B MCAT- Bio, Biochem Flashcards

Question

ribosome

Answer 1

Site of protein synthesis within a cell. Ribosomes are made from rRNA, which are made in the nucleus during transcription.

Answer 2

Experiment which shows you the presence and relative amount of a specific protein. First, run sample on electrophoresis gel. Second, introduce antibody conjugated to a florescent probe, which will bind specifically to protein of interest. Left Lane >>> Right Lane: purified sample > sample of normal cell nuclear lysate> sample of whole cell lysate from normal cell> sample of affected cell nuclear lysate > sample of affected whole cell lysate. Intensity of band indicates amount of protein present. Lower band indicates part of protein missing.

Answer 3

the product of lysis, a cell that has been broken down.

Answer 4

The Bohr Effect describes what happens when there is an off-loading of oxygen from hemoglobin to surrounding tissues. The sigmoidal curve shifts RIGHT (partial pressure of oxygen in surrounding tissue on x axis; % hemoglobin oxygen-bound on y axis). An INCREASE of the following conditions lead to this Bohr effect right shift of the curve: -temperature -pCO2 (i.e. active muscles) -acid -exercise -(2,3) DPG

Answer 5

CO causes the sigmoidal curve to shift left and peak at a lower point. Hemoglobin's affinity for CO is more than 200x that of O2. Therefore, there is less hemoglobin available for O2 to bind to, causing the curve to peak at a lower point. However, a CO bound at the first of four binding sites on a hemoglobin protein will still increase affinity for the remaining sites and the curve will initially rise faster (shift left) than without CO. This leads to the O2 not as readily leaving the hemoglobin to go to surrounding tissue.

Answer 6

cooperativity Ex. Oxyhemoglobin Disassociation Curve

Answer 7

An enzyme involved in DNA excision repair that cut at specific DNA sequences (e.g. to remove a dimer caused by UV radiation).

Answer 8

Tool to start DNA transcription to RNA. 4 pieces (genes) to any operon: regulator > promoter > operator > structural (e.g. enzyme that performs respective duty of the particular operon). 2 categories of operons: 1) Inducible systems--default is that the receptor is bound to the operator and keeps it in the "off" position; the RNA polymerase can not travel past the promoter region of the operon. When inducer is present, receptor binds to it instead and the operon can transcribe. 2) Repressible systems--the repressor can not bind to the operon by itself. 2 prokaryotic operons to know: 1. Lac Operon 2. Trp Operon.

Answer 9

There are four categories of chemical signaling found in multicellular organisms: paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions. Paracrine signaling is between cells that are close together, via Diffusion through the extracellular matrix. Fast acting, short lasting. Signals from distant cells are called endocrine signals, and they originate from endocrine cells. (In the body, many endocrine cells are located in endocrine glands, such as the thyroid gland, the hypothalamus, and the pituitary gland.) These types of signals usually produce a slower response but have a longer-lasting effect. The ligands released in endocrine signaling are called hormones, signaling molecules that are produced in one part of the body but affect other body regions some distance away. Autocrine signals are produced by signaling cells that can also bind to the ligand that is released. This means the signaling cell and the target cell can be the same or a similar cell. Ex. pain sensation. Gap junctions in animals and plasmodesmata in plants are connections between the plasma membranes of neighboring cells. These water-filled channels allow small signaling molecules, called intracellular mediators, to diffuse between the two cells. Small molecules, such as calcium ions (Ca2+), are able to move between cells, but large molecules like proteins and DNA cannot fit through the channels. The specificity of the channels ensures that the cells remain independent but can quickly and easily transmit signals.

Answer 10

Tend to end in "-in". Water soluble, can not cross cell membrane. Require receptor to communicate across a cell membrane. Act very fast.

Answer 11

Hormone insulin and its opposite glucagon are both peptide hormones.

Answer 12

Water soluble. Carried around bloodstream by molecules that are not water soluble. Can cross cell membranes. Slower acting, longer lasting. Secreted by three “steroid glands”—the adrenal cortex, testes, and ovaries—and during pregnancy by the placenta. All steroid hormones are derived from cholesterol. Tend to end in "-one" or "-ol" or "-oid"?

Answer 13

Tend to have "-ine" or "-in" ending? Tend to be a couple amino acids stuck together (vs. a long polypeptide chain).

Answer 14

supports/ regulates homeostasis.

Answer 15

disrupts homeostasis. ex. oxytocin during labor.

Answer 16

a hormone acting on another hormone.

Answer 17

hypothalamus

Answer 18

An inducible operon (default position is "off"). When the structural gene is "on", it produces an enzyme that can break down lactose to make glucose and galactose (if no glucose present on its own).

Answer 19

A repressible operon (default position is "on"); when it is "on" the structural gene codes to make tryptophan. In presence of plenty of tryptophan, the tryptophan becomes co-repressor and binds to the operator gene to repress production of more tryptophan. (negative feedback mechanism)

Answer 20

In eukaryotes, DNA is replicated via transcription to mRNA in the nucleus of the cell. Helicase unwinds the DNA. Single-strand binding proteins keep the integrity of the strands. DNA polymerase transcribes to RNA in a semi-conservative process. DNA ligase puts the strands back together. Eukaryotes have multiple origins of replication. 3 steps to DNA transcription: Initiation, elongation, and termination. After post-translational modifications (intron splicing, 5' cap, poly A tail), the mRNA can leave the cell's nucleus.

Answer 21

3 types of DNA excision repair: base excision nucleotide excision mismatch repair Endonucleases remove the damaged DNA.

Answer 22

AUG = start codon. Always methionine! stop codons: UAA UGA UAG

Answer 23

Amino terminus (nucleophile) attacks the carbonyl carbon on the carboxyl terminus of the next amino acid in a condensation reaction which releases an H2O and forms a peptide bond.

Answer 24

E, Glu, Glutamic acid (glutamate when deprotonated, neg charge, COO- in R group) D, Asp, Aspartic acid (aspartate when deprotonated, neg charge, COO- in R group) Y, Tyr, Tyrosine (aromatic with O- in R group)

Answer 25

H, His, Histidine R, Arg, Arginine K, Lys, Lysine All have N with lone pair nucleophile in side chain.

Answer 26

G, Gly, Glycine A, Ala, Alanine L, Leu, Leucine I, Ile, Isoleucine V, Val, Valine P, Pro, Proline M, Met, Methionine W, Trp, Tryptophan (aromatic) F, Phe, Phenylalanine (aromatic) All have either long carbon chains (aliphatic) or are aromatic.

Answer 27

N, Asn, Asparagine Q, Gln, Glutamine S, Ser, Serine T, Thr, Threonine C, Cys, Cysteine (-SH R group; can form disulfide bonds!) (N, O, or S in side chain.) and more...

Answer 28

Ex: tRNA's anticodon to mRNA's stop codon (AUG) will read... 5'-CAU -3' in tRNA.

Answer 29

Even after translation from mRNA > tRNA > amino acid chain, we don't have a functioning protein until post-translational processing. This includes... Covalent modifications like peptide bonds, N-terminus, C-terminus, and amino acid residues. and non-covalent modifications like protein folding, trafficking (ex. packaging based on where protein is headed), and addition of cofactors. Translation happens in the ribosomes and the post-translational processing happens in the golgi apparatus. (?)

Answer 30

Gel electrophoresis is an electrolytic process used to separate molecules by charge. Gel plate connected to battery or electrical socket to put charge at either end. Cations (+) will migrate to the cathode (-). Anions (-) will migrate to the anode (+). Which molecules are represented by the bands depends on which end you started on.

Answer 31

AGAROSE GEL electrophoresis can separate NUCLEIC ACIDS by size. Mesh-like substance in gel that causes larger nucleic acids to get stuck, while smaller nucleic acids get through and travel further, faster (similar to proteins in acrylamous gel). Read top to bottom (larger to smaller). A "ladder" on the side provides a frame of reference by which to measure the size of each nucleic acid per how many bases it has (in kilobases, kb). Note that nucleic acids are always negatively charged because of the phosphate groups, so always migrating down toward the anode.

Answer 32

Restriction enzymes, a type of endonuclease, cut very specific DNA sequences that are ~3-6 bases in length. "Molecular scissors" in cloning. So, if you know the size of the gene sequence or plasmid you are looking for, you can use gels as a fast diagnostic tool check size.

Answer 33

Southern blot is a test to run after agarose gel electrophoresis to detect the presence of a specific DNA sequence in your fragment. First, run sample with agarose gel electrophoresis to separate by size and identify your predicted fragment. Second, transfer fragments to a solid membrane. Third, construct a radiolabeled DNA probe specific to the sequence of interest. Only fragments complimentary to the probe will be visible. (Northern blots work the same but geared for RNA.)

Answer 34

Differences in restriction sites result in different fragment sizes, and therefore different number of bands. More restriction sites > more bands. Used to confirm cloning experiments or identify genes associated with genetic disorders.

Answer 35

Acrylamide gels are used to separate PROTEINS based on size. Pores of the gel allow for smaller proteins to travel faster and further than larger proteins (similar to nucleic acids in agarose gel). Read top to bottom, with anions (-) always migrating down to the bottom anode; smaller anions migrating further down than the larger ones. Can run in different conditions. 1) Native PAGE - NO denaturant added. Proteins separated by mass and charge. 2) SDS PAGE - Anionic detergent; breaks all non-covalent interactions. Masks charge and separates proteins by size only. 3) Reductive SDS PAGE - SDS + reducing agent; breaks disulfide bonds found in the tertiary and quaternary protein structures. Separates by mass.

Answer 36

Remember SNOW DROP. S (southern) D (dna) N (northern) R (rna) o____________o W (western) P (proteins)

Answer 37

Separates PROTEINS based on isoelectric point (pI). Cathode >>> Anode 14 >>>1 Phosphorylation adds negative charge and causes a decrease the pI. Lowering pI makes the protein negatively charged for a wider range--anions will migrate further toward anode. Recall... When the pH equals pI (pH=pI), the protein is at its isoelectric point; no net charge. Zwitterionic form. When the pH is lower than the pI of the protein (pHPI), it will be negatively charged.

Answer 38

ex: N90G = N asparagine, at position 90, replaced with G glycine.

Answer 39

When two dominant alleles are both expressed. Ex. There are three human alleles for blood type--A, B, and i. You inherit two of the three. If you get AB, both are expressed.

Answer 40

two homogeneous genotypes mate and create a hetrogenome in which you get an inbetween expression. Ex. straight hair + curly hair = wavy hair.

Answer 41

For males, half of their sex-linked chromosomes are X and half are y. For X-linked recessive traits, males can either have the trait and have it expressed, or not have the allele for the trait. Females can have the trait, not have the trait, or be a carrier of the trait. Sex linked traits on Y chromosome are extremely rare. Think: sex-linked = X-linked, unless otherwise explained.

Answer 42

There is not a perfect correlation between genotype and phenotype. Genotype is your given genes; phenotype is what is observable (based on interaction between genotype and the environment.

Answer 43

(think percentage) The portion of the population with a certain genotype who actually express the phenotype.

Answer 44

The degree (intensity) to which a particular trait is expressed.

Answer 45

A mutation that does not show up in proteins.

Answer 46

Germline (germ) cells create gametes—sperm in males and ovule in females. Germ cells are diploid (2n chromosomes) and undergo meiosis to form gamete (n chromosomes). Germ cells are the only cells which can undergo meiosis and mitosis Regarding mutations, the only mutations that are passed along are those which affect the germ cells.

Answer 47

deletion, inversion, duplication All affect a single chromosome.

Answer 48

Insertion of a chunk of one chromosome into a different chromosome. (not to be confused with crossover during cell replication; in that case we are swapping chunks of DNA from the SAME chromosome number, ex. #15)

Answer 49

Two types--missense and nonsense. One nucleotide is swapped with another. Can affect proteins downstream. Though it is possible to have a silent point mutation (typically because of redundancy of wobble base position).

Answer 50

A mistake in nucleotides intending to code for one amino acid, but instead coding for another. Mis-sense mutations tend to be particularly severe and troublesome if the intended and actual amino acids have different characteristics (ex. polar and nonpolar side chains). Can cause severe disruption to the protein structure.

Answer 51

Codes for a premature STOP codon. Protein synthesis stops prematurely (truncates protein during translation). May be less impactful if it happened later in the translation have little to no effect (especially considering post-translational modifications), or could be early on and cause a great deal of damage.

Answer 52

A nucleic acid is deleted, shifting the entire reading frame downstream from that spot. The ribosome reads bases in 3s. Can also result in stop codons in addition to other mutations.

Answer 53

-Autoradiography and self-directed mutagenesis determine potential phosphorylation sites. -RT PCR is used to measure mRNA levels of specific genes. -Generating cell lines with modified proteins can be used to test potential treatment options.

Answer 54

Peptide hormone. Receptor outside cell, fast-acting, short-lasting. Increases glucose uptake by cells, effectively lowering blood glucose.

Answer 55

CO2 increases during exercise. Bohr Effect curve shifts right (hemoglobin releases more oxygen; hemoglobin has less affinity for oxygen). CO2 + H2O > H2CO3 (carbonic acid) > HCO3- + H+ Blood becomes more acidic (pH decreases). (Cell takes up Cl-)

Answer 56

A left shift in the Bohr effect curve indicates that hemoglobin is holding oxygen tighter; more affinity for it. Can be caused by... - Decrease in C02 (hyperventilating). reduction in H+, increase in pH. - High altitudes where there is less O2 present. - Fetal hemoglobin where affinity for O2 must be greater than mom's.

Answer 57

The immune response innate in human's white blood cells (there at birth). Includes skin, mucus, tears, cilia, macrophages, and granulocytes.

Answer 58

A type of white blood cell that surrounds and kills microorganisms, removes dead cells, and stimulates the action of other immune system cells.

Answer 59

The adaptive immune system can learn to recognize an infection we have seen before. Includes lymphocytes (B-cells and T-cells). B-cells form memory to attack foreign material. T-cells attack your body's own cells that have been invaded.

Answer 60

Hypertonic refers to blood having relatively higher osmotic pressure (more concentrated, less water) than surrounding tissue. Hypotonic is blood having lower osmotic pressure (less concentrated, more water) than surrounding tissue. Water will flow from hypotonic to hypertonic spaces.

Answer 61

Vasopressin (ADH) helps regulate plasma osmolarity. As water increases, osmolarity decreases, vasopressin decreases. Aldosterone regulates plasma volume and pressure by increasing sodium reabsorption in the nephron (which, in turn, reabsorbs water).

Answer 62

H2O + CO2 > H2CO3 > H+ + HCO3-

Answer 63

Schwann cells (SCs) are a type of glial cell that surrounds neurons, keeping them alive and sometimes covering them with a myelin sheath. The major glial cell type in the peripheral nervous system. They play essential roles in the development, maintenance, function, and regeneration of peripheral nerves.

Answer 64

the process of evolution by which distantly-related organisms independently evolve similar traits to adapt to similar needs

Answer 65

Epithelial tissues are widespread throughout the body. They form the covering of all body surfaces, line body cavities and hollow organs, respiratory track, and are the major tissue in glands. They perform a variety of functions that include protection, secretion, absorption, excretion, filtration, diffusion, and sensory reception.

Answer 66

Found inside the nucleus of eukaryotes. Produces and assembles ribosomes.

Answer 67

any cell of a living organism other than the reproductive cells.

Answer 68

any of a class of proteins present in the serum and cells of the immune system, which function as antibodies.