Bio/Biochem Flashcards
Prokaryotes vs. Eukaryotes
Prokaryotes do NOT have membrane-bound organelles (such as ER, nucleus, etc). However, both Prokaryotes and Eukaryotes have a cell membrane and for some, a cell wall.
Describe the steps of reverse transcription
In reverse transcription: 1) single stranded RNA is used as a template to generate a complementary DNA strand. This step requires a RNA-dependent DNA Polymerase. 2) There is temporarily an RNA-DNA double helix, but the RNA strand is degraded, and the DNA strand is used as a template to generate a complementary DNA strand to form a DNA double helix. This step requires a DNA-dependent DNA Polymerase.
Megakaryocytes
Large bone marrow cells with a large nucleus that are responsible for the production of platelets necessary for normal blood clotting.
What is a key difference between viral genetics and eukaryotic genetics?
Viruses are NOT diploid, meaning they have ONE copy of a gene/allele.
What is the “fluid mosaic” model referring to
The fluid mosaic model is referring to two specific properties of the plasma membrane: 1) “Fluid” is the ability of certain molecules to travel laterally within the bilayer. 2) “Mosaic” refers to the presence of proteins and lipids/ other molecules scattered in its structure.
How do double bonds impact fluidity of plasma membrane?
More double bonds, more fluid a membrane is due to kinks.
Lytic vs. Lysogenic cycle
In the lytic cycle, the bacteriophage actively copies its genetic material, resulting in the lysing of the host cell. While, lysogenic cycle is a dormant stage, where the bacteriophage incorporates its DNA in the host genome to be activated later.
What is the impact of a stimulant, like cocaine, on glucose metabolism?
Since a stimulant such as cocaine, stimulates the CNS, it increases glucose metabolism in the brain. This effect is similar to the effect of stress!
Sympatric speciation
When reproductive isolation occurs without physical barriers
Allopatric speciation
When physical barriers cause reproductive isolation
Genetic bottleneck
When a reduction in the gene pool diversity occurs due a REDUCTION in population SIZE
Non-sense vs. missense mutation
Non-sense mutation occurs due to a premature STOP codon (UAG, UGA, UAA). Missense mutation is when one amino acid replaces another.
Adaptive radiation
When distinct species that play distinct ecological roles arise from a single ancestor
Five conditions of Hardy-Weinberg Equilibrium
- Large breeding population
- Random mating
- No immigration
- No mutations that change overall allele frequencies
- No natural selection
What direction does water move towards in osmosis?
Water moves towards greater osmotic pressure
Function of the Loop of Henle
Loop of Henle is a structure of nephrons (filtering cells in the kidney) that rely on Sodium pump to reabsorb sodium ions and make concentrated urine.
What Histone proteins are present in human nucleosomes?
H1, H2A, H3, and H4 are histones present in human nucleosomes. However, H1 is outside the bead structure of histones, because their role is to hold the DNA in place & provide stability for the structure.
What is the difference between Chromatin and nucleosomes?
Nucleosomes refers to the DNA-Histone subunits, while Chromatin is fully-packaged DNA.
How are euchromatin and heterochromatin viewed under a light microscope?
The lightly-packaged euchromatin is viewed lighter under a light microscope, while the more condensed heterochromatin is viewed darker.
What is the shape of a rate vs. pH graph for enzymes?
Parabolic- indicated that enzyme activity is optimal at a certain pH, but once the optimal pH is surpassed, the enzyme declines in function.
How is urea formed?
Urea is formed through amino acid metabolism. An enzyme called aminotransferase, replaces the amine group with a carboxyl or carbonyl group, and the free amine group becomes ammonia (NH3). Ammonia is a toxic metabolite that the liver and kidneys transfer to urea (CH4N2O) through combining it with CO2.
What direction do charged AAs travel in an isoelectric gel?
Positively charged AAs move towards cathode, while negatively charged AAs move towards anode.
Homologous Structures
Evolved from a common ancestor but now serve a different function (Ex: forelimbs of mammals such as humans, walruses, bats)
Analogous structure
Evolved individually but serve similar functions (Ex: wings of insects and bats)
What is the function of many plasma proteins in blood buffering?
Proteins with acidic or basic side chains can serve as Bronsted-Lowry bases and acids, absorbing or releasing protons, reducing shifts in pH.
What does Cholesterol do to plasma membrane at physiological temperature?
Similar to at high temperatures, increasing cholesterol at physiological temperature increases membrane rigidity.
How does glycolysis in cancerous cells differ than normal cells?
Cancer cells have a higher rate of glycolysis in comparison to normal cells because they require more energy to proliferate uncontrollably.
Why does a decrease in the number of alveoli in the lungs lead to respiratory distress?
The reduction in surface area in the lungs due to the reduction of alveoli reduces the rate at which O2 and CO2 can diffuse through lunch epithelium.
What biological processes process quicker due to surface area?
- Large number of alveolar sacs in the lungs.
- Presence of microvilli in the small intestine.
- Folding of the inner mitochondrial membrane.
When given a single-stranded DNA, how will the percent composition of the complementary bases differ from double stranded DNA?
In a single-stranded DNA, the complementary bases would not have equal % composition.
What happens when there is a deficiency in fatty acid catabolism (break down)?
There will be an abundance of fatty acids in our system, and less fatty acids can be broken down for energy production, so glucose is relied on for energy production –> less glucose in the blood because more is broken down. At a systematic level, since fatty acids are not broken down, they are stored in the liver and adipose tissue, likely leading to fatty liver disease.
What happens when Insulin is administered or injected into the bloodstream?
Think of insulin as causing the body to build up large molecules (glycogen and lipids) to store energy. Therefore, if there is enough blood sugar, then insulin would promote glycogen storage, or storage of energy in the form of lipids.
What is the function of Troponin?
Troponin is a complex of three proteins (Troponin I, C, and T) and is required for contraction of skeletal and cardiac muscles.
What travels towards the anode and cathode in electrophoresis?
The anode is positive, so negatively charged residues would migrate towards it. The cathode is negative, so positively charged residues would migrate towards it.
Difference between single & double-crossover events
In a double-crossover event, the arms of homologous chromosomes cross twice, so it involves the middle section of chromosomal arms. While single-crossover only occurs once, so it only involves the ends of chromosomal arms.
Why are mitochondrial diseases only inherited maternally?
Mitochondrial diseases are always a result of the child inheriting mitochondria from the ova (female gamete). In a fertilized egg, the mitochondria of ova predominate due to their much larger numbers compared to the mitochondria of sperm. Sperm mitochondria are also associated with ubiquitin protein which causes them to be targeted for destruction post-fertilization.
What is the function of aldosterone?
Aldosterone, released by the adrenal cortex, is released in response to low blood pressure. Its primary function is to increase sodium reabsorption in the distal tubule and collecting duct
What is internalization in the context of biological systems?
Internalization implies that it is NOT expressed on the cell membrane.
Which amino acids are most susceptible to phosphorylation?
The amino acids most prone to phsophorylation are Serine (S), Tyrosine (Y), Threonine (T) due to the presence of an OH group.
What does phosphomimetic mean?
Mimics a phosphate group, so think negatively charged at physiological pH.
Difference between innate and adaptive immunity
The innate immune system is characterized by inflammation that serves as a general response to injection or injury. Adaptive immune system protects against specific pathogens that the body has been exposed to prior.
Totipotent stem cells
Stem cells that are capable of differentiating into all embryonic and adult lineages. (Ex: Zygote)
Pluripotent stem cells
Able to differentiate into all three of the basic embryonic body layers (ectoderm, endoderm, mesoderm) (Ex: Embryonic stem cells)
Multipotent stem cells
Stem cells able to differentiate into multiple specialized cell types in a specific tissue or organ. (Ex: Mesenchymal stem cells)
What results can be inferred from a cross-sectional study?
Cross-sectional studies are observational studies at a single point in time. Only causal relationships can be concluded.
What results can be inferred from an experimental study?
Causal relationships can be inferred if experimental study is well controlled.
What happens in paralyzed patients?
The pathway is not intact and efferent signaling is interrupted. This occurs if spinal cord transection occurred (cutting and nerve damage)
What happens in spinal cord injuries?
The motor cortex is still intact so muscles can still move
What is the pathway from Central Nervous to peripheral?
Cerebral cortex –> spinal cord –> motor neurons (efferent neurons) –> skeletal muscle cells
Guanine Structure
Purine = 2 rings
Adenine Structure
Purine = 2 rings
Cytosine Structure
Pyrimidine = 1 ring
Thymine Structure
Pyrimidine = 1 ring
Uracil Structure
Pyrimidine = 1 ring
Apoenzyme
An enzyme that is devoid of its necessary cofactors and is catalytically inactive
Enzyme responsible for the last step of Glycolysis
Converting PEP to pyruvate is done by Pyruvate Kinase
What step of Citric Acid produces GTP
Conversion of succinyl-CoA to succinate
How do you determine a reversible step when given Gibbs Free Energy?
The reaction with an absolute value closest to 0 is considered reversible
Complex II in ETC
Only complex that does NOT contribute to proton gradient. Primary function is to oxidize FADH2 and reduce ubiquinone. Hypothesized to reduce production of reactive oxygen species
Ubiquinone or Coenzyme Q (CoQ)
Serves as mobile electron carrier, facilitating the transfer of electrons to Complex III & helps facilitate proton pumping, contributing to the gradient by pumping 4 protons into inter- membrane space
Why are diseases associated with splicing so rare?
Splicing is critical for survival, so mutations in core splicing machinery do not allow development of an organism
Relationship between Prokaryotic RNA polymerases and human DNA
Prokaryotic RNA Polymerases can transcribe human DNA
Acidosis
When blood pH is below a 7.35
Alkalosis or Alkaline
When blood pH is above a 7.45
What happens when people hyperventilate?
Respiratory rate increases, so more CO2 is blown off, making the blood more alkaline. Breathing into a bag and re-breathing the air helps some of that CO2 return in your system
Adrenal Medulla
Located on top of each kidney. Produces amino-acid derived hormones, norepinephrine and epinephrine
Adrenal Cortex
Located on the outer parts of the adrenal medulla. Produces corticosteroids, which are involved in stress response and circadian Rhythm,
Atrial natriuretic peptide (ANP)
Regulates fluid homeostasis
Which part of the endocrine system releases Oxytocin?
Posterior pituitary gland
Posterior Pituitary Gland
Secretes oxytocin and antidiuretic hormone (ADH)
Antidiuretic hormone (ADH) or vasopressin
Regulates water balance by increasing water retention when blood osmolarity is too high or blood volume is low. Reduces blood osmolarity & increases blood pressure
High osmolarity
High salt concentration
Which organelles are involved in peptide hormone synthesis?
Rough Endoplasmic Reticulum & Golgi apparatus (for modifications)
Aldosterone function
When blood pressure drop is detected, special cells in Juxtaglomerular apparatus of the distal tubule secretes renin –> Renin triggers angiotensin I, II, and III –> Causes adrenal cortex to secrete aldosterone –> increase membrane proteins absorbing sodium and secreting potassium
Uvula
Works with the soft palate to prevent backflow of food and liquid into nasal cavity
Epiglottis
A cartilage flap that shields the larynx from entrance of food and liquid when someone swallows
Residual Volume in Respiration
The minimum volume of lungs under maximum intrapleural pressure
Find the difference between the minimum and maximum lung volume for an individual with a given weight
subtract the given minimum volume in mL/kg from the maximum volume (mL/kg) and multiply that by the weight to get an answer in volume (mL)
Interphase
Includes G0, G1, S, and G2 phase prior to Mitosis/ Meiosis (M Phase)
Directionality of peptide
N terminus to C terminus. If a residue is labeled in chronological order, the smaller number is closer to the N terminus or the “beginning” of a peptide
Characteristic of anomers
Anomers are a form of epimers which are diastereomers because they differ at one stereocenter only
What component of the ETC is reduced and never oxidized?
Oxygen is reduced to H2O at the end of the ETC. Remember, O2 is an oxidizing agent so it is unlikely for it to be oxidized itself
Suicide Inhibitor
When an inhibitor binds irreversibly to an enzyme via covalent bonding
Competitive Enzyme Inhibitor
Decreases reaction rate by binding to the active site and preventing the substrate to bind
Noncompetitive Enzyme Inhibitor
Decreases reaction rate by binding to enzyme and altering the structure of its active site
Homotropic Regulation
A type of allosteric regulation when the binding of one molecule affects enzyme activity and binding of other substrate binding
Eicosanoids
A large family of lipids derived from arachidonic acid. Examples of Eicosanoids include prostaglandins, which is a signaling molecule that plays a role in inflammation & thromboxanes involved in clotting cascade
Vmax in Michaelis-Menten Curve
The maximum rate of the reaction when the enzyme is saturated with a substrate. Remember: an answer cannot exceed the Vmax!
Do bacterial cells contain introns?
Majority of bacterial cells DO NOT contain introns
A structure within the cell membrane that is similar to gap junctions
Transmembrane proteins (usually glycoproteins) since they pass through the membrane and facilitate transport
Allosteric Inhibition
When an inhibitor binds to an enzyme covalently but NOT at the active site. Usually if the inhibitor and substrate have very different structures they may be an allosteric inhibitor
End product of Meiosis I
2 haploid cells with 23 chromosomes that go on to produce gametes
Competitive Inhibitors effect on Vmax and Km
Competitive inhibitors increase Km while Vmax remains unchanged. In a Line-Weaver Burk plot, the X-axis is -1/Km, so as Km increases it will get closer to 0
Which embryonic layer is the nervous system derived from?
Ectoderm
What is the difference between fetal hemoglobin and adult hemoglobin?
Fetal hemoglobin has a greater affinity for oxygen than adult hemoglobin. For that reason, it is used as a potential treatment for sickle-cell disease
Follicular Phase in Ovarian Cycle
Overlaps with the menses and proliferative phase in uterine cycle. This phase is when the follicle matures to an ova
When are LH and FSH levels increased during female reproductive cycle
FSH and LH are increased in the middle of the ovarian cycle
Broca’s Area
Area of the brain responsible for speech formation
Wernicke’s Area
Area of the brain responsible for speech comprehension
Result of damage to the arcuate fasciculus area of the brain
Inability to repeat words heard but spontaneous word production is intact
Superior Temporal Gyrus
Area of the brain where Wernicke’s Area is located
Hinge Joints
Allows for movement in only one plane (Ex: joints in the elbow)
Gliding Joints
Common at the junction between flat bones and allow the bones to slide past one another (Ex: synovial joints between vertebrae in spinal column)
Ball and Socket Joint
Permits the greatest range of motion and allows for 360 degrees of rotation sometimes (Ex: Hips and shoulders)
Saddle Joint
Formed between reciprocal concave and convex bones (Ex: Joints in the Thumb)
Which lipoprotein has the highest lipid to protein content?
“Very low density lipoprotein” (VLDL) and Chylomicron
Journey of newly synthesized Chylomicron
intestinal epithelium –> lacteals –> lymphatic vessels –> adipose tissue –> liver where their remains are recycled
Lacteals
Blood vessels that drain into the lymphatic system. When chylomicrons are newly synthesized in the small intestine, they enter lacteals
What reaction cleaves disulfide bonds?
Reduction reactions
Functions of lipids
1) Store energy
2) Serve as precursor for hormones (cholesterol)
3) Insulate
4) Generate heat
Where is sperm produced?
Seminiferous tubules
Epididymis
After it’s produced in the seminiferous tubules, sperm is developed and gains motility in the epididymis.
Pathway of sperm through male reproductive system
seminiferous tubules –> epididymis –> vas deferens –> ejaculatory duct –> urethra –> penis.
What type of cells are ovarian cells?
Epithelial cells
Dissociation constant (Kd)
A measurement of affinity between two biomolecules. Lower Kd corresponds to higher affinity
Phosphodiester bonds
Link adjacent nucleotides in DNA
Uncompetitive inhibitors
Reduce BOTH Km and Vmax. Uncompetitive inhibitors only bind target enzymes when the substrate binds to the enzyme first
How are Lactones formed?
Via intramolecular nucleophilic attack
Functions of NADPH
1) Involved in biosynthesis of lipids & cholesterol
2) Production of bactericidal bleach in lysosomes of some white blood cells
3) Maintenance of supply of reduced Glutathione for protection against free radical damage
What is unique about the inner mitochondrial membrane?
It lacks cholesterol
Osteoblasts
Specialized cells that form new bones & add growth to existing bones by absorbing excess calcium in the bloodstream
Osteoclasts
Specialized cells that dissolve damaged bones so osteoblasts can make new bones. INCREASE Calcium levels in bloodstream
What is the role of Calcitonin?
“Tones down” blood calcium levels by activating osteoblasts
What is derived from the neural tube during neurulation?
The brain, spinal cord, and neural crest cells (which become neurons, pigment cells, etc)
Where are MOTILE cilia found?
In the uterine lining (helps egg move through fallopian tube) and trachea
Where is the 5’ and 3’ located on a single nucleotide?
The 5’ end is the 5th carbon of the pentose sugar that is linked to phosphate group via phosphodiester bonds. 3’ end is the 3rd carbon bound to hydroxyl group which would participate in a phosphodiester bond when linked to another nucleotide
How do phosphatases remove phosphate groups?
Via hydrolysis, so they are a subset of hydrolases
Characteristic of Cytochrome C in ETC
Highly water-soluble (polar) protein
What other hormones, beside, glucagon, increase blood glucose levels?
Cortisol & Epinephrine
Effects of Aldosterone secretion
When Aldoesterone is released from adrenal cortex, it triggers the reabsorption of Na+ ions and H2O into the bloodstream. To stabilize K+/Na+, as Na+ is reabsorbed into the bloodstream, K+ decreases.
Post-translational modifications
Ubiquitination, glycosylation, phosphorylation and methylation
Post-transcriptional modifications
Capping, polyadenylation (Poly-A tail), splicing
What interactions are responsible for secondary structures of proteins?
Hydrogen bonding between amino acid back bones. Side chain interactions are responsible for tertiary and quaternary structures
Passive immunity
The transfer of humoral immunity in the form of ready-made antibodies from one individual to another (Ex: mother to fetus)
Microtubule depolymerization
Responsible for separating chromosomes during Anaphase in mitosis and Meiosis I and II
How do you determine the efficiency of an enzyme?
Kcat/Km, where Vmax = kcat[Enzyme]
Which enzyme breaks down glycogen to glucose?
Glycogen Phosphorylase
What are the glycosidic bonds between glucose monosaccharides in glycogen?
alpha (1-4) linearly and alpha (1,6) branched
How is Tm or melting temperature defined for nucleotides specifically?
Melting temperature for nucleotides is the temperature at which 50% of the DNA is unfolded into a single strand
Degeneracy or Degenerate Codon
Refers to more than one codon coding for the same amino acid
What metabolic pathways can happen in the presence and absence of oxygen?
Glycolysis & Gluconeogenesis
Characteristics of Skeletal muscle cells
Multi-nucleated, striated, and voluntary (bones and cartilage, also include the upper third of the esophagus and the pharynx)
Characteristic of cardiac muscle cells
Mono-nucleated, striated, and involuntary
Characteristic of smooth muscle cells
Mono-nucleated, unstriated and involuntary (Visceral organs like stomach)
Why is the fetal circulation designed the way it is?
To bypass the fetal lungs
Adult vs. fetal circulation
The right side of the fetal heart is more pressurized than the left side during prenatal development, allowing oxygenated blood to shunt from pulmonary circulation to systematic circulation through foramen ovale & ductus arteriosus
What direction is the template strand read in by DNA Polymerase?
3’ to 5’
What is the “sense” strand?
The coding strand, so the mRNA sequence would be identical in direction and bases, with the exception of Uracil instead of Thymine. Antisense is the opposite in direction
DNA Polymerase Exonuclease Activity
Proofreading mechanism done by DNA polymerase, where it can replace mismatched bases in the 3’ to 5’ direction
Polygenic
A gene whose individual effect is too small to be observed, but can act together with others to produce an observable variation (Ex: Group of 5 ADH enzymes)
Polycistronic
When a single mRNA can encode more than one polypeptide separately within same RNA (Characteristic of bacterial genome)
How does test-crossing in genotyping work?
To determine the organism with a dominant phenotype, you cross it with an organism that is homozygous recessive for allele of interest
Facultative aerobe
Can use oxygen as final electron acceptor in aerobic respiration & can survive in anaerobic environment
Obligate aerobe
Requires oxygen to survive
Obligate anaerobe
Cannot survive in the presence of oxygen
Facultative anaerobe
Can survive in the presence of oxygen but cannot undergo aerobic respiration
What ion channels are responsible for maintaining resting membrane potential?
Ungated or leakage ion channels
How do Chylomicrons and VLDLs differ?
Both transport triacylglycerol & contain apolipoproteins but Chylomicrons originated in the intestine, while VLDLs originate in liver
Role of peptidyl transferase in protein synthesis
Catalyzes peptide bonds between amino acids
Chaperone proteins
Hold together proteins into their tertiary structures
Exocrine Glands
Glands that secrete molecules (non-hormones) onto the exterior surface of the skin or lungs, stomach, etc (Ex: tears, bile, digestive enzymes)
Transamination
An amino group is transferred from from an amino acid to a-ketoglutarate to synthesize glutamate
Characteristics of Prokaryotes (Bacteria vs. Archaea)
Both domains are unicellular, have circular chromosome, reproduce via binary fission, but Archaea does NOT contain cell wall with peptidoglycan
Digestive Tract Pathway
Mouth –> Esophagus –> Stomach –> Small intestine (duodenum –> jejunam –> ileum) –> Large intestine (cecum –> colon –> rectum)
Terpenes
Precursors in cholesterol and steroid hormone synthesis
Prostaglandins
Nonhydrolyzable lipids & a type of eicosanoids involved in localized inflammatory response
What happens when inspiratory muscles contract?
Inspiratory (inspiration/inhalation) muscle contractions result in negative intrathoracic pressure that results in lung expansion
What happens when expiratory muscles contract?
Expiratory (exhalation) muscle contractions result in positive intrathoracic pressure
Cognitive-Behavioral Therapy
Attempts to change negative beliefs/thoughts & maladaptive behaviors
Humanistic Therapy
An optimistic approach to empower the individual with self-actualization and personal growth
Psychoanalytic Therapy
Attempts to uncover unconscious conflicts rooted in childhood that impacts behavior
Sphingolipids
Structural lipids that help influence the fluidity and structure of biological membranes. The sphingosine backbone contains one hydrolyzable bond with at the amide group
Compare the right and left ventricle
The right ventricle has thinner walls because it pumps blood with less pressure since it is only pumped to the lungs than the left ventricle that pumps blood to all tissues in the body
Difference between fetal & adult circulation
Fetal circulation is pumped from the pulmonary circulation to systemic circulation, since, unlike adults, the right side of the fetal heart pumps blood with greater pressure than the left side
How do uncompetitive inhibitors affect Km and Vmax
Both decrease by the SAME factor, so the Vmax/Km ratio remains unchanged
Kcat in enzyme kinetics
Also known as turnover number, and is the number of substrates an active site can convert into products per unit time. It is = Vmax/ [total enzyme]
Oligodendrocytes
Produce myelin sheath
Structure of GPCRs
Single subunit consisting of seven membrane-spanning alpha helices
Explain for partial pressure of oxygen in alveoli and alveolar capillaries drive gas exchange
Since oxygen diffuses from the alveoli to alveolar capillaries, the partial pressure of oxygen in the alveoli must be greater than the partial pressure of oxygen in alveolar capillaries
Embryonic Development (Starting from Zygote)
1) Zygote: diploid formed from the fusion of two haploid gametes
2) Morula: zygote divides via cleavage, resulting in this solid ball of embryonic cells
3) Blastula: morula develops a fluid-filled cavity, forming this hollow, sphere of cells with a fluid-filled center
4) Gastrula: cells begin to differentiate into the primary germ layers
Cancellous Bone
“Spongy Bone” contains a lattice structure composed of trabeculae spicules with the space between them filled with bone marrow
