Bio/Biochem Flashcards
What happens in geminal part of lymph node?
affinity maturation and somatic hypermutation occurs in germinal part of lymph node
What happens at a palindromic sequence when cutting?
Cutting palindromic will make last 3 nucleotides stay and add 3 new ones honestly I don’t understand the answer at all
What happens over time with antibodies against a bacteria?
Over time, antibodies will increase affinity for bacteria
What does affinity maturation do?
Affinity maturation will make B cells have more affinity for antigen
What does 1 band on SDS PAGE represent?
SDS PAGE with 1 band can be multiple subunits or 1 unit
A researcher compares two antibodies that recognize the same antigen, even though they are made by different animal species. How will these antibodies differ?
Constant region of antibodies can differ but recognize same antigen
What do competitive inhibitors block?
Competitive inhibitors block substrate and Transition state
Where do trypsin and chymotrypsin work?
Trypsin works in stomach, chymotrypsin in small intestine
How to solve given V initial and substrate?
Given S and V initial, use Merchailis menton equation
How are zymogens activated?
Zymogens activated by pH, hydrolytic cleavage, and conformational changes
Effect on Vmax by increasing substrate concentration?
Vmax is not affected by substrate concentration
How are enzymes activated?
Enzyme activates by pH changing. Hydrolytic cleavage will not occur due to pH changing. Only by oxidation/reduction
Fibroblast function?
Fibroblasts make collagen
Endocrine vs exocrine?
endocrine release hormones into blood, exocrine release digestive enzymes
Difference between sequence and fully folded protein?
When comparing 2 proteins, when one is peptide sequence, one is fully folded protein, they differ because tertiary interferes
FSH in blood?
FSH can go in bloodstream without a transport protein and remain soluble
enzyme is more effectively inhibited in uncompetitive when?
enzyme is more effectively inhibited in uncompetitive when substrate concentration increases (only bind to ES complex) or inhibitor concentration decreases
would you use probe to locate transcript?
using a probe to locate a transcript is ineffective because its in cytoplasm
what do nuclear proteins need?
nuclear proteins require nuclear localization domain, DNA binding domain. Saying something is a homodimer means you need protein binding domain. do not need signal sequence domain
nuclear factors function?
nuclear factors differ in each cell type and can control regulation. Not the promotor, enhancer, or gene
How does SDS PAGE separate?
SDS PAGE does not separate based on charge. only by size. Isoelectric focusing and ion exchange do separate based on charge.
Inducer function?
inducer binds to repressor to start transcription in a negative inducible operon. activator binds to recruit promoters to start transcription
f plasmid function?
f plasmid used in conjugation to separate DNA not being incorporated into bacterial DNA
amitotic division result?
amitotic divisions result in unequal distribution of chromosomes
macronuclues function?
macronucleus is used to provide proteins for everyday functioning. not involved in meiosis
Where would proteins in golgi go if they traveled retrograde?
back to RER becasue retrograde means go backwards
Passage implies most strongly?
Look for purpose of experiment
Putting mouse antibody in human won’t work why?
Human body would think of the antibodies as foreign and have immune repsonse to them.
Cell goes into endothelium how?
Must still be bound even with mutation
How many electrons can cytocrome c carry?
1 because cycle between ferrous and ferric state
Best primer to use?
Has most GC content and GC at 5’ and 3’ end
Effect of increased insulin?
decrease blood glucose levels
Increase substrate effect on Km?
no effect
Changing AA from D to L?
would inhibit synthesis
Nervous system response when fewer pigment molecules are available?
Fewer signals of weakly perceived signals are sent to brain. Not the same number of signals.
Proteins affected by color blindness?
Visual receptors in the retina (photoreceptors here)
How to know if there is significant difference?
Look for indication
If you don’t know how to answer question?
Look at chart
With no oxygen, which is not produced?
Acetyl Coa because lactate not transported to mitochondria
Cl- more in systemic arteries or veins?
Veins because more HCO3- in veins
Effect of substituing proline for alanine?
Affect secondary structure
Enzyme used for activating protein?
Protease
Enzyme mutated to have higher affinity for cooperative site will affect reaction how?
Original reaction will occur at a slower rate due to conformational changes of enzyme
Hydrogen bonds are in which protein structure?
Secondary, tertiary is characterized by hydrophobic effects
Polypeptide 4 amino acids long, include start or stop codon?
Include start codon only
Denature over 60% of strand of DNA?
Only part wil reanneal
eukaroytic non coding RNA includes?
microRNA, snoRNA, tRNA, rRNA, but not mRNA/ hnRNA
Nucleic acid that can catalyze reactions?
RNA only, not DNA
G proteins active when?
Only when GTP is bound
Tyrosine kinase phosphorylated can bring signal amplification because?
ample time for the signaling proteins to be activates by phosphorylated receptor
Mito membrane made permeable affects apoptosis how?
Cytochrome c goes to cytosol
Best way to decrease serum cholesterol levels?
Limit the rate limting step in cholesterol synthesis
How steriod hormones transport?
Bind to cystolic receptor to enter nucleus
Changing from alanine to cysteine would affect tertiary structure of protein how?
Change polarity because cysteine is negatively charged polar
Polar residues will be located on outside or inside when interacting with oil?
Inside because do not want polar interactions with oil
Hydrogen bonding of Glu occur with?
NH of another residue. Glu is -COO not COOH at physiological conditions. There is no COOH in the backbone of a peptide
Is meiosis 1 or 2 heterotypic? When does crossing over occur? Is there an S phase in meiosis 1 and 2?
Meiosis 1 is heterotypic (reduces from 2n to n) Crossing over only occurs in meiosis 1. There is no S phase in meiosis 2
Cyclin and cyclin dependent kinase functions?
Necessary for mitosis to occur
Progesterone spike when?
Ovulation and forming corpus luteum
Meiosis 1 result with males?
Make secondary spermatocytes. Sister chromatids still attached
Order in which cells form after fertilization?
Morula, blastula, gastrula
Notochord comes from which germ layer? Spinal chord?
Notochord comes from mesoderm, develops in the vertebral column. spinal chord comes from ectoderm
blastopore forms what?
mouth or anus
Greater amount of wet mass on graph shows?
More solvation
Tertiary structure includes?
covalent interactions between constituent amino acids (disulfide bonds), hydrophobic effect, and ionic bonds between side chains
Given a protein similar to one in experiment, results indicate?
Results would be similar to the one from passage
Given that silicon oxide absorbs polar amino acids, which would be best?
Choose amino acids that are all polar
Charge of something with pka of 3 and 7 at pH 2?
ERROR!
Protein is 5*10^4 amu, how many amino acids in it?
1 AA= 110 Da= 1amu. 5*10^4 amu= 50kDa. 50000 Da/110Da= 450
A person’s BP is high sitting, how would it change laying down?
Would decrease BP because do not have to pump blood against gravity
Diarrhea effect on ions?
Cloride ions go into lumen of large intestine to be released
What should substrate concentration be at when measuring Kcat?
It should be saturating conditions
Anion exchange, what stays and would a peptide of -1 charge or -5 elute faster?
Anions stay, cations leave fast. The peptide of -1 would elute faster than peptide of -5
Drugs causing tubal pregnancy inhibits?
Transfer of ovum from ovary to uterus. (not decreasing FSH secretion)
Renal failure due to?
inadequate blood volume to filter. Not due to salt build up in distal tubule
Human without sweat glands effected how?
Gain instead of lose heat by radiation
Female RS, male RR, how can imbalance of sex chromosomes be compensated?
Inactivation of male R, not female R
Which data set shows most of inactivation?
The one with highest on graph
Which would occur during starvation?
Fatty acid oxidation. This occurs after gluconeogenesis. NOT cori cycle
Pressure 28 atm, 0.5M, now 7 atm, what is M?
0.12M because decrease to 1/4
Prior to secretion, a mature protein will?
delay graph start
Effect of losing plasma protiens on osmotic pressure?
Plasma proteins increase osmotic pressure in blood which then return fluid to circulatory system. With malnutrition, osmotic pressure of blood would decrease, and would increase fluid of body tissues.
Protein aggregation/apoptosis relationship
correlate positively
cells not in noncancerous means what type?
somatic
ATPase activity produces?
ADP + P
initial filtration step
passive flow due to pressure differences (not countercurent exchange)
what can enzymes do?
change pH, co-localize substates, alter substrate shape. does not affect primary structure
ornithine decarboxylase assay is highly specific means that it:
can distinguish ornithine decarboxylase activity from the many other enzymatic reactions in a cell.
Normally, a hypothalamic factor stimulates the release of adrenocorticotropic hormone (ACTH) from the pituitary gland. In a patient with Addison’s disease, the secretion of the hypothalamic factor will?
be higher than normal because adrenal cortex destroyed so more secreted from hypo
involved in elongation?
dna polymerase. not ter protein for termination and initiation proteins for initiation and dicer produces siRNA
found that DNA adds 3 to 5 and read 5 to 3?
flip lead and lag strand
Which must appear for missense? UUU AUG UGA None
none of the above. these are all start/stop
H5 for histone?
only in erythrocytes of birds.
anti-miRs bind where?
to miRNA, which pair with mRNA
secondary structure of nucleic acid?
cloverleaf of tRNA. DNA RNA hybrids is tertiary
plasmid vector contains?
bacterial origin of replication, restriction enzyme sites, host transcription initiating sequence. does not contain a reporter gene
necrosis?
premature death of cells by autolysis. not programmed
what nucleoside triphosphate is hydrolyzed in cap dependent eukaryotic initiation?
GTP (not ATP)
ribosome eukaroyic vs pro?
E: 80S P: 70S
which would inhibit carbonic anhydrase competitively?
Cl-. because active site of enzyme is cation
how is CO2 carried in blood?
binding hemoglobin and dissolving in plasma
Type F carbonic anhydrase deficiency is a recessive disease which is found in 80 of every 500 individuals in a population. Out of every 500 individuals, how many are expected to be phenotypically normal carriers?
80/500 = 16% so q squared= 16 so q= 0.4 so 2.6.4= .48 so 240
According to the passage, which of the following properties of carbonic anhydrase are represented by the value 10^6?
this is Vmax, so Kcat and Et are represented. turnover number= Kcat. Kcat=Vmax/Et
glucagon effect on pyruvate decarboxylase?
decrease it. this occurs to produce acetyl coa for citric acid cycle
given 5*10^4 amu protein, how many AA residues?
1 amu= 110 Da so 5*10^4 amu= 50 kDa. so 50 kDa (1 residue/110 Da) = 450 residues
structure damage to nucleus effect?
hurts ability to divide and perform mitosis
prokaryotes with human DNA?
nucleus won’t be affected, lack spliceosome. Their RNA polymerases can transcribe human genes
which hormone involved in imunosuppression?
cortisol
connects cells?
tight junctions (waterproof), gap junctions (share cytoplasm)
keratin is what type of filament?
intermediate filament
remove parathyroid gland effect?
neurological effect
hydrophobic AA residues go where on protein?
go on inside. hydrophilic go on outside
All of the following hormones exert their downstream signaling action through binding of an extracellular receptor EXCEPT
not thyroxine because it is AA hormone so behave like steroid. Others that do are vasopressin, FSH, melanin
pictures of aldehydes?
can be an alcohol enol form that can form aldehyde
temp change during sublimation?
no temp change because energy is absorbed or emitted
epinephrine effect on gluconeogenesis?
stimulates lipolysis and free fatty acid release, which increase gluconeogenesis
If not properly compensated for, sustained hyperglycemia promotes cellular dehydration by which mechanism?
Glucose increases the osmotic pressure of the extracellular space
The juxtaglomerular cells in the kidney are responsible for the synthesis, storage and secretion of the enzyme renin. These cells are of the same type found in:
small intestine (smooth muscle cells so not nephron)
Which of the following correctly describes the negative feedback loop which regulates appetite and adipose tissue levels?
Decreased adipose tissue causes lower concentrations of leptin hormones, which stimulate appetite until increased adipose mass raises leptin hormone concentrations, and appetite decreases. Leptin inhibits appetite
needed to find delta G?
need concentrations to find equilibrium constant and temp. not ion product
how many NaOH needed to optomize titration in cation chromatography
0.25 because this will allow net positive charge
Which amino acid(s) have side chains that typically include acidic protons at physiological pH?
lysine, not glutamic acid/aspardic acid. they will be deprotonated at 7.4 pH. lysine will have acidic H
Two cysteine residues undergo a reaction to form a disulfide bond. Which of these reactions can be coupled to this process?
NAD+->NADH (need reducing agent)
chymotrypsin cuts at aromatic side chains. cleave at ends?
do not cleave at terminus
Acidic and basic amino acids can be freely found in the bloodstream. How are these molecules involved in buffering the plasma at physiological pH?
Under low-pH conditions, acidic amino acids can decrease H+ concentration. Acidic are - at 7.4 So at low pH, more H+ so they pick up H+
According to Le Châtelier’s principle, which glycolytic disturbances would force the metabolic system to reestablish equilibrium? increase glucose, decrease pyruvate, increase hexokinase, decrease ATP
increase glucose, decrease pyruvate, decrease ATP. NOT increased hexokinase because this is an ezyme, which will NOT affect equilibrium
Which of these scenarios constitutes a demonstration of the second law of thermodynamics?
The second law of thermodynamics states that a spontaneous reaction or cyclic process must yield a net entropy increase. A catabolic process may be coupled with an anabolic reaction, yielding a net increase in entropy.
phosphate with sulfur attached, how to break?
use H2O
cooperative vs non cooperative graph?
cooperative: sigmoidal non cooperative: hyperbolic
A researcher is looking to isolate a protein from a sample of crude tissue lysate. Following a properly conducted western blot, the researcher is unable to obtain any conjugation and the blot yields no signal for the protein of interest. Immunoprecipitation conducted on the sample using the same monoclonal antibody under neutral conditions returns a pure sample of the desired protein; however, results are less successful under mildly alkaline conditions. Which of these statements is a possible explanation for these results?
The protein of interest is a dimer, and the antibody binds at the junction between the two monomers.
In the lab, the technique of immunohistochemistry is used for:
providing a detailed and visual report on the protein expression within a tissue.
How can a scientist running an SDS-PAGE procedure assure that the difference in running distance on the gel is due to the length of the peptide and not its shape?
Detergent is added to the running buffer. SDS is a detergent, having hydrophobic and hydrophilic ends. does not denature primary
A protein from the urine of a chronically ill patient was isolated and run on an SDS-PAGE gel. The result displayed on the gel was a long smear instead of a crisp band. These results can most likely be attributed to the fact that:
protein was partially degraded
why does graph show lots of cells in mitotic phase?
treatment arrests cells in M phase. (not treatment stimulates to M phase becasue they could leave M)
damaged cells are capillaries, are what type of cell?
endothelial cells. capillaries are 1 layer of these.
In a healthy individual, when would you expect ACTH levels to be at their lowest?
8:30 AM because cortisol highest at 8 AM so has negative feedback
Which of the following processes are NOT likely to contribute to hepatic glucose production by mice fed an HFD?
I. Gluconeogenesis using TCA cycle intermediate as substrate
II. Hepatic glycogen breakdown
III. Gluconeogenesis using pyruvate as substrate
IV. Gluconeogenesis using acetyl-CoA as substrate
IV
In eukaryotic cells, where is the highest concentration of phosphorus likely to be found?
nucleus. 1 per base. not cytosol becasue there is only 1 per phosphate
functions of cholecystokinin
suppress hungry, inhibit gastic emptying, stimulate gastric acinar cells. NOT inhibit somatostatin
Which of the following most likely pushes a cardiac myocyte above the threshold membrane potential level?
A neighboring cell’s depolarization allowing some positive ions to enter through gap junctions (Na+ leave not enter through exchange pumps)
hich of the following most probably accounts for the decrease in membrane potential at point 1 on Figure 2?
K+ voltage-gated channels beginning to open before Ca2+ voltage-gated channels open
ovary germ layer?
mesoderm. also Kidneys, bone marrow, spleen. stomach from endoderm
cDNA vs genomic library
genomic is larger, genomic sequence contains both coding and non-coding sequences, whereas a cDNA library includes only coding sequences. A genomic library includes promoters, but a cDNA library does not
why does RNA electrophoresis not require SDS?
SDS detergent is used to ensure that polypeptides have a negative charge proportional to the length of the molecule. RNA molecules already have a net negative charge proportional to the number of nucleotides.
The results shown in Figure 1 most strongly support which of the following conclusions?
as temp goes down, oxygen demand is less. this means damage is done not related to this.
citrid acid cycle occur where
mitochondria
In the experiments described in the passage, what was the purpose of using heat-shocked phage cultures?
To act as a negative control to ensure that there is no effect when no effect should be observed. (negative means to ensure no effect)
The results displayed in Figure 1 most strongly support which of the following conclusions regarding MS-infected cells?
During infection, MS-infected cells create phage proteins, generating high cellular ATP demand. This results in increased cell respiration before cell death. More ATP due to protein phage production, not immune response
toxin that affects actin will hurt what process
cytokinesis, ring of actin pinch cells apart
Gram staining is a common laboratory technique used to classify bacteria. When stained, Gram-positive bacteria appear dark purple under a microscope; in contrast, Gram-negative bacteria appear pink. How can this visible difference between the two bacterial categories be explained?
Gram-negative bacteria have a thinner cell wall, which allows the crystal violet stain to exit the cell.
which are eukarotes? not?
Yes: plants, fungi, hyphaea, protozoa No: archaea, bacteriophages
four cups with bacteria, which are anaerobic?
ones at bottom and spread throughout (dont’ need oxygen)
heterotroph vs autotroph? chemo vs auto?
hetero- dont make their own enery. Auto use organic and chemo use non organic
transduction? transformation?
transduction- a bacteriophage transfers genetic material from one bacterial cell to another during infection.
transformation- occurs when bacteria pick up genetic material from their surroundings.
Of these combinations, which could result in a successful transfer of genetic material through conjugation?
An Hfr bacterium with an F- cell. Hfr has F in circular chromosome
class I transposon?
conversion of DNA to RNA.
a conversion of RNA to DNA.
the production of an additional copy of the transposon. These elements first undergo transcription into RNA using RNA polymerase; as their name implies, they are then reverse transcribed back into DNA and placed in a distinct location elsewhere in the genome.
caspid fact?
most viruses only have 1 or 2 genes coding for caspid proteins
A patient actively infected with human papillomavirus (HPV) was found to have high serum antibody levels. HPV is a non-enveloped DNA virus. Antibodies isolated from this patient would most likely show high affinity for:
a viral caspid protein because the others would not be exposed to surroundings
Which of the following enzymes must be present within the viral capsid of a (-)RNA virus for successful infection and replication to take place?
RNA dependent RNA polymerase (-)RNA used to make (+)RNA. Reverse transcriptase is not necessary; once the new (+)RNA is synthesized, it can be directly translated into protein without a DNA intermediate.
C: Protease and other viral enzymes will be produced by host ribosomes from the (+)RNA and need not be carried in the capsid initially.
D: Integrase is an enzyme responsible for integrating viral dsDNA into the host genome. It is not required for (-)RNA viruses.
reverse transcriptase?
is carried within the retroviral capsid and released into the cytosol following viral penetration.
Uses RNA template to make DNA, then uses DNA template to make DNA
Although Creutzfeld-Jakob Disease is perhaps the best-known prion disease, recent hypotheses suggest that neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease may have prion components. Which of the following, if true, would best refute the claim that prions contribute to the pathology of Parkinson’s disease?
Neurons from Parkinson’s patients show absolutely no increase in expression of heat shock proteins or cellular chaperones. (These help fold misfolded proteins like prions). NOT Knockout mice lacking the PrPC, a prion precursor protein, do not develop Parkinson’s disease when fed intact prions. because “prions induce conformational changes in endogenous precursor proteins that result in their conversion to the prion form. If the precursor protein is absent, the prion has no target and cannot cause pathology”
Researchers hypothesized that the majority of aneuploidies that occur in meiosis I result from malsegregation of individual chromatids rather than a failure of homologous chromosomes to separate. Which of the following is the most likely mechanism that would explain this possibility?
Premature division of homologous chromosomes into constituent chromatids, which then separate randomly in metaphase I. NOT Spindle fibers fail to attach to the centromeres of homologous chromosomes in meiosis I, causing a nondisjunction event because “The meiosis I nondisjunction described results in the failure of homologous chromosomes to separate; and as such would not present an alternative hypothesis.”
Vasodilation, increased capillary permeability, and decreased systemic vascular resistance can be predicted to lead to
Increased tyrosine kinase activity, tissue hypoxia, hypotension
Skeletal muscle is especially rich in phospholipids, of which 10-20% are arachidonic acid. Which of the following changes would lead to a decrease in the fluidity of the sarcolemma?
Converting some of the arachidonic acid present into its all-trans unsaturated geometric isomer. (gets rid of kinks so pack better)
antibodies where?
bloodstream or other exocrine secretions like tears or saliva
All of the following are examples of endosymbiosis EXCEPT:
Endosymbiosis occurs when one organism lives inside another one. Ribosomes are assemblages of RNA and protein that are responsible for translation and have a very ancient origin. All cells contain ribosomes, so they are not an example of endosymbiosis. YES? Dengue fever (a virus) in A. aegypti. mitochondria in eukaryotic cells. B. nitrogen-fixing bacteria in the roots of legumes.
Researchers wish to isolate the protein product of BRCA1, a gene involved in the development of breast cancer. They also want to know this protein’s primary structure. Which analytical technique(s) should they use?
The Edman degradation is a technique used to sequence peptides by progressively removing amino acids
Which of the following would be most appropriate to treat the vascular effects of septic shock
. Aldosterone to increase sodium and water reabsorption in the kidneys.epsis happens when this cascade occurs throughout the body, resulting in a system-wide increase in vascular permeability. This leads to a decrease in blood pressure termed septic shock, as too much fluid, other molecules, and proteins leave the blood. Therefore, the question is really asking how you would treat a severe drop in blood pressure. A medication that raises blood pressure would help reverse the impacts from hypotension and therefore help treat septic shock. Aldosterone works to increase sodium and water reabsorption from the kidneys, leading to an increase in blood pressure.
During development, replication of the small fraction of mtDNA molecules transferred to offspring via a single oocyte can lead to a dramatic decrease in mtDNA diversity between generations. This mechanism of genetic variance is most analogous to:
genetic bottleneck
α-glucosidase inhibitor?
prevents breakdown of dissacharides
Which of the following processes occur in type 2 diabetes?
Impaired secretion of insulin by pancreatic β cells
Insulin resistance
Untreated type I diabetes and unmanaged type II diabetes lead to increased risk of stroke or heart attack. Why?
Endothelial cells in the blood vessel lining take in an excess of glucose, which causes them to overexpress surface glycoproteins, in turn weakening the basement membrane.
While observing chromosomal crossover in a cell undergoing meiosis, students were most likely to have also observed what concurrent event?
spindle formation (prophase I)
Absent any mutagenic effects, HR-mediated repair is likely to have the greatest accuracy when the exchange of identical genetic information occurs between which molecules?
Sister chromatids during G2
Expression of gene X has been shown to stimulate adipocyte growth and differentiation. Given this, gene X expression is likely to be increased by the effect of what hormone?
Insulin. Insulin’s anabolic effects include the stimulation of adipocyte (fat cell) growth. This is consistent with the anabolic needs of the body in the well-fed state - the bodily condition under which insulin levels are normally elevated. NOT cortisol
