BIO/BIOCHEM Flashcards
What is the role of signal sequence ?
Signal sequence : a portion of mRNA that is located in the 5′ region and will signal to the ribosome that translation needs to be continued in the rough endoplasmic reticulum.
What is the nuclear localization signal ?
Nuclear localization signal : is a sequence that tags the protein for it to be transported into the nucleus
What does a mature RNA sequence for a protein located on cell membrane contain ?
mature RNA sequence for a protein that is secreted or that will locate to the cell membrane will contain the SIGNAL SEQUNCCE.
What is the role of calcium during muscle contraction process?
Ca2+ binds to troponin and allows tropomyosin to move, freeing the site of interaction between actin and myosin.
How many fused rings are in steroids ?
4 fused rings (contain 6-6-6-5 fused ring assembly)
What can fix an epileptic issue due to massive firing of neurons in a small area ?
An INCREASE in neuron firing threshold would make it more challenging for a neuron to fire an action potential. This will reduce the frequency of downstream neuron depolarizations, resulting in relief of the symptoms.
Which region of the kidney is glomerular filtrate most concetrated ?
Medullary portion of collecting duct
(last part of tubule where reabsorption of water and salts occur)
What occurs in proximal convoluted tubule ?
portion of tubule where glomerular filtrate First passes through
What is role of collecting duct ?
collecting duct: concentrates filtrate
assuming no denaturation of proteins, what is expected to increase with temperature ?
PROTEIN ACTIVITY (expected to increase with temperature)
How are action potentials stimulated ?
by release of a neurotransmitter that binds to ligand gated channels,
What is the role of Na+/K+ ATPASE during a neuronal action potential ?
aids in The RESTORATION and maintenance of the RESTING POTENTIAL.
This is achieved by moving three Na+ out of the cell for every two K+ ions that are brought into the cell.
What is the function of transcription factors ?
regulate the expression of other genes ( by binding to the promoter or the enhancer of the gene located on the DNA).
How do hydrophobic molecules pass through membrane ?
SIMPLE DIFFUSION
What must occur for regulation of the expression of genes to be possible ?
The downstream target genes must contain DNA REGIONS in their promoter or enhancer, that can interact with transcription factors
What is produced after ATP hydrolysis ?
ADP + Pi (inorganic phosphate)
What are lipid rafts?
lipid rafts: cholesterol rich domains within the membrane
What is the role of microtubules ?
Microtubules: bind to chromosomes at the level of the kinetochore and regulate their migration toward the opposite poles of the cell during anaphase.
What regulates to formation of filtrate in Urinary system ?
The DIFFERENCES IN PRESSURE regulate filtrate formation
what are the main pressures that work in urinary system and how do they work ?
There are three pressures that work together to regulate filtration in the glomerulus:
-glomerular capillary pressure
-capsular hydrostatic pressure
- blood colloid osmotic pressure.
The glomerular capillary pressure will force filtrate from a capillary into Bowman’s capsule; the other two forces promote movement of the filtrate in the opposite direction.
How do enzymes alter the rate of chemical reactions ?
Enzymes :
can alter pH of environment
can co-localize substrates to modify rate of reaction
-alter substrate shape
What is a brief summary of translation ?
Proteins are generated during translation.
In this process, mRNA triplets are read by ribosomes, and tRNA molecules provide the amino acids. Each amino acid is matched to a tRNA molecule carrying a specific anti-codon. A specific amino acid will be added only if it is recognized by its specific codon.
What happens to cells in interphase ?
cells in interphase are NOT actively DIVIDING
What do mature erythrocytes NOT contain ?
Mature erythrocytes do NOT contain DNA since they are enucleated (no nucleus)
What is the role of endothelial cells?
Endothelial cells: cells that are in direct contact with blood and the surrounding matrix so these are the cells that play the most important role in GAS EXCHANGE
What are animal viruses ?
animal viruses are OBLIGATE PARASITES
Animal viruses can only infect animal cells, not bacteria.
How are bacterial chromosomes structured ?
they are CIRCULAR
What is a telomere ? what do they contain ?
telomere refers to a distal end of a chromosome. Telomeres contain non-coding repeats.
How are nucleotides connected in DNA?
Nucleotides are linked to one another by phosphodiester bonds between the sugar base of one nucleotide (thymine) and the phosphate group of the adjacent nucleotide (adenine) (in a way that the 5′ end bears a phosphate, and the 3′ end a hydroxyl group)
What is the role of aldosterone ? What happens in absence of aldosterone ?
aldosterone is responsible for retaining water and sodium in the body (keep levels high in body) and elimination of potassium ions from the body.
Thus, in the absence of aldosterone, the levels of potassium will increase.
Explain the negative feedback that occurs for ACTH?
Release of ACTH from the pituitary is regulated by negative feedback. In normal conditions, high levels of circulating glucose and other stressors activate the production of corticotropin-releasing hormone (CRH) from the hypothalamus.
CRH will stimulate the pituitary gland to release ACTH which will trigger cortisol release from the adrenal cortex.
Finally, the presence of high levels of circulating cortisol will inhibit CRH secretion (negative feedback) thus closing the loop.
What occurs in patient with Addison’s Disease ?
Addison’s disease: the circulating levels of ACTH will be higher than normal because the factor that triggers the inhibition of CRH production, high cortisol levels, is absent or low.
How does high levels of glucocorticoids affect muscles ?
High levels of circulating glucocorticoids will increase protein degradation in various tissues, muscles included.
A direct consequence of protein degradation in muscles is muscle weakness.
What happens if insulin stimulates first step of glycolytic pathway ?
This will result in a decrease of the cellular concentration of glucose. To compensate for the low cellular glucose concentration, glucose uptake is increased.
How can brain still get nourishment in diabetic patient ?
brain has glucose transporters that aer insulin independent
What is the function of end-membrane system?
The endomembrane system: is the portion of the cells that is in charge of modifying proteins that will be secreted.
(Thus, it is most likely that insulin cleavage will occur in the endomembrane system)
What is myoglobin ?
Myoglobin : the substance that holds oxygen in MUSCLES and ORGANs
What controls heart rate ?
Brain stem
What controls muscle coordination ?
cerebellum
What controls appetite ?
hypothalamus
What is extremely sensitive to timing of mRNA turnover?
coordination of cell differentiation during development is extremely sensitive to the timing of mRNA turnover.
What is the best way to incorporate antisense gene into cells of an individual ?
infect an embryo with a virus that carries the antisense gene.
The appropriate virus could become incorporated into the genome of the embryonic cells, thus causing all cells derived from these embryonic cells to contain the antisense gene.
How would an antisense molecule line up with an mRNA sequence ?
When the RNA molecules hybridize, the antisense molecule would line up in an ANTIPARALLEL fashion with the sense molecule, meaning its 3′ end would line up with the 5′ end of its complement.
How does inflation of lungs occur?
Inflation of lungs in mammals is accomplished by NEGATIVE pressure pumping action.
Because the lung stays in contact with the thoracic wall as it enlarges due to contraction of the diaphragm and the external intercostal muscles, a pressure that is lower than atmospheric pressure (negative pressure) is generated within the alveolar sacs
What is transduction ?
Transduction: is the process whereby genes are transferred by a virus
What is transformation ?
transformation: bacteria take up DNA from their surroundings.
What occurs in conjugation ?
Conjugation : production of a special pilus (sex pilus) by one bacterium and transfer through it of DNA to another bacterium.
It requires special genes for the pilus and these are usually present on a plasmid (called F fertility)
What is the most effective method of increasing total amount of water lost through skin?
raising the environmental temperature since it would cause a person to perspire, releasing water to the environment where it can evaporate and cool down the body.
Where would you expect to find ice in a frozen body of freeze-tolerant frog?
You would expect to find ice in the extracellular fluid – ex: blood plasma and lymph
Does the sodium pump DIRECTLY cause action potentials along neurons ?
NO, because action potentials result in an increased permeability of plasma membrane to sodium (leading to depolarization) hence NOT direct
Where is sodium pump most active (body structure)
LOOP OF HENLE
Na+ is reabsorbed from the filtrate moving through the nephron.
What bonds holds DNA backbone
Phosphodiester bonds
What kind of bond is formed by DNA backbone ?
The DNA backbone is formed by phosphodiester linkage between deoxyribonucleotide molecules.
What does structure of pyrimidine look like ?
What does structure of purine look like
differentiate between structures of purines and pyrimidines
Purines have 2 rings
Pyrimidines : have 1 ring
Differentiate between purines and pyrimidines ?
Purines: 2 rings
pyrimidines 1 ring
What kind of side chains are seen in cysteine
Cysteine has SULFYHYDRYL groups (that can form disulfide bridges)
Where does the electron transport chain occur ? How do the complexes in ETC function?
Mitochondrial Inner membrane
the complexes function in a chain (the reactions by complex are Coupled together )
What is the function of Endoplasmic Reticulum ?
endoplasmic reticulum is responsible for the synthesis and transport of various organic molecules, including carbohydrates, lipids, and proteins.
What is function of Golgi apparatus ?
Golgi apparatus: packaging proteins into vesicles for their transport to their proper location
phosphofructokinase 1 inhibition by ATP is an example of :
Allosteric regulation and Feedback inhibition
phosphofructokinase is a major enzyme in glycolysis is part of allosteric reg and has negative feedback loop by ATP
What kind of processes move solute from an area of High concentration to an area of Low concentration ?
Diffusion and Facilitated diffusion
Which process moves solute from an area of Low concentration to high concentration
Active transport (using ATP)
How does solute concentration changed when moving ions from pond water to green algae ?
pond water has low concentration and moves to green algae with high concentration
What is the role of voltage gated K channels in neuronal system ? What would happen if these K channels were Blocked ?
When Voltage-gated potassium channels are activated, this allows for REPOLARIZATION ack to a resting membrane potential.
inhibiting voltage-gated potassium channels would Delay the repolarization phase of the action potential. This would lead to PROLONGATION of the action potential.
What is the relationship between pH and pI (isoelectric point)
If pH > pI : Negative charged (Deprotonated)
if pH < pI : positively charged (protonated)
What is relationship between pka and strength of an acid? How does pH and pka relate ?
Lower the pka, Stronger the acid
pH < pka : protonated
pH > pka : deprotonated
What occurs during ubiquintation ?
Ubiquitination marks proteins for degradation by a proteasome.
What kind of bond are formed in cysteine ?
Cysteine residues contain a thiol group that can form covalent bonds by disulfide bond formation.
What is the role of detergents in experiments
Detergents EXPOSE amino acid residues
What is role of Glyceraldehyde 3 phosphate Dehydrogenase (GAPDH) ?
GAPDH converts glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate during glycolysis and gluconeogenesis (reversible conversion)
What kind of process is histone acetlyatoin ? what method can be used to detect them?
Histone acetylation is a post-translational modification and therefore it can be detected by Western blots.
(remember histones are proteins)
What is role of vasopressin ?
Vasopressin (ADH) : which increases expression of aquaporins in the collecting ducts.
(Vasopressin) is released during dehydration)
What is the role of collecting duct?
The collecting duct is a renal structure responsible for the concentration of urine as it passes from individual nephrons to a minor calyx.
The process of concentrating urine is regulated by aquaporin proteins that mediate water reabsorption from the urine.
What cells are responsible for myelin in peripheral nervous system ?
SCHWANN Cells
which cells responsible for myelination in central nervous cells
OLIGODENDROCYTES
What is a prion ? What is its role?
a prion is A PROTEIN
Prions are misfolded variants of a protein that can cause misfolding when interacting with normally folded variants of the same protein.
Upon infection, prions lead to disease in a host organism.
what is role of small intestine ?
The small intestine : responsible for the absorption of nutrients from the diet.
what happens when nutrients are absorbed from diet? Where does it go?
Once nutrients are absorbed, they are transported to the LIVER via the hepatic portal vein. This allows for nutrient-rich blood to be balanced and detoxified before it is delivered to the rest of the body.
what occurs in antibiotic resistance ?
Antibiotic resistance: is often caused by genetic changes within a pathogen that allow the pathogen to withstand the action of an antibiotic.
What is frame shift mutation ? How does it affect sequence? Which terminus is affected ?
Frameshift mutation : an insertion or deletion in DNA sequence that shifts the way sequence is read
frameshift mutation will alter the specific codon in sequence and downstream codons.
Hence N-termus part of sequence remains the Same, while C-carboxy terminus is ALTERED
How many ATP is formed Anaerobically for 1 mole glucose ?
2 ATP
How many molecules are formed for 1 mole ?
1 mole has 6 x 10^23. molecules
Under anaerobic conditions, how many net molecules of ATP are produced by the consumption of 5 moles of glucose?
Under anaerobic conditions, only 2 net moles of ATP are generated from each mole of glucose. Therefore, after consumption of 5 moles of glucose, 10 net moles of ATP are generated.
Since each mole contains about 6 × 10^23 molecules, it follows that under anaerobic conditions, consumption of 5 moles of glucose yields 6 × 10^24.
What kind of cells are sperm and egg cells ?
Haploid
(sperm and egg cells have same genomic size)
What organs are part of mesoderm?
Heart, kidney and skeletal muscle
What organ is part of endoderm?
brain
What is an example of microfilament ?
actin
What is the role of centrosomes ? How do they a play a role in melanomas?
Centrosomes : are organelles that serve as the primary microtubule organizing center of a cell.
melanosomes most likely move along microtubules produced by and radiating from, the centrosome.
Where in male reproduction system do gametes become motile and capable of fertilization
EPIDIDYMIS
What is the function of reducing agent ?
Addition of a reducing agent will eliminate all disulfide bonds that link the two subunits of a molecule
(can separate parts of a homodimer )
What is role of lyase?
Lyase: enzyme that breaks a covalent bond without water or oxidation
Where in the body does the highest blood pressure occur ?
Aorta (heart)
what happens when arteries are constricted ? how does this affect blood flow ?
Vasoconstriction of arteries : narrows arteries, and adds resistance, resulting in decreased blood flow
where does blood flow during activation of sympathetic nervous system ? Why is this significant ?
when Symp Nerv system activated, blood flows to brain and skeletal muscle.
However, the amount of blood that flows through brain cannot be same as through muscle (brain:must be less)
Which amino acids can be phosphorylated ?
Serine and threonine can be phosphorylated (due to their hydroxyl groups in side chain)
Describe transmembrane domains
Transmembrane domains: regions of a protein that are HYDROPHOBIC
What are Epimers?
Epimers: stereoisomers that differ at their configuration to a chiral carbon
(alpha and beta designators help distinguish this)
What is osmotic pressure ? Formula ?
Osmotic pressure: tendency for water to move into one solution from another by osmosis
Osmotic pressure = i (van’t Hoff factor) x Molarity x R T
if you had Molarity of 0.2 and CaCl2, what is the total concentration of solute particles ?
CaCl2 dissociates into 3 ions, so you would multiply 3 x 0.2 to give value of 0.6 for total concentration
which event is mediated by a ligand gated ion channel
ligand gated ion channels depending on ligand binding
hence ***influx of sodium ions across motor end plate that results in depolarization of muscle fiber membrane will be mediated by this channel. **
this is because depolarization of muscle fiber results in sodium binding to acetylcholine
What is the formula that includes power and force ?
Power = force x velocity
what is necessary for ETC (electron transport chain to occur) ? What will NOT occur in anaerobic environment ?
ETC needs Oxygen for it to occur. Hence if there is NO oxygen, ETC will be turned off and phosphorylation of ADP in ETC will NOT occur
compare fast twitch and slow twitch fibers?
Slow twitch fibers: use aerobic exercise, hence will have greater capillary density (more oxygen and blood flow to fibers, more mitochondria and higher levels of oxygen binding capacity
fast twitch fibers: for quick sprints, will contract faster than slow twitch fibers, and will have higher Ca+ pumping capacity
What is convergent evolution ? Give example of animals that may apply to this process?
Convergent evolution is: process whereby distantly related organisms independently evolve similar traits to adapt to similar needs.
ex: Dolphins and sharks are genetically different, the dolphin being a mammal and the shark being a fish. Both of them, however, have developed similar structures to be able to survive in a similar environment.
What is an operon? What are its components?
Operon: cluster of genes that are transcribed together to give single messenger RNA molecule (mRNA)
operon contains same regulatory region (includes promoter) and structural genes
compare and contrast gene expression in prokaryotes vs eukaryotes? Where do translation and transcription occur ?
Gene expression in Eukaryotes:
- Transcription in Nucleus
-Translation in Cytoplasm
- RNA processing includes splicing of introns, adding 5 methylguanosine Cap and 3 Poly A tail
-
Gene expression in Prokaryotes
-Transcription in Cytoplasm
-Transcription in Cytoplasm
-Transcription and translation occur simultaneously
- NO RNA processing
What are the effects of an increase in contraction ?
increase in contract will cause
-increase availability of intracellular calcium
-decrease in transport of ca+ to extracellular environment
-increase in overall calcium stores to sarcoplasmic reticulum
what is the role of histone acetyltransferases (HATs) ?
Histone acetyltransferases PROMOTE transcription by adding acetyl groups to lysine residue and decreasing the attractive interaction between lysine residues in histones and DNA.
What will decrease transcription ?
condensing of chromatin and tight packing of nucleosomes together will decrease transcription
Which biochemical process CANNOT occur in hypoxic conditions (no oxygen)
Oxidative phosphorylation will not occur (since its oxidative), and if that cannot occur, citric acid cycle and electron transport chain will be DOWNREGULATE D (will be reduced)
Which process can occur under hypoxic conditions (no oxygen present) ?
Under hypoxic conditions, Lactic acid fermentation can occur.
lactic acid fermentation will consume NADH to donate electrons to pyruvate to form lactic acid and regenerate NAD+
Which biochemical pathway is phosphoglucose isomerase part of?
Phosphoglucose isomerase is a part of GLYCOLYSIS
-catalyzes second step where glucose-6 phosphate is converted to fructose 6 phosphate
What is role of tubulin ? Why is it necessary?
Tubulin is a cytoskeletal protein whose expression is similar in different cells. Therefore, tubulin is a housekeeping gene that is often used as a LOADING CONTROL to assess ** Total protein levels in various samples **
(tubulin levels will not change under hypoxic (no o2) levels)
What is a palindromic sequence ? What is an example ? What kind of enzyme cuts DNA at palindromic sequences
Palindromic sequence : if the sequence of nucleotides is the same as the reverse of its complement.
E.g. ACCTAGGT is a palindrome. The complementary strand will have TGGATCCA and if it is reversed then it will be the same as the original sequence.
Restriction enzymes cut DNA at
What is role of succinyl Co-A synthetase ?
Succinyl Co A synthetase: convert succinyl coA into succinate
(remember first word of enzyme is substrate, hence if you overexpress enzyme, you decrease level of that substrate )
What occurs during imprinting? What kind of process is it?
Imprinting: specific parent based inherited genetic modifications that will be passed to offspring based on specific parent trait transmission
-a parental specific transmission of trait
What do RNA viruses need to replicate themselves?
RNA viruses need a REVERSE TRANSCRIPTASE to replicate themselves
What is another name for Reverse trancriptase ?
reverse transcriptase Aka RNA Dependent DNA polymerase (since it depends on RNA and will produce DNA)
What can cause an increase in rate of enzyme activity ?
Increasing the temperature from 20 to 37 degrees Ceslsius can increase rate of enzymatic activity
Most enzymes are active at body temp (37 degrees C) however if enzymes are too hot or too cold, the rate of enzyme activity will change
What type of cells can produce mucus secretions ?
EPITHELIAL CELLS
which specific cells secrete mucus in respiratory epithelium ?
GOBLET cells are the one that secrete mucus in respiratory system and trap irritants and foreign bodies
-they can also be found in lungs to trap and inhbit microbrial infections
what areas of body are connective tissue located in ?
connective tissues are in blood, bone, fat and cartilage
What are the usual mechanisms of neutrotrnasmitter signaling termination?
neutrotransmitter degradation or reuptake
What occurs when an enzyme is inhibited?
When an enzyme is inhibited, the concentration of products Decrease and cocentration of reactants increase
Which enzyme can affect levels of serotonin ? Why is this beneficial ?
Inhibition of monoamine oxidase can cause increase in concentration of serotonin levels
This is beneficially because higher levels of serotonin can help improve depression
What are osteoblasts ?
Osteoblasts are responsible for Building Bones
(they deposit calcium, collagen and protein matrix that make up bones)
What are osteoclasts ?
osteoclasts: break down bone or matrix
what are osteocytes?
Osteocytes: osteoblasts that have become part of bone matrix and are involved in cell communication and mechanical sensing
What must happen for body to increase blood calcium levels ?
LOW osteoblast activity and high osteoclast (break down bone) activity is the best way to increase calcium levels in blood.
What is the function of ligase ?
Ligase: joins okazaki fragments together during replication of Lagging strand
What is role of helicase ?
Helicase: separates DNA strands at the origin of replication (this occurs at beginning of replication)
What is the role of topoisomerase?
Topoisomerase: prevents recoiling of DNA strands during replication
(by addressing strand’s tendency to supercoil)
What kind of enzymes are proteases?
Proteases cleave peptide bonds using water, hence they are HYDROLASES
What process are ketone bodies generated from?
Ketone bodies are generated from OXidation of Fatty acids
which processes occur during initial starvation vs prolonged starvation
intital starvation: glycogenolysis and gluconegenesis will occur to supply energy
during prolonged starvation: oxdiation of fatty acids and ketogenesis (make ketone bodies) will occur
What is rate limiting step in pentose phosphate pathway? What must occur ?
rate limiting step of PPP:
glucose 6 phosphate dehydrogenase catalyze reaction of glucose 6 phosphate to 6 phosphogluconate
-NADP+ must be reduced to NADPH
What are the two main phases of Pentose phosphate pathway ? What are main functions of NADPH?
Nonoxidative phase (irreversible)
and oxidative phase (reversible)
functions of NADPH:
- cholesterol synthesis
-fatty acid synthesis
-reduction of glutathione (protection from reactive oxygen species)
Which amino acids are hydrophillic? Examples ?
polar amino acids are hydrophillic
ex: threoine, lysine and arginine
Which amino acids are hydrophobic ?
proline, leucine, isoleucine, alanine, valine, Methionine
Which enzyme is for complexes I- IV in ETC (electron transport chain)
Complex I : NADH : ubiquinone oxidoreductase
Complex II : succinate dehydrogenase
Complex III: ubiquinol–cytochrome c oxidoreductase,
complex IV: cytochrome C oxidase
What is characterisitc of competitive inhibition ?
competitive inhibition: A drug reversibly binding to the active site of an enzyme
km increases, Vmax stays the same
What is the correct flow of filtrate in the urinary system/
glomerulus–> proximal tubule–>loop of Henle, distal tubule, and then collecting duct.
Which neurotransmitter regulates aggression and hunger ?
SEROTONIN
- serotonin regulates mood (including aggression), hunger/appetite, bowel movements and sleep
What is part of FIVE factor model of personality traits ?
- Openness to experience
2 conscietiousness - Extraversion
- Aggreableness
- Neuroticisim
OCEAN
What is intergenerational mobility ?
Intergenerational mobility: refers to a change in socioeconomic status from one generation to another within a community.
What is horizontal mobility ?
horizontal mobiity : describes a change in position WITHOUT change in social class
ex: someone changes their employment
What is intragenerational mobility ?
Intragenerational mobility: refers to socioeconomic changes (change in their social class) experienced by an individual WITHIN their own generation.
What is role of medulla oblongata ?
Medulla oblongate: regulates basic life functions such as respiration and heart rate
-also associated with reflexes (sneezing, swallowing, coughing and vomiting)
Which brain structures are part of limbic system ?
Amygdala (emotion), hippocampus (memory), Hypothalamus (homeostasis), and thalamus (relay info)
what is iconic memory ?
Iconic memory: is the subtype of sensory memory which stores visual information
