Exam 2 Flashcards
What structures make up an amino acid?
Amino group, central C atom bonded to H, carboxyl group, R group
What structure of the amino acid is unique to each amino acid?
R group
How are products formed from enzymes and substrates?
Enzymes bind with substrates at the active site. The enzyme changes shape during the process, producing the products that leave the active site.
What are the 4 levels of protein structure?
Primary, secondary, tertiary, quaternary
How are the 4 protein structure levels connected conceptually?
(1) An amino acid sequence, (2) that is folded in a beta-pleated sheet, (3) forming a complex 3D shape, (4) along with other 3D shapes to create the final protein
What are the two inhibition types?
Allosteric and competitive
Why does allosteric inhibition not allow a substrate to bind?
A regulatory molecule binds to a place on the enzyme that is not the active site, changing the shape of the enzyme and not allowing the substrate to bind.
Why does competitive inhibition not allow a substrate to bind?
A regulatory molecule directly blocks the active site.
How can allosteric and competitive inhibition be reversed? What will differ between the inhibitions in terms of reversing?
By increasing substrate competition. Competitive reversal can restore enzyme activity to 100%, but allosteric reversal will simply increase (as long as regulatory molecule is still present)
Allosteric/competitive inhibition and adding a phosphate group are examples of _______ inhibition because it ______ affect the enzyme’s primary structure. However cutting the peptide bond between the AAs is an example of _______ inhibition because it _______ affect the enzyme’s primary structure.
Reversible, doesn’t, irreversible, does
Use these terms in a connected sentence: metabolic pathway, steps, specific molecule, chemical reaction, final product
In a metabolic pathway, a specific molecule is altered in a series of steps (each being a chemical reaction) that results in a final product.
The ______ structures of all proteins are manufactured by ________.
Primary, ribosomes
How are AA chains/proteins sorted?
By signal sequences and chemical labels.
Why are AA chains/proteins sorted?
They all do different jobs in different locations, and as such must be sorted so they end up in the correct location.
What is a signal sequence and chemical label made of?
SS - first or last few amino acids in a chain
CL - chemical group added to protein after its finished being made
What organelles are part of the endomembrane system?
Rough endoplasmic reticulum, vesicles, Golgi apparatus, lysosomes
What is the function of the endomembrane system?
Folding, specializing, packaging, transporting, and receiving of proteins
What must all proteins possess in order to go through the endomembrane system?
ER signal
Where will proteins that have an ER signal sequence function?
Endomembrane system or cell membrane
What is the process of a protein in the endomembrane system?
Ribosome manufactures protein, ER signal is made, ER signal binds to signal recognition particle (SRP) pausing translation, SRP binds to RER receptor, AA chain threaded through receptor into RER, SRP detaches/ribosome completes primary structure/AA chain released
Where do proteins receive chemical labels in the endomembrane system?
In the Golgi apparatus
What happens to proteins (in GA) with chemical labels? Without?
With: bud off in vesicles (some may develop into lysosomes)
Without: travel to cell membrane
How do prokaryotic and eukaryotic cells differ in these contexts: making up organisms, organelles, nucleus, mitochondria, DNA presentation, size, intercellular connections
P vs. E: unicellular vs multicellular organisms, non-membrane bound vs membrane bound organelles and nucleus, absence vs presence of mitochondria/chloroplasts, circular single chromosomal DNA vs linear multiple chromosomal DNA, small vs big, flagella/fimbriae vs desmosomes/plasmodesmata
What is the theory of symbiosis?
A bacteria cell entered an archaea cell, evolving into a mitochondria and chloroplast
What is the observational evidence supporting the theory that bacteria evolved into mitochondria/chloroplasts?
Both reproduce by pinching in half, have own circular DNA separate from nuclear DNA, DNA replicates during their reproduction, genomes resemble bacterial genome, proteins within mitochondria are often made by smaller ribosomes within them (opposed to larger ribosomes in the cell)
What did the accidental discovery by microbiologist Kwang Jeon prove between the single-celled amoebae and bacteria?
The amoebae were dependent on the bacteria, and they possessed a endosymbiotic relationship
An increase in size ______ the surface/volume ratio. The ___^___ in the surface/volume ratio _______ the rate at which cells can take in nutrients/gases and excrete waste. Why?
Decreases, decreases; an increase in size decreases SVR, meaning a greater volume and lesser surface area, diffusion as a result is longer and more difficult
What are the two main signal types and how are they distinguished?
Neurotransmitter (faster, nervous system) and hormone (slower, bloodstream)
What is signal transduction? What happens as a result?
Conversion of an extracellular signal to an intracellular signal; activity of proteins in the cell changes
What is the process of signal transduction through G-Protein receptors?
(1) Inactive G-protein is bound to GDP when a signal (hormone) binds to the receptor; (2) GDP becomes GTP causing G-protein to split in half; (3) one of the half/subunit goes to an enzyme that causes a second messenger to be activated (eliciting an intracellular response)
What is the process of signal transduction through RTK receptors?
(1) A signaling molecule binds to RTK receptors, causing dimerization (two RTK monomer subunits come together); (2) RTK molecule phosphorylates itself; (3) bridging proteins bind to RTK and activate RAS molecule, exchanging GDP for GTP; (4) activated RAS triggers phosphorylation and activation of kinase (5) phosphorylation cascade now begins, with kinase phosph. diff kinase until response is triggered in cell
What word can be used to describe the initial signaling that causes the increased signaling/cascade?
Amplification; small extracellular signal -> big intracellular signal
What level of structure(s) does RTK have before the signal binds? (green dot question, lecture 10)
Primary, secondary, tertiary
What level of structure(s) does RTK have after the signal binds? (green dot question, lecture 10)
Primary, secondary, tertiary, quaternary
What are the 3 components of basic nucleic acid structure?
Phosphate group, sugar, and nitrogenous base
What are the differences between DNA and RNA?
Nitrogenous bases (CGAT vs CGAU), sugar (deoxyribose vs ribose), strand (double vs single)
Where on the sugar (of DNA) is the phosphate attached?
5’ Carbon
DNA synthesis results in 2 identical double helices. Does each have 1 new and 1 old strand or does each have 2 of the same new or old strand?
1 new and 1 old strand
i. What does the template/old strand read for the leading strand? What does the synthesized/new strand read for the leading strand?
Template/old strand reads 3’ to 5’
Synthesized/new strand reads 5’ to 3’
i. (Repeat) At a replication fork, how can you tell which strand is leading and which is lagging?
The leading strand has 5 at the closed end/handle, lagging strand has 3 at the closed end/handle
i. (Repeat #2) What does it mean when DNA POLYMERASE only reads 3’ to 5’, and makes 5’ to 3’?
If it only reads 3’ to 5,’ this means the template/old strand must be 3’ to 5.’ If it makes 5’ to 3,’ it means that this is the leading strand.
What are the steps of DNA replication?
1) DNA HELICASE unzips the double helix, TOPOISOMERASE relieves and prevents twisting tension from traveling down the helix
2) SINGLE-STRANDED DNA-BINDING PROTEINS attach to separated strands preventing them from re-attaching
3) PRIMASE lays down primer on both strands
4) DNA POLYMERASE alpha or epsilon synthesizes leading strand, DNA POLYMERASE delta synthesizes lagging strand
5) LIGASE seals the gaps between Okazaki fragments in lagging strand
Why is primase adding primer necessary?
For DNA POLYMERASE to add nucleotides, it needs a a free OH group (which doesn’t exist when the strands are broken apart); primase adds the primer (small sequence of RNA with a free 3’ OH group) that allows DNA POLYMERASE to begin
What are the three repair systems in DNA synthesis?
Proofreading, mismatch repair, nucleotide excision repair
How is proofreading different from mismatch repair?
Proofreading is where DNA POLYMERASE checks itself and fixes its own mistakes, with single nucleotide(s) being replaced. Mismatch repair fixes mistakes after replication is complete, and an entire section of DNA is removed and replaced.
How does nucleotide excision repair differ from proofreading and mismatch repair?
Nucleotide excision repair does not occur during/fix mistakes in DNA replication, but rather mistakes caused by UV light.
What process do prokaryotes replicate by?
Binary fission
What are the phases of the cell cycle?
Interphase, mitosis, cytokinesis
What are the phases within interphase? What is happening in each of the phases?
G1: Cell has uncondensed DNA and decides to replicate
S: DNA replicates
G2: Cell grows to prepare for M phase
How do you distinguish between sister chromatids and homologous chromosomes?
Two sister chromatids make up one of two homologous chromosomes.
SC: I and I in X (2 sister chromatids PER homologous chromosome)
Homologous chromosomes: X and X (a pair of homologous chromosomes contains 4 TOTAL SIS CHROMATIDS)
What is the process of un/condensed and un/replicated DNA?
Uncondensed and unreplicated in G1, uncondensed and replicated in S/G2, condensed and unreplicated in 1/2M, condensed and replicated in 1/2M and C.
(First two uncondensed, last two condensed)
What are the phases of mitosis, and what happens in each?
Prophase (DNA condenses), metaphase (chromosomes lined up in middle), anaphase sister chromatids pulled apart), telophase (nuclear envelope forms around each set of chromosomes)
What happens in cytokinesis?
Cytoplasm is divided equally between the two new cell regions (cleavage furrow separates daughter cells)
What are the cell cycle check points?
G1, G2, M
What does the G1 checkpoint check? What happens after?
If DNA is undamaged; next is S phase and DNA synthesis
What does the G2 checkpoint check? What happens after?
If chromosome replication was successful and DNA is undamaged; next is mitosis
What does the M checkpoint check? What happens after?
If chromosomes separated properly; next is separation/creation of daughter cells
What may a cell do if a checkpoint regulator prevents it from passing the checkpoint (3 things)?
Stay in resting state (G0), fix DNA damage, or undergo cell death/apoptosis
How do cyclins and CDKs work together as a checkpoint regulator?
When cyclin binds to CDK CDK is activated and begins the phosphorylation process.
How does the M phase promoting factor (MPF) act as a checkpoint regulator?
M cyclin binds to CDK, and high levels of M cyclin mean that together with CDK they are the formation of MPF. Next the kinase subunit catalyzes phosphorylation for other proteins to begin M phase.
How is anaphase-promoting complex/cyclosome activated?
MPF activates APC/C during anaphase, which adds the small protein tag ubiquitin to APC/C’s targets. the ubiquitin marks the object for cell death. As such the targeted proteins are destroyed by APC/C.
(Example of APC/C in use is it destroying securin, releasing separase, allowing it to chop up centromere holding sister chromatids together in mitosis)
What are three condensed functions of p53?
Stop transcription/translation, activate repair enzymes, pause the cell cycle so there is time to repair damage
What is the “last resort” function of p53? How does it occur?
Programming of cell death; nuclear DNA is chopped up, organelles split apart, and cell breaks into small chunks that release signals prompting immune cells to engulf the cell
What is the difference between haploid and diploid? And what is an example? Why is the example of haploid haploid?
Haploid means one set of chromosomes, while diploid means two sets of chromosomes. Gamete cells are haploid, and regular human body cells are diploid. Gamete cells are haploid because they join with a gamete of the other sex to create a zygote that is diploid.
