

Chapter. 20 - Cell Communities: Tissues, Stem Cell, and Cancer

Overview - •Extracellular Matrix and Connective Tissue •Epithelial Sheets and Cell Junctions •Stem Cells and Tissue Renewal •Cancer

peroxisome

Oxidative breakdown of toxic molecules. 1% of total cell

Energy via Membrane-based Mechanism

Oxidative phosphorylation - membrane-based process that drives formation of ATP by the transfer of electrons from food molecules to molecular oxygen. •Takes place in the mitochondria of eukaryotic cells •Depends on electron-transport process

Glycine receptor (glycine-gated Cl- channel)

PM of many neurons (@ synapses) Inhibitory synaptic signaling.

Glutamate receptor (glutamate-gated cation channel)

PM of many neurons (synapses) -Excitatory synaptic signaling.

GABA receptor (GABA-gated Cl- channel)

PM of many neurons (synapses). Inhibitory synaptic signaling.

Acetylcholine receptor (acetylcholine-gated cation channel)

PM of muscle cell (@ neuromuscular junction) excitatory synaptic signaling.

Voltage-gated Ca2+ channel

PM of nerve terminal. stimulation of neurotransmitter release.

Precursor cells 8:20

Partially differentiated cell. -Can undergo variety of divisions.

Uniport

Passive transporters (glucose transporter) moves transported molecule into cell.

Protein

Peptides - two or more amino acids joined by peptide bonds Polypeptides - long chains of amino acids joined by peptide bonds Proteins - polypeptides that are folded into particular conformation - more in Chapter 4

Cell-cycle Control Mechanisms - G1 --> S phase

Period during euk. Cell cycle when DNA is synthesized. 1. Environment is favorable --> enters S phase. 2. Unfavorable environment --> Cdk inhibitors block entry to S phase.

3. Metaphase

Period of the euk. Cell cycle when the nucleus and cytoplasm divide. State of mitosis when chromosomes are properly aligned at its equator (midway b/w spindle poles). Kinetochore MT on each sister chromatid attach to opposite poles of the spindle.

Proteins can be regulated by multiple modifications

Phosphate groups, acetyl groups, or ubiquitin, ?

RTKs Activate PI3-Kinase-Akt signaling pathway.

Phosphorylates To Produce Lipid Docking Sites in (PM)--attracting specific sig. proteins from cytosol (i.e. protein kinase AKT--becomes active and relays signal onward. -Stimulate cell growth & survival by activating PI3-kinase--phosphorylates specific inositol phospholipids in cytosolic leaflet of PM lipid bilayer. Pathway: Activated RTK --> PI 3-kinase (activated) --> phosphorylated inositol phospholipid --> protein kinase 1 --> AKT kinase --> trans regulator or target proteins Relay of onward signal in cytosol. Protein kinase 1 - Can form many target proteins.

Chloroplast

Plant cells; ATP synthesis and carbon fixation via photosynthesis.

Voltage-gated Na+ channel

Plasma membrane of nerve cell axon. Generation of action potential.

Voltage-gated K+ channel

Plasma membrane of nerve cell axon. Return of membrane to resting potentian after initain of action potenetial.

Phosphatidylcholine

Polar (hydrophilic) head: Choline and phosphate. No charge: glycerol. Non-polar (hydrophobic) tail: hydrocarbon tail w double bond (kink). -Most common phospholipid in cell membranes.

Cell membranes are packed with phospholipids.

Polar Hydrophilic head and nonpolar hydrophobic tails.

Myosin filament

Polymer composed of interactions molecules of myosin-II; interaction w actin promotes contraction in muscle and nonmuscle cells.

transmembrane protein w beta barrel conformation instead of an alpha helical conformation

Porin proteins form water-filled channels in the outer membrane of a bacterium.

Cytoplasm

Position Organelles via MT and motor proteins (MP).

7-methyl G (guanosine)

Positioned @ 5' cap.

Heterozygous

Possessing dissimilar alleles for a given gene.

Homozygous

Possessing identical alleles for a given gene.

Transmembrane Integrin protein

Present on cell surfaces- enable cells to make & break attachments to extracellular matrix- Allows cells to crawl through tissue--binding to fibronectin outside of the cell. i.e. links extra. matrix proteins: collagen and fibronectin to the intracellular cytoskeleton of cells that contact the matrix.

Levels of Protein Organization

Primary structure - amino acid sequence of a protein (polypeptide) Secondary structure - α-helices and β-sheets that form w/i certain segments of polypeptide chain. Tertiary structure - 3D conformation of a completely folded protein (entire polypeptide chain) +Incl: alpha helices, beta sheets, and all other loops and folds that form b/w the N- and C-termini. Quaternary structure - interaction of two or more proteins (polypeptides) +Protein molecule exists as complex of more than 1 polypeptide chain that interacts forming structure.

Law of segregation

Principle that the maternal and paternal alleles for a trait separate from one another during gamete formation and then reunite during fertilization. +Mendel's first law of inheritance. +States the maternal and paternal alleles for each trait separate from one another during gamete formation and then reunite randomly during fertilization.

Law of independent assortment

Principle that, during gamete formation, the alleles for diff. Traits segregate independently of one another. +Mendel's second law of inheritance. +Unraveled the laws of heredity by studying the inheritance of discrete traits in pea plants. +During gamete formation, dif. Pairs of alleles segregate independently of one another.

Terminal differentiation

Proceed to S phase? Pause? Withdraw to G0? Withdraw permanently and terminally differentiated?

Chromosome condensation

Process by which a duplicated chromosome becomes packed into a more compact structure prior to cell division.

Cell respiration:

Process by which cells harvest the energy stored in food molecules; usually accompanied by the uptake of O2 and release of CO2.

Carbon fixation:

Process by which green plants and other photosynthetic organisms incorporate carbon atoms from atmospheric carbon dioxide into sugars. Second stage of photosynthesis.

Photosynthesis

Process by which plants, algae, and some bacteria use the energy of sunlight to drive synthesis of organic molecules from CO2 and H2O. plants generally involves the green pigment chlorophyll and generates oxygen as a byproduct.

Centrosome cycle

Process by which the centrosome duplicates (interphase) and the two new centrosomes separate (@ beginning of mitosis) to form the poles of mitotic spindle.

Cytokinesis

Process by which the cytoplasm of a plant or animal cell divides in 2 to forming individual daughter cells.

Cellular repiration

Process making E from glucose and O2 --> ATP and CO2. NADH utilized in each step. 3 stages: 1. Glycolysis; glucose to 2 pyruvate, ATP, and NADH carried to Mitochondria 2. Citric acid cycle; (2 pyruvate enter mitochondria) making acetyl Co-A --> 2 GTP + 1 FADH2 + 4 CO2 + 6 NADH. 3. Oxidative phosphorylation; makes the most ATP from e- carried by NADH. -End step for NADH and FADH2 donates protons; passed among molecules in inner membrane and release E in intermembrane space causing chemical gradient (more H+ in intermembrane space than mitochondria) E used for ATP synthase. -O2 at end of chain releasing H2O. ATP synthase: Flow of H+ from ETC making ATP.

Induced pluripotent stem cells (iPS) 20:07

Process of somatic cell (differentiated) reprogrammed to resemble and behave like embryonic stem cell through artificial introduction of a set of genes (transcription factors) a pluripotent stem cell that was generated by manipulation of a differentiated somatic cell by injecting genes that code for certain transcription factors can be created by artificially expressing a suite of three to four transcription factors in adult cells such as fibroblasts. The iPS cells can then be converted into the desired cell type. Both ES and iPS cells - can be induced forming organoids: in vitro cultured cells that self-assemble into 3D organs. Organoids - ways researches can take apart the diff. processes of multicellular cells. i.e. Retina - ES cells (img) -major problem with using foreign cells grown in culture for transplantation in humans - investigators are exploring the use of induced pluripotent stem cells to generate personalized ES cells, which could be induced to produce the differentiated cell types needed by the host and be genetically identical to the host's other cells.

Osmosis

Process that Water Moves Across Cell Membranes Down Its Concentration Gradient. Aquaporin channels in PM of some cells: Allows water molecules to diffuse rapidly through

Crossing-over

Process when 2 homologous chromosomes break @ corresponding sites and rejoin producing 2 recombined chromosomes having physically exchanged segments of DNA. Enhancing genetic mixing helps ensure the proper segregation of chromosomes during meiosis.

Endocrine signals

Produced in animal cells. i.e. pancreas, an endocrine gland that produces several hormones — insulin, that regulates glucose uptake in cells all over the body. Akin to broadcasting info. over the radio. Signal send throughout entire body of multicellular organism e.g. insulin. -Endocrine cell with local mediator or hormone (inside cell) is excreted and passes thru membrane into bloodstream and bind to receptors of diff. target cells. Multicellular organisms, the most "public" style of cell-cell communication involves broadcasting the signal throughout the whole body by secreting it into an animal's bloodstream or a plant's sap.

Poly-A-binding protein

Promotes export from the nucleus, translation, and stability

Bad enzyme and inactive Bcl2

Promotion of cell survival by inhibition of apoptosis.

Denaturation

Protein - by treatment w solvents disrupting noncovalent interactions holding folded chain together.

Electrophoresis

Protein Separation.

Condensin

Protein complex that helps configure duplicated chromosomes for segregation by making them more compact.

Cohesin

Protein complex that holds sister chromatids together after DNA has been replicated in the cell cycle.

Cytochrome c oxidase complex

Protein complex that serves as the final electron carrier in the respiratory chain; removes electrons from cytochrome c and passes them to O2 producing H2O. This is one of the three respiratory complexes found in the electron-transport chain. It is the last complex in the chain. It receives electrons from cytochrome c, where protons are oxidized and the oxygen we breathe is reduced to form 2 molecules of water (4 electrons from the carrier and two protons from the aqueous environment).

G1-Cdk complex

Protein complex whose activity drives the cell through the first gap phase of the cell cycle. Consists of a G1 cyclin plus a cyclin-dependent protein kinase (Cdk). Major cyclins and Cdks of vertebrates. Drive cells through G1. -Cyclin D: * 3 forms of cyclin D in mammals (cyclins D1, D2, and D3) -Cdk4, Cdk6

nuclear receptors

Protein inside a eukaryotic cell that, on binding to a signal molecule, enters the nucleus and regulates transcription.

Motor protein

Protein like myosin or kinesin; uses E from hydrolysis of a tightly bound ATP molecule to propel itself along a protein filament or polymeric molecule.

motor proteins

Protein such as myosin or kinesin that uses energy derived from ATP hydrolysis to propel itself along a protein filament or polymeric molecule.

Plectin

Protein that aids in the bundling of intermediate filaments and links these filaments to other cytoskeletal protein networks. Linker Proteins Connect Cytoskeletal Filaments and Bridge the Nuclear Envelope. Microtubule + motor proteins --> Chromatin (nucleus) (Microtubule + motor proteins), plectin, actin complex --> nuclear lamina (nucleus)

Actin-binding protein

Protein that interacts w actin monomers or filaments to control the assembly, structure, and behavior of actin filaments and networks.

actin binding proteins

Protein that interacts with actin monomers or filaments to control the assembly, structure, and behavior of actin filaments and networks.

Scaffold protein

Protein that organizes groups of interacting intracellular signaling proteins into signaling complexes.

exterior cell wall serves the same purposes for bacteria, yeast and plant cells

Protein, sugars, and other macromolecules. -Movie 11.7

Secretory pathways 2

Proteins Are Further Modified and Sorted in the Golgi Apparatus. Near ER; Cis golgi network. Near PM; trans golgi network.

Protein Separation

Proteins can be separated by column chromatography based on differences in charge, size or ability to bind to particular chemical groups.

lateral mobility of plasma membrane proteins can be restricted in several ways.

Proteins can be tethered (A) to the cell cortex inside the cell, (B) to extracellular matrix molecules outside the cell, or (C) to proteins on the surface of another cell. (D) Diffusion barriers (shown as black bars) can restrict proteins to a particular membrane domain.

Tubulin

Proteins made from microtubules.

renaturation

Proteins often refold spontaneously to original conformation. By removing high concentration of solvent. Although requires correct conditions & works best for small proteins.

Oligomeric Proteins

Proteins with multiple polypeptide chains/quaternary structure

Dimer

Proteins with one binding site

rings

Proteins with two different binding sites positioned asymmetrically

beta-catenin

Proto-oncogene Activating mutations in gene makes beta-catenin protein resist to degradation, promotes proliferation

Activated Carriers and ATP Production

Pyruvate (a breakdown product of glucose) and fatty acids (a break down product of lipids) are •Transported across the inner mitochondrial membrane. •Broken down in the citric acid cycle to form NADH. •High energy electrons in NADH are passed through the electron transport chain in the inner membrane to O2. •A proton gradient is generated during electron transport. •ATP is generated by ATP synthase, which couples its synthesis to proton transport.

DNA Repair

The Problem and the Solution: •Extensive genetic changes in the short-term to an organism's DNA are harmful. • •Mutations arise from mistakes in DNA replication (proofreading does not eliminate these entirely) or chemical changes to DNA inside the cell. • •Most DNA damage is eliminated by DNA repair mechanisms

Mismatch repair

The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides.

mismatch repair

The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides.

Peptide bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid

equilibrium potential

The electrical potential difference across the cell membrane that exactly balances the concentration gradient for an ion. -potential gradient that forces ions to passively move in one direction: positive ions are attracted by the 'negative' side of the membrane and negative ions by the 'positive' one. -A resting (non-signaling) neuron has a voltage across its membrane called the resting membrane potential, or simply the resting potential. +The resting potential is determined by concentration gradients of ions across the membrane and by membrane permeability to each type of ion. a neuron establishes and maintains a stable voltage across its membran

Which of the following is a mobile electron carrier in the electron-transport chain?

The electron-transport chain is composed of three integral membrane complexes: NADH dehydrogenase complex, cytochrome c reductase complex, and cytochrome c oxidase complex, with two mobile carriers, ubiquinone and cytochrome c.

Which activated carrier contains a high-energy bond whose hydrolysis releases a large amount of free energy?

The energy released by the hydrolysis of ATP to ADP can be harnessed to drive many otherwise energetically unfavorable chemical reactions in cells.

Stroma

The fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water In a chloroplast, the large interior space that contains the enzymes needed to incorporate CO2 → sugars during the carbon-fixation state of photosynthesis. Equiv. To the matrix of mitochondria. +ATP and NADPH made via photosynthesis--used w/i stroma--driving carbon-fixation cycle: CO2 + H2O → carbohydrates then exported from stroma into cytosol--providing the starting material used for the synthesis of many other organic molecules & production of materials used by plant mitochondria to produce ATP

Double helix

The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape.

Fertilization

The fusion of 2 gametes (sperm & egg) produces a new individual organism.

Euchromatin

The less condensed form of eukaryotic chromatin that is actively transcribed

Germ line

The lineage of reproductive cells that contributes to the formation of a new generation of organisms, as distinct from somatic cells, which form the body and leave no descendants in the next generation.

Leading strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.

The anaphase-promoting complex (APC) triggers the onset of anaphase by doing which of the following?

The onset of anaphase by triggering the destruction of the cohesins that hold the sister chromatids together. This release allows the chromatids to be pulled toward the opposite poles of the dividing cell.

Cell cycle

The orderly sequence of events by which a cell duplicates its contents and divides into two.

pH scale

The pH scale is used to indicate the acidity or basicity (alkalinity) of a solution. Values range from 0 to 14 0 to <7 = Acidic 7 = Neutral >7 to 14 = Basic (or alkaline) pH is a measure of hydrogen ion concentration in a solution. When water ionizes or dissociates, it releases an equal number of hydrogen (H^+) ions and hydroxide (OH^-) ions. Proton Movement In Aqueous Solutions

Active site

The part of an enzyme or antibody where the chemical reaction occurs.

Conformation

The particular three-dimentional shape of a protein molecule

Biosynthesis

The process by which living organisms produce larger molecules from smaller ones.

ubiquitination

The process of adding ubiquitin chains to a protein targeted for degradation.

MT display dynamic instability

The rapid switching between growth and shrinkage shown by microtubules. Alternating rapidly b/w growth & shrinkage. -Shrinkage-promoted via hydrolysis of GTP (tightly bound to tubulin dimers) reducing the affinity of the dimer for their neighbors, promoting MT disassembly. -Stabilized via localized proteins--capture plus ends, helping position MT and harness them for specific functions. Growing MT: GTP-tubulin (tubulin dimer w bound GTP) --> adds to growing end of MT --> proceeds faster than GTP hydrolysis by dimers (forms GTP cap) Shrinking MT: GTP hydrolysis is faster than add of new GTP-tubulin dimers --> (GTP cap lost) protofilaments (GDP-tubulin) peel away from MT wall --> GDP-tubulin is released to cytosol.

DNA repair

The removal and replacement of damaged DNA by the correct sequence

initiation site

The site on the DNA from which the first RNA nucleotide is transcribed is called the +1 site. -upstream - Nucleotides that come before the initiation site are given negative numbers. -downstream - Nucleotides that come after the initiation site are marked with positive numbers.

Cytosol

The soluble portion of the cytoplasm, which includes molecules and small particles, such as ribosomes, but not the organelles covered with membranes. -Exports mature eukaryotic mRNAs from nucleus then are degraded in cytosol.

Lagging strand

The strand in replication that is copied 3' to 5' as Okazaki fragments and then joined up.

Chloroplast Structures

The structure of the chloroplast - three membrane-bound compartments: •outer membrane •inner membrane •thylakoid membrane (this last one differs from mitochondria) •Stroma - space inside the inner membrane where Calvin cycle takes place •similar to matrix of mitochondria •Thylakoids - flattened, disc-like sacs whose membranes contain proteins for light reactions

Equilibrium constant, K

The value when equilibrium concentrations are substituted into the reaction quotient

During photosynthesis, what happens in the water-splitting step?

The water-splitting enzyme contains a cluster of manganese atoms that holds onto two water molecules from which electrons are extracted one at a time. Once four electrons have been removed from these water molecules, oxygen is released.

Globular protein

These proteins are small spheres with little to no water inside. They have hydrophobic amino acids in the inside and hydrophilic R groups on the outside.

Inactive monomeric GTPase

This activity is controlled by two regulatory proteins. GTPase-activating proteins (GAPs): *Active monomeric GTPase stimulate hydrolysis of GTP —> GDP, switches protein off; inactive monomeric GTPase --[GEF]-> GDP to GTP then activates monomeric GTPase --[GAP] dephosphorylates to inactivated GTPase.

Mitochondria origin

Thought that when an aerobic bacterium was engulfed by a larger anaerobic eukaryotic cell.

Synaptic signaling

Thousands of synpases form on the cell body and dendrites of a motor neuron in the spinal cord. Affected by most Psychoactive Drugs by Binding to Neurotransmitter Receptors. The Complexity Enables Us to Think, Act, Learn, and Remember.

Sequence Elements Required for Replication and Segregation

Three DNA elements required •Replication origin - where DNA replication begins - multiple elements along chromosomes •Telomeres - DNA sequence that marks the ends of the chromosome and prevents misidentification as broken DNA needing repair •Centromere - DNA sequence used for separating duplicated chromosomes during Mitosis

Cadherin

Tight Junction. A family member of Ca2+-dependent proteins that mediate mechanical attachment of one epithelial cell to another in animal tissues proteins in the plasma membrane that bind other cadherins extracellularly and actin intracellularly to form cell-cell contacts. link epithelial cells together by binding to similar cadherins in adjacent epithelial cells. Inside the cell, cadherins are attached to the cytoskeleton.

Iron-sulfur center

Tightly bound metal complex that carries electrons in proteins that operate early in the electron-transport chain; has a relatively weak affinity for electrons.

Connective tissues

Tissues i.e. bone, tendons, and dermis of skin, in which ETC makes up bulk of the tissue and carries the mechanical load. A major distinction between the connective tissues in an animal and other main tissue types such as epithelium, nervous tissue, or muscle is the amount of extracellular matrix in connective tissues. -Animal: provide mechanical support to organs & limbs-consist mainly of extracellular matrix that is secreted by a sparse scattering of embedded cells.

RNA polymerase II (Movie 7.3)

Transcribes all protein-coding genes.

RNA polymerase I

Transcribes most rRNA genes.

RNA polymerase III

Transcribes tRNA genes.

Extracellular Signal Molecules Cross the Plasma Membrane and Bind to Intracellular Receptors.

Transcription of target gene.

Regulatory sequence

Transcription regulator

P53

Transcription regulator that controls the cell's response to DNA damage, preventing the cell from entering S phase until damage is repaired or inducing suicide (extensive damage). Mutations in the gene encoding this protein are found in human cancers. Tumor suppressor gene - inactivation of both copies of p53 allows cancer to continue to survive and divide, even in the presence of damanged DNA.

Enzyme-couple receptors

Transmembrane protein, when stimulated by the binding of a ligand, activates an intracellular enzyme (either a separate enzyme or part of the receptor itself). Either act as enzymes or associate w enzymes inside the cell; when stimulated, the enzymes can activate a variety of intra. sig. pathways. Once binds its extra. sig. molecule, an enzyme activity is switched on @ the other end of the receptor, inside cell. Many receptors have their own enzyme activity (left), while others rely on an enzyme that becomes associated w the activated receptor (right). -Plants, like animals used this to recognize the extra. sig. mole.--that controls growth & development; often act by relieving the transcriptional repression of specific genes. -Receptor tyrosine kinases (RTKs): Activated RTKs Recruit a Complex of Intracellular Signaling Proteins I.e. 1. Inactive catalytic domain binds w signal molecule (dimer) --> activated. OR 2. Inactive receptor binds w signal molecule --> Active receptor and associated enzyme complex.

transmembrane proteins

Transmembrane proteins are integral protein. hydrophobic side chains (light green) of the amino acids forming the α helix contact the hydrophobic hydrocarbon tails of the phospholipid molecules, while the hydrophilic parts of the polypeptide backbone form hydrogen bonds with one another. -Transmembrane polypeptide chain: cross lipid bilayer as alpha helix.

Ion-channel receptors

Transmembrane receptor protein or protein complex- opens in response to the binding of a ligand to its external face, allowing the passage of a specific inorganic ion. Change the permeability of the PM to selected ions, alters the membrane potential, if conditions are right, producing an electrical current. Transmitter-gated ion channels. Responsible for the rapid transmission of signals across synapses in the nervous system. Transduce a chemical signal, in the form of a pulse of secreted neurotransmitter molecules delivered to a target cell, directly into an electrical signal, in the form of a change in voltage across target cell's PM. When neurotransmitter binds to ion-channel-coupled receptors on the surface of target cell, the receptor alters to open conformation, allowing it permeable to specific ions, i.e. Na+, K+, and Ca2+. Driven by their electrochemical gradients, the ions rush into or out of cell, creating a change in the membrane potential w/i. m/sec. i.e. Ca2+ channels changes in the concentration in target-cell cytosol altering activities. Change in potential may trigger a nerve impulse or make it easier (or harder) for other neurotransmitters to do so. -Convert Chemical Signals into Electrical Ones. -Closed channel and open channels (Ions, signal molecule) -change permeability of PM to selected ions, altering the membrane potential, if conditions are right, producing an electrical current. -Important in nerve cells and other electrically excitable cells (muscle cells), G-protein-coupled receptors and enzyme-coupled receptors are important to practically every cell type in the body.

Neuronal signals

Transmitted electrically along a nerve cell axon - this electrical signal reaches the nerve terminal and causes the release of neurotransmitters onto adjacent target cells. Third form of cell communication. Like endocrine cells, nerve cells (neurons), deliver messages over long distances. A message is not broadcast widely but is instead delivered quickly and specifically to individual target cells through private lines. The axon of a neuron terminates at specialized junctions (synapses) on target cells that can lie far from the neuronal cell body. The axons that extend from the spinal cord to the big tie in an adult human, can be more than a meter in length. When activated by signals from the environment or from other nerve cells, a neuron sends electrical impulses racing along axon at speeds up to 100 m/sec. On reaching the axon terminal, these electrical signals convert into chemical form: each electrical impulse stimulates the nerve terminal to release a pulse of an extracellular signal molecules called NEUROTRANSMITTER. Long-distance but personal, i.e. a phone call, text msg... -Signal sent to individual cells of a multicellular organism through synapses to other neurons or other cell types (e.g. muscle) via neurotransmitter at nerve terminal.

Membrane-enclosed organelles import proteins via

Transport thru nuclear pores. Across membranes, and by vesicles. Synthesis of almost all proteins starts on ribosomes in the cytosol exceptions: some mitochondrial and chloroplast proteins on organelle ribosomes Short amino acid sequence in the protein being synthesized starts the protein sorting process = signal sequence

Vesicle Docking Depends on Tethers and SNAREs

Transport vesicle must RECOGIZE its target (e.g. organelle or PM) and then FUSE w target membrane to release its cargo. Recognition of molecular markers on vesicle and target membranes. -Rab proteins on vesicle (GTPases). -Tethering proteins on target membrane (cytosolic surface). Additional recognition by SNARE proteins - v-SNAREs and t-SNAREs Also catalyze membrane fusion Delivers vesicle contents and vesicle membrane Rab proteins, tethering proteins, and SNAREs help direct transport vesicles to their target membranes.

Ca2+ signals

Triggers Many Biological Processes. i.e. Fertilization of an egg by a sperm triggers an increase in cytosolic Ca2+ in the egg. The effects of Ca2+ in the cytosol are indirect mediated through calmodulin & other Ca2+ responsive proteins. -Important calmodulin target: Ca2+ /calmodulin dependent protein kinases (CaM-kinases) Enzyme that phosphorylates target proteins in response to an increase in Ca2+ ion concentration through its interaction with the Ca2+-binding protein calmodulin. Calcium binding changes shape of the calmodulin protein.

Collagen

Triple-stranded, fibrous protein that is a major component of the ETC and connective tissues. Main protein in animal tissues, and diff. forms found in skin, tendon, bone, cartilage, and blood vessels.

Trp operon

Trp operator (promoter) of E. coli DNA binds with mRNA molecule forming series of enzymes required for tryptophan biosynthesis. Switches allow cells to respond to changes in their environment.

Operon off

Tryptophan high - excess binds to active Trp repressor.

Brca 1 and Brca2

Tumor suppressor gene - inactivation of both copies of Brca 1 or Brca2 allows cancer cells to continue to survive and divide in presence of massively damaged DNA

Condensation rxn

Two COVALENT molecules combine and water is removed. MONOMER --> POLYMER

Redox pair

Two molecules that can be interconverted by the gain or loss of an electron. NADH and NAD+.

Myosin-II

Type of myosin that exists as a dimer w 2 actin-binding heads and a coiled-coil tail; can associate to form long myosin filaments.

Myosin-II

Type of myosin that exists as a dimer w 2 actin-binding heads and a coiled-coil tail; can associate to form long myosin filaments. double head and single tail (like kinesins and dyneins). clusters of dimers form filaments with two sets of myosins, with heads oriented away from the filament center

phosphorylation common mechanism

Typical eukaryotic cell are modified via covalent addition of one or more phosphate group. Involves enzyme-catalyzed transfer of terminal phosphate group of ATP to OH on serine, threonine, or tyrosine side chain of the protein. 1. General reaction: Protein kinase- Transfer of phosphate group from ATP to amino acid side chain of target protein Protein phosphatase- Enzyme catalyzes causes removal of phosphate group 2. Can either increase or decrease protein activity- depending on site f phosphorylation and structure of protein.

Mitochondrial precursor proteins

Unfolded during import

Other noncoding RNAs

Used in RNA splicing, gene regulation, telomere maintainance, and many other processes.

Polypeptide chain

Usually Crosses the Lipid Bilayer as an alpha Helix

Lipids and Fatty Acids

Variety of structures Large, nonpolar molecules that are insoluble in water (hydrophobic) -Lipid bilayer -Glycerol + fatty acid.

Protein coat

Vesicle budding Is Driven by the Assembly of a Protein Coat. Functions; shapes membrane into a bud captures molecules for transport. Clathrin is a coat protein Golgi —> outward Plasma membraneàinward COP is another class of coat proteins ER <—> Golgi Golgi <—> Golgi

Organelles must maintain their specific identities (components)

Vesicular transport. need specific packaging of proteins in/on vesicles need recognition mechanisms on surface of vesicles

Proliferating precusor cell

Via this precursor: In many tissues, nondividing, terminally differentiated cells are generated from stem cells

Hydrophobic

Water hating

Hydrophilic

Water loving

What does the phosphorylation of Cdc25 by M-Cdk do?

When phosphorylated, Cdc25 becomes activated, which in turn can then remove the inhibitory phosphates from M-Cdk, thereby activating more M-Cdk.

Operon ON

When tryptophan is low - inactive Trp repressor and RNA polymerase

Signals in DNA tell RNA polymerase

Where to start & stop transcription.

Chiasma (plural chiasmata)

X-shaped connection b/w paired homologous chromosome during meiosis. Represents a site of crossing-over b/w 2 non-sister chromatids.

Most RTKs Activate the Monomeric GTPase Ras.

Yield onward transmission of signal.

RTKs Activate PI 3-Kinase to Produce Lipid Docking Sites in the Plasma Membrane.

Yield signal relayed onward by activated Akt.

Both GPCRs and RTK's activated intra. Sig. pathways.

Yield transcription regulators and many target proteins.

Ras activates a MAP-kinase signaling module.

Yields in changes in either protein activity or gene expression.

Plasma membrane

a container and act as selective barrier. -Eukaryotic cell: Plasma & internal membrane. -Bacterial cell: Only plasma membrane.

cilium

a hairlike structure arranged in tightly packed rows that projects from the surface of some cells, moves fluid over it surface like epithelium in lungs.

free energy change (delta G)

a measure of the change in free energy as a chemical reaction or physical change occurs

Bacterium

a microscopic prokaryote

Coupled reaction

a pair of reactions, one exergonic and one endergonic, that are linked together such that the energy produced by the exergonic reaction provides the energy needed to drive the endergonic reaction

Exon junction complex

a protein complex that assembles at exon-exon junctions during splicing and assists in RNA transport, localization, and degradation

Epithelium

a sheet of cells that covers an exposed surface or lines an internal cavity or passageway

Ubiquinone

a small hydrophobic molecule that can move in the lipid bilayer, to carry two electrons to the next complex.

Equilibrium

a state in which opposing forces or influences are balanced.

Nucleosomes

a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones.

Mass spectrometry

a technique that separates particles according to their mass

Transition state

a term sometimes used to refer to the activated complex

Nonhomologous end joining

a way of repairing a DNA double-strand break and is often error-prone

Nuclear import receptors

able to disrupt meshwork of nuclear pore proteins and carry cargo protein through pore. Proteins remain properly folded during transport. Prospective nuclear proteins are imported from the cytosol through nuclear pores.

RNA polymerase

about polarity of template strand. Directionality: -always builds a new RNA strand in the 5' to 3' direction. Can only add RNA nucleotides (A, U, C, or G) to the 3' end of the strand.

Lamellipodium

activation of Rho-family member Rac causes what type of actin organization Dynamic sheetlike extension on the surface of animal cells, especially one migrating over a surface. A web of polymerizing actin filaments pushes the leading edge of lamell. forward.

Pump

active transport mechanism that works against electrochemical gradients.

Newly synthesized phospholipids

added to the cytosolic side of the ER membrane and then redistributed by transporters that transfer them from one half of the lipid bilayer to the other. Some new membrane stays in ER; the rest is used to supply other organelles.

Mass Spectroscopy

allows proteins to be identified based on its digestion fingerprint and amino acid sequence information, based on comparisons with the proteins predicted from genomic sequences.

Primary structure

amino acid sequence of a protein (polypeptide)

organoid

an artificially grown mass of cells or tissue that resembles an organ

DNA ligase

an enzyme that eventually joins the sugar-phosphate backbones of the Okazaki fragments. -uses the energy of ATP hydrolysis to join together Okazaki fragments.

two key ends of tRNA

anticodon loop and 3' end (amino acid attachment site).. Match Amino Acids to Codons in mRNA.

Organelles

are almost one-half the volume of a typical eukaryotic cell

Procollagen precursors

are cleaved to form mature collagen outside the cell.

G-protein-coupled receptors. (GPCrs)

are found in eukaryotes from yeast to mammals. In animals GPCRs are used in endocrine, paracrine, and neuronal signaling.

Collagen Fibrils

are organized into bundles.

Nucleic Acids

are polymers of nucleotides. Two varieties of nucleic acids: DNA (DeoxyriboNucleic Acid) Genetic material that stores information for its own replication and for the sequence of amino acids in proteins RNA (RiboNucleic Acid) Performs a wide range of functions within cells which include protein synthesis and regulation of gene expression

Sarcomeres assembly

assemblies of Plus ends of actin filaments anchored at Z discs (edge of sarcomere) and myosin filaments at the center of sarcomere Muscle contraction = shortening of all sarcomeres actin filaments sliding past myosin filaments.

Sarcomeres

assemblies of Plus ends of actin filaments anchored at Z discs (edge of sarcomere) and myosin filaments at the center of sarcomere. (Actin; thin filaments and myosin-II; thick filament) Highly organized assembly of actin and myosin filaments serves as a contractile unit of myofibril in muscle cells. -Myosin filament at center of sarcomere. -Plus ends of actin filaments anchored at Z discs (edge of sarcomere

Gene Expression Can Be Regulated

at Various Steps from DNA to RNA to Protein. in eukaryotic cells can be controlled at various steps.

protein cortex MOV 11.7

attached to cytosolic side of membrane provides cell shape and stabilizes plasma membrane. Animal cells. -An exterior cell wall serves the same purposes for for bacteria, yeast and plant cells. protein, sugars and other macromolecules. -Made largely from spectrin: Characteristic shape of RBC in humans. -A cortex made largely of spectrin gives human red blood cells their characteristic shape. a form of anemia results in humans with certain spectrum mutant forms -Most other animal cells have a cortex containing actin and myosin proteins better for facilitating shape changes, movement, and other processes

Mechanically-gated cation channel

auditory hair cell in inner ear. detection of sound vibrations.

Element

basic substance of matter that cannot be broken down by ordinary chemical means Each element has unique properties: Density, solubility, melting point, and reactivity

Most other animal cells have a cortex containing actin and myosin proteins

better for facilitating shape changes, movement, and other processes

Ran-GTP

binds to nuclear import receptor proteins in the nucleus. carried into nucleus by a nuclear import receptor specific for Ran-GDP single member of the Ran subfamily, and the most abundant small GTPase in the cell. Like the other small GTPases, Ran functions as a molecular switch, converting between the active GTP-bound and inactive GDP-bound conformations.

Amino acids

building blocks of proteins

Glycosaminoglycans (GAGs)

built from repeating disaccharide units. Polysaccharide chain--can form a gel that acts as a "space filler" in extracellular matrix of connective tissues--helps animal tissues resist compression. Covalently linked to proteins forming proteoglycans-act as space-fillers & provide resist compression. Additional ECM Proteins

Most Psychoactive Drugs Affect Synaptic Signaling

by Binding to Neurotransmitter Receptors

rate at which a solute crosses a protein-free, artificial lipid bilayer

by simple diffusion depends on its size and solubility.

viral nucleic acids

can be DNA or RNA, double-stranded or single-stranded.

iPS pathway

can be created by artificially expressing a suite of three to four transcription factors in adult cells such as fibroblasts. The iPS cells can then be converted into the desired cell type.

transmembrane hydrophilic pore

can be formed by multiple amphipathic α helices. hydrophobic amino acid side chains on one side of each helix (green) come in contact with the hydrophobic lipid tails of the lipid bilayer, while the hydrophilic side chains on the opposite side of the helices (red ) form a water-filled pore.

Protein phosphorylation

can control protein activity by triggering a conformational change due to change in electrostatic attractions. The addition of the negative charge can cause the protein to change its shape, thereby activating or inactivating its function. •is only one of several covalent protein modifications that control activity, interactions with other molecules, protein levels, and subcellular localization. •Proteins can be regulated by multiple modifications

single prokaryotic mRNA molecule

can encode several different proteins, each translated separately, because of operon structure of many prokaryotic genes. -Ribosome-binding sites before start codon AUG on mRNA sequence.

Mutation

change in a DNA sequence that affects genetic information. from Chemical Modifications DNA: •Incorrect incorporation of a nucleotide during DNA replication •The consequences if not repaired: Incorporation of an incorrect nucleotide or deletion of a nucleotide during DNA replication

Signal

changes in electric potential across the neuron's plasma membrane

Organic molecule

chemical compound that contains carbon and hydrogen

Hydrolysis reaction

chemical reaction in which a water molecule is added to break a covalent bond Used to breakdown polymers into monomers

Condensation reaction

chemical reaction in which subunits are joined by the formation of a covalent bond and water is produced during the reaction •Used to connect monomers together to form polymers

NADP+

coenzyme that functions as a universal electron carrier, accepting electrons and hydrogen atoms to form NADPH, or nicotinamide adenine dinucleotide phosphate. NADP+ is created in anabolic reactions, or reaction that build large molecules from small molecules.

Amino Acids

consist of a carboxylic acid group and an amino group attached to a central α-carbon atom that also has specific side chain •side chains give amino acids specific characteristics.

cell membrane

consists of a lipid bilayer in which proteins are embedded.

Phagocytosis is a process by which cells do which of the following?

consume large particles, such as microbes and cell debris. The most dramatic form of endocytosis, phagocytosis, was first observed more than a hundred years ago. In protozoa, phagocytosis is a form of feeding: these unicellular eukaryotes ingest large particles such as bacteria by taking them up into phagosomes. The phagosomes then fuse with lysosomes, where the food particles are digested. Few cells in multicellular organisms are able to ingest large particles efficiently. In the animal gut, for example, large particles of food have to be broken down to individual molecules by extracellular enzymes before they can be taken up by pinocytosis by the absorptive cells lining the gut. Nevertheless, phagocytosis is important in most animals for purposes other than nutrition. Phagocytic cells—including macrophages, which are widely distributed in tissues, and other white blood cells, such as neutrophils—defend us against infection by ingesting invading microorganisms.

Cell membrane

contain membrane transport proteins that selectively promote: -Passive diffusion (blue) -Pumping (purple or green)

Central cylinder

contains vascular tissue

Sigma factor

controls the binding of RNA polymerase to the promoter.

Photosynthesis

converts solar energy to chemical energy. In (H2O) out (O2; cytoplasm) and (CO2; makes sugar & inorganic molecules)

ATP-driven pump

couple uphill transport to the hydrolysis of ATP

Phosphoproteins

covalently bound phosphate groups used to activate or deactivate a protein or provide binding sites for protein attachment.

eukaryotic cells, internal membranes

create enclosed compartments that segregate different metabolic processes.

Concentration of free actin

dictates growth of actin filaments High [free actin] --> growth at plus and minus ends Intermediate [free actin] --> growth at plus end, disassembly at minus end Low [free actin] --> disassembly at plus and minus ends (treadmilling) 50% of actin is free monomers; 50% of actin is in filaments

** Antibiotics

differences in ribosomes and protein synthesis b/w eukarotes and prokaryotes can be exploited to fight against bacteria. Inhibit bacterial protein or RNA synthesis.

Concentration gradients

differences in solute concentrations across their membranes

An ER signal sequence and an SRP

direct a ribosome to the ER membrane (to a protein translocator via SRP receptor in the ER membrane).

Phospholipids and glycolipids

distributed asymmetrically in the lipid bilayer of an animal cell plasma membrane.

Lipid bilayer

double-layered sheet that forms the core of nearly all cell membranes

Membranes retain their orientation

during transfer between cell compartments.

nonpolar covalent bond

electrons are shared equally between atoms. Examples: hydrogen gas, oxygen gas, methane.

Polar Covalent Bonds

electrons are shared unequally. Example: water (due to electronegativity)

Two types of glucose transporters

enable gut epithelial cells to transfer glucose across the epithelial lining of the gut.

LDL receptor

endocytosis

The outer membrane of the nucleus is continuous with the membrane of which other organelle?

endoplasmic reticulum. The nucleus, generally the most prominent organelle in eukaryotic cells, is surrounded by a double membrane known as the nuclear envelope. The outer nuclear membrane is continuous with the membrane of the endoplasmic reticulum (ER), a system of interconnected membranous sacs and tubes that often extends throughout most of the cell. The ER is the major site of synthesis of new membranes in the cell. The nuclear membranes and the membranes of the ER, Golgi apparatus, endosomes, and lysosomes most likely originated by invagination of the plasma membrane.

First Law of Thermodynamics: Conservation of energy

energy cannot be created or destroyed, but can be changed from one form to another. Total Amount of Energy Conserved

Free energy, G

energy released available to do work

ΔG Changes and Equilibrium

equilibrium does not mean there are equal concentrations of reactants and products, but rather the conversion between the two is equal

genetic code

every codon does not specify an amino acid (stop codons do not). -The full set of relationships between codons and amino acids (or stop signals) -allows DNA and RNA sequences to be "decoded" into the amino acids of a protein. -In transcription, the DNA sequence of a gene is "rewritten" in RNA. In eukaryotes, the RNA must go through additional processing steps to become a messenger RNA, or mRNA. -In translation, the sequence of nucleotides in the mRNA is "translated" into a sequence of amino acids in a polypeptide (protein chain) [reading frame] determines how the mRNA sequence is divided up into codons during translation.

Nuclear membrane and the ER

evolved through invagination of the plasma membrane. This process is thought to apply to other organelles of the "endomembrane system" (that is , all organelles except mitochondria & chloroplasts)

Fibronectin

extracellular matrix protein that helps cells attach to matrix by acting as a "linker"- binds to a cell-surface integrin molecule on one end and to a matrix component, i.e. collagen, on the other.

Wnt proteins

extracellular signal proteins with many roles in development, including regulation of proliferation and the maintenance of stem cells in a proliferative state

Cdc42 activation (Rho-family)

filopodia actin organization

1. Prophase - Mitotic Spindle Formation

first and longest phase of mitosis, during which the chromosomes become visible and the centrioles separate and take up positions on the opposite sides of the nucleus -1st stage of mitosis, the duplicated chromosomes condense and formation of mitotic spindle. -Duplicated chromosomes, each consisting of two closely associated sister chromatids, condense. Outside the nucleus, the mitotic spindle assembles b/w the two centrosomes, that have begun to move apart. -Array of microtubules and associated molecules that forms b/w the opposite poles of euk. Cell during mitosis and pulls duplicated chromosome sets apart.

Signal sequences

for import into ER Lumen & mitochondria ; Located at N terminus. Swapping changes the location of the protein. Therefore, signal sequences are both necessary and sufficient for directing protein traffic Normal signal sequence; ER protein, ER signal sequence in ER and cytosolic protein (no signal sequence) in cytosol —-ER signal seq. removed from ER protein and attached to cytosolic protein —> Relocated signal seq.; ER protein w signal seq. removed in cytosol and Cytosolic protein w added ER signal seq. in ER.

Equilibrium Constant, K

for reversible reactions, ratio of substrate to product when the rates of the forward and reverse reactions are equal For Y à X and equilibrium occurs when product (X) is 10x that of the substrate (Y)

Internal membranes

form many different compartments in a eukaryotic cell. Endoplasmic reticulum, nucleus, peroxisome, lysosome, endosome, golgi apparatus, plasma membrane, mitochondrion, and transport vesicle.

Splicing factors

forms lariat from intron.

Beta (β) Sheets

found in fibroin (major constituent of silk. •Formed by hydrogen bonding between segments of polypeptide chains that lie side by side •Can be antiparallel or parallel depending on orientation of N-termini and C-termini relative to each strand

Alpha helix

found in α-keratin (skin, hair, nails)

Reduction

gain of an electron

noncytosolic face of a membrane

glycolipids are found exclusively

Chromatin

granular material visible within the nucleus; consists of DNA tightly coiled around proteins

double-pass transmembrane protein

has an internal ER signal sequence (start -transfer sequence).

Amphipathic

has both a hydrophilic region and a hydrophobic region. -Incl all diff. types of membrane lipids

Bacterial promoters and terminators

have specific nucleotide sequences that are recognized by RNA polymerase.

Plasma membrane proteins

have a variety of functions. -Transporters & channels. -Anchors. -Receptors. -Enzymes.

Polar

having a pair of equal and opposite charges

intermediate filament assembly process

helical monomer x2 coiled coil dimer X2 staggered antiparallel tetramer (2 coiled coil dimers) X8 intermediate filament

Inner Life of the Cell (video)

https://xvivo.com/inner-life-of-the-cell/

Hydrogen Bonding

hydrogen bond - a weak attraction between a slightly positive hydrogen atom and a slightly negative atom. -can occur between atoms of different molecules or within the same molecule. -A single hydrogen bond is easily broken, while multiple hydrogen bonds are collectively quite strong. -helps to maintain the proper structure and function of complex molecules such as proteins and DNA.

Hydronium ion

hydrogen ion combines with a water molecule to form a hydronium ion, H3O(+)

Hydrophobic force

hydrophobic collapse- proteins fold to push hydrophilic sections to the exterior and hydrophobic sections to the interior solvation shell- water molecules interact unfavorably with hydrophobic sections, so water molecules forced to lock their orientation and form shells around the protein this low entropy and high free energy state is relieved by protein folding

Light-driven pump

i.e. Bacteriorhodopsin is a light-driven proton pump. Located in PM of some bacteria. Functions as active export of H+ ions.

Scanning Electron Microscopy (SEM)

images the outside surface of tissues/cells/organisms

Transmission Electron Microscopy (TEM)

images thin sections of tissues/cells

Protein-free, artificial lipid bilayer (liposome)

impermeable to most water-soluble molecules

Voltage-gated Ca2+ Channel

in Nerve Terminals Convert an Electrical Signal into a Chemical Signal. Neurons connect to their target cells at synapses. electrical signal is converted into a secreted chemical signal at a nerve terminal.

Transmitter-gated Ion Channel

in Postsynaptic Membrane Convert the Chemical Signal Back into an Electrical Signal via postsynaptic transmitter-gated ion channels at a synapse. a subcategory of ligand-gated ion channels

action potential propagates along the length of an axon

increased [Na+] in region adjacent to region of membrane depolarization begins propagation of an action potential.

Action potention proprogates

increased [Na+] in region adjacent to region of membrane depolarization begins propagation of an action potential.

Quaternary structure

interaction of two or more proteins (polypeptides)

Transmitter-gated ion channel

intracellular signaling molecules

G-protein-coupled receptors (GCPR)*****

intracellular signaling molecules Cell-surface receptor. Works w intracellular trimeric GTP-binding protein (G protein) after activation by an extracellular ligand. Embedded in membrane by 7 transmembrane alpha helices.

intron in a pre-mRNA molecule

intron in a pre-mRNA molecule forms a branched structure during RNA splicing

Complementary surface conformations and the same weak noncovalent bonds

involved in secondary, tertiary and quaternary structure produce the binding. 1. dimer 2. helix 3. ring 4. spherical 5. tubular

Cryo Electron microscopy (cryo-EM)

involves the observation of samples flash-frozen in water solution. Tomography combines multiple images by computation to achieve high resolution.

Rac activation (lamellipodium )

is a cytoskeletal protein actin projection on the leading edge of the cell. It contains a quasi-two-dimensional actin mesh; the whole structure propels the cell across a substrate.

Rho family proteins

is a member of the Ras superfamily of small GTPases. Small GTPases are monomeric proteins and function as molecular switches that turn "on" or turn "off" Intracellular signaling pathways converge on Rho protein family members = Monomeric GTPases

Cytosol

is concentrated aqueous gel of large and small molecules •Aqueous part of cytoplasm that is left if you remove organelles from a cell •Contains many large and small molecules •Acts more like a gel than liquid •Constantly in motion

single-pass transmembrane protein

is retained in the lipid bilayer.

Epitheal tissue

is specialized in absorption, secretion,and protection. example - inside of mouth and outside of your intestines

Interphase chromatin

largely in the form of 30nm fiber

Nuclear envelope

layer of two membranes that surrounds the nucleus of a cell

Intermediate filament assembly process Exam info: Know process

like ropes made of long, twisted strands of protein.

Polypeptide chain

long chain of amino acids linked by peptide bonds

Polyribosomes

mRNAs are being transcribed from several different genes. Although transcription is still in progress, ribosomes have attached each mRNA and begun to translate it into protein. When an mRNA is being translated by multiple ribosomes, the mRNA and ribosomes together are said to form.

Nuclear pore

made of ~30 different proteins (nuclear pore complex) Cytosolic fibrils; Disordered amino acid tails of proteins surrounding the pore create a meshwork blocking free passage of large molecules through the pore. Large cargo pass through: ribosome subunits, for example, and also HIV core particles complex forms a gate through which selected macromolecules and larger complexes enter or exit the nucleus.

Difference between a malignant and benign tumor?

malignant tumor invades and colonizes other tissues, while a benign tumor does not. The resulting secondary tumors, called metastases, can be difficult to eradicate, as they may invade multiple organs.

Turnover number

maximum number of substrate molecules an enzyme molecule converts to product each second

Archaeon

member of a group of single-celled organisms that lack a nucleus but are more closely related to eukaryotes than to bacteria

Enzymes

molecules that speed up chemical reactions and are required for dehydration and hydrolysis reactions

Nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a nucleotide linked to phosphate group, and a nitrogenous base

Simple diffusion

movement of a solute from an area of high concentration to an area of low concentration

Procollagen

must be cleaved by the proteinase to form mature collagen. Thus, overactivity of the proteinase would cause an increase in collagen and less stretchy skin.

Electron

negatively charged particle

Neuron

nerve cell that receives, integrates, and transmits signals. has a cell body, a single axon, and multiple dendrites.

acetylation

of DNA and histones causes nucleosomes to loosen and spread apart

Deamination

of cytosine to produce uracil (so uracil cannot be used in DNA because it needs to be recognized as an error).

acetylcholine receptor in the plasma membrane

of vertebrate skeletal muscle cells opens when it binds the neurotransmitter acetylcholine

Cell recognition

one cell specifically binds to another cell of a certain type

Micrometer

one millionth of a meter

Voltage-gated

open; resting PM. close; depolarized PM. in response to voltage changes underlie the leaf-closing response in the touch-sensitive plant Mimosa pudica.

Second messenger molecules**

part of the cascade of events that translates ligand binding into a cellular response

Nucleolus

parts of different chromosomes carrying ribosomal genes cluster together, making ribosomal RNA that combines with ribosomal proteins to form the ribosomes -Located on 10 diff. chromosomes that then cluster yielding dark region. -Light microscope.

Receptor proteins

performs the primary step in signal transduction Recognizes the extracellular signal & generates new intracellular signals in response that process usually works like a molecular relay race. +Message is passed "downstream" from one intracellular signaling molecule to another, (fig. 16-2B). Each activating or generating the next signaling molecule in the pathway, until a metabolic enzyme is kicked into action: -Target-cell responses: Metabolic enzyme —> altered metabolism. cytoskeletal protein —> tweaked into a new configuration or movement. Transcription regulator —> altered gene expression by switching it on or off. Final outcome: THE RESPONSE OF THE CELL.

Protein-attached

peripheral membrane proteins.

Receptor serine/threonine kinases

phosphorylate serine and threonine residues on cytoplasmic target organs, important mediators of cell growth and differentiation, implicated in cancer progression and metastasis

K+ leak channel

plasma membrane of most animal cells. maintenance of resting membrane potential.

K+ concentration gradient and K+ leak channel

play major parts in generating the resting membrane potential across the plasma membrane in animal cells Closed: PM potential = 0 (balanced by pos. & neg. charges) Open: Membrane potential exactly balances the tendency of K+ to leave. Force tending to drive ion across membrane via electrical membrane potential and concentration gradient of ion. At equilibrium, two forces balance and satify Nernst equation assuming that the ion carries a single pos. charge @ 37 celcius. V = 62log[10](C[o]/C[i]) -V; membrane potential (mV) -C[o] and C[i]; inside and outside concentration of the ion.

Proton

positively charged particle

Gene expression

process by which a gene produces its product and the product carries out its function

Homologous recombination

process that results in genetic exchange between homologous DNA from two different sources

pre-mRNAs undergo alternative RNA splicing

produce different mRNAs and proteins from the same gene.

Hydrophilic and hydrophobic parts of lipids

promote their assembly into bilayers.

ribozymes in cells

protein hydrolysis not catalyzed by ribozyme

Histone

protein molecule around which DNA is tightly coiled in chromatin. abundant, highly conserved chromosomal proteins around which DNA wraps to form nucleosomes •Positively charged molecules that are able to bind negatively charged DNA. •Noncovalent interaction and stable structure.

Atomic weight

protons + neutrons

In the electron-transport chain, as electrons move along a series of carriers, they release energy that is used to do what?

pump protons across a membrane The resulting electrochemical proton gradient represents a form of stored energy.

Depurination

reactions remove Adenines and Guanines from DNA

Binding site

region on the surface of a protein, typically a cavity or groove, that interacts with another molecule through the formation of multiple noncovalent bonds

microRNAs (miRNAs)

regulate gene expression

Entropy

relative amount of disorganization Second Law of Thermodynamics: Entropy - isolated systems will change spontaneously toward those arrangements that have the greatest possibility or energy cannot be changed from one form to another without a loss of usable energy

Protein phosphatase

remove a phosphate group from a molecule to return. Deactivated conformation

Double strand break (DSB) repair

repairs DNA breaks generated by x-rays, reactive oxygen species

Nucleosome

repeating subunit of chromatin fibers, consisting of DNA coiled around histones. - beadlike, structural unit of a eukaryotic chromosome composed of short length of DNA wrapped around an octameric (8) core of histone proteins -two sets of 4 proteins that make up octameric core.

Telomere

repetitive DNA at the end of a eukaryotic chromosome

Free ribosomes

ribosomes suspended in the cytosol

cAMP levels ___ and ___ upon signaling changes due to serotonin

rise and fall rapidly

transfer RNAs (tRNAs)

serve as adaptors b/w mRNA & amino acids in protein synthesis. Match Amino Acids to Codons in mRNA. Key ends - Anticodon loop & 3' end (amino acid attachment site)

Phosphotyrosine on RTKs

serve as docking sites for various intra. sig. proteins.

Lysozyme

severs polysaccharide chains that form the cell walls of bacteria •Hydrolyzes bond between adjacent sugar molecules •Transition state - some substrate molecules need to be distorted to access the bond to be broken by an enzyme

Formation of mouse-human hybrid cells

shows that some plasma membrane proteins can move laterally in the lipid bilayer. However, very often cells confine proteins to particular locations in the plasma membrane or in the membranes of organelles

RNA

single-stranded nucleic acid that contains the sugar ribose

Different Types of Muscle Cells Perform Different Functions

smooth muscle -contraction activated by phosphorylation of myosin protein -slow activation and sustained contraction (phosphorylation -dephosphorylation cycle slower than Ca2+ inflow to cytosol and subsequent pumping out of cytosol non-muscle cells (with contractile bundles) have similar activation of contraction as smooth muscle (phosphorylation of myosin) non-muscle cells (with contractile bundles) have similar activation of contraction as smooth muscle (phosphorylation of myosin)

On an individual chromosome

some genes are transcribed using one DNA strand as a template, and others are transcribed from the other DNA strand.

Promoter (recognition sites)

specific region of a DNA where RNA polymerase bind and begin transcription. -Tells polymerase where to "sit down" on DNA to begin transcribing.

Replication origin

specific sequence of DNA at which DNA synthesis begins

function of aminoacyl-tRNA synthetases

specificity is through recognition of anticodon loop. • Specific Enzymes Couple tRNAs to the Correct Amino Acid

Phospholipid bilayers

spontaneously close in on themselves to form sealed compartments. -Energetically unfavorable- In a planar phospholipid bilayer, hydrophobic tails (white layer) are exposed to water along edges. -Energetically favorable- Formation of a sealed compartment shields hydrophobic tails from water.

Coiled-coil

stable, rodlike protein structure formed when two or more alpha helices twist around each other

Golgi apparatus

stack of membranes in the cell that modifies, sorts, and packages proteins from the endoplasmic reticulum

Aster

star-shaped structure formed in the cytoplasm of a cell microtubules that surround the centrosome during mitosis

Positive Allosteric Regulation

stimulation of a glucose - metabolizing enzyme by ADP, which accumulates when metabolism has not generated enough ATP.

Catalyst

substance that speeds up the rate of a chemical reaction

Acid

substances that dissociate in water, releasing hydrogen ions (high H^+ concentration).

Base

substances that either take up hydrogen ions (H^+) or release hydroxide ions (OH^-) (low〖 H〗^+ concentration) .

Cytoskeleton

systems of protein filaments in a cell, composed of: •Actin filaments - central part of machinery that regulate muscle contraction •Microtubules - thickest filaments formed as hollow tubes •Intermediate filaments - strengthen animal cells

Homologous

term used to refer to chromosomes that each have a corresponding chromosome from the opposite-sex parent

Membrane Potential Is Governed by

the Permeability of a Membrane to Specific Ions. Exact balance of charges on each side of membrane: membrane potential = 0. A few pos. ions (red) cross membrane from right to left, setting up a nonzero membrane potential. distribution of ions on either side of a cell membrane gives rise to its membrane potential. A Venus flytrap uses electrical signaling to capture its prey.

Electrostatic attraction

the attraction between positive and negative charges. the attractive or repulsive force between two electrically charged objects. Like charges repel each other while unlike charges attract each other.

Chemical bond

the attractive force that holds atoms or ions together

Standard free-energy change , (delta G zero)

the change in free energy that will occur for one unit of reaction if the reactants in their standard states are converted to products in their standard states

Electron Transport Chain (ETC)

the chlorophyll reaction center strips electrons off and attaches them to the first in a long string of proteins that pass the electrons from one to the next protein

true about electrons as they move through the electron-transport chain?

the electron-transport chain, electrons are passed from carriers with weaker electron affinity to those with stronger electron affinity, losing energy with each transfer.

N-terminus

the end of a polypeptide or protein that has a free amino group

C-terminus

the end of a polypeptide or protein that has a free carboxyl group

endoplasmic reticulum in euk. cells

the most extensive membrane network. Two initial fates of proteins that are sorted to the ER: 1. completely translocated across ER membrane soluble proteins 2. partially translocated across ER membrane transmembrane proteins -Plant cell ER lumen in green. -Dog pancreas cell - specialized for secretion of digestive enzymes.

semiconservative

the new DNA strand contain one strand that is old and one that is new

Base-pairing rules

the rules stating that in DNA cytosine pairs with guanine and adenine pairs with thymine and that in RNA cytosine pairs with guanine and adenine pairs with uracil

Atom

the smallest part of an element that displays the property of the element. An element and its atoms share the same name. Composed of subatomic particles: protons, neutrons, electrons

Molecular weight

the sum of the atomic weights of all the atoms in a molecule # w/o units

A basal lamina

thin layer of specialized connective-tissue cells w particular proteins and extracellular matrix underlying an epithelium; secreted via epithelial cells, upon which these cells sit. -Connective tissue: Typically has lots of extracellular matrix w very little cells. 1. Underlying connective tissue: Cells are more sparse and lots of proteins and molecules that holds it together. 2. Overlying epithelial cells: Epithelial tissue. ECM composed of specialized collagen (type IV collagen) and laminin (provides sites for integrin binding - similar to fibronectin) i.e. bone, fluid in eye.

Repeated regulatory sequences

transcription regulator dimer

Protein kinase

transfer a phosphate group from ATP to an amino acid side chain which has an hydroxyl group.

Protein transporT

translation details for proteins destined for nuclei and mitochonria

: The acetylcholine receptor in the plasma membrane of vertebrate skeletal muscle cells opens when it binds the neurotransmitter acetylcholine.

transmitter-gated ion channel, a subcategory of ligand-gated ion channels. A. Overall: B. Closed: Neg. charged amino acids side chains and gate --2 acetylcholine--> open conformation (allowing for NA+ to go through.

Clathrin-coated vesicles

transport selected cargo molecules. Cargo receptors, adaptins, and clathrin work together to choose specific cargo molecules for transport. cargo molecules (e.g. proteins) have transport signals recognized by cargo receptors Adaptins then capture (bind) the cargo receptors Adaptins also bind clathrin securing it to the membrane. Lastly Coat proteins and adaptins are removed after budding.

Mass spectrometry

used to identify proteins by determining the precise masses of peptides derived from them.

Patch-clamp recording

used to monitor ion channel activity. behavior of a single ion channel can be observed. Open and close states of channel.

Cell respiration

uses energy stored in chemical bonds to drive reactions inside cells set of metabolic reactions and processes that take place in the cells of organisms to convert chemical energy from oxygen molecules or nutrients into adenosine triphosphate (ATP), and then release waste products.

glucose-Na+ symport

uses the electrochemical Na+ gradient to drive the active import of glucose. Drives the Transport of Glucose Across the Plasma Membrane of Animal Cells. Located; apical PM of kidney & intestinal cells. E from Na+ gradient, import of glucose.

Electron Shells

valence shell - the outermost energy shell of any atom and it determines many of an atom's chemical properties. octet rule - the outermost shell is most stable when it has eight electrons. Exception: If an atom has only one shell, the outermost valence shell is complete when it has two electrons.

How are newly made lipids supplied to the plasma membrane?

via the constitutive pathway of exocytosis In all eukaryotic cells, a steady stream of vesicles buds from the trans Golgi network and fuses with the plasma membrane in the process of exocytosis. This constitutive exocytosis pathway supplies the plasma membrane with newly made lipids and proteins, enabling the plasma membrane to expand prior to cell division and refreshing old lipids and proteins in nonproliferating cells. The regulated exocytosis pathway also adds phospholipids to the plasma membrane; however, this pathway only operates in cells specialized for secretion.

RNA Synthesis and Processing Takes Place in "Factories"

w/i nucleus.

Van der Waals attraction

weak attractions between atoms due to oppositely polarized electron clouds noncovalent

Secondary structure

α-helices and β-sheets

A single nuclear pore

• Proteins Enter the Nucleus Through Nuclear Pores. spans both the outer and inner membrane -Inner nuclear membrane contains a lipid bilayer -Outer nuclear membrane also contains a lipid bilayer and is continuous with the ER

Endocytic pathway

• Specialized Phagocytic Cells Ingest Large Particles (>250nm) (Pseudopods) • Fluid and Macromolecules Are Taken Up by Pinocytosis (<150nm) (Clathrin) • Receptor-mediated Endocytosis Provides a Specific Route into Animal Cells. Endocytosed Macromolecules Are Sorted in Endosomes. Lysosomes Are the Principal Sites of Intracellular Digestion.

Subunit

•- each polypeptide chain (protein) of a complex •Complexes can contain multiple proteins of the same type or different types

Amino Acids table

•20 different amino acids are found in nature •Differences in side chains confer physical and chemical properties. -side chain properties for each amino acid and how changing an amino acid within a polypeptide sequence can alter protein structure

DNA Composition

•A molecule of deoxyribonucleic acid (DNA) contains two polynucleotide chains held together by hydrogen bonds between the nucleotide bases. • •Building blocks: Sugar phosphate and base à nucleotide then gets strung together forming orientation. •Double-stranded, sugar-phosphate backbone covalently bonded. Hydrogen-bond b/w base pairs. • •Each strand has a polarity that is in antiparallel 3' à 5'

ATP as Activated Carrier

•ADP à ATP is energetically unfavorable •But, ATP à ADP has a large negative ΔGº, so energetically favorable. •ATP is most widely used activated carrier • •Within triphosphates of ATP - unfavorable repulsion between negative charges of phosphate molecules • •ATP hydrolysis removes repulsion •Carries high-energy phosphate groups, whereas NADH and NADPH carry high-energy electrons. •Favorable hydrogen-bond formation with water stabilizes inorganic phosphate (Pi)

Transfer of Terminal Phosphate from ATP

•ATP hydrolysis often coupled to transfer of terminal phosphate (rather than release of the phosphate) •Phosphorylation - reaction that involves the transfer of a phosphate group to a molecule

Chemical Reactions Result in Loss of Free Energy

•Above reaction occurs in one direction •Products will not spontaneous revert back to paper •Chemical energy released is lost irretrievably to the universe in the form of heat - random thermal motions of molecules •Chemical reactions proceed "downhill" = loss of free energy

Connective tissue

•Abundant extracellular matrix •Establishes a structural framework •Transports fluids and dissolved materials •Protects delicate organs •Supports, surrounds, and interconnects tissues •Stores energy reserves Varieties of Connective Tissues: •Tough/flexible - tendons or skin •Hard and dense - bone •Soft and transparent - fluid in eye interior

homologous recombination

•After DNA replication but before cell division, the replicated DNAs are still close to each other. •Unlike nonhomologous end joining, there is no loss of DNA •also used during meiosis to exchange genetic information during formation of germ cells (sperm and egg).

Cells similar Basic Chemistry

•All cells utilize DNA for storage of genes •Follow Central Dogma of Molecular Biology: •DNA --> RNA --> Protein •Same set of nucleotides are incorporated into DNA and RNA •Same set of amino acids are utilized to produce proteins •Same set of codons used to "read" mRNA

Apical and Basal Epithelia

•Apical - surface exposed to air or bodily fluid. •Basal - surface attached to sheet of connective tissue called basal lamina •Basal lamina - ECM composed of specialized collagen (type IV collagen) and laminin (provides sites for integrin binding - similar to fibronectin)

G2 phase

•Between S phase and onset of mitosis. •Cell synthesizes proteins, including microtubules, necessary for division.

Integrin Activation

•Binding and release allows cell to move through matrix •Binding causes conformational change to integrin - on either side of membrane 1.Intracellular binding results in activation on extracellular side 2.Extracellular binding results in signal cascade intracellularly

Bond Length and Orientations

•Bond length - characteristic distance between nuclei of bonded atoms •Hydrogen can only form 1 covalent bond •Other common atoms can form multiple covalent bonds. [-O-, N-] •Covalent bonds between atoms have characteristic bond lengths, angles, and energies. [Water (H2O) and propane (CH3-CH2-CH3)]

Enzymes Lower Activation Energy

•CO2 - Most energetically favorable form of carbon •H2O - most energetically favorable form of hydrogen •But, neither can be changed to lower energy state without initial input of energy •Activation energy - energy that must be acquired by a molecule to undergo a chemical reaction

Chloroplast

•Capture sunlight and use energy to synthesize energy-rich sugar molecules •Process called photosynthesis •Contain their own DNA

Photosystem II *

•Captures light energy to energize electrons in chlorophyll •Energized electrons pass through the ETC •carriers pump protons to create an electrochemical gradient •which is used to produce ATP by ATP synthase (like the process in mitochondria). -Extracts Electrons from Water. -passes electrons to the mobile electron carrier plastoquinone, which transfers them to the only proton pump involved in the photosynthetic electron-transport chain.

Sugars and Carbohydrates

•Carbohydrates - fuel and building material - include sugars and sugar polymers Monosaccharides - the simplest carbohydrates, single sugar molecules (simple sugars) example: glucose Disaccharides - two monosaccharides joined together example: maltose (2 glucose molecules) Polysaccharides - polymers composed of many sugar building blocks Example: starch

carbon atoms

•Cell formed from carbon compounds Properties: •Small, 6 electrons (2 in first shell, 4 in outer shell) •Can form 4 covalent bonds •can be single, double, triple or ring structure •C-C bond is very stable •Organic molecules - those that contain carbon •Chemical groups - specific combination of atoms attached to molecules with specific chemical and physical characteristics

G1 phase

•Cell is in recovery from previous division •Cell doubles it organelles •Cell grows in size •Cell accumulates raw materials for DNA synthesis

Prokaryotic Cells

•Cells can divide quickly (~20 minutes) •Within a relatively short time can produce more cells than humans alive •Most diverse and numerous •Mostly single-celled organisms

Biomolecules in Cells

•Cells contain four major families of small organic molecules

Sequential Reactions

•Cells couple reactions to drive unfavorable forward •Free energy changes in these reactions are additive

Cells and Entropy

•Cells do not defy the second law of thermodynamics because cells are not isolated systems •As order increases inside cell, released heat energy increases the entropy in the surrounding environment

Regulation of Chromosome Structure

•Changes in nucleosome structure allow access to DNA •Chromatin remodeling complexes utilize ATP hydrolysis to loosen DNA around nucleosomes and push it along to expose DNA to other factors

Free Energy and Catalysis

•Chemical reactions proceed in the direction that causes a loss of free energy •Enzymes reduce the energy needed to initiate spontaneous reactions •The free-energy change for a reaction determines whether it can occur •ΔG changes as a reaction proceeds toward equilibrium •The standard free-energy change, ΔG°, makes it possible to compare the energetics of different reactions •The equilibrium constant is directly proportional to ΔG°

DNA Packaged Into Chromosomes in Eukaryotes.

•Chromosomes typically contain long linear DNA molecules associated with proteins that fold the DNA into a more compact structure (chromatin). •Most human cells contain two copies of each chromosome - one copy from your mother, one from your father. Here, DNA from each chromosome type is labeled with a different fluorescent dye.

Cytokinesis - Animals

•Cleavage furrow appears between daughter nuclei •Actin and myosin filaments form contractile ring divides cytoplasm. •Like pulling on a drawstring •Pinches mother cell in two w one nucleus. -Mediated via contractile ring of actin and myosin filaments--assembles midway b/w spindle poles. -In plant cells, differs b/c a new cell wall forms inside the parent cell to divide the cytoplasm in two.

Chromosome Numbers Vary Greatly

•Closely related species with similar overall genome size (total amount of DNA) can have very different chromosome numbers and structures •No simple relationship between gene number, chromosome number, and total genome size

Cohesions and Condensins

•Cohesins - protein complexes that hold sister chromatids together - encircle 2 sister chromatids •Condensins - protein complexes that help chromosomes condense to compact bodies that are easily segregated during mitosis - encircle 1 sister chromatid -Both are needed for proper DNA segregation

Cyclins and Cyclin-dependent Kinases **lect 9, 20-24 pathway

•Cyclins - involved in switch kinases on and off, no inherent enzymatic activity, concentration varies throughout the cell cycle (degraded @ varies times on cell cycle). Allosteric protein inducing conformational change. i.e. Some cyclins are ubiquitylated and degraded in proteasomes. •Cyclin-dependent protein kinases (Cdks) - Enzyme that can trigger cell cycle events by phosphorylating and activating specific target proteins. -Trigger diff/ steps of the cell cycle. -Interphase --> binding of cyclin complexes of downstream targets. ie. important of signaling launch to next phase.

Reactions in Context of Cytosol

•Cytosol consists of many large and small molecules •Enzymes must find substrates within cytosol •Remember: cytosol is not static •Chemical reactions are constantly occurring and releasing heat (thermal) energy à movement of molecules à molecular collisions

DNA Replication is Semiconservative

•DNA replication is semiconservative, with each strand acting as a template for synthesis of the other, complementary strand. •Each newly synthesized DNA molecule contains one "old" strand and one "new" strand - semiconservative

S phase

•DNA replication takes place. •Proteins associated with DNA are synthesized.

Fidelity of DNA Replication and Repair

•DNA sequences are highly conserved between organisms •Sex-determination genes in humans and whales are highly similar

DNA Base-Pairing

•DNA strands held together by hydrogen bonds •C pairs with G (three H bonds) and A pairs with T (two hydrogen bonds) •each pair contains a bulky base (purine - G or A) paired with a smaller base (pyrimidine - C or T) to maintain a constant width of DNA strands. •2' attachment of ribosomes i.e. hydroxyl group or deoxy group.

Types of DNA Damage

•Depurination reactions remove Adenines and Guanines from DNA •Deamination of cytosine to produce uracil (so uracil cannot be used in DNA because it needs to be recognized as an error).

Covalent Cross-Linkage

•Disulfide bonds - covalent cross-link formed between the sulfhydryl groups on two cysteine side chains •Reinforces protein structure of secreted proteins or joins two different proteins together Not formed by proteins inside a cell

X-Inactivation

•Dividing cells pass along their histone modifications and heterochromatin to daughter cells •X-inactivation - involves formation of heterochromatin on one of two X chromosomes in females such that only one X is expressed in that cell and all its progeny, Occur randomly. •Example: Calico cats

Photosystem II Extracts Electrons from Water

•Electrons removed from the reaction center are replaced by electrons removed from water, in the process generating protons and O2.

Mechanical Model of Coupled Synthesis

•Energetically favorable reaction - rocks falling from cliff •Energetically unfavorable reaction - raising of water bucket •Energy conserved from middle panel can be used to drive otherwise unfavorable reactions

Enzyme

•Enzymes - proteins that lower activation energy (catalysts) •Substrates - molecules bound by enzymes •Products - molecules produced from chemical reactions

Enzymes Convert Substrates to Products

•Enzymes - proteins that lower activation energy (catalysts) •Substrates - molecules bound by enzymes •Products - molecules produced from chemical reactions

Enzymes Do NOT Change Equilibrium

•Enzymes lower activation energy for Y à X, but also for X à Y •Direction of reaction is dependent on concentrations of substrates and products •Equilibrium point is unchanged by enzymes

Most Genes Encode Proteins

•Exact correspondence between the 4-letter DNA alphabet and 20-amino acid alphabet was not clear from DNA structure (Genetic code - chapter 7)

Consequences of Unrepaired DNA

•Failure to repair DNA damage can have consequences for the organism. •Change of even a single nucleotide can be consequential if it affects an amino acid that is critical for the structure/function of a protein. Sickle Cell Anemia •Single amino acid change: Glutamic acid to Valine •Negatively charged a.a. ànonpolar a.a. •Less soluble protein than wild type and forms intracellular aggregates in the homozygous condition •The affected cells are more fragile than wild type cells; lyse to cause anemia and blockage of blood vessels (bad). •But in the homozygous or heterozygous condition (mutant/wt) the mutation confers resistance to malaria (good), so there is some positive selection in African populations.

Elongated Fibrous Shapes

•Fibrous proteins - protein with elongated, rod-like shape, such a collagen or keratin filament •Particularly abundant outside cell in extracellular matrix that helps bind cells together in tissues •Collagen - extremely strong and hold tissues together •Elastin - form rubber-like network by covalently cross-linked loose, unstructured polypeptide chains

Activated Carriers and Biosynthesis

•Formation of an activated carrier is coupled to an energetically favorable reaction •Activated carrier - small molecule that stores energy of chemical groups in a form that can be donated to many different metabolic reactions

Cytokinesis - Plants

•Formation of phragmoplast (cell plate) +In dividing a plant cell, a structure made of microtubules and membrane vesicles that guides the formation of a new cell wall. -Formed from remains of interpolar microtubules. •Many small membrane-bound vesicles made by Golgi apparatus •Eventually fuse into one thin vesicle extending across mother cell

Alpha Helices in Proteins

•Formed from turning of single polypeptide chain around itself into a structurally rigid cylinder •Hydrogen bond forms between amino group (N-H of one amino acid with the C=O of another amino acid) •Complete turn approximately every 3.6 a.a. (every 4th amino acid forms the hydrogen bond) •Can form region that is integrated into plasma membrane •Can intertwine with each other

Free Energy

•Free energy (G) - energy that can be harnessed to do work •Free-energy change (ΔG - delta G) - difference in free energy between reactants and products of a chemical reaction •Energetically favorable reactions - create disorder in universe by decreasing free energy of the system - have a negative ΔG) •Energetically unfavorable reactions - create order in universe - have a positive ΔG)

Chromosomes Organize Genes

•Genome - the total genetic information carried by all the chromosomes in a cell. •Some organisms have closely packed genes and other (generally more complex) have more spaced out genes •Complexity of an organism is generally proportional (but not always) to the number of genes in its genome. •In addition to genes, genomic DNA from more complex eukaryotes (eg, humans) can contain lots of "junk" DNA whose purpose is not clear. •Only one of the two strands serves as the template for the mRNA. • •Orange region (genes) used as template for DNA and grey is spliced out.

Periodic Table of Elements

•Groups - vertical columns, same number of electrons to fill outer shell and behave similarly when bonding to other atoms •Periods - atomic numbers increase from left to right, top to bottom

Alpha Helices

•Helix formed when many similar subunits are located next to one another •Can have different numbers of subunits in each turn of the helix •Resembles spiral staircase •Can be left-handed or right-handed - unchanged by turning upside down, but changes with mirror

Further Packing of DNA

•Histone H1 pulls nucleosomes together into compact chromatin fiber •Condensation: Fibers folded into loops that further compact into the mitotic chromosome

Heterochromatin Spreads

•Histone tail modifications establish and maintain chromatin structure •Heterochromatin modifications attract set of heterochromatin-specific proteins •Heterochromatin histone modifications added to neighboring nucleosomes •Chromatin condensation propagates along chromosome until it reaches barrier DNA sequence

Histone Modifications

•Histones contain "tails" that extend out of the nucleosome and can be reversibly modified • •E.g. Phosphorylation (serine), acetylation (lysine), and methylation (arsine) modifications alter chromatin structure directly or create binding sites for regulatory proteins. Some positions can be modified alternatively by more than one type of modification - leading to different consequences

Double-Strand DNA Breaks

•If the chromosomes become fractured by something like radiation, there can be loss of genes if the double-stranded pieces become separated. •To prevent this, non-homologus end joining (NEHJ)rapidly sticks the ends together before they drift apart (emergency repair). •Risk: loss of nucleotides at repair site •If the double-stranded break occurs just after DNA has been replicated, the undamaged helix can serve as a template to repair the damaged helix with homologous recombination

Cancer Incidence Increases with Age

•In order to be passed from one generation to the next, a mutation must be carried in the germ line, which produces the gametes (sperm and eggs). •But somatic cell mutations can cause problems too (e.g., cancers, caused by a gradual accumulation of multiple mutations leading to uncontrolled division and migration of cells). •The steep dependence of cancer with age is a consequence of the constant rate of change in DNA coupled with the need for multiple changes. •If a change leads to increased cell division, it replicates itself - so rare changes can amplify and become important.

Complex Chemical Reactions

•Inside cells, a more common reaction involves combining two reactants into one product Need to include concentrations of both reactants in equation

Cellular Attachment to ECM

•Integrin - transmembrane receptor protein ie. Fibronectin provides a linkage between the cell and collagen; part of the fibronectin molecule binds to collagen, while another part forms an attachment site for integrins. •Extracellular domain interacts with components of matrix •Intracellular domain interacts with cytoskeleton •Fibronectin - extracellular matrix protein that connects cell to ECM via integrins

Allosteric Enzymes

•Late products of enzymatic pathways typically inhibit early enzymes within pathway via binding to enzyme •Typically binds at different site from active site •Allosteric regulation - "other" binding - can be positive or negative. The regulator affects the active site by causing a conformational change in the protein when it binds.

Electron Sharing in Covalent Bonds

•Most covalent bonds share one pair of electrons (ethane) •Some covalent bonds share more than one pair of electrons (ethene) •Alternative intermediate between single and double, typically results in ring structure (benzene) •Differences in shared electrons affects •Bond strength Bond angles

Prokaryote

•Most diverse and numerous cells on Earth •Divided into two domains: Bacteria and Archaea

Interphase

•Most of the cell cycle is interphase •Cell performs usual functions •Time varies by cell type Long period of the cell cycle b/w one mitosis and the next. Includes G1, S, and G2 phases. •Some cells exit cell cycle - remain in G0 phase

Cells are Self-Replicating Collections of Catalysts

•New cells only come from existing cells (Cell Theory) •Production of new cells requires duplication of genome and other cellular components •Also requires molecules for energy to drive reactions forward

Polar and Nonpolar Interactions

•Nonpolar side chains disrupt hydrogen bonding of water molecules and typically reside towards the interior of folded proteins •Polar side chains are able to hydrogen bond with water and are typically located towards the exterior of folded proteins •When located interiorly, hydrogen bonds form between polar side chains or with peptide backbone

Eukaryotic Cells

•Nucleus stores genetic information •Mitochondria generate usable energy from food molecules •Chloroplasts generate energy from sunlight •Internal membranes create intracellular compartments with different functions •Cytosol is concentrated aqueous gel of large and small molecules •Cytoskeleton is responsible for directed cell movement •Eukaryotic cells might have originated as predators

Chlorophyll and Light Wavelengths

•Pigments (e.g. chlorophyll): chemicals that absorb certain wavelengths of light •Pigments found in chlorophyll absorb various portions of visible light •Wavelengths that are not absorbed are reflected or transmitted

S Phase - DNA Replication

•Pre-replication complex (origin recognition complex) forms at origin of replication •Recruits proteins like Cdc6 •Formed during G1 phase and is ready for activation as cell moves into S phase •S-Cdk (Cyclin A-Cdk2) - activates DNA helicase in pre-replication complex (G1 phase) and promotes assembly of remaining proteins needed for replication fork --> completion of DNA replication (S phate)

Mitochondria - Generate Usable Energy

•Present in essentially all eukaryotic cells •Enclosed within two membranes •Inner membrane folds toward interior of the organelle •Carry out cellular respiration •Contain their own DNA. Early anaerobic eukaryotic cell w nucleus engulfs Aerobic bacterium forming internal membranes around nucleus

Enzyme-Catalyzed Pathway

•Protein molecules function as catalysts. •The reactants of an enzymatically catalyzed reaction are called substrates. •Each enzyme accelerates a specific reaction. •Each reaction in a metabolic pathway requires a unique and specific enzyme. i.e. enzyme 1 catalysis molecule A to B. •The final end product will not be formed unless ALL enzymes in the pathway are present and functional. • •Animals use cellular respiration. Plants use photosynthesis.

DNA Replication Summary

•Proteins at a replication fork cooperate to form a replication machine. •DNA helicases and single-stranded binding proteins (SSBs) unwind the helix and keep the DNA in the unwound state. •Sliding clamps keep the DNA polymerase fully attached to DNA template (added by clamp loader). •The proteins involved in DNA replication are held together in a large multienzyme complex

Protein Folding

•Proteins fold into the lowest energy state possible (minimal ΔG) •Conformation - final folded state of a protein •Exposure of proteins to solvents or heat can denature the protein - cause unfolding of protein •Proteins will refold (renaturation) into proper conformation once denaturing stimulus is removed •Indicates the information needed to fold properly is contained within the protein sequence •In cells, however, chaperone proteins are present to help partially folded protein adopt the correct conformation

Photosystem I

•Receives electrons from terminal acceptor in Photosystem II •Captures light energy to regenerate energized electrons •Energized electrons used to reduce NADP+ (plants) to NADPH (animal cell or mitochondria) , rather than pump protons

Replication at Chromosome Ends

•Replication of chromosome ends presents a special problem that is resolved by the enzyme telomerase. •The problem: The lagging strand loses the DNA encoded by the RNA primer in each round or replication (progressive loss of DNA would occur). •The problem is resolved by telomerase, an enzyme with a bound RNA template (a reverse transcriptase) that allows extra copies of the telomere repeat to be added to the telomere template strand.

What is the Genetic Material?

•Requirements for the genetic material: 1.Must be able to store genetic information 2.Must be stable and able to be replicated accurately during cell division and transmitted from generation to generation 3.Must be able to undergo mutations to provide genetic variability • •By the 1940s, researcher knew: • genes are on chromosomes •chromosomes contain both proteins and nucleic acids locating in nuclei. •Proteins - initially thought to be genetic material b/c there are 20 different amino acids that can be ordered in different ways. • •Nucleic acids (DNA and RNA) - contain only 4 types of nucleotide as basic building blocks - not enough variability to store information • •Researchers were eventually able to show that DNA is the genetic material using transformation experiments - see "How We Know" at the end of Chapter 5)

Protein Families

•Serine proteases - while only part of the protein sequence is similar (green in image), conformation is highly similar and have similar functions •Each protein family has distinct activities

Flexibility of Long Polypeptides

•Single C-C bonds are very flexible - atoms can rotate around bond •Proteins fold up into distinct 3-D shapes •Protein backbone and side chains involved in folding •Non-covalent interactions •Hydrogen bonds •Electrostatic interactions •van der Waals interactions Hydrophobic forces

Light Microscopes

•Some cellular detail can be seen by light microscopes •Scientists have developed assays that utilize fluorescent markers to visualize different cellular components

DNA Replication and Segregation

•Specialized DNA sequences are replicated and are required for DNA replication and chromosome segregation •Replication of DNA occurs during the Interphase stage of the cell cycle •Chromosome segregation occurs during Mitosis

Evolution of Energy Generating Systems 58:06

•The first cells probably generated ATP by anaerobic fermentation (no O2) and used ATP to pump protons out generating gradient of stored E making ATP. •Electron transport proteins that pump protons without ATP hydrolysis evolved •Then the ATP pumps could work in the opposite direction to synthesize ATP

Topoisomerases

•The localized unwinding of DNA tightens the helix on the other side of the open region •DNA topoisomerases relieve the tension by creating nicks.

Evolution of Photochemical System

•The major breakthrough was the evolution of photochemical reaction centers that could use light energy to produce energized electrons • •The availability of O2 in the atmosphere as a result of photosynthesis allowed organisms to use aerobic metabolism to make ATP.

Linear Messages

•The structure of DNA suggested how genetic information is carried and copied. •The linear sequence of nucleotides in a gene must determine the sequence of a protein. •DNA can replicate because each strand carries the information for the other.

Regulation of Cyclin Concentrations

•Transcription/translation of cyclins leads to gradual increase in concentrations. •Targeted destruction by Anaphase-Promoting Complex/Cyclosome (APC/C) A ubiquitin ligase that triggers progression from metaphase to anaphase by signaling the degradation of cyclin B and cohesins. Pathway: Active cyclin-Cdk complex --[ubiquitylation (ubiquitin chain) via APC/C]--> Destruction of cyclin in proteasome --> inactive Cdk + degraded cyclin

Thymine Dimer Formation

•Ultraviolet light promotes covalent linkages between adjacent thymines. •Individuals with xeroderma pigmentosum carry different mutations affecting the repair of these; skin is highly sensitive to sunlight (lots of skin lesions and cancer).

DNA Synthesis Uses RNA Primers

•Unlike DNA polymerases, RNA polymerases do not need a base-paired end to begin synthesis (no proofreading function). •Primase is an RNA polymerase that synthesizes short RNA primers from DNA templates.

Electron microscope

•Utilizes beams of electrons, rather than light, to visualize cellular detail. Transmission Electron Microscopy (TEM) & Scanning Electron Microscopy (SEM)

Cells Vary in Appearance and Function

•Vary in size - range from a few micrometers (μm) to about 1 millimeter (mm) •Vary in shape - many projections like neurons to submarine-like shape of paramecium •Vary in chemical requirements - as simple as CO2, sunlight and water to more complex macromolecules from •Vary in function - production of molecules needed by the organism or regulation of movement of the organism by mechanical or electrical forces

Electron Transfer and Proton Pumping

•Water provides a large reservoir of mobile protons, which would tend to bond with any atom in the electron transport chain that becomes reduced. •So placement of an electron acceptor on the inside of the inner mitochondrial membrane and an electron donor on the outside could move a co-transported proton to the outside.

Multiprotein Complexes

•Weak noncovalent bonds also hold proteins in complexes •Subunit - each polypeptide chain (protein) of a complex •Complexes can contain multiple proteins of the same type or different types •Binding site - region on the surface of a protein, typically a cavity or groove, that interacts with another molecule through the formation of multiple noncovalent bonds

Replication Forks

•Y-shaped junction at site of DNA synthesis •2 replication forks formed at each replication origin •Replication machinery moves along DNA to open up double helix DNA synthesis is bidirectional

DNA polymerase

•enzyme catalyzes consecutive additions while remaining attached to DNA strand. •Takes pyrophosphate (2 phosphate) released à polynucleotide. Synthesizes DNA •Importance of base-pairing between incoming nucleotide and template. •Nucleotides added to 3' end of growing strand. •Phosphodiester bond between 3' end of growing stand and 5'-phosphate group of incoming nucleotide •Energy from hydrolysis of high-energy phosphate bonds of incoming nucleoside triphosphate (NTP) Self-Correcting proofreads during synthesis, removing incorrectly added nucleotides and resynthesizing that addition. A hypothetical DNA DNA polymerase synthesizing in the 3' to 5' position could not proofread because the 5' triphosphate would be gone after the first addition.

NADPH

•nicotinamide adenine dinucleotide phosphate, oxidized to NADP+ •utilized during photosynthesis for anabolism of complex molecules Reduced electron carrier -Activated carrier: electrons & hydrogens

NADH

•nicotinamide adenine dinucleotide, oxidized to NAD+ •utilized during cellular respiration for catalysis of food molecules. -Activated carrier: electrons & hydrogens

Intrinsically disordered sequence

•region in a polypeptide chain that lacks a definite structure •Connect different domains within larger proteins Unstructured Regions of Proteins

Protein domain

•segment of polypeptide chain that folds into a compact, stable structure and often carries out a specific function •Different domains often have distinct functions

Antibody

•structure: •Y-shaped molecule composed of polypeptide chains (two heavy and two light chains) •Two variable, antigen-binding sites at the end of each arm of Y-shaped structure •Different in different antibody molecules - bind antigens in specific conformation •Variable regions of both heavy and light chain generated by genomic rearrangements - "hypervariable loops" •Produce enormous variation due to the combinatorial diversity of rearrangements and antigen-binding capacity

Cell

•vary enormously in appearance and function •Living cells all have a similar basic chemistry •Living cells are self-replicating collections of catalysts •All living cells have apparently evolved from the same ancestral cell •Genes provide instructions for the form, function, and behavior of cells and organisms

Replication Origins

•where DNA replication begins - multiple elements along chromosomes •Initiator proteins separate strands of double helix •DNA sequences that are easy to open - A-T rich regions - only 2 hydrogen bonds between bases •Bacterial genome contains 1 origin •Human genome has ~220 origins/chromosome

Standard Free-Energy Change (ΔGº)

•ΔG is dependent on concentrations of molecules involved in chemical reactions •Standard free-energy change (ΔGº - delta G zero) - free-energy change measured at a defined concentration, temperature, and pressure. ΔGº = kilojoules/moles [Y] and [X] = concentrations of molecules ln = natural logarithm R = gas constant T = absolute temperature RT = 2.58 @ 37ºC