BSI EXAM 1 Flashcards
What helps the protein from being degraded by enzymes?
Glycosylation
What is phagocytosis?
Phagocytosis is the process by which bacteria, dead tissue, or other bits oif microscopic material are engulfed by cells
Pair of Centrioles and Pericentriolar material is called the ______
Centrosome
What is autophagy?
Autophagy is controlled digestion of damaged organelles within a cell.
This contains digestive enzymes.
Lysosomes
This is made up of cylindrical array of microtubules.
Centrioles
Glycosylation
Adding of a sugar group to the protein.
Trans face of the Golgi Apparatus faces the ER. T or F?
FALSE, The CIS face, faces the ER
Glycosylation usually happens with membrane proteins and __________.
Lipids
What is the mitotic spindle?
The mitotic spindle is the macromolecular machine that segregates chromosomes to two daughter cells during mitosis. It is made up of microtubule polymers.
Gln192 is a __ residue located 192 amino acids from the __ terminus
Glutamine; N
which of the following pairs of aa can form an ionic bond with each other
a) Lys and Glu
b) Ser and Arg
c) Gln and Lys
D) Pro and Cys
a)
What functional group is the “N-terminus”?
Amino group
If you add a chemical that breaks a noncovalent bond, what structural level is affected?
Secondary, tertiary, quaternary
Name the 10 amino acid with nonpolar side chain.
Alanine (Ala), Glycine (Gly), Valine (Val), Leucine (Leu), Isoleucine (Lle), Proline (Pro), Phenylalanine (Phe), Methionine (Met), Tryptophan (Trp), Cysteine (Cys)
T or F; Reduced form has a disulfide bond.
False, Oxidized form has disulfide bonds.
Which structures are determined by unique amino acid sequence?
Tertiary and quaternary
What are the 4 amino acids that does NOT start with the first 3 letters of their name?
Asparagine (Asn), Glutamine (Gln), Isoleucine (Ile), Tryptophan (Trp)
Which 3 amino acid contains an OH group that can be phosphorylated?
Serine (Ser), Threonine (Thr), Tyrosine (Tyr)
N-terminus, is that the beginning or the end of the protein?
Beginning
(Ser-Gln-Asn) and (Leu-Phe-Gsy), which one is more likely to be a membrane protein and why?
Leu-Phe-Gsy because it’s nonpolar and prefer membrane environment.
What functional group is the “C-terminus”?
Carboxyl Group
Adding a chemical solution to denature a protein that is in its functional quarternary structure as a heterodimer. The protein does not contain cysteine. The chemical solution interferes with noncovalent bonds. In what form would you most likely predict the protein to end up.
As two separate polypeptide chains with no secondary or tertiary structure.
T or F? A protein can only have one function
False, proteins can have multiple domains.
Name the 8 essential amino acid
Threonine, Methionine, Lysine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan
Define Domain
Part of the protein that can fold up on its own and have its own function.
Which amino acid contains SH and can form disulfide bonds?
Cysteine (Cys)
Name the 2 amino acid with negative side chain
Aspartic Acid (Asp) and Glutamic acid (Glu)
A polar protein that loves water and avoids lipids, would most likely be what kind of protein?
Cytosolic
Name the 5 amino acid with uncharged polar side chain
Asparagine (Asn), Glutamine (Gln), Serine (Ser), Threonine (Thr), Tyrosine (Tyr)
Name the 3 amino acid with positive side chain
Arginine (Arg), Lysine (Lys), Histidine (His)
What is the three letter abbreviation for Alanine?
Ala
What is the three letter abbreviation for Glutamic acid?
Glu
What are the 8 essential AAs?
Threonine, Methionine, Lysine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan
What is the three letter abbreviation for Tryptophan?
Trp
What is the three letter abbreviation for Asparagine?
Asn
What 3 AAs contain an -OH group which can be phosphorylated?
Ser, Thr, Tyr
What is the three letter abbreviation for Leucine?
Leu
What is the three letter abbreviation for Proline
Pro
What is the three letter abbreviation for Glutamine?
Gln
What is the three letter abbreviation for Histidine?
His
What is the three letter abbreviation for Serine?
Ser
What is the three letter abbreviation for Glycine?
Gly
What is the three letter abbreviation for Tyrosine
Tyr
What is the three letter abbreviation for Phenylalanine?
Phe
What is the three letter abbreviation for Valine?
Val
What is the three letter abbreviation for Isoleucine?
Ile
What 5 AAs have an uncharged polar side chain?
Asparagine (Asn), Glutamine (Gln), Serine (Ser), Threonine (Thr), Tyrosine (Tyr)
What is the three letter abbreviation for Cysteine?
Cys
What 2 Amino Acids have a negative side chain?
Aspartic acid (Asp) and Glutamic acid (Glu)
What is the three letter abbreviation for Methionine?
Met
What 3 AAs have a positive side chain?
Arginine (Arg), Lysine (Lys), and Histidine (His)
What 10 AAs have a nonpolar side chain?
Alanine (Ala), Glycine (Gly), Valine (Val), Leucine (Leu), Isoleucine (Ile), Proline (Pro), Phenylalinine (Phe), Methionine (Met), Tryptophan (Trp), Cysteine (Cys)
What is the three letter abbreviation for Threonine?
Thr
What is the three letter abbreviation for Lysine?
Lys
What is the three letter abbreviation for Aspartic acid?
Asp
What is the three letter abbreviation for Arginine?
Arg
What recognizes tag (chain of ubiquitin) and degrades the protein?
Proteasome
Degraded proteins are turned back into ____________
peptides
Covalent bonds are the type of bonds that holds the ligand in binding site.
False, noncovalent bonds.
Define: Denaturation
The process in which a protein loses its quaternary, tertiary, and secondary structure present in their native state.
What is a small molecule that functions as a transient carrier of a functional group?
Coenzyme
What enzyme recognizes specific degradation signals on proteins and then adds a chain of ubiquitin?
Ubiquitin ligases.
What is the first step in the UPS?
Protein is tagged with ubiquitin.
What is disrupted during denaturation.
Nonconvalent bonds maintaining secondary, tertiary, and quaternary structure.
INCORRECT
Proteins interact with what molecule(s) to carry out its function?
Ligands
What is the function of the Ubiquitin-proteasome system?
To identify degradation signals on protein to begin the process of degrading a protein
Denaturation can be cause by ______, _______, and _______
Temperature, pH, Electrolyte concentration.
What are inorganic ion or molecule that is required for enzyme activity?
Cofactor
Where do the mitotic spindle binds?
Centromere
Level 3 packaging, Chromatin fiber forms loops (300nm), T or F?
True
Genes that are considered “off” are located in areas of ______________
heterochromatin
What is a linker region?
A linker region is the DNA you see between the two histones or “beads”
Loops are condensed into chromosomes (700nm). At what level does this occur?
Level 4
What level of mitotic chromosome does euchromatin resemble?
Level 2
What level of packaging is it when threadlike mass of genetic material (DNA and histone proteins) form “beads on a string” (11nm structure)?
Level 1
The DNA sequence encoding the stop codon can be located:
A. in the termination sequence of the gene.
B. in an intron toward the 3’ end of the gene.
C. in an exon towards the 5’ end of the gene.
D. In the TATA box sequence within the promoter of the gene.
E. Two of the above → One of two or more alternative forms of a gene that arise by mutation and are found in the same place on a chromosome.
in an exon towards the 5’ end of the gene.
Level 2 packaging, what chromatin fiber width is _____?
30nm
What is a nucleosome?
Basic structural unit of a chromosome. Histones, DNA, Linker Region
Do genes encode lipids and carbohydrates?
No, only proteins are encoded. Lipids and carbohydrates are synthesized.
What are the three phases of gene transcription?
Initiation, Elongation and Termination
initiation for trasncrption
RNA Polymerase ll binds to promotor
elongation for transcription
Move along DNA from 3’-5’
Reads single strand of DNA AND add complementary nucloetides to growing pre-mRNA
Pre-mRNA: 5’-3’
Uracil instead of thymine
Pre-mRNA Processing
5’ capping of Guanine nucleotide with a methyl group. Polyadenylation, which is a series of repeated adenine nucleotides attached to 3’ end. Splicing which is the removal of introns in the pre-mRNA and ligates exons together The process is important for nuclear export.
Termination for Transcription
RNA Polymerase ll termination sequence and releases DNA
Spliceosome structure consists of _____________ and proteins.
mall nuclear RNAs (snRNAs)
Phases of translation
Initiation, Elongation and Termination
initiation for translation
- tRNAiMET is loaded on small ribosome along with eIFs (initiation factors) to form initication complex
- Initiation complex recognizes and binds mRNA at 5’ end of mRNA
- Initiation complex then slides along the mRNA until it find start codon AGU
- once small subunit reaches start codon, elFs dissociated with tRNAiMET in P-site
- Poly-A comes in and helicases to relax secondary strucuture allowing small subunit to scan along mRNA to find start codon
tRNAiMET VS tRNAmet
tRNAiMET: initiator RNA only used at start codon
tRNAmet: incorporated MET into growing polypeptide during elongation
Elongation of translation
- growing tRNA on P-site and new amino acid of tRNA on A-site
- peptidyl transferase forms peptide bond bewteen carboxyl terminal of polypeptide chain and amino group of new aa
polypeptide grow amino to carboxyl terminus - placing empty E-site, tRNA polypeptide chain on P-site, leaving A-site for incoming tRNA
Elongation: Ribosome undergoes ______ _______ to shift the mRNA one codon at a time.
onformational change
Elongation factors (EFs) ______ accuracy and ______ of the translational process.
increase; speed
Termination of translation
- Releasing factors come in when there is stop codons in A-site
- Releasing factors binds to any ribosome with stop codon on A-site and make peptidyl transferase to polypeptide to water
- Ribosome dissembles and release mRNA
What are the two reasons why more than one codon can code for a specific amino acid?
Wobble and tRNA’s with different anticodons can carry same amino acid.
What is wobble?
The ability of one tRNA with a specific anticodon to complementary base pair with more than one codon. Matching the 1st and 2nd codon.
Post translational modifications
protein folding cofactor binding covalent modifications -glycosylation -phosphorylation -acetylation form quaternary structure
If a SNP is in a noncoding sequence of a gene, can it affect the phenotype of a cell?
Yes
________ patterns can alter expression pattern of genes.
Methylation
Phosphorylation of _____ inhibits translation initiation.
eIF-2
Will a SNP always change the amino acid sequence of a protein?
**No, due to synonymous and nonsynonymous codes
Methylation of DNA typically _____ genes ____
shuts; off
All of the mRNA molecules produced from a specific gene will always contain the same nucleotide sequence. T or F
False, due to alternative splicing.
An SNP is a variation at a specific nucleotide in the DNA sequence between two genes on the same chromosome. T or F?
False, between one gene
Epigenetics: Methylation patterns can be ______.
Heritable
T or F; Cells express all genes.
False, cells DO NOT express all genes.
Methylation patterns of some genes can be modified by _________
environment (diet, stress, toxins, etc)
Can one gene give rise to multiple mature mRNAs with difference nucleotide sequences?
Yes due to alternative splicing
miRNA
binds to mRNA and inihibits tranlation causing degradation of mRNA
Many receptors have 12 transmembrane domains, while many sugar transporters for example have 7 transmembrane domains. T or F?
False, reversed, 7;12
Membrane protein movement is limited by _____ ______ where adjacent cell membranes are actually fused providing a physical barrier.
tight junctions
T or F: The inner and outer membrane of the cell are symmetrical.
False; different proteins and lipids forming the bilayer makes them asymmetrical
What is an amphipathic molecule?
This is a molecule that is both water AND lipid soluble. Membrane lipids are typically amphipathic with both hydrocarbon fatty acids which are lipid soluble AND one or more charged groups which are water soluble (they are therefore schizophrenic in nature!).
Amphipathic membrane lipids will naturally form a bilayer with hydrophilic parts, these lipids arranged externally to interact with water while the hydrophobic parts self-associate to form the true barrier away from water; this is _______ favorable.
Energetically
How do membranes “work”? (based on what principle/s)
Cellular chemistry/biochemistry occurs in water so by making membranes primarily out of lipids/fats it separates aqueous environments as it is energetically unfavorable for water soluble/lipid insoluble molecules to cross lipid membranes.
Why are membranes important?
They allow cells to compartmentalize and control their chemical environment making it conducive (favorable) for life.
How do you overcome membrane impermeability?
There are 2 mechanisms; one is utilizing transport proteins while the other involves fusing with membranous vesicles (endocytosis for exporting and endocytosis for importing).
An amphipathic molecule has: A. A hydrophobic and a lipophobic region B. A hydrophobic and hydrophilic region C. A lipophilic and hydrophilic region D. A lipophobic and lipophilic region E. All of the above (A to D)
E. All of the above (A to D)
Many transmembrane proteins are receptors allowing chemical signals that cannot enter the cell to be recognized and produce an effect inside the cell: this is ___ ____
signal transduction
_______ move half of lipids to the non-cytosolic face so both sides of the membrane are expanded equally.
Flippases
Can you predict what can and cannot cross a cell membrane?
Only relatively small, hydrophobic molecules (ethanol) plus the polar, universal solvent water: certainly nothing charged (ions) or larger polar molecules (glucose).
Diffusion of a freely membrane permeable substance exhibits saturation kinetics?
A. True
B. False
B. False
Unlike for membrane-permeable substances, transported substances rely on a finite number of transporting proteins and therefore are subject to _____ _______
saturation kinetics.
Dissociation into two ions, (as happens when NaCl is dissolved), ________ the osmotic pressure.
doubles
Diffusion is more rapid the smaller the substance. T or F?
True
Ion channels do not exhibit saturation kinetics?
A. True
B. False
A. True
Moving ions out of a cell will do what to its osmotic pressure?
A. Increase it
B. Not change it
C. Decrease it
C. Decrease it
Diffusion is effective over long (intracellular/cellular) but not over short distances. T or F
False. Effective over short distances but not over long distances. (1mm in diameter or less diffusion of O2 is sufficient)
Diffusion time _______ by the square of the distance but _____ with increased area.
increases; decreases
Coupled transport slide: Ion Channels: Which way does Ca2+ flow?
Outside in
How many TMD’s does SGLT1 have and how is it different from other transporter?
14, normal sugar transporter has 12 TMD’s
_________ exerts its effects by increasing the number of transporter molecules in the cell membrane.
Insulin
Sugar transporters are composed of how many transmembrane domain.
12
If to co-transport of X out of a cell required it be linked to K+ movement what type of transport/transporter would this be? (transporter does NOT use ATP)
Secondary active transport/coupled symport; linked to K+ efflux (K+ gradient maintained by primary active transport)
Coupled transport slide: Secondary Active Transport: Which way does H+ flow?
Inside Out
Facilitated diffusion only happens in efflux. T or F?
False, transport can usually occur in either direction depending on the gradient, (if not coupled).
What forms of membrane transport would cyanide affect?
Primary and secondary not facilitated.
Saturation Kinetics is due to a _________ number of transporter molecules.
finite ((Will have a maximum rate(Vmax) and an affinity, (Km))
GLUT3 (GLUT14)
high affinity
neurons
insulin insensitive
GLUT4
fat muscle
regulated by insulin
GLUT 2
low affinity
intestine,kidney
uptake and efflux
_____ protein uses ____ hydrolysis to form a “neck” around the forming vesicle and helps it pinch off.
Dynamin; GTP
identification of the correct destination of a vesicle depends on low molecular weight G-proteins of the ____ family
Rab
Constitutive exocytosis fusion with the cell membrane also releases the contents extracellularly and is therefore responsible for ____ secretion.
unregulated
Some specialized cells can ingest old cells, (for recycling), malfunctioning cells, (cancerous), and even invading pathogens such as bacteria, (macrophages and neutrophils: see Immunology): this is _____.
phagocytosis
The destination of a vesicle is determined by ______ associated with it
protein
LDLs are recognized by cell-surface receptors and are internalized via a clathrin-coated vesicle during receptor-mediated exocytosis. T or F?
False, endocytosis
Vesicles: Additional recognition is via the _____ proteins: ____ on vesicles bind to complementary______ on target membranes and draw them closely together, excluding water, to promote fusion.
RAB; v-SNARES; tSNARES
The contents of vesicles, (not embedded proteins), are determined by proteins from the _____ family.
adaptin
Proteins with a TMD, a “hydrophilic start” sequence, (followed by an appropriate “stop” sequence), allows the partially translocated peptide/protein to form an appropriate hydrophobic alpha-helix within the membrane and be retained: only one TMD is formed as the “start” sequence is now removed. T or F?
False, “Hydrophobic start” sequence
Exocytosis: Constitutive secretions occurs ______ to renew the plasma membrane or for unregulated export.
continueously
Phagocytosis is ______ and requires recognition via surface proteins/glycoproteins.
specific
How are movement between layers of the Golgi apparatus achieved?
By budding and subsequent fusion of vesicles
Phagocytic cells extend arm-like projections of their cell membranes called _____ which form the intracellular phagosome after internalization.
pseudopods
_________, like the constitutive exocytosis pathway, occurs constantly recycling the cell membrane
Pinocytosis
Exocytosis: Regulated secretions requires a _____.
signal
A specific endocytosis pathway known as _____-_____ endocytosis requires recognition by specific cell surface receptors: this is an efficient system for concentrating a substance within a cell, (x1000 compared to constitutive pinocytosis).
receptor mediated
Nuclear transport receptor actively transport proteins through the nuclear pores using what energy source?
GTP hydrolysis
How are vesicles formed?
mechanism of vesicle formation via clathrin-coated pits. “Cargo molecules” (proteins to be transported) are recognized by receptors which, via adaptin, organize clathrin molecules to form a supporting “cage” helping form the vesicle. After dynamin pinches off the vesicle the clathrin is removed and recycled leaving the naked vesicle.
Vesicle formation is aided by _____-_____ pits.
clathrin-coated
Exocytosis results from the fusion of vesicles released from the cis Golgi Apparatus with the cell membrane. T or F
false, trans
Describe the mechanism of vesicle fusion.
Vesicles are then transported to their correct destinations via moleccular motors. It requires ATP.
Tethering proteins on target membrane
-t snares
v snares on vesicles
Some pathogens utilize _______-______ endocytosis pathway to gain access to cells such as the influenza viruses and HIV.
Receptor; mediated
exocytosis pathway found only in where?
endocrine cells
