BIO final Flashcards

Question

Why is compartmentalization important?

Answer 1

Lysosome: Restricts activity, for example, lysosomes keep digestive enzymes in itself because if they get out, everything will be digested by them pH should be maintained, lower pH means more work, more efficiency Nucleus: Regulation for expression of genes, for example if there's something that shouldn’t be translated, it can be stopped Protects DNA from being damaged from nucleases, prevents from degradation Peroxisome: hydrogen peroxide changes the structure of macromolecules and damages them, so being inside peroxisomes is good so that it doesn’t get out Mitochondria: maximizes surface area, with the foldings, it can have more space. Same thing with thylakoids inside chloroplasts Thylakoids need storing compartment Endoplasmic reticulum: oxidizing environment, disulfide bridges get formed

Answer 2

Don't have nucleus Has cytoplasm, cell membrane, ribosomes, has DNA (not in compartment, but instead, nucleoid) Some prokaryotes have additional specific features like cell wall, capsules, internal membrane, cytoskeleton, flagella, pili, and fimbriae

Answer 3

Consists of peptidoglycan two sugars (NAG and NAM) linked, one NAM and then NAG and then NAM and so on NAM is linked to 4 amino acids, peptide These chains are linked with other amino acids Surrounds plasma membrane Some bacteria has only this, or can have another membrane layer Gram-positive bacteria have thick peptidoglycan layer (stay stained after being colored, which is why it’s positive) Gram-negative bacteria have thin peptidoglycan layer and another layer (lose dye, become discolored)

Answer 4

Rich in sugar Helps bacteria to protect itself Helps it to stay hydrated Helps with sticking to each other

Answer 5

Can be homologous to the eukaryotic cytoskeletal proteins Some have filamentous proteins Involved in cell division, movement, and shape maintenance

Answer 6

Involved in attaching bacteria together, adhesion Bacterial conjugation, make contact between bacteria, genetic material goes from one bacteria to another, sexual pili, genetic exchange

Answer 7

Help with infection and contact

Answer 8

Bacteria can have one, two on both ends, a cluster of them, or all around it Involved in movement, moves towards nutrients, moves away from toxic molecule Has a tail and hook (linked to structure that makes hook move when it moves) The reason why hook must move is because protons diffuse in bacteria

Answer 9

Size- Prokaryotes are much smaller Shape Nutritional requirements Prokaryotes feed from light (photoautotroph), use inorganic material to survive Animal cells use glucose for energy (chemoautotroph, independent), dependent on plants (chemoheterotroph) Photoheterotrophs use light source of energy and organic molecules instead of inorganic molecules

Answer 10

If bigger volume increases more than the surface area, this is bad because the biochemical activity in the cell increases, and it will need more outside nutrients. It’s better if it’s small because then cells can get what they need from outside

Answer 11

Endoplasmic reticulum RIBOSOMES Golgi apparatus CENTROSOMES CYTOSKELETON Mitochondria NUCLEOLUS Nucleus

Answer 12

Type of hemolytic anemia- lack of blood cells\ Symptoms: Yellowing of eyes Spleen becomes enlarged Fatigue Dizziness Hair loss Shortness of breathe Red blood cells aren’t donut shaped, they become round The proteins that are under the cell membrane that give the red blood cells their shape are dysfunctional Spectrin and ankyrin

Answer 13

Under the red blood cells, there are proteins like ankyrin, spectrin, and actin (cell cortex, cortical cytoskeleton) Underneath the red blood cell membrane, theres a network of proteins that are a part of the cytoskeleton, rich in actin and actin-binding proteins, also myosin Then, there’s plasma membrane Then there’s glycocalyx

Answer 14

The lipids found are phospholipids, cholesterol, and glycolipids, all of them have a hydrophobic and hydrophilic part (amphipathic) Example of phospholipid: phosphatidylcholine, most common type of phospholipid in biological membranes Its head is composed of a choline molecule and a phosphate group Glycerol links the head and tails The tails are made up of two fatty acids with about 14-24 carbon atoms (usually 18-20), usually single bond, but there may be a couple double bonds (unsaturated). Usually one tail is saturated and the other is unsaturated When a tail is unsaturated, it has a kink structure, important for fluidity The layer of the bilayer thats facing the cytosol is called the cytosolic monolayer and the layer facing the exterior of the cell/lumen of an organelle is called the non-cytosolic monolayer Phospholipids can move laterally (freely around membrane), flexion (moving fatty acid chains), rotation, or flip-flop (very rare, moves from one layer to another, happens with enzymes) During flip flop, The polar side has to touch the non-polar side, which is not energetically favourable Because they can move, we can say the lipid bilayer is fluid

Answer 15

Fluidity can be regulated Temperature When temperature increases, fluidity increases. Lipid composition What is in the membrane For example, cholesterol stiffens plasma membrane Phospholipid tail saturation degree When all saturated, they pack together and fluidity decreases When there's a double bond (unsaturated), there’s space to move around and the fluidity increases Phospholipid tail length Shorter tails are more fluid Fluidity is important because too little will cause less transport because it will be too rigid, and receptors won’t find each other.

Answer 16

Membrane of smooth endoplasmic reticulum How phosphatidylcholine is made First step is to get a fatty acid and add it to a glycerol and phosphate group, make amphipathic molecule Insert it in cytosolic layer This prephospholipid moves around, and a phosphatase (enzyme) finds it, removes its phosphate group and gives diacyl glycerol A third enzyme adds choline to it All of these molecules are added to the cytosolic layer of the membrane To have both layers of the membrane grow about the same, an enzyme takes the newly made phospholipids and puts them in the non-cytosolic layer This enzyme works randomly This enzyme is called scramblase Membrane layers must be about equivalent in length Not all types of phospholipids are distributed randomly Phosphatidylcholine is only in the non-cytosolic layer For the phospholipids to be distributed to their place, the endoplasmic reticulum membrane must go to the golgi apparatus

Answer 17

For the phospholipids to go to their right place, the ER buds to the membrane of the golgi apparatus The golgi apparatus has specific enzymes that are able to flip the phospholipids to the layers that they must be in. For example, if there’s a phospholipid that is in the cytosolic layer but belongs in the non-cytosolic, a specific enzyme in the golgi will flip it. This is maturation The specific enzymes are flippase enzymes

Answer 18

It buds from golgi apparatus and flows to another organelle or plasma membrane Keeps the same structure as it was before, keeps same orientation The cytosolic part will stay in the cytosolic layer and the non-cytosolic part will either face the extracellular fluid or will be in the interior of a new organelle What do the different phospholipids on either face of the membrane say about it? Since there are different phospholipids that can only be on one face and not the other, this makes the membrane asymmetrical

Answer 19

phosphatidylcholine - non-cytosolic layer phosphatidylinositols- cytosolic layer

Answer 20

Cell signaling Transport Cell growth and motility Cell-cell recognition Cell-cell adhesion

Answer 21

They make an alpha helix shape, where hydrophobic amino acids in side chains interact with hydrophobic tails Single pass make receptors In rough endoplasmic reticulum

Answer 22

Integral - linked to lipid bilayer and must have a detergent to separate them CanHow are proteins associated with lipid bilayer? cross the membrane (transmembrane) Can be monolayer-associated (only on one layer) Can be covalently linked (linked to lipid) Peripheral - attached to lipid bilayer (protein or lipid attached proteins) Weakly attached to proteins or lipids Protein distribution is also asymmetrical *NOTE: detergents are amphipathic* *NOTE: lipid linked means covalently attached, lipid attached is by hydrogen bonds

Answer 23

With the help of proteins Help by being: Transporters Ion channels Receptors Enzymes

Answer 24

Have both hydrophobic and hydrophilic amino acids When making alpha helix, the hydrophobic amino acids are on the outside while hydrophilic is inside

Answer 25

When there’s an infection, it signals the epithelial cells lining the blood vessels They then respond by making receptors called lectin, which recognizes sugar in carbohydrate layer of neutrophil cells Neutrophil starts interacting with epithelial cells, protein-protein interaction They slip between two epithelial cells and go to the site of infection to combat that infection They make the surface of the cell viscous

Answer 26

Coated with carbohydrates Sugar coating called carbohydrate layer/glycocalyx Involved in cell-cell adhesion and recognition

Answer 27

Binding the cell cortex Binding extracellular matrix molecules Binding proteins on the surface of another cell Tight junctions act as a barrier

Answer 28

Example: sponges When the glycocalyx is separated in sponges, they come together when they can interact with each other, and each one recognise the one it was attached to, so they make the same structure that it was initially If two different sponges were doing that, two sponges would be created because they have different glycocalyx, so they wouldn’t mix.

Answer 29

No covalent bonds Hydrogen bonds Vanderwaal bonds because non polar

Answer 30

Since the proteins in the membrane can move, they must be restricted. One way to restrict them is by binding them to the cell cortex. Without it, fluidity would increase and they would move

Answer 31

Genetic disorder The chloride ion channel doesn’t let ions out of the cell Water doesn’t get out of these cells and mucus thickens in air ways Harder to breathe More infections Digestive issues because digestive ducts are clogged with thick mucus

Answer 32

Mostly ion channels Create hydrophilic pores

Answer 33

Charges are attracted to each other and also repulse each other If there’s too much of negative charge, for example, the cell will burst

Answer 34

The inside of the membrane is more negative than the outside More of this will cause hyperpolarization, which is important for nerve signaling

Answer 35

Allow transport of ions and small molecules Active and passive

Answer 36

Since sodium molecules are positive and there’s more outside, they want to go to the area with lower concentrations, so the gradient is higher Potassium is negative and want to get out of the cell, but they are repulsed, so the gradient is low

Answer 37

The inside of the pores are positive, and they react with the negative charge of the oxygen in water Aquaporins Common in kidneys in the nephron tissue

Answer 38

Ion channels facilitate diffusion Don’t need to use energy Channels are membrane proteins Integral Multipass membrane proteins The pore of the channels are specific, only the right size and right charged ions can cross the channels Ion channels are selective The pores can open and close, triggered by ligand or difference in voltage Can open from mechanical pressure like light or vibration Sometimes they don’t have a trigger, they just open and close

Answer 39

They must change conformation Sometimes use energy and move ions against concentration gradient Can move substances to the same side or two substances to opposite sides at the same time

Answer 40

ATP Phosphorylation happens Calcium transporters in smooth endoplasmic reticulum This is important for muscle contraction, fertilization, and nerve cell communication Sodium-potassium pump Sodium moves along its gradient while potassium goes against its gradient Antiporter because its taking two substances and moving them in opposite directions from each other Light Bacteriorhodopsin: in archaea, retinal absorbs light and triggers a conformational change in the transporter Electrochemical gradient Sodium-glucose transporter Sodium goes with concentration gradient while glucose against it The electrical chemical gradient of sodium is helping glucose to go against its concentration gradient

Answer 41

Active transport Electrochemical gradient of sodium Passive transport for glucose When going from the lumen to the membrane, glucose must be going actively. When exiting the membrane to extracellular fluid, its going passively

Answer 42

LDL: low density lipoprotein, Cholesterol is made in the liver by smooth endoplasmic reticulum Cholesterol is an amphipathic molecule Has to be packaged, LDL is the name of that package Once it has been packaged, it’s released to blood, cells have to receive it Cells use receptor mediated endocytosis to get that cholesterol This and phagocytosis can bring in large things like polar things, nucleic acids Phagocytosis: macrophages takes in cells that are used up like red blood cells, digestive enzymes break it down

Answer 43

Primary uses ATP to help with Na-K pump Secondary uses primary to drive the glucose against concentration gradient

Answer 44

This will make it do the same function that it would have done in the apical domain, which is taking in glucose into the membrane. This is bad because it shouldn’t take glucose from the extracellular fluid This is disturbance

Answer 45

cytoplasm nucleolus nucleolus cytoplasm

Answer 46

Ligand-gated sodium channel “Ligand” = a molecule that binds to a receptor “Gated” = it opens or closes in response to something “Ion channel” = allows ions (like sodium) to move in or out of the cell Can’t be voltage because voltage opens in response to change in the electrical charge

Answer 47

Chromosomes aren’t mixed together in the nucleus A network of filamentous proteins support the shape of the nucleus Nucleolus isn’t bound by a layer of phospholipids The rough and smooth endoplasmic reticulum are both connected to the nuclear envelop

Answer 48

Signal between two neurons During rest, neuron is polarized When triggered, sodium channels open and sodium rushes in, so more positive inside, this is depolarization because it becomes more positive Action potential is triggered, sudden change in membrane potential When the cell is at rest, ion potassium channels leak When the cell is triggered, and some depolarization happens, sodium potassium channels open. Depolarizes even further opens other voltage gated sodium channels Potassium voltage gated ion channels open, potassium gets out, hyperpolarization happens, restoring resting potential Calcium voltage gated ion channels are located at the end of the terminal When depolarized, calcium rushes in because low concentration inside Vesicles with lots of neurotransmitters fuse with membrane of nerve terminal and they are released into synapse Neurotransmitters bind with ligand gated ion channel (sodium) Depolarization of the membrane happens When enough, another action potential is triggered inside the neuron That action potential travels and goes downstream to the end of neuron Electrical signal is converted into chemical signal to release neurotransmitters

Answer 49

Calcium influx triggers this Exocytosis is also triggered to release neurotransmitters

Answer 50

Membrane is hydrophobic and chlorine is charged

Answer 51

Active transporters

Answer 52

moving downward = along gradient moving upward = against gradient

Answer 53

Happens in three steps In the mouth and the gut In the cytosol In the mitochondria The cell cannot break down sugar to generate heat because it cannot increase temperature Instead it uses enzymes to break down sugar

Answer 54

Chemical reaction that release energy to surroundings Energetically favourable reactions because increase disorder Products have lower free energy level (more stable) than reactants Release free energy (potential energy) contained in chemical bonds All exergonic reactions are catabolic (breaking down molecules)

Answer 55

Disease of a built up fat tissue High risk of cancer and fertility issues, metabolic problems, depression White adipose tissue stores energy as fat and brown adipose tissue burns fat to produce heat Brown adipose tissue has more mitochondria There’s an energy transporter in the mitochondria that allows energy of food to be converted to heat instead of ATP Converting white to brown adipose tissue is good strategy to combat obesity Exercise allows white to become brown adipose tissue, exposure to cold, some food like in chili pepper (capsicin), berries

Answer 56

Chemical reaction that absorbs energy from its surroundings Energetically unfavourable reactions because they make order Products have higher free energy level than reactants Store energy in molecules All endergonic reactions are anabolic (making small and large organic molecules) cells couple exergonic and endergonic reactions. For example, when adding glucose and fructose to make sucrose, ATP breaks down to ADP. Making sucrose without breaking down ATP will not work, so they both happen at the same time in order to make sucrose*

Answer 57

Sometimes enzymes cannot do coupled reactions, so they store energy released by exergonic reactions

Answer 58

Enzymes provide activation energy Enzyme reduced activation energy to make a reactant become product It can do this by providing a better environment that, for example, disincludes water, or puts bond that has to work under stress

Answer 59

Begins glucose catabolism Converts glucose to two pyruvate and a small amount of energy Does not require oxygen In cytoplasm Involves 10 enzyme-catalyzed reactions First phase: 2 ATP molecules are used Second phase Cleavage phase, biphosphorylated molecules breaks down to 2 molecules of 3 carbon atoms Third phase Energy releasing to produce ATP and NADH Step 6 and 7 Oxidized: oxygen is added, addition of inorganic phosphate to molecule, exergonic reaction Reduced: NAD+ to NADH In step 7, ADP to ATP is endergonic reaction

Answer 60

Does not include oxygen Pyruvate stays and gets converted to lactic acid or ethanol

Answer 61

Uses oxygen from environment (aerobic) Converts 1 pyruvate to 3 CO2 Includes pyruvate oxidation, citric acid cycle, oxidative phosphorylation

Answer 62

Outer membrane has lots of pores Permeable to almost all molecules Intermembrane space, between inner and outer membrane, full of enzymes that use ATP from glycolysis to phosphorylate nucleotides In matrix, citric acid cycle, pyruvate oxidation

Answer 63

Links glycolysis and citric acid cycle Loses one carbon atom when in matrix Makes Acetyl CoA Makes one NADH, one CO2

Answer 64

8 reactions 2 carbons in acetyl CoA gets converted to 2 CO2 3 NADH, 1 GTP, and 1 FADH2 are made from one Acetyl CoA 2 Acetyl CoA’s per glucose, so there will be 10 NADH, 6 CO2 (come from the 6 carbon atoms from glucose molecule), 2 FADH2, and 4 ATP (2 from GTP)

Answer 65

Protons are pumped from matrix to intermembrane space, the come back to matrix Complex 1 receives electrons and gives it to another protein, carries it to complex 3 Complex 3 pumps more electrons, the transferred to complex 4 Complex 4 pumps more electrons and transfers them to oxygen to water Chemiosmosis: protons diffuse back to the mitochondrial matrix and ATP is synthesized

Answer 66

Each time electron is transferred from one complex to another, that complex binds to proton and electron at the same time, and proton is released to other side of membrane while electron goes to next complex As NADH moves across complexes, it loses energy because that energy is used to pump protons

Answer 67

Each complex is more electronegative than the one before NADH wants to get rid of its electrons and gives it to complex 1, complex 3 wants it more than complex 1, and same thing with complex 4 and then oxygen Affinity for electrons is one higher than the other

Answer 68

Energy doesn’t get converted to ATP, instead its heat energy

Answer 69

Allows ATP production without oxygen 2 pyruvates to lactic acid Important for cells because NADH will build up without fermentation, so must use NADH to make NAD+. This is important because NAD+ is needed for glycolysis

Answer 70

Because no electron transfer happens, NADH is not oxidized, and pumping of protons stops. Pumping of protons is used to make ATP (source of energy) and bring in pyruvate. The transporter that brings in pyruvate has an electrochemical gradient of protons. Basically, without electron transfer, no NADH is oxidized, so protons stop pumping to make ATP. That energy from pumping protons is used to bring in pyruvate, so without that, pyruvate stays where it is and doesn’t enter the matrix.

Answer 71

Normally, the pH of the matrix is higher than the intermembrane space because protons are pumped to intermembrane space, so more H+ is there so they have lower pH. The concentration of protons decreases if there’s no oxygen because it’s the final electron acceptor, so without it, protons won’t be pumped into intermembrane space, and the matrix becomes more acidic (less pH) The intermembrane space will be less acidic so higher pH

Answer 72

Reduced plant growth Less plants = less CO2 absorption When plants are under stress, they close stomata that releases water and oxygen and takes in CO2

Answer 73

ATP production Stops because ADP cannot come into matrix, so won’t be able to make ATP Proton electrochemical gradient Gradient increases at first because protons continue to pump into intermembrane space, but then slows down because too much protons and no gradient pH of the mitochondrial intermembrane space pH decreases because protons stay in the intermembrane space since ATP synthase can’t happen Electron transport chain Slows down and stops because the gradient of the protons is low, so pumping them is hard Oxygen consumption Decreases because electron transport chain slows down

Answer 74

Appears green bc of chlorophyll Two stages First one is light dependent and requires water and thylakoid membrane Produces ATP and NADH, which are required for the light independent reaction for photosynthesis Makes oxygen Second stage is carbon dioxide fixation to produce sugars and other organic compounds Begins in chloroplast stroma and continues in the cytosol

Answer 75

Molecule that absorbs visible light During fall, chlorophyll is broken down and the carotenoids are made

Answer 76

Have huge complexes called photosystems Each photosystem has two parts: In photosystem II: - Harvest energy from light Electron comes back and gives its energy to next chlorophyll Reaction center - Reaction center: proteins and two chlorophylls When energy reaches these two chlorophylls, they get excited and electron leaves chlorophylls, and doesn’t come back Given to electron carrier and another complex to create electrochemical gradient After that, there's a positive charge, so water is split to get electrons for chlorophylls in the reaction center (water is oxidized). This happens in the Thylakoid space The electron that went goes to plastoquinone and goes to cytochrome b6f complex to be used for its energy to pump protons from stroma into thylakoid space The protons go to ATP synthase to make ATP in the stroma Photosystem I Second photosystem - Harvest energy from light Take energy and transfer it to reaction center - Reaction center Once excited, leaves photosystem I, given to another electron carrier called ferrodoxin Ferrodoxin gives it Thioredoxin, but alternatively to another protein, NADP+ reductase Gets reduced to NADPH (second activated carrier) in the stroma The electron that was lost in photosystem II will come to replace electron lost in photosystem I Photosystem I boosts the energy of electrons that came from Photosystem II

Answer 77

Made up of packets of energy called photons Photons have dual nature, particle-like behavior When a molecule absorbs energy from photon, it gets excited The electron then leaves the molecule or it comes back to its original shell and loses energy by heat and free energy that is used by another molecule Chlorophyll absorb these energies and their electrons move from their ground state to an excited state Chlorophyll doesn’t absorb green light, only every other light

Answer 78

Splitting of water increases concentration of protons in the lumen H+ in the stroma is used up because it is added to NADP+ Protons are pumped

Answer 79

Calvin cycle 3 CO2 added to molecules will be phosphorylated and reduced by NADPH. Result of precursor for sugar, amino acids, nucleotides, which is glyceraldehyde 3-phosphate There will be regeneration of ribulose 1,5- bisphosphate For each G3P, 3CO2, 9 ATP, and 6 NADPH are made ATP and NADPH link light dependent and light-independent reactions pH increases in the stroma because protons go to Thylakoid space Since stroma pH is increasing, it makes some things in the calvin cycle “triggered” and work Thioredoxin Protein that has a disulfide bridge in it and when they receive electrons, they become reduced and the bridge breaks down, which changes conformation of protein. This change makes protein active or inactive

Answer 80

ATP made in chloroplast cannot get out, they will be used during carbon fixation

Answer 81

Both need membrane Oxidative phosphorylation happens in inner mitochondrial membrane, while photosynthesis happens in Thylakoid membrane Protons build up in Thylakoid space while in mitochondria, protons build up in intermembrane space In mitochondria, protons are pumped from the matrix to intermembrane space In chloroplasts, protons are pumped from stroma to Thylakoid space Protons are pumped from the interior of the organelle ATP is produced in chloroplasts and mitochondria Both include redox reactions Both use ATP synthase powered by electrochemical gradient ATP is formed in the stroma and matrix Water is the donor to give oxygen for electrons while in mitochondria, NADH gives electrons In chloroplasts, NADP+ is an electron acceptor from water while in mitochondria, oxygen receives electrons to turn to water from NADH and FADH2 Electrons are not energized in mitochondria but they are in chloroplasts

Answer 82

The process by which a cell converts an external signal into a functional internal response. The conversion of one type of signal to another

Answer 83

The molecules inside the cell that carry and process the signal (e.g., second messengers, kinases, G-proteins).

Answer 84

The sequence of molecular events (receptors → intermediates → effectors) triggered by a signal.

Answer 85

Cells receive signals from: neighboring cells, distant cells (via bloodstream), the extracellular matrix, or even themselves. Main types: Endocrine: Hormones travel through bloodstream to distant cells (slow, long-lasting). Paracrine: Signals act on nearby cells (local regulators like growth factors). Autocrine: A cell signals to itself. Synaptic: Neurons release neurotransmitters to a specific target cell (fast, short-range). Contact-dependent: Signal molecule is membrane-bound; cells must touch.

Answer 86

Intracellular receptors: Ligands: small, nonpolar molecules that cross membranes (e.g., steroids, NO). Can be proteins or small messenger molecules (like cyclic GMP or cyclic AMP) Function: ligand binds receptor inside cytosol or nucleus; often regulates gene transcription. They relay, amplify, integrate, receive feedback, and distribute the signal Responses: slower, long-lasting. Cell-surface receptors: Ligands: hydrophilic molecules that cannot cross membranes (peptides, proteins, many neurotransmitters). Function: receptor binds ligand outside and activates intracellular cascades. The last intracellular signaling molecule in the pathway activates an effector protein (enzyme, transcription factor, or protein of the cytoskeleton) Responses: fast or slow depending on pathway. Has three types: G-protein-coupled receptors, enzyme-coupled receptors, and ion-channel coupled receptors (ligand-gated ion channels)

Answer 87

Endothelial cells receive signal from acetylcholine to release NO → NO diffuses across membranes of smooth muscle cells → binds and activates intracellular enzyme guanylyl cyclase → increases cGMP by converting GTP to cGMP→ cGMP causes smooth muscle relaxation (e.g., in blood vessel walls → vasodilation).

Answer 88

Cortisol crosses membrane → binds intracellular receptor → receptor–cortisol complex enters nucleus → binds specific DNA sequences → changes transcription of target genes → alters metabolism or stress-response pathways.

Answer 89

Relayed: Receptor activates the next molecule in the chain (e.g., G-protein activates enzyme). Amplified: One activated molecule creates many second messengers → strong response. Distributed: Divergent pathways allow one signal to produce multiple effects (e.g., activating many target proteins). Modulated: Feedback loops adjust the strength or duration (positive feedback enhances; negative feedback reduces/ends signaling).

Answer 90

Cells receive many signals at once. Intracellular signaling proteins can act as “coincidence detectors,” responding only when several pathways are active. Integration allows coordinated outcomes like cell division, differentiation, survival, or apoptosis.

Answer 91

Switches turn “on” or “off” depending on their state: Phosphorylation switches: kinases add phosphates to activate; phosphatases remove them to deactivate. GTP-binding proteins: active when bound to GTP; inactive when GTP is hydrolyzed to GDP.

Answer 92

Different cells have different receptors, signaling proteins, and effector molecules. Therefore, the same ligand can produce distinct outcomes. Examples: Acetylcholine: slows heart rate (cardiac muscle), causes contraction (skeletal muscle), causes secretion (salivary glands). Adrenaline (epinephrine): causes glycogen breakdown in liver, increases heart contraction, dilates some blood vessels, constricts others.

Answer 93

Change in cell movement Change in cell shape Change in cell metabolism Secretion Differentiation (slow) Division (slow) Growth (slow) Survival

Answer 94

Transcription factors, metabolic enzymes, and proteins of the cytoskeleton Impact directly

Answer 95

An enzyme that phosphorylates proteins Example of intracellular signaling molecule that amplifies an extracellular signal

Answer 96

proteins (ex: insulin involved in glycemia control) peptides (ex: oxytocin involved in lactation and social bonding) amino acids (ex: glutamate involved in learning and memory) steroids (ex: cortisol involved in metabolism, inflammation and response to stress) fatty acid derivatives (ex: prostaglandins involved in inflammation, pain and fever) gases (ex: nitric oxide in blood vessel dilation)

Answer 97

GPCRs (G-protein–coupled receptors) are membrane proteins with: - 7 transmembrane α-helices - Single polypeptide chain that crosses the lipid bilayer seven times - ⅓ of the drugs work via GPCRs - An extracellular ligand-binding region - A cytoplasmic region that interacts with G proteins - It activates G proteins (G proteins are a protein that binds GTP and hydrolyzes it) - GPCRs are the largest family of cell-surface receptors They bind diverse ligands, including: - Small molecules (adrenaline, acetylcholine, dopamine) - Peptide hormones (glucagon) - Large protein hormones - Odorants, tastants - Photons (for rhodopsin in the retina—light acts as the “ligand”)

Answer 98

Trimeric G proteins have three subunits: - α (alpha): binds GDP/GTP and interacts with target enzymes - β (beta) - γ (gamma) When a ligand activates a GPCR: - GPCR changes shape. - It causes Gα to exchange GDP for GTP. - Gα–GTP dissociates from βγ. - Both Gα–GTP and βγ can activate downstream targets.

Answer 99

Adenylyl cyclase (AC) - Produces cyclic AMP (cAMP) from ATP. Phospholipase C (PLC-β) - Produces IP₃ (inositol trisphosphate) and DAG (diacylglycerol).

Answer 100

- A signal binds GPCR. - GPCR activates Gαₛ by allowing GDP→GTP exchange. - Gαₛ–GTP binds and activates adenylyl cyclase. - Adenylyl cyclase converts ATP → cAMP. - cAMP activates PKA, which phosphorylates cellular targets.

Answer 101

- IP₃: soluble; diffuses into the cytoplasm; binds IP₃ receptors on the ER → triggers release of Ca²⁺. - DAG: remains in the plasma membrane; activates protein kinase C (PKC) (with the help of Ca²⁺). - Together, Ca²⁺ + DAG activate PKC → changes in gene expression, secretion, or metabolism.

Answer 102

- Two main classes of G proteins: monomeric and trimeric - Monomeric G proteins are made of one subunit (protein) - Monomeric G proteins are activated by some enzyme coupled receptors - Trimeric G proteins are made of three subunits, alpha (a), beta (ß) and gamma (v). - The alpha subunit binds and hydrolyzes GTP (has a GTPase activity) - Trimeric G proteins are activated by GPCRs - GPCR's activation changes the conformation of the trimeric G protein and causes the exchange of GDP for GTP. - Upon GTP binding, the a subunit separates from the ßy complex. - The a subunit and the By complex are both intracellular signaling proteins and can interact with target proteins. - In mammals, there are 20 different types of trimeric G proteins based on differences in their a subunit. - Each type of G protein is activated by a set of receptors and activates a set of target proteins. - In pacemaker cells, the By complex opens K+ channels, leading to plasma membrane hyperpolarization, a reduced frequency of action potentials and decreased heart rate

Answer 103

- Caffeine is a phosphodiesterase (PDE) inhibitor. - PDE normally breaks down cAMP → AMP. When caffeine blocks PDE: - cAMP levels stay high - PKA remains active longer - This increases alertness and metabolic activity.

Answer 104

- In salivary gland cells, Tastants bind GPCRs on taste buds → activate G proteins → stimulate PLC → release Ca²⁺ → neurotransmitter release (excocytosis of saliva) - In tase receptor cells, sweet, umami, and bitter flavors bind to GPCRs, which activates the phosphatidylinositol pathway and leads to intracellular Ca+ concentration increase. This leads to neurotransmitter release to sensory neurons

Answer 105

(olfaction): Odorant molecules bind GPCRs in olfactory neurons → activate G proteins → increase cAMP → opens cyclic nucleotide-gated ion channels → depolarization and initiation of odor signals. generates nerve signals.

Answer 106

Amplification steps: - One photon activates one rhodopsin. - One activated rhodopsin activates hundreds of transducin molecules. - Each transducin activates phosphodiesterase (PDE). - PDE breaks down thousands of cGMP molecules. - Reduced cGMP causes many ion channels to close, greatly amplifying the signal. - This huge amplification allows rods to respond to very dim light.

Answer 107

- Rhodopsin is a GPCR in rod cells. Light causes retinal inside rhodopsin to change shape → activates G protein transducin → lowers cGMP levels → closes ion channels → produces the visual signal. - In the absence of a light signal, cyclic GMP is continuously produced - The cyclic GMP binds to cation channels and keeps them open - In the presence of light, the GPCR (rhodopsin) and then the G protein (transducin) are activated - G protein activates cyclic GMP phosphodiesterase, which breaks down cyclic GMP to GMP - In the absence of cyclic GMP, Na+ channels close, leading to cell hyperpolarization - The rate of neurotransmitter release from the base of the cell changes as membrane potential changes - As the rod cell hyperpolarizes, the rate of neurotransmitter release from the base of the cell decreases - The light signal is greatly amplified by the signal transduction pathway in rod photoreceptor cells. Each light-activated GPCR (rhodopsin) can activate several hundred copies of the G protein. Each G protein activates a large number of cyclic GMP phosphodiesterase enzyme. Each cyclic GMP phosphodiesterase hydrolyzes several hundred molecules of cyclic GMP per second. Hence, a single photon of light can result in the closure of a huge number of Na+ channels.

Answer 108

- Ligand (e.g., EGF, insulin) binds extracellular domain. - Two RTKs dimerize. - Their kinase domains become active and autophosphorylate tyrosines. - Phosphorylated tyrosines act as docking sites for signaling proteins with SH2 domains.

Answer 109

1. Adaptor protein Grb2 binds phosphotyrosine on RTK. 2. Grb2 recruits SOS, a guanine nucleotide exchange factor (GEF). 3. SOS activates Ras (monomeric G-protein) by exchanging GDP → GTP. 4. Active Ras-GTP triggers kinase cascade: - Raf (MAPKKK) - MEK (MAPKK) - ERK (MAPK) 5. Activated ERK enters nucleus → phosphorylates transcription factors → gene expression changes (e.g., proliferation).

Answer 110

GPCRs (G-protein–coupled receptors) Structure: 7 transmembrane helices. Function: Activate trimeric G proteins → second messengers (cAMP, IP₃, DAG). Typical signals: hormones, neurotransmitters, odorants, photons. 2. RTKs (Receptor Tyrosine Kinases) Structure: Single-pass transmembrane proteins with intracellular tyrosine kinase domain. Function: Dimerize on ligand binding → kinase domains autophosphorylate → recruit signaling proteins. These proteins can either bind to the activated receptor and relay the signal OR bind to the activated receptor, become phosphorylated, activated, and relay the signal Typical signals: growth factors and hormones (EGF, PDGF, insulin). 3. Ion-channel–coupled receptors Structure: Transmembrane proteins that form an ion pore. Function: Open/close when ligand binds → rapid changes in ion flow. Typical signals: neurotransmitters (ACh, GABA, glutamate). 4. Enzyme-coupled receptors (non-RTK) Structure: Single-pass; intracellular domain associates with enzymes (e.g., JAK-STAT receptors). Function: Activate attached enzymes rather than having intrinsic kinase activity.

Answer 111

1. RTK activates PI3K (binds to phosphotyrosines). 2. PI3K phosphorylates PIP₂ → PIP₃ at membrane. 3. PIP₃ recruits Akt and PDK1. 4. PDK1 + mTORC2 phosphorylate and activate Akt. 5. Akt promotes cell survival and growth by: - inactivating pro-apoptotic proteins (e.g., Bad, which promotes cell to kill itself through apotosis) - stimulating protein synthesis (via mTOR pathway)

Answer 112

- Receptor internalization: endocytosis removes RTKs from surface. - Receptor degradation: sent to lysosomes. - Phosphatases: remove phosphates from RTKs and pathway proteins. - Ras-GAPs: stimulate Ras to hydrolyze GTP → GDP (inactivating Ras). - Short-lived second messengers: e.g., lipid messengers get rapidly dephosphorylated. - RTK inactivation occurs through the hydrolysis of its GTP - GTP hydrolysis is stimulated by Ras-GAP - About 30% of human cancers contain mutations affecting Ras GTPase activity

Answer 113

Receptor tyrosine kinases (RTKs) Receptor serine/threonine kinases (RSTKs) Cytokine receptors (associated with tyrosine kinases)

Answer 114

The cytoskeleton is essential because it: - Maintains cell shape (resists deformation; provides mechanical strength). - Organizes internal contents (positions organelles; forms tracks for vesicle transport). - Enables cell movement (crawling, contraction, beating of cilia/flagella, chromosome separation). - Allows cell division (mitotic spindle for chromosome segregation; actin–myosin contractile ring for cytokinesis). Without the cytoskeleton, the cell would collapse, fail to move materials, and be unable to divide.

Answer 115

Subunit: α/β-tubulin heterodimers (polymerize to form protofilament) Width: ~25 nm (widest). Length: Long, stiff hollow tubes spanning the cell. Polarity: Yes (plus and minus ends). Location: throughout cytoplasm Function: Tracks for organelle/vesicle transport, mitotic spindle, cell polarity, cilia/flagella movement, cell division

Answer 116

(Actin filaments) Subunit: actin monomers (G-actin). Width: ~7 nm (thinnest). Length: Shorter, often bundled or branched. Polarity: Yes. Location: Cortex (just beneath plasma membrane), muscle cells, protrusions (microvilli). Function: Cell shape changes, muscle contraction, cell crawling, cytokinetic ring, tension support.

Answer 117

Subunit: fibrous proteins (keratin, vimentin, neurofilaments). Width: ~10 nm. Length: Rope-like, very long and stable. Polarity: No (symmetrical structure). Location: Cytoplasm (skin cells, neurons); nuclear lamina. Function: Mechanical strength, resistance to stress, anchoring, nuclear shape.

Answer 118

IF subunits are extended coiled-coil dimers. Two dimers → tetramer with staggered, antiparallel arrangement. Tetramers pack into rope-like fibers with many noncovalent interactions. Lack of polarity and tight lateral packing make them flexible but extremely hard to break, ideal for mechanical reinforcement (e.g., skin, axons).

Answer 119

Microtubules Require GTP-bound tubulin to assemble. Grow from centrosomes at the minus end; grow at plus end. Rapid assembly and disassembly controlled by GTP hydrolysis (dynamic instability). Actin filaments Require ATP-actin to assemble. Grow faster at plus end; slower at minus end. Assembly controlled by actin-binding proteins (nucleators, severing proteins, capping proteins). Intermediate filaments Do not bind nucleotides to assemble. More stable and less dynamic. Assemble by lateral packing, not end growth; disassembly mainly regulated by phosphorylation (e.g., nuclear lamina breaks down in mitosis).

Answer 120

(microtubule-based) Move toward plus end of microtubules. Transport vesicles, organelles toward cell periphery.

Answer 121

(microtubule-based) Move toward minus end (toward centrosome). Drive cilia/flagella beating; transport cargo inward.

Answer 122

(actin-based) Most move toward plus end of actin. Muscle contraction, cell cortex tension, vesicle transport along actin

Answer 123

Kinesin and dynein use microtubules; myosin uses actin. Kinesin = outward; dynein = inward transport. Myosin primarily generates force and contraction rather than long-distance transport.

Answer 124

Dynamic instability = alternating rapid growth and rapid shrinkage of individual microtubules. How it works: Tubulin adds to the plus end in the GTP-bound form. As the microtubule grows, a GTP cap forms. If GTP is hydrolyzed to GDP faster than new dimers add → the GTP cap is lost. Without the cap, the unstable GDP-tubulin causes the microtubule to catastrophically shrink Why dynamic instability matters: Allows microtubules to search and capture chromosomes or targets during mitosis. Enables rapid reorganization of the cytoskeleton to change cell shape or polarity. Controlled by: Rate of GTP hydrolysis Tubulin concentration Microtubule-associated proteins (MAPs) that stabilize or destabilize the filament Drugs (taxol stabilizes; colchicine depolymerizes)

Answer 125

G1 (Gap 1) Cell grows, monitors environment, prepares for DNA replication. Decision point: divide, delay, or enter G0. S (Synthesis) DNA is replicated. Centrosomes duplicate. G2 (Gap 2) Cell checks DNA for errors. Prepares machinery for mitosis. M (Mitosis + Cytokinesis) Chromosomes segregate; cell physically divides.

Answer 126

Prophase Chromosomes condense; mitotic spindle begins to form. Prometaphase Nuclear envelope breaks down; microtubules attach to kinetochores. Metaphase Chromosomes align at metaphase plate; each sister kinetochore attached to opposite spindle poles. Anaphase Sister chromatids separate and move toward opposite poles. Telophase Nuclear envelopes re-form; chromosomes decondense. Followed by cytokinesis (actin–myosin ring divides cell)

Answer 127

Mitosis One division → two genetically identical diploid daughter cells. Sister chromatids separate in anaphase. No crossing-over (except in recombination repair). Meiosis Two divisions → four genetically diverse haploid gametes. Homologous chromosomes pair up (synapsis) and undergo crossing-over in meiosis I. Meiosis I: homologs separate. Meiosis II: sister chromatids separate. Produces genetic variation; reduces chromosome number by half.

Answer 128

The control system is a network that ensures events happen in the correct order. Main components: Cyclin-dependent kinases (Cdks): enzymes that drive cell cycle forward. Cyclins: regulatory proteins that activate Cdks. Cdk inhibitors (CKIs): block Cdk activity (e.g., p21, p27). Phosphatases (Cdc25): remove inhibitory phosphates to activate Cdks. Kinases (Wee1): add inhibitory phosphates. APC/C (anaphase-promoting complex): ubiquitin ligase that destroys cyclins and securin.

Answer 129

1. Cyclin binding: required for Cdk activation. 2. Phosphorylation/dephosphorylation: - Activating kinases add activating phosphates. - Wee1 adds inhibitory phosphate, Cdc25 removes it. 3. Cdk inhibitors (CKIs): physically block active site. 4. Cyclin degradation: ubiquitin-mediated destruction by APC/C or SCF. 5. Localization: cyclins/Cdks must be in the right place at the right time.

Answer 130

G1 checkpoint (Start/Restriction point) - Checks environment (growth factors), nutrients, DNA integrity. - Decision: enter S-phase or pause/enter G0. G2/M checkpoint - Ensures DNA replication is complete and undamaged before mitosis. 3. Spindle assembly checkpoint (metaphase–anaphase) - Ensures all chromosomes are attached to spindle with correct tension. - Blocks anaphase until all kinetochores are properly attached.

Answer 131

- Mitogens activate signaling pathways (often via RTKs). These activate transcription of G1 cyclins (e.g., cyclin D). - Cyclin–Cdk complexes inactivate the tumor suppressor Rb by phosphorylating it. - Rb releases the transcription factor E2F. - E2F turns on genes needed for S-phase (including cyclin E, cyclin A). This commits the cell to DNA replication.

Answer 132

1. DNA damage activates ATM/ATR kinases. 2. These activate Chk1/Chk2, which activate p53. 3. p53 induces transcription of p21. 4. p21 inhibits G1/S-Cdks and S-Cdks. 5. The cell cannot enter S-phase until damage is repaired.

Answer 133

- Unattached kinetochores generate a “wait” signal”. - This signal blocks APC/C activation. - Without APC/C, securin is not degraded → separase stays inactive. - Sister chromatids cannot separate → anaphase is delayed. - This prevents chromosome missegregation.

Answer 134

1. Cdk or cyclin mutants - No cyclin / inactive Cdk → arrest at that checkpoint (e.g., no S-cyclin → cannot enter S-phase). - Non-degradable cyclin → failure to exit that phase (e.g., non-degradable M-cyclin → stuck in mitosis). 2. Mutants in Rb pathway - Loss of Rb → uncontrolled entry into S-phase (hyperproliferation). 3. p53 or p21 mutants - Loss of p53 or p21 → cells fail to arrest after DNA damage → replication with damaged DNA; major genomic instability. 4. APC/C mutants - Inactive APC/C → cells cannot enter anaphase → sister chromatids stay attached. - Hyperactive APC/C → premature chromatid separation. 5. Cdc25 or Wee1 mutants - No Cdc25 → Cdk stays inhibited → cannot enter mitosis. - No Wee1 → premature mitosis; cells divide before ready.

Answer 135

A replication bubble forms when DNA strands separate at the origin of replication. Two replication forks move outward in opposite directions from the origin. Each parental strand serves as a template for a daughter strand. The leading strand is synthesized continuously in the 5' → 3' direction toward the fork, while the lagging strand is synthesized discontinuously away from the fork as Okazaki fragments, each also built 5' → 3'. The most recently formed Okazaki fragment is the one closest to the replication fork. Polarity must be labeled: original strands run antiparallel (one 5' → 3', the other 3' → 5').

Answer 136

Base-pairing rules: A pairs with T, and G pairs with C. The complementary strand runs antiparallel to the original. If given a sequence in the 5' → 3' direction, write the complementary bases and label that strand as 3' → 5'. Reverse it if asked to provide the complementary strand in the 5' → 3' direction.

Answer 137

Loss of helicase prevents strand separation and halts replication. Loss of single-strand binding proteins allows strands to re-anneal or form secondary structures. Loss of primase prevents RNA primer formation, so DNA polymerase cannot begin synthesis. Loss of DNA polymerase stops elongation of new DNA strands. Loss of ligase prevents joining of Okazaki fragments, leaving the lagging strand fragmented. Loss of topoisomerase leads to excessive supercoiling and possible DNA breakage ahead of replication forks.

Answer 138

Replication forks move bidirectionally outward from the origin. DNA polymerase synthesizes new DNA 5' → 3', which can be either in the same direction as the fork (leading strand) or opposite the fork (lagging strand). Fork movement is direction of unwinding; synthesis direction is determined by polymerase polarity.

Answer 139

Linear chromosomes cannot fully replicate their 3' ends because DNA polymerase needs a primer and cannot replace the final RNA primer on the lagging strand. This causes chromosomes to shorten with each cell division. Telomerase solves this by extending telomeres using an RNA template, allowing completion of the lagging end and preventing loss of essential genes.

Answer 140

DNA contains deoxyribose, is double-stranded, and uses bases A, T, G, and C. RNA contains ribose, is usually single-stranded, and uses A, U, G, and C. DNA has thymine, while RNA has uracil. RNA can form complex secondary structures (hairpins, loops), whereas DNA forms a stable double helix. DNA is chemically more stable due to the missing 2'-OH; the 2'-OH in RNA makes it more reactive.

Answer 141

The coding (sense) strand has the same sequence as the mRNA except T → U. The non-coding (template or antisense) strand is the one RNA polymerase reads 3' → 5' to synthesize mRNA 5' → 3'. To write the mRNA: take the coding strand and replace T’s with U’s. If only the template strand is given, write the complementary RNA sequence (A↔U, G↔C) and give it in the 5' → 3' direction.

Answer 142

RNA polymerase binds promoter sequences (e.g., −35 and −10 in prokaryotes; core promoter + transcription factors in eukaryotes). Promoter elements are asymmetrical, so binding orientation determines which strand will be used as the template and where initiation begins. Sigma factor (prokaryotes) or transcription factors (eukaryotes) guide the polymerase to the correct promoter.

Answer 143

Both enzymes synthesize nucleic acid 5' → 3' and use a template strand. DNA polymerase requires a primer; RNA polymerase does not. DNA polymerase uses dNTPs; RNA polymerase uses NTPs. Both reactions are driven by hydrolysis of the high-energy triphosphate (release of pyrophosphate). DNA polymerase proofreads; RNA polymerase generally does not.

Answer 144

Prokaryotes: initiation uses sigma factor; transcription and translation occur together; termination occurs via Rho-dependent or intrinsic (hairpin + U-run) mechanisms. Eukaryotes: initiation requires many transcription factors and promoter elements (TATA box, enhancers); transcription and translation are separated; termination involves cleavage of the transcript and downstream dissociation mechanisms, not a simple hairpin.

Answer 145

Eukaryotic pre-mRNA undergoes 5' capping, intron removal by spliceosomes, and addition of a poly-A tail at the 3' end. These modifications protect RNA from degradation, allow export from the nucleus, and ensure proper translation.

Answer 146

Defective capping leads to rapid degradation and poor ribosome binding. Defective splicing can cause intron retention, exon loss, or frameshifts, often producing nonfunctional or truncated proteins. Defective polyadenylation results in unstable RNA, reduced translation, and possible failure of nuclear export.

Answer 147

tRNAs are short RNAs (~75–90 nt) that fold into a cloverleaf secondary structure and L-shaped 3D shape. They contain an anticodon loop that base-pairs with codons on mRNA and a 3' CCA end where the amino acid is attached. Their function is to deliver specific amino acids to the ribosome. Ribosomes are ribonucleoprotein complexes composed of large and small subunits. They contain rRNA and proteins. The small subunit binds mRNA and aligns codons; the large subunit performs peptide-bond formation. Ribosomes have A, P, and E sites that coordinate tRNA movement during translation.

Answer 148

Initiation: the small ribosomal subunit binds mRNA and the initiator tRNA; the large subunit joins to form the full ribosome. Elongation: aminoacyl-tRNAs enter the A site, peptide bonds form between the growing chain in the P site and the amino acid in the A site, and the ribosome translocates along mRNA. Termination: a stop codon enters the A site, release factors bind, the polypeptide is cleaved from the tRNA, and the ribosome subunits dissociate.

Answer 149

Wobble refers to non-standard base pairing at the 3rd position of the codon (5' position of the anticodon). This flexibility allows one tRNA to recognize multiple codons that code for the same amino acid. Wobble reduces the number of unique tRNAs a cell needs.

Answer 150

A synthetase attaching the wrong amino acid causes that amino acid to be incorporated wherever that tRNA’s anticodon pairs—a translation-level error producing faulty proteins. A mutation in the anticodon changes which codon that tRNA recognizes, potentially inserting the wrong amino acid at specific codons. Single-base mutations in mRNA may cause silent, missense, nonsense, or frameshift outcomes depending on the type and position of the mutation, affecting protein sequence and function.

Answer 151

Uncharged tRNA is aminoacylated by its aminoacyl-tRNA synthetase, attaching the correct amino acid using ATP. The charged tRNA enters the ribosome’s A site during elongation. After peptide bond formation, the growing chain is transferred onto its amino acid and the tRNA shifts to the P site. After translocation, the now-uncharged tRNA moves to the E site. It then exits the ribosome back into the cytosol.

Answer 152

Single-strand damage includes base modifications (oxidation, alkylation), base loss (abasic sites), and single-strand breaks. These are repaired by base excision repair, nucleotide excision repair, or single-strand break repair enzymes. Double-strand breaks arise from ionizing radiation, replication fork collapse, or mechanical stress. These are repaired by homologous recombination or nonhomologous end joining. Unrepaired damage can block replication and transcription, create mutations, cause chromosomal instability, or lead to cell death or cancerous transformation.

Answer 153

Proteins destined for the ER begin translation in the cytosol. When the signal peptide emerges, the signal recognition particle (SRP) binds it and pauses translation. The ribosome–SRP complex docks at the SRP receptor on the ER membrane. The ribosome attaches to the translocon channel, SRP is released, and translation resumes. Proteins either pass completely through the translocon into the ER lumen or integrate into the membrane via hydrophobic stop-transfer or start-transfer sequences. After synthesis, signal peptides may be cleaved and the protein folds inside the ER

Answer 154

Silent mutations change a nucleotide but not the amino acid; protein structure and function are usually unaffected, so phenotype is unchanged. Missense mutations change one amino acid; effects range from harmless to severe depending on the role of the altered residue. Nonsense mutations convert a codon into a stop codon, producing a truncated protein that is usually nonfunctional. Loss-of-stop mutations remove or alter the stop codon, causing translation to continue into the 3′ UTR, producing extra amino acids and often an unstable or nonfunctional protein. Frameshift mutations (insertions or deletions not in multiples of 3) shift the reading frame, altering all downstream amino acids and usually creating premature stops; this generally yields nonfunctional proteins and strong phenotypic effects.

Answer 155

The most common replication error is base mispairing. DNA polymerase proofreading detects incorrect bases and removes them with its 3'→5' exonuclease activity. Mismatch repair fixes errors missed by proofreading by identifying the newly synthesized strand and correcting the mismatch. Failure to repair creates permanent point mutations passed to daughter cells.

Answer 156

Deletion removes a chromosomal segment, causing loss of genes and often severe phenotypes. Duplication repeats a segment, increasing gene dosage and potentially altering development or metabolic balance. Inversion flips a segment around within the chromosome; usually no gene dosage change, but breakpoints can disrupt genes or alter regulation. Translocation exchanges segments between nonhomologous chromosomes; may create fusion genes, disrupt regulation, or cause infertility due to meiotic mispairing.

Answer 157

NHEJ directly ligates broken DNA ends without needing sequence homology; fast but error-prone because nucleotides may be lost or added, often leading to mutations. HR uses a homologous sequence (usually the sister chromatid) as a template, allowing accurate repair with no sequence loss; restricted to S and G2 phases when a sister chromatid is available

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