Bio/Biochem Review Flashcards
1
Q
How do catalyts and inhibitors affect reaction rates?
How is ∆G affected by enzymes?
A
Catalysts increase the reaction rate, inhibitors decrease the reaction rate
∆G is not affected by enzymes
2
Q
Name the cellular location and end products (per glucose) for the following:
Glycolysis, pyruvate dehydrogenase complex, Krebs cycle, electron transport, fermentation
A
Glycolysis: Cytoplasm, 2 NADH, 2 pyruvate, 2 ATP (net)
PDC: Mitochondrial matrix, 2 NADH, 2 acetyl-CoA and 2 CO2
Krebs Cycle: Mitochondrial matrix, 6 NADH, 2 FADH, 2 GTP, 4 CO2
Electron Transport Chain: Inner mitochondrial membrane, end product is a proton gradient (30 ATP generated)
Fermentation: Cytoplasm, end products are 2 ATP, 2 lactic acid (muscle) or 2 ethanol (yeast)
3
Q
Name the cellular location and main products of the following biochemical pathways:
Gluconeogenesis, glycogenesis, glycogenolysis, fatty acid oxidation, fatty acid synthesis, and the pentose phosphate pathway
A
All reactions occur in the cytosol besides fatty acid oxidation, which occurs in the mitochondrial matrix
Gluconeogenesis - Glucose-6-phosphate
Glycogenesis - glycogen
Glycogenolysis - Glucose-1-phosphate
Fatty acid oxidation - Acetyl-CoA units
Fatty acid synthesis - 16-C fatty acid (palmitate)
Pentose phosphate pathway - NADPH (oxidative) ribulose-5-phosphate (non-oxidative)
4
Q
Define replication, transcription, and translation. At which stage is protein synthesis primarily regulated?
A
Replication = DNA to DNA
Transcription = DNA to RNA
Translation = RNA into protein
Regulation of protein synthesis if primarily at the level of transcription.
5
Q
What does semiconservative replication mean?
A
After DNA replication, one strand of a DNA double helix is composed of old DNA and the other is composed of newly-synthesized DNA
6
Q
What are the differences between DNA and RNA?
Name 3 types of RNA and their functions
A
DNA is double stranded, thymine, sugar is deoxyribose
RNA is single stranded, uracil, sugar is ribose
mRNA = translated to make proteins
rRNA = needed to make a functional ribosome (Without, cell can’t make proteins, and cell function will be inhibited)
tRNA = carries an amino acid to a ribosome to be incorportated into a growing protein
7
Q
Name at least 5 differences between prokaryotes and eukaryotes
A
Prokaryotes don’t have a nucleus or organelles, have a single circular chromosome, 3 different DNA polymerases and 1 RNA polymerase. Transcription and translation are simultaneous, their mRNA is polycistronic, and there is no mRNA processing
Eukaryotes have a nucleus and other organelles, have several linear chromosomes, 1 DNA polymerase and 3 different RNA polymerases. mRNA is monocistronic, and mRNA must be processed before translation.
8
Q
What is the basic structure of a virus?
A
A virus is a piece of nucleic acid surrounded by a protein shell (capsid)
Viruses are obligate parasites
9
Q
Name three different life cycles of a virus. Which of these is of an animal virus life cycle only?
A
Lytic, lysogenic, productive
Productive is for animal viruses only
10
Q
What is a prion? What is a viroid?
A
A prion is an abnormally folded version of a normal protein that is able to convert other prions to its abnormal form. (Infectious protein)
They are highly resistant to degradation by heat, acids, etc and are implicated in degenerative brain disorders
Viroids are short, single stranded RNAs that have highly complimentary sequences. They are plant pathogens that are though to affect protein synthesis by binding and silencing normal cellular RNAs.
11
Q
Name the 3 shapes of bacteria
A
Coccus (round)
Bacillus (Rod-shaped) (E. Coli is a gram negative bacillus)
Spiral (Spirochete)
12
Q
Define obligate aerobe, facultative anaerobe, tolerant anaerobe, and obligate anaerobe
A
Obligate aerobe - must use oxygen to survive
Facultative anaerobe - prefers oxygen, but will ferment to survive
Tolerant anaerobe - can tolerate oxygen, but ferments to survive
Obligate anaerobe - will die in the presence of oxygen
13
Q
Name the cell organelles and their functions
A
Nucleus = control center, contains DNA and is the site of replication and transcription
Ribosome = protein synthesis
Rough ER = holds ribosomes that are synthesizing secreted or membrane proteins, functions in protein modification
Golgi apparatus = sorts and packages proteins, protein modification
Lysosome = digestive enzyme container
Mitochondria = energy production
Smooth ER = lipid metabolism
Centrosome = mitotic spindle formation
Peroxisome = eliminated free radicals
14
Q
What are the four main colligative properties?
What do they depend on?
A
Vapor-pressure depression, boiling point elevation, freezing-point depression, and osmotic pressure.
They depend only on the number of solute particles in a solution and not on the type of particle
15
Q
What is the difference between osmosis and diffusion?
What is the van’t Hoff factor?
A
Osmosis is the movement of water from an area of low solute concentration to an area of high solute concentration
Diffusion is the movement of solute from an area of high solute concentration to an area of low solute concentration
The van’t Hoff factor is the ionizability factor, it tells how many ions one unit of substance will produce in solution
16
Q
What types of molecules can easily cross the plasma membrane? Which cannot?
A
Small, nonpolar molecules can easily cross the plasma membrane (Oxygen, CO2)
Large, and/or polar molecules cannot
17
Q
What is an oncogene?
What is a tumor supressor gene?
A
An oncogene is a mutated proto-oncogene that are permanately active.
Proto-oncogenes regulate the cell cycle, and activate it during times of development, growth, or healing.
The cell cycle is permanently on, and cell growth and division occurs without control. Gain of function mutation
Tumor suppressor genes code for proteins to slow or stop the cell cycle until DNA damage is repaired. If DNA is not repairable, they trigger apoptosis. Loss of function mutation
18
Q
Name the stages of mitosis and describe the location of the chromosomes in each.
What is the end product of mitosis?
Where is there heavy regulation?
What is the difference between mitosis and meiosis?
A
Prophase = replicated chromosomes condense in a deteriorating nucleus (Build spindle, condense DNA, break down nuclear membrane)
Metaphase = chromosomes randomly align at the cell center
Anaphase = separate sister chromatids by pulling at the centromeres (Cytokinesis begins)
Telophase = Reverse prophase. Decondense DNA, break down the spindle, and rebuild the nuclear membrane. Finish cytokinesis
DNA replication occurs during the S phase of interphase
The end product of mitosis is two daughter cells that are identical to each other and identical to the parent cell
There is heavy regulation at the G1-S phase, because the cell isn’t going to replicate if it doesn’t need to.
Mitosis is the division of s**omatic (body) cells, meiosis is the division of gametes (germ cells)
19
Q
Name the stages of meiosis and describe the location of the chromosomes in each.
When is the cell considered to be haploid?
What is the end result of meiosis?
A
Prophase I - Build spindle, condense DNA, break down nuclear membrane (Synapsis - pairing of homologous chromosomes/Crossing over occurs - DNA exchange) (Specific) *Longest phase of meiosis
Metaphase I - Tetrads randomly align at the cell center. (In mitosis it would be individual chromosomes)
Anaphase I - separate homologs partners, pulled to opposite sides of the cell. Begin cytokinesis
Telophase I - New nucleus forms. (Possibly reverse mitotic prophase)and finish cytokinesis
Prophase II, metaphase II, anaphase II, and telophase II = chromosome movements are identical to movements during mitosis, but the amount of DNA is reduced by half. (starting with less)
Cell is haploid after telophase I
Is diploid during G1 and G2
4 cells that are very different from each other and from the parent cell
20
Q
Define gene, traitr, allele, genotype, and phenotype
A
Gene = piece of DNA that codes for some product
Trait = physical characteristic of an organism
Allele = version of a gene
Genotype = combination of alleles an organism has
Phenotype = physical characteristics of an organism dictates by alleles
21
Q
State the rules of multiplication and addition.
How can they be used?
A
Rule of multiplication: probability of A and B = (Prob A) x (Prob B)
Rule of addition - Probability of A or B = (Prob A) + (Prob B) - (Prob A and B)
These are used to solve genetic probability problems by reducing them to a series of simple single gene crosses, the results of which can be combined using the rules.
22
Q
What are the outcomes of the four basic single gene crosses?
A
- Homozygote x Homozygote = 100% same homozygote
- Homozygous dominant x homozygouse recessive = 100% heterozygote
- Homozygote x heterozygote = 50% same homozygote, 50% heterozygote
- Heterozygote x Heterozygote = 25% homozygous dominant, 50% heterozygotes + 25% homozygous recessive
23
Q
Name two ways to determine whether genes are linked
A
If after a cross involving two different genes, the progeny do not match what would be expected ratios for unlinked genes. (The alleles don’t sort independently)
RF value < 50%
Recombination frequency = # recombinants/total progeny x 100
24
Q
What are the two Hardy Weinberg equations?
What are the 5 conditions for these equations
A
Allele frequency: p + q = 1
Genotype frequency: p2 + 2pq + q2 = 1
Large population, random mating, no migration, no mutations, no natural selection
25
What is the basic theory behind evolution by natural selection?
Organisms that are better adapts to an environment will survive better than organisms that are poorly adapted. Because they survive, genes will be passed on to their offspring. Over time, this can substantially alter a population.
26
Describe the basic structure of a neuron
Dendrites send impulses toward the cell body, and axons send impulses away from the cell body
27
Define depolarize, hyperpolarize, and repolarize. What ion channels control the action potential?
Depolarize = move away from rest potential in the positive direction
Hyperpolarize = move away from rest potential in the negative direction
Repolarize = return to rest potential
Voltage gated sodium (depolarize) and voltage gated potassium channels (hyperpolarize/repolarize) control the action potential.
28
Differentiate between the sympathetic and parasympathetic NS. Which system is the adrenal medulla part of?
Sympathetic = fright, fight, flight, and sex - speeds up body processes
(Increases heart rate, respiratory rate, etc) diverts blood flow to skeletal muscle, uses NE as a neurotransmitter in postganglionic neurons.
Parasympathetic = rest and digest; slows down body processes.
Diverts blodo flow to digestive and visceral organs and uses only ACh as a neurotransmitter.
The adrenal medulla is part of the sympathetic division, it produces epinephrine, which can bind to NE receptors to prolong and increase sympathetic effects
29
Name the five classes of sensory receptors, what they respond to, and some examples of each
Mechanoreceptors respond to shape changes (Hearing receptors, touch receptors)
Thermoreceptors = temperature, hot/cold receptors
Nociceptors = pain receptors, are all over the body
Chemoreceptors = chemical changes, smell taste, and CO2 receptors
Photoreceptors = light, rods and cones
30
Describe the anatomy of the eye
* _Iris_ is the colored part of the eye and regulates pupil diameter
* _Lens_ is a biconvex structure that focuses light on the retina
* _Cornea_ is the external transparent layer of the eye
* _Pupil_ is the black opening in the middle of the eye
* _Ciliary muscles_ regulate the curvature of the lens
* _Fovea_ is responsible for visual acuity
* _Retina_ is the layer at the back of the eye that is sensitive to light
* _Optic disc_ = blind spot - place on the retina where the optic nerve forms (no photoreceptors)
* _Optic nerve_ - a bundle of axons leaving the eye toward the brain
31
Describe the anatomy of the ear
The outer ear (pinna) captures sound waves
Waves travel down the auditory canal where they vibrate the tympanic membrane
Vibrations are transmitted through the auditory ossicles (malleus, incus, and stapes) to the cochlea, which houses the basilar membrane and the hearing receptors.
Semicircular canals monitory dynamic equilibrium
32
What is the difference between an endocrine and exocrine gland?
Endocrine secretes hormones directly into the blood
Exocrine secrete various products through ducts onto a body surface or cavity
33
What are the differences between peptide and steroid hormones? Give some examples of each
Peptide hormones are amino acid based, bind to extracellular receptors, are fast-acting and temporary (Adrenaline, insulin, oxytocin)
Steroid hormones are cholesterol based, bind to intracellular receptors, are slow acting and more permanent. (Estrogen, testosterone, aldosterone, cortisol)
34
For each of the following hormones, state where they come from, what causes their release, what their target organs are, and their function
Growth hormone, prolactin, TSH, ACTH, FSH, LH, oxytocin, ADH, thyroid hormone, aldosterone, cortisol, estrogen, progesterone, testosterone, insulin, and glucagon
Growth hormone - secreted from the anterior pituitary, is released due to exercise or other hormones, targets all cells, functions in growth and cell turnover
Prolactin - Anterior pituitary, nursing causes release, targets the mammary glands, and produces breat milk
TSH - anterior pituitary, stimulated by low thyroid hormone, targets the thyroid, increases thyroid hormone
ACTH - anterior pituitary, stimulated by low amounts of corticosteroids, targets the adrenal cortex, causes release of corticosteroids
FSH - anterior pituitary, low sex steroids triggers release, targets the ovaries/testes, causes egg/sperm maturation
LH - anterior pituitary, low sex steroids, targets ovaries/testes, stimulates ovulation and the release of progesterone/testosterone
Oxytocin = posterior pituitary, nursing/labor, targets reproductive smooth muscle, labor/milk ejection
ADH = posterior pituitary, stimulated by high blood osmolarity, targets kidney tubules to retain water
Thyroid hormone - thyroid gland, stimulated by low metabolism, targets all cells to increase metabolism
Aldosterone - adrenal cortex, released due to low blood pressure, targets the kidney tubules, to increase sodium retention
Cortisol - adrenal cortex, stimulated by stress, targets the liver, increase blood glucose
Estrogen - released from developing follice, triggered by FSH, targets the uterus and other body cells, functions in lining and female sex characteristics
Progesterone - corpus luteum, stimulated by LH, targets the uterus, maintains lining.
Testosterone - interstitial (Leydig) cells (testes), stimulated by LH, targets sperm/other body cells, functions in sperm production and male sex characteristics
Insulin - secreted from the pancreas due to increased blood glucose, targets all cells to reduce blood glucose
Glucagon - secreted from the pancreas due to low blood glucose, targets the liver to increase blood glucose.
35
State the differences between arteries, veins, and lymphatic vessels in terms of structure, pressure, and fluid movement.
Arteries have a thick muscle layer to regulate flow, high blood pressure, pressure moves blood away from the heart, and is elastic
Veins/lymphatic vessels have a thin muscle layer, lower in pressure, move fluid through body movements, have valves, return fluid to the heart, are not elastic
36
Trace the path of blood from the body, to the heart, to the lungs, back to the heart, and out to the body
Body, superior/inferior vena cava, R atrium. Tricuspid valve, R ventricle. Pulmonary semilunar valve, pulmonary artery, lungs. Pulmonary veins, L atrium, mitral/bicuspid valve, L ventricle, aortic semilunar valve, aorta, body
37
Which two things is blood pressure directly proportional to?
Cardiac output (SV x HR) x Peripheral resistance
38
How do a cardiac action potential and a neural action potential differ?
Neural AP is much quicker (2-3 msec); sharp upward spike due to Na/K channels
Cardiac AP is much longer (300 msec); plateau, Na+ K+, Ca2+ channels
39
Trace the pathway of the cardiac conduction system
SA node, AV node, Bundle of His, Left and Right bundle branches, Purkinje fibers
40
Name the primary functions of plasma, erythrocytes, leukocytes, and platelets
Plasma = transport cells, proteins, etc
Erythrocytes carry oxygen
Leukocytes are our disease defense
Platelets function in blood clotting
41
How are oxygen and carbon dioxide carried through the blood stream?
Oxygen: 3% dissolved in plasma, 97% carried on hemoglobin in RBCs
Carbon dioxide: 7% dissolved in plasma, 20% carried on hemoglobin, 73% carried as bicarbonate ions in the plasma
42
What is the basic structure of an antibody? What is its function? Which cells produce antibodies?
Antibodies bind specifically to a particular antigen and mark it for destruction or removal.
B cells produce antibodies
43
What is autoimmunity?
Autoimmunity is an inappropriate immune reaction targeted at normal body structures
44
Name three processes used by the kidney to form urine, and the region of the nephron in which these processes occur.
Filtration = glomerulus
Reabsorption and recretion = all other parts of the nephron tubule
45
How and where do ADH and aldosterone affect the kidney?
**ADH** makes the **collecting duct** more permeable to water, causing increased water reabsorption
**Aldosterone** allows the distal convoluted tubule to reabsorb sodium
46
When renin is released, how does it affect the body?
Renin is released when blood pressure is low, causing the conversion of angiotensinogen to angiotensin I
Angiotensin I is further converted to angiotensin II by ACE in the lungs.
Angiotensin II is a powerful vasoconstrictor, which raises blood pressure.
Angiotensin II also causes the release of aldosterone to retain sodium
Retention of sodium causes release of ADH and retention of water, causing increased blood volume and increased blood pressure.
47
Name the organs of the alimentary canal, their functions, and the layers of the canal from the lumen outward
Mouth = chew, moisten food, and starch digestion
Esophagus moves food to the stomach
Stomach is our food storage, acid hydrolysis, and protein digestion
Small intestines are the main site of digestion and absorption
Large intestine = water reabsorption and fecal storage
Layers of canal from lumen outward = mucosa, submucosa, circular muscularis, longitudinal muscularis, serosa
48
What are the digestive functions of the liver, pancreas, gallbladder, and salivary glands?
Liver produces bile (emulsifies fat for easier digestion)
Pancreas produces digestive enzymes and bicarbonate to raise intestinal pH
Gallblader stores and concentrates bile (Without, makes it more difficult to digest fats)
Salivary glands produce lysozymes to kill bacteria, amylase to digest starch, and water/mucus to bind/moisten food
49
Describe the steps of the sliding filament theory of muscle contraction
Calcium is required
Myosin binds to actin, pulls actin toward the center of the sarcomere, releases actin **(requiring ATP)**, resets and repeats
50
Name the three muscle fiber types
Red slow twitch, Type IIA fibers, and type IIB fibers (white fast twitch)
51
What are the differences between skeletal muscle, cardiac muscle, and smooth muscle
Skeletal muscle is multinucleate, voluntary, striated, and attached to bones
Cardiac muscle is uninucleate, involuntary, striated, and only in the heart
Smooth muscle is uninucleate, involuntary, nonstriated, and in hollow organs
52
What are the functions of the skeletal system?
Support, protection, movement, mineral storage, and blood formation
53
What is the difference between the conduction zone and respiratory zone?
Conduction zone - air tubes only, no gas exchange
Respiratory zone = gas exchange between lungs and blood
54
How is respiratory (ventilation) rate regulated?
Name the receptors involved
Regulated primarily by the amount of CO2 (as acid) in the blood.
The peripheral (aortic/carotid bodies) and central chemoreceptors
55
What are the differences between spermatogenesis and oogenesis?
Spermatogenesis occurs from puberty to death of males, million of sperm are produced daily, and for mature gametes (sperm) from a single precursor cell
Oogenesis = beings prenatally, meiosis is paused at prophase I, only finished if the oocyte if fertilized, and one oocyte is produced monthly
56
Name and briefly describe the three phases of the uterine cycle and ovarian cycle. Which hormones control which phase?
Uterine cycle:
Menstruation, shed the old endometrium, very low estrogen and progesterone levels.
Proliferative phase: rebuild the endometrium, rising estrogen levels
Secretory phase: maintain and enhance the endometrium, stable levels of estrogen and progesterone
Ovarian cycle:
Follicular phase: build the follicle, controlled by FSH
Ovulation: release the oocyte, controlled by LH
Luteal phase, forms corpus luteum, controlled by LH
57
How long is the embryonic period? The fetal period?
The embryonic period is the first eight weeks after fertilization
The fetal period lasts from the end of the embryonic until birth
58
What is the difference between determination and differentiation?
Determined is when a cell is committed to a particular developmental fate, but may not ahve yet started the path to changing
Differentiation is the process by which a determined cell becomes its final mature version
59
Which structures are part of the endoderm, mesoderm, and ectoderm
Endoderm - inner linings of respiratory, digestive, and urinary tract. Composes all glands
Mesoderm = bond, muscle, blood vessels, and non-gland organs (the heart)
Ectoderm = skin, hair, nails, nervous system
60
What specifically do enzymes do to alter reaction rates?
Enzymes reduce activation energy to speed up reaction rates
61
What is found at the active site of enzymes?
Anything that would stabilize the transition state: ions, charges amino acids, etc
62
How do competitive, noncompetitive, and uncompetitive inhibitors differ by where they bind, and how do they affect Vmax and Km
Competitive: binds to active site, does not change Vmax, increases Km
Noncompetitive: binds to allosteric site, decreases Vmax, no change to Km
Uncompetitive inhibitors: bind to enzyme-substrate complex, decreases Vmax and decreases Km
63
For glycolysis: what happens to the carbon chain? Where does ATP enter and exit? What are the end products? How are they prepared for the Krebs cycle
Six carbons (glucose) is phosphorylated twice, spltiting to 3 carbons and desphosphorylated to form pyruvate
ATP enters twice to phosphorylate glucose
ATP exits when the phosphorlyated carbon chain is split
End products are 2 net ATP, 2 NADH, and 2 pyruvate. Pyruvate must be decarboxylated to enter the Krebs cycle
64
For Krebs: What happens to the carbon chain? Where do you make NADH, FADH2, and GTP? How many NADH, FADH2 and GTP are made per molecule of glucose?
Two carbons (acetyl-CoA) are added to 4 carbons (OAA) to make 6 carbons (citric acid). Is decarboxylated twice and isomerized back to OAA. 2 NADH during decarboxylation, 1 NADH, FADH, and 1 GTP during isomerization
6 NADH, 2 FADH2 and 2 GTP per glucose
65
For electron transport: Where are NADH/FADH2 oxidized? How many ATP are made for each molecule? How are the ATP produced?
NADH is oxidized at the first proton pump in the inner mitochondrial membrane.
FADH2 skips the first proton pump and is oxidized at coenzyme Q
2.5 ATP per NADH, 1.5 ATP per FADH2
ATP is produced when protons move down the concentration gradient back into the matrix across an ATP synthase
66
How many total ATP are made per glucose for aerobic respiration? How many for fermentation?
30 ATP for eukaryotes, 32 for prokaryotes. Total ATP for fermentation = 2
67
What are the end products of fermentation for yeast? For muscle cells?
Yeast = 2 ethanol, 2 ATP
Muscle cells = 2 lactic acid, 2 ATP
68
What are the main steps in regulation for gluconeogenesis, glycogenesis, glycogenolysis, and the pentose phosphate pathway?
Gluconeogenesis: PFK and F-1,6-BPase; an abundance of ATP or lack of glucose stimulated gluconeogenesis
Glycogenesis: stimulated by insulin, stimulates glycogen synthase
Glycogenolysis: Stimulated by glucagon (caused by low blood glucose), which stimulates glycogen phosphorylase
Pentose Phosphate Pathway: regulated primarily by NADPH; high levels turn off the pathway, low levels stimulate it.
69
How do purines and pyrimidines differ in structure? How do they specifically bond DNA
Purines are a double ring
Pyrmidines are a single ring
Cytosine binds guanine (3H bonds)
Thymind binds adenine (2H bonds)
70
Name and define the three types of point mutations. How serious are they? How serious are frameshift mutations? What is a translocation? What do transposons do?
Missense = new amino acid
Nonsense = stop codon
Silent = no change
Missense and nonsense severity depends on where in the protein the amino acid is affected and how drastic the change is
Silent mutations do not affect protein shape or function
Frameshift mutations are usually serious because every amino acid from that point forward is altered
Translocation moves large pieces of DNA from one chromosome to another
Transposon is a jumping gene that can excise itself (or copy itself) from one chromosome and insert itself in another. Depending on where it inserts it can cause genetic dysregulation
71
Name and describe the different types of DNA repair
Direct reversal - enzyme directly fixes a mutation
Homology dependent repair - undamaged strand is used as a template to repair a damaged strand
DS break repair - can repair homologously or join broken ends, regardless if they are the correct ends or not
72
What are some similarties and differences between replication and transcription? Briefly describe how they take place
Similarities - Both occur in the 5' to 3' direction and have definite start sites
Differences - replication is proofread and transcription is not; there is no stop site in replication, and transcription has a definite stop site. There is no primer needed for transcription
Replication begins at an origin, primase puts down an RNA primer. DNA polymerase replicates in both directions away from the origin. One strand leads one legs. The entire molecule is replicated
In transcription, RNA polymerase binds to a promoter, transcription begins at a start site and continues to the stop site. Only one strand of DNA is transcribed.
73
Describe translation. Name the start and three stop codons
mRNA binds to the small ribosomal subunit, the first loaded tRNA binds at the P-site, and then all bind to the large subunit. The next loaded tRNA binds at the A-site, and then a peptide bond forms between first and second amino acids.
This breaks the bond between the first tRNA and the first AA. The entire complex shifts so that the second codon is now on the P-site. This repeats until the entire proton is translated.
Start codon = AUG = methionine
Stop codon = UAA, UGA\< and UAG
4 x # AAs = amount of ATP needed
74
Describe the lytic, lysogenic, and productive cycles
All cycles begin the same way with attachment and injection.
Lytic cycle = viral genome is immediately translated, new viral particles are made, the host cell is lysed to release new viruses
Lysogenic cycle = v iral genome is inserted into the host genome and replicated every time the host cell reproduces. At some point the viral genome is excised and enters the lytic cycle.
Productive cycle = Viral genome is immediately translated, new viral particles are made, and the virus buds out from the host cell and becomes covered in plasma membrane.
75
What problems do +RNA and -RNA viruses have when trying to replicate? What special enzymes do they need?
To replicate +/- RNA viruses must be able to make a strand of RNA from a strand of RNA, which the host cell cannot do. Thus, the viruses need to make a special enzyme (RNA dependent RNA polymerase)
+RNA viruses only need to code for the enzyme since they are essentially mRNA and can be immediately translated
-RNA viruses just carry the enzyme with them since they are the template for mRNA and cannot be immediately translated; the + strand must be made first
76
Classify bacteria by cell wall/membranes, preferred temperature, and energy/nutrient requirements
Gram+ = thick cell wall, inner membrane (purple)
Gram(-) = thin cell wall, inner/outer membranes (more resistant to antibiotics due to periplasmic space)
Thermophiles = hot temps
Mesophiles = medium temps
Psychrophiles = cold temps
Photoautotrophs use light energy and CO2 to make their own carbon chains
Chemoheterotrophs rely on chemical energy (ATP) and consume other organisms to get their carbon chains (humans)
Chemoautotrophs rely on ATP and make their own food (deep sea vent bacteria)
Photoheterotrophs use light energy and eat other organisms (venus fly trap)
Supercript- = bacteria can't do something; can't make arginine, can't metabolize lactose
77
What is the difference between bacterial asexual reproduction and conjugation?
Bacterial asexual reproduction = binary fission, increases population size without mixing up the genetic information
Conjugdation = only purpose is to exchange DNA, does not result in a bigger population
78
Name the three fibers in the cytoskeleton and their functions.
What are tight junctions? Gap junctions?
Microtubules = spindle, flagella, cilia, organelle movement
Microfilaments = contraction
Intermediate filaments = structure and shape
Tight junctions seal space between two cells so that molecules cannot pass between the cells (Intestines, blood brain barrier)
Gap junctions are like protein tunnels connecting two cells that allow cytoplasm and other substances to flow freely (cell-to-cell communication) (the heart)
79
Describe the structure of the plasma membrane
A mosaic of phospholipids (lipid bilayer), cholesterol, proteins (which may pass all the way through or associate with one side) and carbohydrates (Only on extracellular side, attached to proteins or lipids)
80
Define simple diffusion, facilitated diffusion, exocytosis, endocytosis, primary active transport, and secondary active transport
Simple diffusion = molecule crosses membrane according to concentration gradient
Facilitated diffusion = molecule crosses the membrane through a special protein according to concentration gradient
Exocytosis = cell secretes a product from a vesicle
Endocytosis = cell takes up a substance in a vesicle
Primary active transport = cell uses ATP directly to pump molecules against a concentration gradient (Na/K ATPase)
Secondary active transport = relies on Na+ gradient set up by primary active transport to drive co-transport of other molecules across the membrane
81
Describe a basic second messenger system (G proteins)
A molecule binds to an extracellular receptor, which causes an associated G protein on the intracellular side to bind to GTP.
The G protein with GTP bound now activated adenylate cyclase, which causes the production of cAMP
cAMP activates cAMP-dependent protein kinases, phosphorylate enzymes, turning them on or off.
This is also an example of signal amplification, since at every step the number of activated molecules increases and the binding of a single ligand to a receptor results in multiple enzymes being affected.
82
What are the subphases of interphase?
In which phase do nondividing cells remain?
Subphases are G1 S and G2
Nondividing cells (muscle, nerves, etc) stay in G1
83
Briefly describe the process of apoptosis
Apoptosis is triggered when a stressor (toxin, DNA damage) reaches a critical level
Proteins called caspases are involved.
Initiator caspases activate effector caspases, which are digestive enzymes.
Effector caspases cleave cellular proteins and trigger the shrinking of the cell membrane by breaking down the nucleus and cytoskeleton and signal phagocytotic cells that the dead cell is ready to be cleared away
84
What does 2n and 1n mean?
How many chromosomes are in human cells?
2n = diploid (2 homologous copies of each type of chromosome)
1n = haploid (1 copy of each chromosome)
n = # of different types of chromosomes
Humans have 2(23) = 46 total chromosomes
85
In meiosis, when do homolgous chromosomes separate?
At anaphase I
86
Define classical dominance, incomplete dominance, codominance, and epistasis
Classical dominance = One allele is expressed, one is silent.
Incomplete dominance = neither allele is silent, both are expressed as a blended phenotype (flower color)
Codominance = neither allele is silent, both expressed equally and distinctly (blood type AB)
Epistasis = suppression of the effect of a gene by a nonallelic gene (Baldness and hair color)
87
What is a testcross?
A cross between a homozygous recessive and an unknown genotype
88
Why do sex-linked diseases and conditions affect males more frequently than they effect females?
If a disease is on the Y chromosome, only males have a Y
If a disease is on the X chromosome, males only have one X, so whatever they have is expressed. (Females have two, so one good X and compensate for a bad X)
89
State Mendel's Law of segregation and the Law of Independent Assortment
Law of segregation = alleles are separated during meiosis
Law of independent assortment = how alleles for one gene are separated has no bearing on how alleles for other genes are separated
90
When can you suspect that two genes are linked?
What is the recombination frequency of linked genes?
After a cross between two difference genes, the expected Mendelian ratios are not what would be expected between unlinked genes. In other words, the alleles do not sort independently.
Or when the RF \< 50%
RF = (# recombinants)/(total offspring)
91
What is rest potential and how is it maintained?
Rest potential is the potential difference of -70 mV across the cell membrane
It is maintained by the **Na/K+ ATPase** and the **K+ leak channels**
92
What is the difference between **absolute** and **relative refractory periods?**
Absolute = absolutely impossible to fire a second action potential; Na channels are **inactivated,** the cell is in positive potentials.
Relative = possible, but difficult to fire a second AP; Sodium channels are now **closed;** the cell is **hyperpolarized** and farther from threshold.
93
Describe transmission at a chemical synapse. How can the postsynaptic neuron be excited or inhibited?
An AP in the presynaptic axon opens VG-Calcium channels, allowing the influx of calcium
Increased [Calcium] breaks the bonds holding the neurotransmitter vesicles to the cytoskeleton. Vesicles migrate to the membrane and exocytose, releasing neurotransmitters into the synaptic cleft, where it binds to receptors on the postsynaptic cell.
Binding of neurotransmitter to receptor causes EPSPs or IPSPs on the postsynaptic cell.
Postsynaptic cell is excited or inhibited depending on the sum of all EPSPs and IPSPs
94
What is the difference between an afferent and efferent neuron?
**Afferent** neurons send impulses toward the CNS **(Sensory)**
**Efferent** neurons send impulses away from the CNS **(Motor)**
95
What are the major functions of the medulla, pons, midbrain, cerebellum, epithalimus, thalamus, hypothalamus, lobes of the cerebral cortex, and the corpus callosum?
Medulla - basical vital functions, special respiratory/digestive functions
Pons = facial movement and balance
Midbrain = visual/auditory startle reflexes
Cerebellum = smooth body movement, coordination
Epithalimus = sleep/wake cycles
Thalamus = sensory relay station (Besides olfactory)
Hypothalamus = Homeostasis
Frontal lobe = voluntary movement, reasoning
Parietal lobe = general sensation and taste
Temporal lobe = auditory sensation, memory, and smell
Occipital lobe = vision
Corpus callosum = relays information between cerebral hemispheres
96
What are the functions of the auditory tube, cochlea, and semicircular canals?
Describe auditory processing. How does the basilar membrane work?
**Auditory tube** = equalizes pressure on either side of the tympanic mebrane
**Cochlea** = hearing
**Semicircular canals** = equilbrium
Sound waves set up vibration in the cochlear fluid, which sets up waves along the basilar membrane. Hair cells on the basilar membrane move when the membrane moves, and the bending of the hair cells sends an action potential along the auditory nerve.
Pitch is determined by the region of the basilar membrane most stimulated. The basilar membrane is thick and stiff at the round window and floppy at the end.
High frequency tones tend to vibrate the thicker area more, and low frequency tones vibrate the apex more
97
Describe visual processing
Light striking a photoreceptor c*auses a sodium channel to close*; the normal open state of this channel means the cell is **depolarized at rest.** Closure of the channel causes the cells to hyperpolarize and *stop releasing an inhibitory neurotransmitter* onto the **bipolar cells.** This causes bipolar cells to fire an action potential, **stimulating ganglion cells** and sends an action potential into the brain along the optic nerve
98
What type of tissue is the anterior pituitary gland made of? The posterior pituitary gland?
Compare control of the anterior and posterior pituitary glands
Anterior pituitary = gland tissue (adenohypophysis)
Posterior pituitary - nervous tissue (neurohypophysis)
Anterior is controlled by hormones released from the hypothalamus
Posterior is controlled by action potentials from the hypothalamus
99
What is the difference between diastole and systole?
What causes heart sounds?
Diastole is when the ventricles are relaxed
Systole is when the ventricles are contracted.
The first heart sound in the closing of AV valves and the beginning of systole
The second heart sound is the closing of semilunar valves and the beginning of diastole
100
How can cardiac output be calculated? What is Starling's Law of the Heart?
How can peripheral resistance be changed?
CO = Stroke volume x heart right
Starling's Law: More blood in, more blood out (Increased venous return increases cardiac contractility and stroke volume)
Peripheral resistance is changed by changing arterial diameter; vasodilation leads to a drop in resistance
101
How do cardiac action potentials differ from neural action potentials?
What other ion channel is involved?
Cardiac action potentials are longer, as they have a plateau phase due to VG-Calcium channels
102
Give three reasons for the elaborate cardiac conduction pathway
1. It is impossible to directly transmit an impulse from atria to ventricles, so the only way the impulse can get into the ventricles is through the conduction system
2. The AV node delays the impulse slightly so that the atria can contract first, allowing the ventricles to fill completely.
3. The impulse travels to the bottom of the ventricles before entering ventricular muscle cells so that the ventricles contract from bottom to top (Better ejection efficiency)
103
Name the nonspecific disease defense systems of the body.
What cells are involved in immunity and what are their functions?
Nonspecific defense:
**Barriers:** skin, hair, earwax, skin oil, mucus,
**Chemicals:** lysozymes, gastric stomach acid, pepsin, proteases, the complement system (enhances the ability of antibodies and phagocytic cells)
**Cells:** macrophages, neutrophils, eosinophils, dendritic cells, NK cells
Immunity is a _specific defense;_
* B cells:* humoral immunity; make antibodies, can only produce one type of antibody, but can alter their genes to produce different types; have an antigen receptor on their cell surface
* T Cells* - cell-mediated immunity, look to kill antigens directly; have a self receptor and antigen receptor, both must be stimulated for the cell to be active
* Killer T cells* **(CD8)** bind and kill abnormal self-cells; associated w/ **MHC1** - _found on all cells;_ allowing cells to display their contents on the cell surface
* Helper T* **(CD4)** - secrete cytokines that help B cells and killer T cells proliferate; associated with **MHC2** - MHC2 is _found on macrophages and B Cells;_ allows cells to display what is eaten on the cell surface
104
Besides urine production, what are the other functions of the kidney?
Regulated blood presure, pH, ion/water balance, activated viatmin D, and secretes eryhtropoietin (EPO) to increase red blood cell formation
105
What is unique about the bklood supply to and from the glomerulus?
It is both supplied and drained by arteries, allowing regulation of blood flow in and out
106
List the skeletal muscle hierarchy
Myosin, actin, sarcomere, myofibrils, muscle cell, fascicle, muscle
107
What is excitation-contraction coupling?
What types of motor units do the fingers have? The legs?
The coupling of contraction (sliding filaments) with excitation (a neural AP) through use of Calcium.
Fingers have **many small** motor units, legs have a **few large** motor units
108
What are the sources of muscle energy, from fastest source to slowest source? What is the oxygen debt and how is it repaid?
Muscle gets energy (ATP) by substrate-level phosphorylation (taking phosphate off creatine phosphate and putting it on an ADP to generate an instant ATP), by glycolysis, and by aerobic cellular respiration.
Oxygen debt is the additional oxygen required after exercise to replenish oxygen stores on myoglobin and to convert lactic acid into something useful.
The debt is repaid through the Bohr effect (Increased CO2, increased temperature, and decreased pH), which causes hemoglobin to have a lower affinity for oxygen and release more oxygen to the tissues
109
Describe the three skeletal muscle fiber types in terms of their energy usage and contraction speeds
Red slow twitch fibers contract slowly, use oxidative metabolism, and are fatigue resistant (Posture muscles)
Type IIB (White fast twitch) contract rapidly, are glycolytic only, and fatigue quickly.
Type IIA fibers contract quickly, are oxidative, and are more fatigue resistant than type IIB, but not as much as red slow twitch.
110
# Define osteoblast, osteocyte, and osteo clast.
What hormones affect these cells and how?
Osteoblast = immature bone-producing cell
Osteocyte = masture bone cell in lacuna
Osteoclast = bone-dissolving cell
PTH increases blood calcium levels by stimulating osteoclasts and inhibiting osteoblasts
Calcitonin decreases b lood calcium levels by stimulating osteoblasts and inhibiting osteoclasts
111
Name the structures of the conduction zone and respiratory zone
Conduction zone: nose, nasal cavity, pharynx, larynx, trachea, primary bronchi, secondary bronchi, tertiary bronchi, terminal bronchioles
Respiratory zone = respiratory bronchioles, alveolar ducts, alveoli
112
How does surfactant make breathing easier?
It reduces the surface tension on the inside wall of the alveoli, preventing them from collapsing and reducing the effort required to inflate them
113
Which muscles control inspiration? Expiration? Forced Expiration?
Inspiration = diaphragm/external intercostals
Expiration = none
Forced expiration = abdominals/ internal intercostals
114
Define tidal volume, residual volume, vital capacity, and total lung capacity
Tidal volume = normal resting breath volume (500 mL)
Residual volume = amount remaining in the lungs after complete exhale (1200 mL)
Vital capacity = maximal inhale after a maximal exhale, (4500 mL)
Total lung capacity = total lung volume (5700 mL)
115
Name the layers of the skin and their tissues
How does the skin help regulate body temperature?
Epidermis = epithelial tissue
Dermis = connective tissue
Hypodermis = fat
The skin helps in thermoregulation by sweating and vasodilation in hot temperatures/ not sweating and vasoconstriction in cold temperatures
116
Name the structures and functions of the male reproductive system
Scrotum = regulates temperature of thetestes
Testes = produce sperm and testosterone
Epididymis = sperm storage
Vas deferns = contracts for ejaculation
Seminal vesicle = produces 60% of semen
Prostate = produces 35% of semen
Bulbourethral glands - produce alkaline mucus to lubricate, neutralize the urethra
Penis = becomes ereject to inject sperm/semen
117
Name the structures and functions of the female reproductive system
Labia = protects the vulva
Clitoris = erectile tissue
Vestibular glands = lubrication
Vagina = birth canal
Cervix = opening to the uterus
Ovaries = egg, estrogen, and progesterone production
Mammary glands produce breast milk
118
What causes differentiation of a fetus into a male?
The presence of a Y chromosome triggers the production of the testes.
The testes secrete testosterone, which allows the Wolffian (male) ducts to develop, as well as Mullerian Inhibiting Factor (MIF) which causes the Mullerian ducts to degenerate
119
Which division of the autonomic NS controls arousal, orgasm, and resolution respectively
Arousal = parasympathetic
Orgasm and resolution = sympathetic
120
Describe the proces of fertilization, cleavage, blastulation, gastrulation, and neurulation
Fertilization: Sperm penetrates the egg, the egg finishes meiosis, the nuclei fuse
This can occur about 14-16 days after menstruation
Cleavage is the rapid cell division of the zygote, occuring the first week after fertilization
Blastulation is the formation of a hollow sphere with inner cell mass and an outer cell layer, occurs during the last few days of cleavage before implantation
Gastrulation is the formation of the three distinct germ layers, occurs in weeks 1-3 after implantation
Neurulation = formation of the nervous system, occurs weeks 4-8 after implantation
121
What is the difference between totipotency, pluripotency, and multipotency?
Totipotent cells can become any cell type in the embryo or placenta
The zygote is totipotent
Pluripotent cells can differentiate into any of the cells in the three primary germ layers, and can become any of the 200+ cell types in the human body; The cells of the inner cell mass (Embryonic stem cells) are pluripotent
Multipotent cells are more specialized and can become many, but not all cell types. The cells of different germ layers are multipotent; ie the cells of the mesoderm can become bone or muscle cells, but not neurons or liver cells
122
What hormonal changes occur in a woman during pregnancy?
Which hormone is used to test for pregnancy?
Developing embryo cells secrete hCG, which prolongs the life of the corpus luteum so that it continues to secrete progesterone and estrogens. hCG levels stay high for the first trimester until the placenta is formed.
The placenta secretes large amounts of estrogen to develop the mammary glands, progesterone to maintain the uterine lining, and relaxin to soften joints.
The high levels of estrogen and progesterone inhibit the release of FSH and LH
123
What factors trigger labor?
Describe the positive feedback system in operation during labor
1. Growing fetus stretches the uterus
2. Stretch of the cervix increases uterine contractions
3. Increased oxytocin secretion
4. Increased estrogen relative to progesterone
Baby's head presses on the cervix, stimulating uterine contractions and oxytocin release.
Contraction of the uterus pushes the baby's head against the cervix, stimulating further contractions
124
What changes occur in the fetal circulation after birth?
What changes occur in the month after birth?
1. Ductus arteriosis closes, redirecting blood through the lungs
2. Foramen ovale closes, separating the right and left atria
3. Ductus venosus closes, redirecting blood through the liver
4. Umbilical arteries and veins constrict
5. Baby stops making fetal hemoglobin
In the mother: delivery of the placenta causes estrogen and progesterone levels to drop dramatically. Drop in these hormones releases inhibition of prolactin, causing the release of prolactin, causing breast milk production.
125
What is *nondisjunction*?
When can this occur and what is the result?
Nondisjunction is the failure to properly separate DNA during gamete formation.
**Anaphase I failure** - 4 abnormal gametes
**Anaphase II failure** - produces 2 abnormal gametes
126
Describe the **secretory pathway**
ER --\> Golgi --\> Secretory vesicles --\> exterior via exocytosis or storage or lysosomes
127
Ribosomes of the rough ER secrete what kinds of proteins?
Membrane-bound, secreted, and integral proteins
128
What are the components of the **cytoskeleton** and what are their features/functions?
**Microtubules** are composed of ***alpha and beta tubulin***
Have a _large diameter_ and form the mitotic spindle, participate in intracellular transport and ***make up cilia and flagella***
**Microfilaments** are composed of ***actin*** and have a _small diameter_
Function in ***muscle contraction, pseudopod formation (macrophages), and cytokinesis***
**Intermediate filaments** are composed of many types of proteins, serve _structural roles,_ and are *more permanent* than other parts of the cytoskeleton.
129
130
What are the characteristics of G protein receptors?
G proteins have **inherent GTPase activity**, where it constantly hydrolyzes GTP into GDP. As such, _at rest GDP is bound to the alpha receptor subunit_
G proteins are **multisubunit proteins**, allowing one subunit to migrate and activate Adenylyl Cyclase.
cAMP is a **second messenger system**, because the ligand can't cross the cell membrane and has to drive the release of a second messenger.
Is a form of **signal amplification** (activation of multiple G-proteins by the bound receptor)
Are **fast and temporary;** fast because you simply activate the pathway, and temporary due to the inherent GTPase activity
131
What three amino acids can be phosphorylated?
Serine, threonine, and tyrosine
132
Which proteins finish translation in the Rough ER?
Describe their signal sequence
*Secreted proteins, lysosomal proteins, and transmembrane proteins* finish translation in the rough ER.
Signal sequence of **secreted and lysosomal proteins:**
is the _first few amino acids translated_ and _is removed upon completion of translation_
**Membrane-bound proteins:**
Signal sequence _can be anywhere in the amino acid sequence_
Signal sequence _can appear multiple times_
Signal _remains as part of the transmembrane part of the protein_ (Removal would cause the protein to fall apart.)
133
Define zymogens
Zymogens are **inactive precursors of enzymes** that are usually **activated by cleavage** and are involved in the breakdown of proteins.
