Biology Exam 2
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What bond holds amino acids together?
What is the structure of an amino acid?
- NH2 ---- C----- COOH
What are the categories of amino acids and their meanings?
- Hydrophobic: Avoids Water
- Polar: Uncharged
- Negatively Charged: Acidic
- Positively Charged: Basic
What is the primary structure?
The sequence of amino acids of a protien
What is the secondary structure? and an example
The "local" fold of a protein (for example beta sheets and alpha helices- both of whose structures are maintained by hydrogen bonds)
What bond is in secondary structure?
What is Tertiary Structure?
The "overall" fold of a protein
What bonds are in tertiary structure?
What structure is the "overall conformation" of a protein?
What is the Quaternary Structure?
The manner in which 2 or more polypeptide chains may come together to form a protein molecule
What is Native Conformation (aka native fold or shape)?
- The fold of a protein in its natural stage
- ---> for example within the cell
How many amino acids are proteins made up of?
What is the molecular mass (Da) of a protein?
- 75-204 Da
- Tryptophan is the largest
- Average is 137 but use 100 to estimate
How does a protein stay folded?
An unfolded protein will move around but when one part is in the right place it will stay there while the other parts move around to find their right places.
What are the forces that determine how proteins fold/keeps the protein in conformation?
- Hydrogen bonds (weak): Attractions between polar amino acids
- Electrostatic Bonds (weak): positively charged amino acids repel eachother; neg charged amino acids repel eachother; oppositely charged amino acids attract
- Hydrophobic Bonds (weak): Hydrophobic amino acids tend to stay together, avoid water, and usually bury themselves in the inner portions of the folded protein
- Vanderwaals Forces (weak): Attraction and repel between atoms and molecules due to fluctuating polarization of nearby molecules
- Disulfide Bond (Strong): Two cysteines can form a strong covalent S-S bond. This is a covalent bond while the others are non covalent
What agents denature proteins?
- Strong or not so strong acids and bases
- --->They disrupt hydrogen bonds
- --->They disrupt the electrostatic bonds
- --->Disrupts hydrphobic bonds
- --->Disrupts all non- covalent bonds (so all except disulfide)
What is a Gain of Function mutation?
- muatations that result in defective proteins that do something harmful and which is different from the normal protein
- ---> a new bad function
What is an example of a disease that results from a mutant protein?
- Sickle cell anemia
- ---> also is a gain of function
What organ does sickle cell anemia affect?
Red Blood Cells
What is the defect of sickle cell anemia?
Hemoglobin (protein that carries oxyen) is defective
What is some info on Sickle cell anemia?
- Affects primary African Americans (fitness benefit from one copy of HbS gene)
- Symptoms: pain, anemia, organ damage
- Lifespan: 5-85 years depending on severity and medical care
What is hemoglobin?
- Protein responsible for carrying oxygen
- abundant in rbc's
What are the parts of hemoglobin?
- Heme: small molecule, contains iron which carries oxygen (iron coated in oxygen)
- Globin: Large molecule, a protein
What are the types of globin?
- Both of these are very similar, but not exactly the same, you can have diseases that affect just your a-globin and b can be fine and vise versa
What is the total composition of a hemoglobin molecule?
- Two identical molecules of a-globin
- Two identical molecules of b-globin
- Four hemes (one for each globin)
What happens with the blood cells in sickle cell anemia
the cells are sickle shaped not round, they dont flow smoothely through the capillaries and can get blocked up, they are also destroyed more quickly by the body resulting in deprivation of oxygen, anemia and organ damage
What part of hemaglobin is mutated in sickle cell anemia?
- The b- globin: a hydrophobic patch is added to b- globins making hemaglobins stick together
- --->the 6th amino acid on the beta chain is changed from a glu to a val creating this hydrophobic patch
When do symptoms of sickle cell anemia appear? why?
- at least 6 months
- bc it takes that time for fetal globin to stop and for you to make your own red blood cells which in infected people will be sickle, not the mothers normal rbcs
What are the benefits of understanding a proteins structure?
- Helps explain its function
- explains certain diseases such as sickle cell
- allow the design of drugs that affect the protein
How is the HIV virus replicated?
it makes strings of protein which are cut by HIV protease into the normal HIV proteins that are then assembled into the actual virus?
What is HIV protease?
- Enzyme that cuts the proteins
- essential for replication
What is the most direct way to stop a virus?
To inhibit a viral protein it needs to survive or replicate?
What were the goals of things to block for drugs for HIV
- 1. First anti-HIV drugs blocked the "target" reverse transcriptase protein which was essential for DNA replication
- 2. The second "target" is to find drugs to block the protease sitting in the active site for the enzyme
What is one drug that is used for HIV?
- Crixivan: it sits in the active site of HIV protease and blocks this protein from binding
- without the protease, HIV cant replicate
What is Bcr-Abl kinase?
- a mutant protein which may be responsible for chronic myologenous leukemia (CML)
- It is purified from CML cells and its structure is determined by X-ray diffraction
- knowing its structure helps for rational drug design
What is a new anti-cancer drug for CML?
- --->lowered number of leukemia cells
- you can relapse if the tumor becomes resistant to the drug
What are the 7 categories of proteins?
- Protein hormones
- Structural Proteins
- Motor Proteins
- Signal Pathway Proteins
What are enzymes?
- Proteins that catalyze chemical reactions in living things
- ---> catalyze- speeds up a Rx without changing itself
What is a substrate?
- The reactants or substance upon which the enzyme acts
- substrates fit precisely into the active site of the enzyme
What is the active site?
the site (place) on the enzyme into which the substrate fits and where it reacts
What is the product?
Substances produced from substrate by the enzyme
Give 5 examples of enzymes, their substrates and products
- Amylase: substrate- starch; product- maltose
- Peroxidase: substrate- hydrogen peroxide; product- water and oxygen
- Beta-Galactosidase (or lactase): substrate- lactose; product- glucose and galactose
- Glycogen Synthestase (triggered by insulin): substrate- glucose (6-P); product- glycogen
- Glycogen Phosphorylase: substrate- glycogen; product- glucose (6-P)
What are protein hormones? examples?
- A hormone that is a protein
- ex: insulin, glucagon
- there are also hormones that are not proteins such as adrenaline
What is a hormone?
substance produced by cells that travels through the blood to signal other cells to some action
Name 5 hormone proteins and what they signal for
- Insulin: glucose storage
- Growth hormone: Bone growth
- Erythropoietin: Red blood cell formation (given to anemics and chemotherapy patients)
- Thyroid Stimulating Hormone: stimulates thyroid
- Thromobpoietin: Platelet formation
What are receptors?
Proteins found usually on the surface of cells (sometimes within cells) that bind signal molecules (hormones, neurotransmitters, growth factors) and trigger the cells responses
What is a ligand?
Another word for a signal molecule that fits into a receptor
Examples of receptors?
Insulin binds to insulin receptors (on liver, muscle, etc) which triggers glucose uptake into these cells
What is unique about each receptor?
- A given receptor will only bind to its particular molecule
- --->ex: insulin receptor will only bind to insulin
What are some key points of receptors?
- Usually found on cell surface
- Specific- bind to one particular molecule/ion
- Can be active (on/open) or inactive (off/closed)
- Typical signal molecules are hormones, growth factors, neurotransmitters, cytokines (like hormones but dont need to travel by blood), and chemokines(chemical attractants for cells)
- When receptors are defective, disease usually resultsfor example cancer
What is aceylcholine?
- neurotransmitter released by neurons. the vesicles in the neuron move to the surface of the terminal and pop releasing these neurotranmitters.
- it is released and binds to its acetylcholine receptor in muscle cells
What is unique about acetylcholine?
- it is a receptor and a carrier becuase it is a channel that allows sodium to enter
- it is normally a closed carrier but it opens up when aceytlcholine binds to it and allows Na+ to enter the cell
How does acetylcholine relate to muscle contraction?
the neurotransmitter binds to the receptor (A quarternary structure) in muscle cells and triggers muscle contraction
What blocks Acetylcholine?
- Cobratoxin fits into the acetylcholine receptor and blocks it from binding resulting in paralysis
- Curare does this too, this was used in poison darts for south americans to paralyze respiratory muscles of prey, however non toxic if eaten
What is an antagonist?
enemy substance that blocks the signal molecule from binding to the receptor
What are Carrier proteins?
- proteins that carry or transport something from one place or another, usually from outside to inside the cell
- can sit inside the membrane and flip, take the substance and flip back, allowing substances inside, or also act as a channel
Example of a carrier protein?
Aquaporin-1 and porin: form pores in cell membranes allowing water molecules to move through the cell membrane
What are 5 examples of transport proteins and their ligands
- ligand: glucose; transport protein: glucose transport protein
- ligand: fructose; transport protein: fructose transport protein
- ligand: maltose; transport protein: maltose transport protein
- ligand: lactose; transport protein: lactose transport protein
- ligand: phosphate; transport protein: phosphate transport protein
What is protein binding in enzymes?
- active site with substrate
- substrate is chemically altered
What is protein binding in carriers?
- binding site with ligand
- carrier in cell membrane
What is protein binding in receptors?
binding site with ligand witha receptor where the ligand may be taken in by endocytosis and may be destroyed
What are key points of re carrier proteins?
- specific re what they carry, ex only glucose
- May carry something from one place of the body to another ex: hemaglobin
- May change conformation in order to move substance (lactose transport protein does this)
- May act as a channel for a specific substance (such as aquaporin for water)
- May be open or closed
What are structural Proteins? examples?
- proteins that form important structures in or around cells
- ex: tubulin (microtubule protein)
- actin and myosin (muscle proteins)
How can microtubule proteins move things?
- growing longer
- walking like way
What are cillia?
What is the structure of a microtubule?
- 9+2 structure
- the same in all microtubules
- means 9 doublets on edges then 2 central microtubules in the middle
What are key points of structural proteins?
- found in structures such as muscle filaments, microtubules, cytoskeletons, cilia, flagella, etc
- Actin (thin filaments) and myosin (thick filaments) are major muscle proteins that slide over eachother in muscle contraction
- Microtubule protiens such as tubulin assemble into microtubules which move flagella, cillia, and in mitosis, chromosomes (spindle microtubules)
- Collagen is found outside cells and is the glue that holds cells together
- keratin is a tough strucutral protein in rhino horn, fish scales, fingernails, hair, etc
- These proteins can have other functions, can also be enzymes (such as myosin) signal molecules(such as collagen) and carriers (tubulin)
What are motor proteins?
- Protiens that generate movement.
- convert chemical energy into movement
- (atp able to move the heads along active filament or microtubule)
What are signal pathway proteins?
- transmit receptor signal to cellular respose
- between signal protein receptor connection and cells action
What is protease?
enzyme that breaks down proteins by hydrolyzing bonds between amino acids
What is synthase
enzymes that synthesize molecules in anabolic reactions by condensing two smaller molecules togehter
What is kinase?
- enzymes that catalyze the addition of phosphate groups to molecules
- protein kinases are an important group of kinases that attach phosphate groups to proteins
What is enzyme activity?
- the action of an enzyme
- a denatured enzyme loses enzyme activity
- temp (microbes on snow have enzymes that can function in cold) and pH (stomach enzymes are best in acid) affect enzyme activity
What are the ways that enzymes can be regulated?
- Compartmentalization: enzyme can be kept in an organelle until needed (ex- amylase kept in salivary glands until starch present) (Ex: digestive enzymes held in lysosomes)
- Modification of "Activity": attachment of small molecules such as a phosphate can alter the conformation and turn an enzyme on or off (Ex: happens in glucose regulation)
- Cells can decide whether or not to make an enzyme (Bacteria ecoli and betagalactosidase)
What happens in modification of activity?
- possible to take an enzyme and chemically modify it in such a way that it has little to no activity and to later modify it agian to be very active giving it an on/off state
- most common way to do this is add a phosphate (added by kinase) to alter conformation
Why does a phosphate change the fold of the enzyme?
bc its negatively charged so depending on other charges it can change the conformation
Is phosphate the only thing that can be added?
- methyl, acetate, amino groups, etc can be added
What happens when you feast in enzyme and glucose regulation?
When you feast, there is glucose in the blood and insulin sends the signal for glucose uptake. a phosphate is removed as a result of signal transduction pathways making glycogen synthase active and glycogen phosphorylase inactive causing glucose to be converted to glycogen
What happens in glucose and enzyme regulation when you fast?
The pancrese secrtetes glucagon which triggers the addition of phosphate to the proteins making glycogen synthase inactive and glycogen phosphorylase active and then glycogen would be converted to glucose
- Converts glucose to glycogen
- active when phosphate is removed
- inactive when phosphate added
- converts glycogen to glucose
- active when phosphate added
- inactive when phosphate removed
Explain e-coli and their control of enzyme
they have an enzyme (betagalactosidase) that digests lactose but they only use it when lacotse is present because it takes energy. if there is just glucose they will not make the enzyme and just get their nutrition from that
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