Bio exam Flashcards
(128 cards)
1
Q
What are Light-Dependent Reactions?
A
Location: In the thylakoid membranes of the chloroplasts.
Main Purpose: Convert light energy into chemical energy in the form of ATP and NADPH (used in the Calvin cycle).
Process Overview:
- Photons (light energy) excite electrons in chlorophyll molecules in Photosystem II.
- These excited electrons are passed through the electron transport chain (ETC).
- Water molecules are split (photolysis), releasing oxygen as a by-product.
- The excited electrons travel through the ETC, leading to the production of ATP via ATP synthase (this is called photophosphorylation).
- The electrons then reach Photosystem I, where they are re-excited by more light and ultimately used to produce NADPH.
Key Points to Remember:
- Photolysis: Splitting of water molecules to release oxygen, protons, and electrons.
- Photophosphorylation: The production of ATP using light energy through the electron transport chain and ATP synthase.
- Products: ATP and NADPH, which are then used in the Calvin cycle.
- Oxygen is released as a by-product.
2
Q
What is the Calvin Cycle?
A
- Light-Independent Reactions
Location: In the stroma of the chloroplasts (fluid-filled space surrounding the thylakoid membranes).
Main Purpose: To fix carbon dioxide and convert it into glucose using the ATP and NADPH produced in the light-dependent reactions.
Process Overview:
1. Carbon Fixation: CO₂ is attached to a 5-carbon sugar, ribulose bisphosphate (RuBP), by the enzyme RuBisCO, forming an unstable 6-carbon compound that splits into two 3-carbon molecules.
2. Reduction: ATP and NADPH from the light reactions are used to convert the 3-carbon molecules into glyceraldehyde-3-phosphate (G3P).
3. Regeneration of RuBP: Some G3P molecules are used to regenerate RuBP, allowing the cycle to continue.
4. Glucose Formation: The remaining G3P molecules are used to form glucose or other sugars.
Key Points to Remember: - The Calvin cycle does not directly require light but uses the ATP and NADPH from the light-dependent reactions.
- It fixes carbon dioxide into a 3-carbon compound (G3P), which can later be used to form glucose.
- RuBisCO is the key enzyme that catalyzes the fixation of CO₂.
- ATP and NADPH from the light-dependent reactions are crucial in this cycle to produce glucose.
2
Q
What is substrate level phosphorylation?
A
During the metabolic processes for sugar, a phosphate group is removed from a substance molecule and combined with an ADP molecule to form ATP
Phosphorylation means the addition of a phosphate group
Shown an ‘P’ inside a circle
This recycles the hydrolyzed ADP from previous reactions, back into useable ATP
3
Q
What is oxidative phosphorylation?
A
Build up from the pumping of H+ out is a electrochemical gradient, large amounts of positive charges create a chemical gradient
Large H+ concentration creates a chemical gradient
All the electrons from NADH and FADH2 are transferred through a chain of membrane proteins on the inner mitochondrial membrane
Two stages: electron transport chain and chemiosmosis
This helps to drive phosphorylation of ADP to ATP
Electron transport chain: the chain of enzymes and their cofactors in the membrane
The ETC gets more and more electronegative than the last component- this helps to make electrons go through the chain
The final electron acceptor, O2, is one of the most electronegative substances on earth
4
Q
What is an enzyme?
A
- Enzymes are catalysts – these are chemicals that speed up a chemical reaction without being used up in the process
- Most biological processes involve the successful collision between reactant molecules in order for products to form
- To ensure the success of such collisions, enzymes need to become involved
- The molecule that the enzyme acts on is called the substrate molecule.
- Enzymes are very specific for the substance to which they bind
- The site where the enzyme binds to the substrate is called the active site
- The notch in the protein is compatible with the shape of the substrate, such they fit together
- When the two are attached, this creates the enzyme-substrate complex
- Some enzymes require the presence of certain substances before they can work properly – these behave like “switches” that turn an enzyme on and off.
- Enzymes can be inorganic (cofactors) or organic (coenzymes). Vitamins and minerals tend to be inorganic because they are human made. Calcium is also inorganic as calcium is added on. Calcium can be organic if body breaks it down from bones
- organic means it’s made in the body, while inorganic means it must be digested
- cofactors help enzymes
- Enzymes prepare substrates for reaction by changing the substrate, its environment, or both in some way
- Enzymes reduce the activation energy required for a reaction to begin.
- Less energy needed for reactions to occur
5
Q
What is an inhibitor?
A
Molecules that bind to the allosteric or active site of an enzyme and causes a decrease in the activity of that enzyme
6
Q
What is an allosteric site?
A
a site on an enzyme that is not the active site, where other molecules can interact with and regulate the activity of the enzyme
7
Q
What is competitive inhibition?
A
interferes with the active site of the enzyme so substrate cannot bind
8
Q
What is non-competitive inhibition?
A
changes the shape of the enzyme so it cannot bind to substrate.
9
Q
What is an activator?
A
- Non competitive activation
- Molecules can also bind to an allosteric site
- It is a molecule that keeps an enzyme active or causes an increase in the activity of that enzyme
10
Q
What are factors affecting enzyme activity?
A
- An enzyme is a protein.
- If it becomes denatured, it will not function to catalyze the reaction properly.
3 important factors affecting activity:
Temperature
- As temperatures increase, so does the vibrational energy of each atom
- This causes the intermolecular forces holding the protein together to break.
- The result is a denatured protein. In this case, an inefficient enzyme.
- Likewise if the temperature is too low
pH
- Some enzymes function best in acidic environments, others basic ones.
- Example: pepsin thrives in the stomach - pH =2
- Trypsin thrives in small intestines - pH =8
- As pH changes, the enzyme’s amino acid R-groups gain or lose protons (H+), which change their shape.
- this is due to differing intermolecular forces
Substrate Concentration
- If there are more molecules present in solution, there is a higher chance that one will interact with the enzyme
- At a certain point (x), there are not enough enzyme molecules to catalyze all of the substrate molecules.
- The enzyme becomes the limiting factor
11
Q
What is Electrical Nature?
A
- Nerves conduct electrical impulses to carry the message
- By changing the concentration of Na+ and K+ inside and outside of the cell, electric current flows down an axon
12
Q
What is a membrane potential?
A
- difference in charge separation across a cell membrane
- Potential energy
- Conduct due to axon structure
13
Q
What is an action potential?
A
- a change in charge that occurs when gates of K+ channels close and Na+ open after depolarization (caused by a stimulus)
- A nerve impulse (signal) consists of a series of action potentials.
- Nerve cells are polarized because of a difference in charge across the membrane
- inside more negative than outside
Depolarization is when they are less polarized - Membrane potential is less than resting potential
- Inside of cell less negative than outside
When a membrane has a charge imbalance, it has potential energy
- charge imbalance, also called electric chemical gradient, makes potential energy. This energy can be used to allow a electric impulse to move through a neuron
13
Q
What are the releasing hormones?
A
- GNRH- comes from hypothalamus
- after release, anterior pituitary gland releases: FSH and LH both in males and females
- In males, testes begin sperm production which releases testosterone
- In females, ovaries produce estrogen and progesterone
- The Menstrual Cycle: a 28 day long cycle*
- Hormones stimulate the development of the uterine wall and release of an egg from the ovary
- If the egg is not fertilized, the uterine lining is shed (along with the unfertilized egg)
14
Q
What are trp Operons?
A
- negative feedback loop because it’s inhibited and is always on but off if needed
- Trp Operon in E. coli contains five genes that are involved in the synthesis of essential amino acid tryptophan.
- This operon is normally transcribed, until the cell has sufficient tryptophan. Once enough tryptophan is present for normal cell functioning, the extra tryptophan binds to the repressor protein allowing it to attach to the operator and inhibit transcription.
The trp operon is “OFF”
- Regulates genes for tryptophan (an amino acid) production in prokaryotes
- The trp operon is inhibited when high levels of tryptophan are present
- Tryptophan is a co-repressor because it binds with the trp repressor protein and activates this repressor protein (transcription proceeds)
- This complex will the deactivate (turn off) gene expression of the trp operon
The trp Operon is “ON”
- Lack of tryptophan deactivates the repressor and activates transcription via RNA Polymerase
- RNA polymerase transcribes trp operon genes
15
Q
What are Lac operons?
A
- positive feedback loop because it’s not inhibited and is always off but on whenever needed
- An example of an inducible system to regulate gene expression
- The lac operon contains three genes (Z, Y, and A) needed for the breakdown of lactose in E. coli. All three genes are under the control of one promoter. Therefore, they undergo the same level of regulation. When lactose is not present, the lac repressor inhibits transcription.
- CAP = catabolite activator protein (protein that binds to help produce proteins to catabolize, or breakdown, lactose)
- used a lot in research b/c simple, not very big, not complex, grows quickly, this helps to manipulate DNA easier
Lac Operon “OFF”
- When lactose is absent this inhibits lac protein expression. A repressor protein (Lac1 protein) binds to the operator site.
- this blocks RNA polymerase from binding to the promoter
- no β-galactosidase is produced
- Negative feedback loop. In conditions of low lactose, there is increased activity of the repressor protein, which is decreasing the output of this operon.
Lac Operon “ON”
- The presence of lactose acts as an inducer. A derivative of lactose, allolactose binds to the Lac1 protein (repressor) so it can no longer bind to the operator of the lac operon DNA
- RNA polymerase can now bind to the promoter region and transcribe the lacZ, lacY, lacA enzymes
CAP is an activator
- When the cell detects low glucose, it will attempt to increase lactose metabolism and will therefore need these lactose metabolizing enzymes in high amounts.
- In conditions of low glucose, there tends to be high cAMP which binds to the CAP protein and allows it to attach to the CAP site and greatly increase the binding of RNA Polymerase to the promoter
16
Q
What is a cell membrane?
A
- Separates contents of the cell from the extracellular environment
- A phospholipid bilayer, 0.006nm thick
- Fatty acid tails (hydrophobic) point inwards
- Polar head groups (hydrophilic) face inside and outside environment of cell (mostly water)
- Many of the membrane properties can be explained by the functioning of lipids
- Phospholipids are held together by weak intermolecular forces NOT covalent bonds
- Molecules embedded in the membrane can move around freely without breaking structure
- Push phospholipids out of the way
Mosaic: - a variety of macromolecules make up the membrane inside and surface - Proteins, glycoproteins, cholesterol
16
Q
What are Membrane proteins?
A
- Integral membrane proteins are embedded, with hydrophobic ends within the membrane
- all channel proteins are integral proteins, but not all integral proteins are channel proteins
- Peripheral membrane proteins are loosely bound to the surface, and they have a polar surface
- Regulate transport of substances
- Reaction catalysis
- Cell recognition: proteins recognize certain carbohydrate chains. Help differentiate from foreign cells
- Signal reception and transduction: bind hormones and initiate a cellular response
17
Q
What are Channel Proteins?
A
- Facilitated diffusion – protein membranes help aid diffusion without the use of energy
- Channel proteins – forms a channel across a cell membrane, which allows specific ions or molecules to cross the membrane along the concentration gradient
- The shape and size of the hole will determine which ions/molecules will pass through
- Channel proteins allow substances such as Na+ and K
- all channel proteins are integral proteins, but not all integral proteins are channel proteins
- they can have the interior be polar or nonpolar, depending on the lining. The substance coming in needs to be the same polar type as the lining in order to pass through channel protein
18
Q
What are Carrier Proteins?
A
- binds to specific molecules, transport them across the membrane, and then release them on the other side. Thus, the proteins carry the molecules across
- Channel proteins can transport ions or small polar molecules
- The exterior of a carrier protein is usually composed of non-polar amino acids that interact with the non-polar interior of the membrane
- The interior of the carrier protein is lined with amino acids that can bind to the particle to be transported
19
Q
What is Endocytosis?
A
- Process by which a cell engulfs material by folding the cell membrane around it and then pinching off to form a vesicle inside the cell
1.Phagocytosis – involves solid particles
2.Pinocytosis – involves liquid particles
3.Receptor-mediated endocytosis – use of receptor proteins on a portion of a cell that bind with specific molecules outside the cell
20
Q
What is Exocytosis?
A
- Transport method in which a vacuole fuses with the cell membrane and releases its contents outside the cell.
- This is important in plants to construct cell walls
- In animal cells provides a mechanism for secreting and releasing many hormones, neurotransmitters, digestive enzymes, and other substances
21
Q
What is Passive Transport?
A
- The movement of ions or molecules across a cell membrane from a region of higher concentration to a region of lower concentration, without the input of energy.
- The ions or molecules move as a result of a concentration gradient
- A difference in concentration between one side of a membrane and the other
22
What is Active transport?
- The transport of a solute across a membrane against its gradient
- This occurs usually with the aid of ATP (adenosine triphosphate), the main source of energy for cells
- With the aid of water, ATP undergoes hydrolysis to create ADP which releases energy for the cell
23
What is a Endomembrane system?
- contains nuclear envelope, endoplasmic reticulum, golgi apparatus, and vesicles
- the transportation and product-processing section of the cell
- helps to make sure cell's functions are at a restricted to specific regions
- The organelles that are a part of the system are connected to one another either directly or by transport vesicles
1. surface of the rough er, polypeptides are produced by bound ribosomes and extruded into lumen, rather than being released into the cytosol
2. polypeptides travel through lumen to the smooth er, where they are stored and processed. When proteins are ready for transport, pieces of the smooth er pinch off to form vesicles containing the protein
3. vesicles from smooth er travel across the cell to the cis face of the golgi apparatus. The vesicles merge with the membrane of the golgi apparatus and release their contents into the interior. In ga, some proteins are stored and others are modified further.
4. When the modified proteins are ready for transport, pieces of the golgi apparatus pinch off from the trans face to form vesicles. the vesicles transport the proteins to the cell membrane r to other destinations within the cell
24
What is Initiation of DNA replication?
- During S-phase during interphase
- Replication starts at a specific nucleotide sequence called The Origin of Replication
- DNA helicase unwinds the double helix by breaking the H bonds between the complementary base pairs holding the two DNA strands together. It has a hole which has things like teeth that unwind the DNA, unzips DNA. For example, the triple bond between G and C will be broken by helicase
- Behind helicase is the replication fork,
- Single stranded binding proteins (SSBs) keep the individual strands apart by blocking the hydrogen bonding between the bases. Since the strands want to be helicase structure, SSBs help each strand to make the hydrogen bonds not connect
- Topoisomerase II (also called Gyrase)– relieves stress of the unwinding on the parent DNA molecule by cutting and un-twisting the molecule. When unwinding, the ends of the DNA strands will supercoil, which will cause it to break. Can be solved by having gyrase to relieve it by cutting the DNA, usually binds at the ends
- Replication starts at a specific nucleotide sequence - the origin of replication
- As the two strands of DNA are disrupted, the junction where they are still joined is called the replication fork
- In eukaryotes, DNA replication occurs at more than one site at a time, resulting in hundreds of replication forks across a DNA strand. This is important because it speeds up the process.
- When 2 replication forks form, a replication bubble is also formed
- If the helicase is seen on the left, DNA is unzipping on the left and is headed towards the left direction, INTO THE FORK
25
What is elongation of DNA replication?
- DNA polymerase III - main player that adds nucleotides to the new strand of DNA. can only add nucleotides in the 5′ to 3′ direction, and requires RNA primase as starting points, and requires condensation reactions to go through the 5' to 3' direction. RNA primers are the starting site because DNA polymerase III will immediately know that it should combine to it
- DNA is always synthesized in the 5′ to 3′ direction
- The leading strand is built continuously by Polymerase III toward the replication fork, starting with 1 RNA primer
- The lagging strand is synthesized by Polymerase III discontinuously in short fragments in the opposite direction to the replication fork
- These short fragments are called Okazaki fragments which each require RNA primers
- The enzyme Primase lays down RNA primers that will be used by DNA polymerase III as a starting point to build the new complementary strands
26
What is Termination of DNA replication?
- Replication process is completed
- Two new DNA molecules separate from each other
- Replication machine is dismantled
- Occurs upon completion of the new DNA strands
- New DNA molecules separate from each other
- Replication machine is dismantled
- Everything falls off (helicase, DNA polymerase III, etc.)
- The three DNA polymerase proofread the nucleotides
- While elongating DNA, polymerase III proof reads DNA (initial proofread)
- When polymerase I removes RNA primers to add DNA, the second proofreading happens
- The third time happens when DNA polymerase II is at the end to proofread
26
Why do we need RNA Primers?
- Allows DNA Polymerase III to bind to the strand
- DNA polymerase can only add new nucleotides to a free 3′ end of a growing chain of DNA
- DNA polymerase I removes the RNA primers from the leading strand and from the lagging strand’s fragments. It will then fill in the space with DNA nucleotides by extending the neighbouring DNA fragment
- DNA ligase enzyme joins the Lagging strand’s Okazaki fragments into one strand (if making RNA, then it's RNA ligase)
- Synthesis of one strand of DNA (leading strand) proceeds continuously in the 5′ to 3′ direction
- Synthesis of the complementary strand (lagging strand) is more complex because it is running opposite to the leading strand, and DNA polymerase can ONLY add new nucleotides to a free 3′ end
- To solve this dilemma, the polymerase builds the lagging strand using many small pieces called Okazaki fragments
- DNA polymerase I will come and remove the RNA primers at the end of elongation
- On the leading strand, there's only 1 RNA primer. If a bubble, there's 2 on it.
- Primers are always on the 5' end of the newly synthesized DNA
27
What is initiation of translation?
- Small ribosomal subunits bind to the 5′ cap of the mRNA transcript and translation commences
- mRNA codon AUG-codes for methionine amino acid (START)
- tRNA with anticodon UAC, carrying methionine will bind AUG site on mRNA
- Large ribosomal subunit binds the small subunit now, and activates the complex
28
What is elongation of transcription?
- RNA polymerase reads the template strand and adds complementary RNA nucleotides in the 5’-3’ direction
- Thymine (T) is replaced by Uracil (U)
- No Okazaki fragments form
- As soon as this begins, another RNA polymerase can bind to the promoter region and start building another strand of RNA (rapid production of RNA)
- RNA Polymerase can synthesize new strands much faster than DNA Polymerase could during DNA Replication
- RNA Polymerase does not proofread the RNA! This is because when there's a mistake, the RNA turns to protein unlike DNA, which would cause the cell to die if there's a mistake
- During elongation, an RNA polymerase complex moves along the DNA strand, the DNA helix unwinds, and complementary RNA nucleotides are joined together. After the RNA polymerase has passed, the DNA double helix reforms.
28
What is termination of transcription?
- Specific sequence signals the end – STOP sequence
- When RNA polymerases reach this sequence, they detach
- The newly synthesized RNA is released and ready to be processed into mRNA
DNA double helix reforms
28
What is the occipital lobe?
- back of brain
- visual association area
- primary visual cortex (visual input)
28
What is initiation of transcription?
mRNA initiation
- DNA transcription only occurs on one strand: the template strand
- There is no need to transcribe from the coding strand because it is identical to the mRNA being formed (except it has Thymine not Uracil)
- RNA polymerase: The main enzyme that catalyzes the formation of RNA from DNA
- DNA is unwound by RNA Polymerase to expose the template strand
- Also remember that the template strand must be 3’-5’. This allows the mRNA to be built 5’-3
29
What is the adrenal cortex?
(outer layer) - long term stress
Nervous system is NOT impacted
Releases ACTH- adrenal cortex hormone
Produces:
- Glucocorticoids (↑ blood sugar)- Helps to maintain energy, too much is stored as fat, which is why there's a link to weight gain. Also causes suppression of calcium absorption, slow wound healing, muscle weakness.
- Mineralocorticoids (↑ blood pressure)- helps to keep blood flowing because the area that has more minerals will attract water to it, making it more flowy, blood pressure up. Increases sodium absorption in blood
29
What is cortisol?
Raises blood glucose levels
The most abundant glucocorticoid stress hormone. It is produced via long-term stress response. Releasing hormones stimulate secretion of ACTH from the anterior pituitary gland. ACTH is released to stimulate the cortisol release (too much ACTH is a long term stress response). The cortisol breaks down muscle protein into amino acids, which are then removed from the blood by the liver. Glucose is released by the blood. Cortisol can help with breaking down fat cells. Negative feedback loop happens when the increased levels of cortisol helps to suppress ACTH and its release. Cortisol also reduces allergic/inflammatory immune system responses that are caused from damaged tissues.
29
What is the adrenal medulla?
(inner layer) - short term stress
Connection between endocrine + nervous systems
Affects the nervous system because since epinephrine and norepinephrine are released, they re hormones and neurotransmitters that affect it
The production of those two hormones by the adrenal medulla regulate “Right, Flight, or Freeze” response
29
What is elongation of translation?
- Ribosome moves along mRNA from 5’ to 3’, reading the code in triplet codons
When the start codon is in the P site, tRNA has delivered methionine
- Second codon is now in the A site
- Appropriate tRNA delivers the next amino acid in the protein sequence
- Peptide bond is formed between methionine and the second amino acid in the P site
- Then, the Ribosome subunits shift down one codon (moving in 5′ to 3′ direction of mRNA strand)
- mRNA is read 5’-3’
- The polypeptide chain grows while it is in the P site
- The start codon establishes the reading frame – all codons read by the ribosome to form the protein
- Methionine is transferred to the A-site amino acid, the first tRNA exits, the ribosome moves one codon (3 base pairs) along mRNA
- First tRNA goes to pick up another amino acid (met)
- This puts the amino acid chain in the P-site, and frees up the A site for the next tRNA
- As elongation continues, the growing peptide is continually transferred to the A-site tRNA, the ribosome moves along the mRNA, new tRNAs enter, and peptide bonds are formed
- Process of elongation continues until a stop codon is read in the A site
- Stop codons are UAG, UGA and UAA
29
What are post-transcriptional modifications?
mRNA undergoes changes in the nucleus (only mRNA)
Alternative splicing can produce different mRNA molecules
- 5’ Cap and 3’ poly-A tail are purposefully not added
- RNA interference – the regulation of gene expression by small RNA’s (sRNA); it inhibits gene expression by degrading mRNA or inhibiting translation by binding to it, inhibits the mature RNA from making protein
- Small RNA’s (micro RNA) and small interfering RNA can inhibit translation and interact with specific mRNA’s
- if ribosomal subunits attach, where methionine attaches to p site, translation can be blocked by a site. If a site is blocked, only methionine is in, but won't be enough to fold so it won't be functional
30
What is termination of translation?
- Elongation ends when a stop codon is encountered in the A-site
- A release factor enters the A-site and causes the ribosome subunits to disassemble (small and large subunits fall apart) and translation is terminated, releasing the mRNA and newly formed protein
- Protein is folded and modified and then targeted to areas of the cell where it is required
- mRNA can be retranslated, or can be degraded immediately
- The anticodon is also in RNA format
- PROTEIN SEQUENCE IS STILL READ FROM MRNA MOLECULE
30
What are adrenal glands?
pair of organs that regulate stress response and blood sugar levels. They are located on top of the kidneys, and they are connected to them.
deal with short and long term stress response
can deal with epinephrine and norepinephrine
can secrete cortisol
Composed of two layers
30
What is pyruvate oxidation?
- When oxygen is available, the 2 pyruvates produced in glycolysis in the cytosol are transported into the mitochondrial matrix and oxidized to 2 Acetyl-Coenzyme A’s
- 3-Carbon pyruvate is converted into 2-Carbon Acetyl-Coenzyme A complex (Ac-CoA)
- This releases 1 carbon in the form of CO2
- NAD+ is reduced (gains electrons) to NADH
- This reaction is coupled to the release of carbon dioxide
- The 2 carbon acetyl group associates with CoA
- **this produces 2 NADH and 2 Ac-CoA since two pyruvate molecules enter from glycolysis
30
What are the levels in mitochondria?
from outer to inner:
- outer mitochondrial membrane
- intermembrane space
- inner mitochondrial membrane
- Matrix
30
What is the Frontal lobe?
-top front of brain
- general motor association area
- primary motor area
- frontal association area (planning, personality)
- Broca's area (expressing language)
31
What is a nephron?
- The smallest functional unit of a kidney
- Embedded within renal cortex and extending into renal medulla
- Over 1 million per kidney
- Intertwined with capillaries for fast diffusion
- Filters various substances from blood, transforming it to urine
- 3 main regions: filter, tubule, collecting duct
31
What happens when you are jump-scared?
1. Stimulus occurs, the Amygdala interprets images and sound as stressful, which sends distress signal to hypothalamus
2. Hypothalamus activates the sympathetic nervous system via autonomic nerves, carrying signal from hypothalamus to adrenal medulla glands, bypasses pituitary gland and through spinal cord
3. Neurons stimulate adrenal medulla to secrete epinephrine and norepinephrine
- remember: adrenal medulla is responsible for making epinephrine and norepinephrine, NOT BRAIN
4. Triggers stress response – increase body activity
Results:
- Rapid release and effects due to nervous system control
- Effects last many times longer than nervous system effects
31
What is the parietal lobe?
- top of brain
- primary somatosensory area
- taste
- general sensory association area
31
What is the krebs cycle?
The cyclic metabolic pathway that oxidizes acetyl-CoA and breaks it down
- It converts released energy to be stored as ATP, NADH, and FADH2.
- Occurs in the mitochondrial matrix
- 2 ATPs produced (substrate level phosphorylation) (1 in each turn of the Krebs cycle)
- 6 NADH produced (3 in each turn of the Krebs cycle) - 2 FADH2 produced (1 in each turn of the Krebs cycle
31
What is the temporal lobe?
- both sides of brain (left and right)
- smell
- auditory area (hearing input)
- auditory association area
- facial recognition area (on inner side of cortex)
- Wernicke's area (understanding language)
31
What is lactate fermentation?
- Pyruvate is converted to lactate (or lactic acid) in the absence of oxygen
- Reacts with NADH to oxidize to NAD+
- Lactate is acidic and must be transported out of cells to protect the surrounding tissue
- *Lactic Acid contributes to the burning and soreness you feel in your muscles as you work out*
31
What is glycolysis?
- the metabolic pathway that breaks glucose down to 2 pyruvate molecules
- The 2 Pyruvates are passed onto the next cycle for further processing
- There are 10 reactions that occur during glycolysis
- Glycolysis occurs in the cytoplasm and the products proceed into the mitochondria for further breakdown
- ATP (energy) is both used (2) and produced (4)
- NADH and FADH2 (electron carriers) are produced
- The overall process for glycolysis from start to finish uses 2 molecules of ATP and produces 4 molecules of ATP for a net reaction of 2 ATP
- The next step is entirely dependent on the presence of oxygen.
- The role of glycolysis is NOT ATP production, it is the preparation phase for the next pathways
- glucose is broken down to pyruvate, which is then processed for ATP
31
What is ATP synthase?
- ATP is formed (oxidative phosphorylation)
- As the H+ re-enter the matrix through special protein channels that are coupled with ATP synthase (Fo subunit)
- It spins at high speed, creating enough energy to phosphorylate ATP molecules (F1 subunit), integral membrane protein
- potential energy gets converted to kinetic energy to make F0 spin. That kinetic energy gets converted back to potential energy in F1. This happens by having proteins come into the F0 subunit. After the energy gets converted back to potential in F1, protons go to the matrix. That proton was with the protein, but it went away into the matrix. The energy in F1 makes ADP and Pi form to make ATP, which uses that energy as storage (potential energy)
31
What is complex 4?
Cytochrome oxidase
31
What is oxidative phosphorylation?
- Electrons from NADH and FADH2 are transferred through a chain of membrane proteins on the inner mitochondrial membrane
- This occurs in 2 stages:
*The Electron Transport Chain
*Chemiosmosis
- This process drives the phosphorylation of ADP into ATP
- The chain of enzymes and their cofactors in the membrane is called the Electron Transport Chain
- Each component of the ETC is more electronegative than the previous
- This is what drives the electron transfer down the chain
- The Final electron acceptor, O2, is one of the most electronegative substances on earth
31
What is chemiosmosis?
- H+ ions diffuse across the membrane, down the electrochemical gradient
- Just like water built up behind a dam, it is now ready to flow when a specific gate is opened
- This turns a turbine, which drives a generator to convert kinetic energy into electrical energy
- Similarly, to water in a dam, this gradient drives the phosphorylation of ADP to ATP
- The ‘gate’ that allows H+ is an enzyme called ATP Synthase
- The process of phosphorylating ADP to ATP, driven by hydrogen ions moving down the electrochemical gradient through ATP Synthase
- 1 NADH through the ETC Yields 3 ATP
-1 FADH through the ETC Yields 2 ATP
31
What is complex 1?
NADH reductase
31
What is complex 2?
succinate dehydrogenase
31
How is urine released?
- Wastes filtered by the kidneys travel along the ureters to the urinary bladder
- A urinary sphincter is found at the base of the bladder
- When the sphincter relaxes, urine enters the urethra and it is voided
31
What is complex 3?
Cytochrome reductase
32
What are the regions of the kidney?
Renal Cortex
- Outer layer
Medulla
- Inner layer
- Contains cone shaped tissue
Renal Pelvis
32
What is ethanol fermentation?
Acetaldehyde + NADH Ethanol
- Some bacteria and yeast function under aerobic and anaerobic conditions
- Facultative aerobes
- 2 step anaerobic process:
- pyruvate converted to acetaldehyde (removal of CO2)
- Acetaldehyde oxidizes NADH to NAD+, forming ethanol (drinking alcohol)
32
What are the functions of the kidney?
- Regulate water-salt balance
- Maintain pH
- Release hormones to maintain homeostasis
32
What are kidneys?
- Kidneys form urine to eliminate waste material carried by the blood
- Bean shaped, reddish brown color
- Renal artery enters kidney, brings blood in
- Renal vein and ureter exit kidney, brings filtered/good blood out
- Kidneys regulate acid-base balance in blood
- Kidneys monitor blood pH @ 7.4
- Human urine usually has pH of 6 or lower
- Because of uric acid in urea makes pee acidic
- Anything nitrogenous makes urine more acidic
- Kidneys secrete two hormones: calcitriol (Vitamin D as a hormones) and erythropoietin
- Calcitriol active form of Vitamin D, promotes calcium absorption from digestive tract
- Erythropoietin stimulates red blood cells in response to increased oxygen demand
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What is reabsorption?
Reabsorption occurs until the threshold level of a substance is reached, excess NaCl remains in the nephron and is excreted with the urine.
32
What are capillary pores?
- in the glomerulus/ loop of Henle
- The pores are too small to allow proteins, red blood cells through… only metabolic waste (ions, small molecules, urea etc.)
- The pressure here is 4x greater than anywhere else – forces materials along a concentration gradient (high to low) and into the Bowman’s capsule
32
What is a tubule?
- Bowman’s Capsule connected to a narrow tubule
- Tubule has 3 sections: proximal tubule, descending loop of Henle, ascending loop of Henle, distal tubule
- surrounded by capillaries
- if too much sodium, it will diffuse into nephron through capillary
- there can still be diffusion
- Uses a concentration gradient to absorb and secrete materials into/out of urine
32
How does blood reabsorb into nephrons?
- The transfer of essential solutes and water from the nephron back into the blood is called reabsorption. occurs at the loop of Henle
- Both active (glucose, amino acids, NaCl) and passive transport (water via osmosis) help reabsorb the fluid back into the blood.
32
What is absorption of salts?
- Water will diffuse (osmosis) to the area with higher salt concentration
- Aldosterone – stimulates salt reabsorption at the distal tubule
- Excrete K+
- Reabsorb Na+
- This affects the water balance, as water follows solute concentrations
- Recall that aldosterone is a mineralocorticoid (hormone).
- The Loop of Henle uses reabsorption of solutes to move water into and out of vessels
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What is a duct?
- Tubule empties into collecting duct
- Functions as water-conservation device
- if too much water, it can leave to go to body
- if too concentrated, water can come in
- only reabsorb or secrete water
- Filtrate that remains here is a suspension of water and solutes
- Called urine at this point
- Highly concentrated, as little water as necessary unless there is an excess in the body
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How does blood supply affect nephrons?
- Afferent arterioles branch off the renal artery and supplies the nephrons with blood
- Afferent arterioles branch into a capillary bed known as the glomerulus
- Blood leaves the glomerulus via efferent arterioles to the capillaries that wrap around the nephron
- The glomerulus is surrounded by the cup-shaped Bowman’s capsule
- The Bowman’s capsule, afferent arterioles and efferent arteriole are in the renal cortex
- Wastes (“future urine”) enter the Bowman’s capsule from the blood. (Diffuse in)
- The capsule tapers off into the proximal tubule, which carries the filtrate to the loop of Henle
- The loop of Henle descends into the medulla and connects to the distal tubule and then into the collecting ducts
- The collecting ducts collect urine from many nephrons, which merge in the renal pelvis
- This is how Substance-filled blood enters the kidney, and gets filtered from here.
- The waste will diffuse out of the blood into the Bowman’s Capsule, which is filled with fluid (due to concentration gradient)
- The Bowman’s Capsule is thin where it is in contact with the cells to allow for rapid diffusion
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What is filtration
- The movement of fluids from the blood into the Bowman’s capsule is called filtration.
- Each nephron of the kidney has an independent blood supply, and blood moves through the glomerulus, a high pressure filter.
- The pressure in the Bowman’s capsule is about 4x as much as in normal capillary beds.
- Plasma proteins, blood cells, and platelets are too large to move through the walls of the glomerulus.
- Smaller molecules pass through the walls and enter the nephron.
- high pressure
- red blood cells, platelets, and protein cannot get through
32
What is reabsorption into blood?
The transfer of essential solutes and water from the nephron back into the blood is called reabsorption. occurs at the loop of Henle
If none of the filtrate are reabsorbed, you would form 120mL of urine each minute, and would be requiring 1L of fluids every 10 minutes to maintain water balance.
Both active (glucose, amino acids, NaCl) and passive transport (water via osmosis) help reabsorb the fluid back into the blood.
32
What is secretion?
- The movement of materials from the blood back into the nephron is called secretion.
- through capillaries
- happens throughout nephron
- Nitrogen-containing waste (from metabolism of proteins, creating ammonia NH3), excess H+ ions, and other minerals are excreted via urine
- Secretion occurs by active transport –molecules are shuttled from the blood into the nephron
33
What are protein hormones?
Also called water-soluble hormones
dissolve in water
contain amino acid-type groups with polar side chains
Ex. epinephrine, hGH, thyroxine, and insulin
Cannot diffuse across cell membrane because it is a large polar molecule
Binds to receptor protein on surface of target cell
Triggers a series of reactions that amplifies the signal inside the cell
Called a cascade
33
What is water reabsorption?
- Regulated by ADH (antidiuretic hormone)
- Released from anterior pituitary gland when blood becomes too concentrated (too many solutes) (dehydrated) – detected by osmoreceptors
- Increases permeability of distal tubule and collecting duct to reabsorb water
- water is reabsorbed by blood
- pee is dark
If too concentrated in blood:
- too little h2O in blood
- too much osmotic pressure
- release ADH
- osmoreceptors in hypothalamus sense too much osmotic pressure
- sends signal to anterior pituitary gland, releases ADH
- makes kidneys more permeable, water is being reabsorbed
- Osmotic pressure is normal
If too dilute in blood:
- too hydrated
- low osmotic pressure (low solute)
- osmoreceptors in hypothalamus send signal to anterior pituitary gland to stop releasing ADH
- diarrhea
- blood secretes more water
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What is PCR?
Polymerase Chain Reaction
Automated method for amplifying specific regions of DNA from very small quantities
- Produces billions of copies of a section of DNA in a test tube within hours
- Very important in Forensics = amplify a very very small amount of a suspects DNA into a quantity that is testable for distinguishing markers
The Polymerase Chain Reaction
1. Double strand DNA heated to 94-96⁰C to denature it into single strands (split it up)
2. Cooled to 50-60⁰C to allow RNA primers to anneal(bind) to the strands
3. Heated to 72⁰C, where a special heat-resistant DNA polymerase (Taq Polymerase) can optimally function and add complementary nucleotides from the primers
4. Cycle repeats 30 cycles to produce 1 billion copies of initial strand
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What are steroid hormones?
made of carbon-hydrogen ring structures
lipid based hormones (a.k.a. lipid soluble)
ex. testosterone, estrogen, cortisol
Can easily diffuse through cell membranes
Bind to receptor proteins inside the nucleus
Hormone-receptor activates gene expression and synthesis of specific mRNA
enter in through cell membrane and target nucleus
1. Hormone diffuses through membrane because it is lipid soluble
2. Hormone binds receptor protein
3. Hormone-receptor complex enters nucleus and activates gene (transcription occurs)
4-6. mRNA is translated to protein by the ribosome in cytoplasm
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What is the hypothalamus?
- Part of the endocrine system (hormone system) that maintains homeostasis throughout the body
- controls everything in the body like hormones
Often serves as the coordinating/control centre:
- Receives messages from sensors/monitors
- Initiates a hormonal/nervous response
- sends response to pituitary gland, which sends the information to the rest of the body
- If there was a tumor that was affecting most of the body, it's most likely to be pushing against the hypothalamus
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What is the anterior pituitary gland?
- At the front
- Hormone synthesizing gland
- Produces tropic hormones: TSH, ACTH, PRL, hGH, FSH, and LH
- makes its own hormones, stimulating/tropic hormones
- Releasing hormones from hypothalamus go to the anterior pituitary and stimulate/inhibit the release of tropic hormones into the bloodstream
33
What is the pituitary gland?
- connected and controlled by hypothalamus and sends information to the rest of the body
- main gland that controls a lot of the homeostasis within the body.
- releases tropic hormones (signaling target glands to release other hormones)
- Made up of two lobes: anterior and posterior
- Attached to hypothalamus by neurosecretory cells
- A neurosecretory cell is a neuron that releases a hormone at the final synapse. This hormone diffuses into the bloodstream through the capillaries
- Releases tropic hormones for: Metabolism, Growth, Development, Reproduction
33
What is the posterior pituitary gland?
- At the back
- Part of the nervous system
- Does not produce hormones
- Stores and secretes the hormones ADH and oxytocin, which are produced in hypothalamus
- Antidiuretic hormone (arginine vasopressin) tells kidneys how much water to conserve.
- Oxytocin = love hormone, released during labor/reproductive purposes
- The hypothalamus secretes a releasing hormone into the anterior pituitary to tell it to release a hormone
- Anterior pituitary releases 2nd hormone into bloodstream
- Stimulates a target gland somewhere else in the body to release 3rd hormone into blood
- 3rd hormone travels to another cell and produces an effect
- Build up of 3rd hormone prevents further release of 1st two hormones
34
How are insulin and glucagon different?
The pancreas functions in the digestive system to secrete enzymes for digestion and also endocrine system to release insulin and glucagon
Has beta cells (for releasing insulin) and alpha cells (for releasing glucagon)
Over 2000 clusters of endocrine cells, called the islets of Langerhans, scattered throughout the pancreas
secret antagonistic hormones:
insulin (secreted by beta cells) lowers blood glucose by making target cells more permeable to glucose. If blood sugar is too high, it happens after eating a meal, beta cells in pancreas release insulin which goes to the liver so that it stores extra glucose as glucagon. Insulin also goes to muscle cells to uptake extra glucose. Insulin goes to fat tissue to store extra sugar, this lowers blood sugar back to normal
glucagon (secreted by alpha cells) increases blood glucose by stimulating the liver to convert glycogen to glucose. If blood sugar is too low, alpha cells in pancreas release glucagon, which goes to fat tissue to break it down to glucose. also goes to liver to break down glycogen
Recall: calcitonin and PTH are also antagonistic hormones (opposite effects)
35
What is logistic growth?
the growth pattern exhibited by a population for which growth is limited by carrying capacity or limited resources.
36
What is exponential growth?
the growth pattern exhibited by a population growing at its biotic potential. A population growing at biotic potential tends to grow exponentially. Bacteria in a lab tends to grow exponentially since it grows under ideal conditions
37
What is catabolism?
- metabolic pathway
- process of breaking down compounds into smaller molecules to release energy
- Our body works to break down the glycogen polymer into glucose monomers for use (catabolism, or catabolic reaction)
- when eating lots of food, you release energy
- like a polymer to monomer
38
What is anabolism?
- metabolic pathway
- the process of using energy to build large molecules from smaller molecules
- condensation is anabolism, but anabolism is not only condensation
38
What are photosystems?
clusters of proteins and pigments (like chlorophyll) in the thylakoid membranes of chloroplasts that play a crucial role in photosynthesis. They absorb light energy and use it to generate high-energy electrons, which are key to producing chemical energy for the plant. Z diagram because of how energy flows in this system
39
What is photosystem II?
(PSII, p680):
- Function: PSII absorbs light energy to excite electrons, which are then passed along the electron transport chain.
- Key Role: It also splits water molecules (photolysis), releasing oxygen, protons, and electrons.
- Outcome: The excited electrons from PSII eventually help in the production of ATP (through a process called photophosphorylation).
40
What is photosystem I?
(PSI, p700):
- Function: PSI absorbs light energy to excite electrons as well, but it specifically contributes to the reduction of NADP+ to NADPH.
- Key Role: The excited electrons from PSI are used to help form NADPH, which is essential for the Calvin cycle, the next stage of photosynthesis.
- Outcome: PSI primarily contributes to the production of NADPH, which pairs with ATP to drive the synthesis of glucose.
40
What are C3 plants?
Process: C3 plants use the Calvin cycle to fix CO2, which directly enters the cycle as the first stable product (a 3-carbon compound, hence the name "C3").
Timing of CO2 Fixation: CO2 is fixed during the day when the stomata (tiny pores on the leaf surface) are open to allow gas exchange.
Stomatal Opening: Stomata are open during the day to take in CO2 for photosynthesis, which also leads to water loss through transpiration.
Efficiency in Different Environments: C3 photosynthesis works well in cooler, moist environments with moderate sunlight.
Water Use: C3 plants tend to lose a lot of water due to open stomata during the day, making them less efficient in hot, dry climates.
Examples: Most temperate plants (e.g., wheat, rice, and soybeans).
40
What are CAM plants?
Process: CAM plants also use the Calvin cycle, but they store CO2 as organic acids (like malic acid) at night and release it during the day to use in the Calvin cycle.
Timing of CO2 Fixation: CAM plants fix CO2 at night when stomata are open. This allows them to avoid water loss during the hot, dry daytime.
Stomatal Opening: Stomata open at night to take in CO2, and close during the day to prevent water loss.
Efficiency in Different Environments: CAM is highly efficient in hot, dry environments (e.g., deserts) where conserving water is critical.
Water Use: CAM plants are much more water-efficient than C3 plants because they take in CO2 at night and close their stomata during the day, minimizing water loss.
Examples: Succulents like cacti, agave, and pineapple.
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What are the differences between C3 and CAM plants?
CO2 Fixation Timing:
- C3: CO2 is fixed during the day.
- CAM: CO2 is fixed at night.
Water Efficiency:
- C3: More susceptible to water loss since stomata remain open during the day.
- CAM: More water-efficient as stomata remain closed during the day and open only at night.
Environmental Adaptation:
- C3: Best in cooler, wetter climates.
- CAM: Best in hot, dry, or arid environments.
41
What is DNA helicase?
- DNA helicase unwinds the double helix by breaking the H bonds between the complementary base pairs holding the two DNA strands together. It has a hole which has things like teeth that unwind the DNA, unzips DNA. For example, the triple bond between G and C will be broken by helicase
- Behind helicase is the replication fork,
- Single stranded binding proteins (SSBs) keep the individual strands apart by blocking the hydrogen bonding between the bases. Since the strands want to be helicase structure, SSBs help each strand to make the hydrogen bonds not connect
42
What is DNA gyrase?
- Topoisomerase II (also called Gyrase)– relieves stress of the unwinding on the parent DNA molecule by cutting and un-twisting the molecule. When unwinding, the ends of the DNA strands will supercoil, which will cause it to break. Can be solved by having gyrase to relieve it by cutting the DNA, usually binds at the ends
42
What is the hGH hormone?
Human Growth Hormone
Secreted by anterior pituitary
Affects almost every body tissue
Most effects are tropic
For example, it stimulate liver to secrete growth factor hormones
Stimulates growth of bone and cartilage, protein production
43
What is mimicry?
A species evolves to look like another species
Batesian mimicry: when a harmless species mimics a harmful species. The harm can be poison or attacking, while the harmless has neither.
Mullerian mimicry: two harmless species that have the same predators look alike
44
What is camouflage?
An organism mimics its environment to look invisible to predators
44
What is carrying capacity?
maximum population size that a habitat can sustain indefinitely
44
What is Fecundity?
The average number of offspring produced by a female member of a population over her lifetime. This helps to control population in a habitat.
45
What are the monomers of carbohydrates?
monosaccharide
- One Sugar
- a carbohydrate composed of between three and seven carbon atoms.
- “They are “simple” sugars such as glucose, fructose, and galactose
- Glucose, fructose, and galactose are isomers of each other
46
What is the linkage for carbohydrates?
Glycosidic bond
- The bond linking each monosaccharide to another
- Forms between the 1-Carbon of one sugar, and the 4 or 6-Carbon of the second
- The 1-Carbon is to the right of the oxygen in the ring
46
What are the functional groups for carbohydrates?
- carbonyl
- carboxyl
- amino
- phosphate
47
What are the polymers of carbohydrates?
- Cellulose: structural support for plant cells
- Starch: main energy storage for plants
- Glycogen: energy reserve
47
What are the monomers for lipids?
Glycerol- a ‘triol’ – molecule that contains 3 hydroxyl groups
Fatty acids:
- a hydrocarbon chain ending in a carboxyl group
- Fatty Acids with double bonds in their structure are called unsaturated fatty acids
–0 double bonds = saturated
–1 double bond = monounsaturated (Cis or Trans)
–2 or more double bonds = polyunsaturated (Cis or Trans)
48
What is the linkage for lipids?
ester and phosphodiester bonds
49
What are the functional groups for lipids?
- ester
- Carboxyl
- Phosphate
- amide
50
What are the polymers for lipids?
Phospholipids
- Is a lipid composed of a glycerol molecule bonded to two fatty acids and a phosphate group with an R group
- *The difference is that a phosphate group replaces the third fatty acid of a triglyceride.
- *The “head” of the phospholipid molecule is polar, while the lower “tail” portion has only nonpolar C-C and C-H bonds.*Thus the head is hydrophilic, and the tail is hydrophobic.
51
What are the monomers for proteins?
Amino acids- They are a diverse group of macromolecules as they vary in shape and size.
*a hydrogen atom
*an amino group
*a carboxyl group
*and a variable R group.
- All amino acids are somewhat polar, due to the polar C=O, C-O, C-N, and N-H bonds
52
What is the linkage for proteins?
Peptide bond
- Amide bond
- In order to form a protein, amino acids are joined by covalent bonds called peptide bonds
- This results in the formation of long polymer chains
- A peptide bond forms between the carboxyl group of one amino acid and the amino group on another
- The link is formed by removing a water molecule
53
What are the polymers for proteins?
Proteins are polymers of amino acids
*Catalyze chemical reactions
*Provide structural support
*Transport substances in the body
*Enable organisms to move
*Regulate cellular processes
*Provide defense from disease
53
What are the functional groups for proteins?
- amino
- carboxyl
54
What are the monomers for nucleic acids?
Nucleotides- composed of a sugar bonded to a phosphate group and a nitrogen containing base.
DNA- A with T, G with C
RNA - A with U, G with C
G and C have 3 hydrogen bonds, while A and T have 2.
55
What is the linkage for nucleic acids?
Phosphodiester bond - covalent bond between 2 nucleic acids
- A bond between the phosphate group of one nucleic acid and the sugar or the next
- this connects one strand, while hydrogen bonding connects two strands together
56
What are the functional groups for nucleic acids?
- phosphate
- nitrogen base
- sugar molecule
57
What are the polymers for nucleic acids?
- DNA is composed of nucleotides containing the sugar deoxyribose
- RNA is composed of nucleotides containing the sugar ribose.
- DNA is the genetic material of living organisms that carry hereditary information and instructions for the organism to carry out
58
What is cellular respiration?
Location: glycolysis occurs in the membrane of the cell, pyruvate phosphorylation and the krebs cycle in the mitochondrial matrix, and oxidative phosphorylation in the inner mitochondrial membrane.
reactants/products: C6H12O6 (s) + 6O2 (g) -> 6CO2(g) + 6H2O (l) + energy
H2 + CO2-> CH4 + H2O (anaerobic)
Organisms: animals, plants, fungi, some bacteria
Type of process: catabolic
58
What are chromosomal mutations?
- A change to the number of chromosomes is always negative, and often lethal
- Eg. trisomy 21 = Down’s Syndrome
- There can also be mutations of entire chromosome sections, which would affect several/many genes (Deletion, Duplication, Inversion, Translocation)
59
What is photosynthesis?
Definition: Photosynthesis is the process by which plants, algae, and some bacteria convert light energy into chemical energy stored in glucose, using carbon dioxide and water.
Type of Process: Anabolic (building molecules using energy)
Location in the Cell: Chloroplasts (specifically in the thylakoid membranes for the light-dependent reactions, and the stroma for the Calvin cycle)
Reactants: Carbon Dioxide (CO₂), Water (H₂O), Light Energy (from the sun)
Products: Glucose (C₆H₁₂O₆), Oxygen (O₂)
Types of Organisms: Plants, algae, and cyanobacteria (some bacteria can also photosynthesize).
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What are silent mutations?
- Mutation that has no effect on amino acid sequence of a protein
- Can be a change of 1 or more base pairs
61
What are mutagens?
Cause mutations
Physical Mutagens
- They physically change the structure of DNA and range from point mutations to loss of large portions of chromosomes
- get into nucleus and change structure of DNA, more prominent than chemical mutagens
- e.g., X rays, UV Rays, Gamma Rays
Chemical Mutagens
- Can enter the nucleus of a cell and induce mutations by reacting chemically with the DNA. They can cause nucleotide substitutions or a frameshift mutation
- e.g., nitrites, gasoline fumes, cigarette smoke, and any other carcinogens (cancer causing substance).
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What are DNA mutations?
- CHANGES IN THE GENETIC MATERIAL OF AN ORGANISM
TWO CATEGORIES:
- Single-Gene Mutations involve changes in the nucleotide sequence of one gene
- Chromosome Mutations involve changes in chromosomes, and may involve many genes
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What are missense mutations?
- Mutation that changes the amino acid sequence of a protein
- This can be good or bad
- It may introduce a new protein that will help an organism survive its environment
64
What is a nonsense mutation?
Mutation that shortens a protein by introducing a stop codon
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What are point mutations?
- Single-gene mutation resulting from a change in a single base pair
- happen at a specific area in the genetic code, happen within the nucleotides
- Can involve substitution/insertion/deletion of a single base pair
- Substitutions have a fairly minor effect on cell due to redundancy of genetic code
- Eg. A mutation of GGA (glycine) to GGG (glycine), will have no effect on the organism
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What is a frameshift mutation?
- Insertion or deletion of nucleotides
- Causes the entire reading frame of genes to be altered (yikes!)
- Causes changes to neighbouring triplets as well
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How to repair mutations?
- Photorepair – A specific repair mechanism that repairs damage to DNA caused by exposure to UV radiation. A photolyase enzyme recognizes the damage, binds to the site and corrects it
- Excision repair – Non-specific repair mechanism whereby parts of damaged DNA are removed and DNA polymerase puts down new/correct nucleotides
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What is gel electrophoresis and fragment migration?
1. Gel is treated with ethidium bromide and added to wells
- The dye binds the backbone of DNA and fluoresces(glows) under UV light
- Helps us to see the DNA on the gel
2. Gel is placed in buffer and electric current is run from cathode(-) to anode(+)
- Negatively charged DNA (due to phosphate groups) will move from the negative end towards the positive end
- Buffer maintains pH of solution (keeps DNA from denaturing)
3. Smaller DNA fragments move faster/further than larger fragments
- They fit through the agarose gel easier
4. Gel is removed from buffer and exposed to UV light
- Ethidium bromide in the DNA backbone glows and allows us to see the DNA
- A ladder is a lane that contains DNA of known size (base pair length)
- We compare the fragments in the gel to this standard
EcoRI
- Each restriction enzyme that we discover is known to recognize a specific sequence
- EcoRI is a restriction endonuclease that will recognize this DNA sequence (notice that it is a palindrome
- Recognition sequence always the same 5’ to 3’
- Restriction fragments with sticky ends form base pairs w/ other single stranded regions with the correct complementary sequence
- This is very specific, as all the nucleotides must match to bond
- Blunt cuts reduce specificity
- No sticky ends that can form complementary base pairs
- Two fragments with blunt end can combine
- Less efficient
- Only 2 nucleotides must match, higher chance that unwanted DNA will bind to this site
