Download BCHM 270 Midterm Test: TCA Cycle, Electron Transport Chain, Enzymes, and Energy Metabolism and more Exams Nursing in PDF only on Docsity!
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TCA Cycle Step 1 - ANSWER citrate synthase
oxaloacetate + Acetyl = Citrate + CoA
TCA Cycle Step 3 - ANSWER isocitrate dehydrogenase
isocitrate --> alpha-ketoglutarate + NADH + CO
TCA Cycle Step 4 - ANSWER alpha-ketogluterate dehydrogenase
alpha-ketoglutarate --> Succinyl CoA + NADH + CO
TCA Cycle Step 5 - ANSWER Succinate thiokinase
Succinyl CoA --> Succinate + GTP
-cleaves high energy thioester bond (S-CoA) to drive reaction forward
TCA Cycle Step 6 - ANSWER succinate dehydrogenase
succinate --> fumarate + FADH2
TCA Cycle Step 8 - ANSWER malate dehydrogenase
L-Malate --> Oxaloacetate + NADH
Direction of electron flow in electron transport chain - ANSWER from compounds with lower redox potentials to compounds with higher redox potentials (low free energy to high free energy) which is used to move protons from the matrix into the inter membrane space to generate the
chemiosmotic gradient
ATP synthase activity - ANSWER Flow of protons back into the matrix causes movement within the enzyme that creates kinetic energy which cause the beta subunits to cycle between 3 conformational states to bind ADP to Pi. Proton motive force provides the energy to allow it to cycle and release ATP.
NADH and FADH2 difference - ANSWER - NADH produces 3 ATP as its electrons are passed to complex 1 and FADH2 produces 2 ATP as its electrons are passed to complex 2 (pumps fewer protons)
- Only NADH produced locally can produce 3 ATP as the inner mitochondrial membrane lacks an NADH transporter and therefore its electrons use two shuttle systems in the cytoplasm
Uncoupling proteins - ANSWER brown fat is used by infants to generate heat which is done by uncoupling proteins in the ETC which bypass ATP synthase and allow protons to reenter the the matrix without generating ATP (energy dissipated as heat rather than ATP).
Oligomycin - ANSWER Blocks proton channel in ATP synthase. Gradient becomes too great and thus no ATP made.
Synthetic uncouplers - ANSWER Allows electrons in ETC to move through the membrane without pumping protons. Heat is produced.
What is an enzyme? - ANSWER Typically globular proteins with multiple domains that act as catalysts for chemical reactions. Can increase reactions rates by 103-108 times.
What do enzymes do? - ANSWER Catalyze a reaction by binding to substrate and lowering activation energy which is done by enzyme stabilization of the
Homotropic effectors - ANSWER - substrates for the enzyme and will affect the enzymes other active sites' affinity to bind the substrate
- are normally positive (hemoglobin's ability to bind multiple oxygens)
Heterotropic effectors - ANSWER - Different from the enzyme's substrate
- Often are downstream product of the pathway the enzyme is involved with
Rate of reaction is proportional to - ANSWER the enzyme substrate complex
Michaelis-Menten equation - ANSWER v0 = (Vmax [S])/(Km + [S])
Km - ANSWER - Substrate concentration at 1/2 Vmax
- enzyme affinity towards the substrate
Linewearver-Burk Plot - ANSWER - allows for quick determination of Km and Vmax
- reciprocal of Michaelis-Menten equation
Allosteric enzyme curve - ANSWER - sigmoidal
- described by the hill equation
Hill equation - ANSWER n = degree of cooperatively
Positive if n > 1
Negative if n < 1
irreversible inhibition - ANSWER forms permanent bond with enzyme. Occurs when an enzyme binds an inhibitor that is a substrate analogue
Competitive inhibitors - ANSWER - structure which prevents substrate from entering the active site
- are substrate analogues
- Km increases
- No change to Vmax
Uncompetitive inhibitors - ANSWER - Bind to the enzyme when its active site is occupied
- Bind to allosteric site
- Lowers Km and Vmax
_ "U"niversally lower
Noncompetitive inhibitors - ANSWER - bind to the enzyme and enzyme substrate complex equally well
- Bind to an allosteric site
- decrease Vmax
- no change to Km
Four major tissues that play a role in energy metabolism - ANSWER Liver, Adipose, Muscle and Brain
- integration of energy metabolism is controlled by two peptide hormones: insulin and glucagon
Insulin - ANSWER An anabolic hormone produced by the pancreas
Mononucleotides - ANSWER are unbound to other nucleotides and can have one, two or three phosphate groups
Deoxyribose vs Ribose - ANSWER Ribose has a hydroxy group on the second carbon
Purines - ANSWER Adenine and Guanine
Pyrimidines - ANSWER Tymine/Uracil and Cytosine
Sugar phosphate backbone of DNA - ANSWER Formed by phosphodiester bonds
- formed by dehydration reactions between the phosphate group of one nucleotide and the hydroxyl group on the 3' carbon
Polymorphism - ANSWER DNA changes that are not known to cause harm; variants in the genetic code (blood types)
restriction endonucleases - ANSWER - enzymes that cleave double stranded DNA to produce DNA segments termed restriction fragments
- Can be used to combine new DNA sequences together for DNA cloning
- Recognize palindromes (4-6 base pair sequences) (same backwards as they are forwards)
gel electrophoresis - ANSWER Procedure used to separate and analyze DNA fragments by charge by placing a mixture of DNA fragments at one end of a porous agarose or polyacrylamide gel and applying an electrical voltage to the gel
DNA cloning - ANSWER - used to isolate a DNA sequence and introduce it into a cell to amplify that DNA sequence
- Cloned DNA can be expressed for protein or used for other DNA cloning experiments, isolated and analyzed
DNA probe - ANSWER - single stranded DNA molecules that are labelled with radioisotopes or non-radioactive labels
- have sequences complimentary to the target DNA
- Allele specific oligonucleotides can be designed to bind to only one version of an allele
- can be used for allele specific PCR
Blotting - ANSWER - transfer of macromolecules, such as nucleic acids or
CRISPR-Cas9 - ANSWER - can directly edit human genome of a cell for a specific sequence
- CRISPR are sequences found in bacteria and are used as a method of protection against viruses
- Cas9 is and RNA guided DNA endonuclease enzyme which can cleave foreign DNA
Northern blotting - ANSWER - used to show and detect a specific RNA sequence
- way to probe for a gene being expressed in the tissue or cells of interest
Quantitative PCR - ANSWER - used to understand how experimental conditions alter how cells and tissues behave
- Quantitative Real Time PCR used to determine the gene expression of cells
cDNA microarrays - ANSWER - contain thousands of immobilized DNA sequences on a small chip
- used for gene expression analysis
- allows researchers to discover patterns of gene expression in normal and cancerous cells, or cells under different controlled conditions
- intensity and colour of fluorescent pattern determines relative amounts of
cDNA in a particular sample which gives the amount of mRNA gene expression
SDS-Polyacrylamide Gel Electrophoresis - ANSWER - proteins are separated by size using polyacrylamide gels with a detergent called sodium dedecyl sulphate (SDS)
- smaller proteins migrate more quickly through the gel
- allows for measurement of size of proteins
Antibodies - ANSWER - used for protein detection
- high specificity for their respective antigens
Western Blots - ANSWER - probe for protein
- take place after transferring the results of SDS-Page to a nitrocellulose or PVDF membrane
- use antigen specific enzyme labelled antibody which generates a band at the position of the antigen
- bands are used to determine the presence and size of protein
Enzyme Linked Immunosorbent Assay (ELISA) - ANSWER - 96 well microplane assay technique used to quantify protein expression and detect for protein-protein or protein-antigen interactions
the hydrophobic molecules and the hydrophobic molecules will spontaneously associate together
- driving force has to do with the 2nd law of thermodynamics
- important for membrane formation and protein folding
Protein structure - ANSWER linear polymer of amino acids where the R group interactions with the environment will dictate how the protein will fold
Peptide bonds - ANSWER amino acids are joined by peptide bonds that form between the carboxyl group of one amino acid and the amino group of the other
(this is a condensation reaction)
Nonpolar amino acids - ANSWER In soluble proteins, non polar amino acids cluster together in the core of the protein, whereas in membrane proteins they interact with the hydrophobic tails of lipids
Uncharged amino acids - ANSWER do not form salt bridges because they have no net charge at physiological pH
- polar and are usually found on the outside of proteins
Acidic amino acids - ANSWER form salt bridges
Basic amino acids - ANSWER interact with negative molecules
Aromatic side chain amino acids - ANSWER very large and can cause steric hindrance. Gain or loss of these can cause deformities in the protein structure.
Chirality of amino acids - ANSWER except glycine, alpha carbon has 4 different groups --> chiral
post-translational modifications - ANSWER protein folding- chaperones assist in finding proper shape
- disulphide bonds form between thiol groups of cysteine which help stabilize the folded protein making it resistant to denaturation
- Glycosylation is a carbohydrate is covalently attached to a protein (can be added to amide group in asparagine or to hydroxyl group in serine or threonine
- Phosphorylation is the addition of phosphate to hydroxyl group in serine, threonine and tyrosine and is used to turn on or off proteins and enzymes
sickle cell anemia - ANSWER aggregation of hemoglobin within the red blood cells which results from substitution of glutamic acid to valine
Alpha helix - ANSWER right handed spiral where hydrogen bonds are formed between carbonyl O of the first residue and an amide H 4 residues away (parallel to axis of spiral).
Beta sheets - ANSWER series of turns where hydrophilic amino acids group together on one side of the sheet and same for hydrophobic amino acids
Helix breakers - ANSWER - Proline, as it is a rigid structure and doesn't fit into a right handed helix spiral
- Charged sequence clusters
- Too many bulky amino acids creates steric hinderance as well
- Valine, tryptophan, tyrosine, leucine and phenylalanine
Motifs - ANSWER combinations of alpha helices and beta sheets to form super secondary structures. Are not functional units.
tertiary structure - ANSWER The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.
quartenary structure - ANSWER two or more polypeptides interact to form a
functional protein
Alzheimer's disease - ANSWER abnormal cleave of the amyloid precursor protein in the brain. New protein adopts beta sheet structure and forms plaques. It is a neurotoxin.
Prion disease - ANSWER Proteins are able to fold in multiple distinct different structures and one form can cause other PrP proteins to fold into the same form. Alpha helices are refolded into beta sheets into an infectious form and is resistant to degradation and accumulates.
