exam 2 -study guide 7 Flashcards
What is the elemental composition of proteins? What is an amino acid? What is the chemical structure of an amino acid? How many different amino acids are commonly found in proteins? What type of bond joins amino acids together in a protein? What is a polypeptide?
Elemental composition – C, H, O, and N. Often sulfur.
AA – building blocks of protein
Chemical AA structure – central carbon, an amino group, a carboxyl group, a hydrogen, and a unique R group.
20 common AA’s
Linked by peptide bonds
Polypeptides are fundamental structures of proteins
What are the different levels of protein structure?
Primary – sequence of amino acids within a polypeptide chain
Secondary – beta-pleated sheets and alpha helix
Tertiary – sheets and helixes together – enzymatic activity
Quaternary – the association of several protein chains
What are the chemical determinants of protein structure
Hydrogen bonding, polar groups, non-polar groups, covalent bonds, and a linear sequence of amino acids.
What is protein denaturation, and what chemical and/or physical conditions can cause protein denaturation?
Protein denaturation is the process of a protein’s three-dimensional structure being altered. Often caused by high temperature, extreme pH, solvents breaking bonds, etc.
What is a protein chaperone, and what does a protein chaperone do
A protein that helps other proteins fold properly.
What is a prion? What is it composed of? What effects can it have on the structure of other proteins?
A prion is a misfolded protein that induces misfolding in normal variants of the same protein, leading to cellular death.
What slow, degenerative diseases in humans and/or animals are caused by prions
Transmissible spongiform encephalopathy.
glycoproteins
proteins with sugar molecules covalently bonded to their side chains
lipoproteins
proteins with lipid molecules covalently bonded to their side chains
What are the spikes on the SARS-CoV-2 virion composed of? How many polypeptide chains are present in one spike? Are they identical? What receptors on human cells do the spikes bind to?
What are some of the biological effects that SARS-CoV-2 spike proteins have on human beings?
Spikes composed of glycoproteins
Each protein is composed of two polypeptide chains
1. S1: binds to human cell receptors
2. S2: facilitates fusion of the virus with host cell membrane
Human cell receptors are called to ACE2.
Biological effects include thrombosis, vascular endothelium inflammation, mitochondrial damage, myocarditis, DNA damage, increase production of reactive oxygen species.
What are catalysts? What are enzymes? – What are the main properties and characteristics of enzymes? What is the size in metric units of the size/diameter of a typical enzyme? What is the expected range of number of copies of an enzyme present in a cell?
Catalysts accelerate conversion of substrate into product by lowering activation energy.
Enzymes are proteins that catalytically speed up specific chemical reactions in living cells.
Characteristics – lower the activation energy required for a chemical reaction to proceed, enable metabolic reactions, shape, specificity, provide an active site for substrates, larger than substrates, can be recycled, may require cofactors, greatly affected by temp and pH, can be regulated by feedback and genetics.
3-8 um.
1000-10000 molecules
What are virulence factors? What are some protein molecules that can act as virulence factors?
Molecules or protein produced by pathogen that enhance their ability to cause disease, colonize hosts, evade the immune system, and obtain nutrients.
What is an exotoxin? What is an exoenzyme (also called an extracellular enzyme)? What are some examples of exoenzymes that act as virulence factors?
Exotoxins are soluble poisonous protein substances secreted by a microorganism or released after cell lysis.
Exoenzymes act outside the cell that produces it.
Factors
* Hemolysins – rupture RBCs
* Hyaluronidase – breaks down hyaluronic acid (polysaccharide that bonds host cells together
* Collagenase – breaks down collagen in CT and muscless
substate
the substance on which an enzyme acts; the surface on which an organism will grow
active site
the site on an enzyme shaped to fit with the substrate
allosteric site
A site that allows molecules to either activate or inhibit enzyme activity
apoenzyme
protein portion of the enzyme
cofactor
chemical species needed by some enzyme for enzymes to catalytic
coenzyme
organic cofactors
holoenzyme
apoenzymes + cofactor
How do enzymes increase reaction rate?
Increasing the frequency of collisions between reactants, orienting reactants properly in space to facilitate reaction, lowering activation energy requirement, allowing reactions to occur at biological temp and pressure quickly.
how many classes of enzymes are known to exist
6 functional classes
names of important coenzymes
Nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD), Coenzyme A, thiamine pyrophosphate, pyridoxal phosphate, tetrahydrofolate
enzyme activity affected by enzyme concentration
increased, reaction rate increases
enzyme activity affected by substrate concentration
There is a maximum substrate level that will cap off the amount of enzymatic activity; the active site will be continually occupied
enzyme activity affected by pH
affects the ionization of groups that help stabilize the tertiary structure
enzyme activity affected by temperature
There is an optimal temp for most enzymatic activity for each activity. Ift temp is too high, change in conformation occurs
enzyme activity affected by inhibitors
bind at allosteric site which changes the enzymes activity
What are competitive enzyme inhibitors
Compete with normal substrate for active site.
- Have similar size/shape/structure as substrate
- Sulfonamide & PABA
What are non-competitive enzyme inhibitors?
Binds to site other than active site. Often that is at allosteric site which alters structure of active site. Is reversible.
What are enzyme poisons, and some examples of these?
Enzyme poisons are non-competitive inhibitors that are not reversible.
* Mercury converts oxidizes the S—H groups of cysteine which converts it to cystine which cannot form disulfide bonds
What is the difference between reversible and non-reversible non-competitive inhibitors?
Reversible – inactivates enzymes through noncovalent, reversible interactions, bind weakly and dissociate
Non-reversible – form strong, covalent bonds that permanently inactivate the enzyme.
selective toxicity
The ability of a drug to targets sites that are relative specific to the microorganism responsible for the infection
How does sulfanilamide work as a bacteriostatic agent?.– Is it a competitive or non-competitive inhibitor? Why do sulfa drugs have high selective toxicity? What normal substrate does sulfanilamide resemble in having almost the same shape and size as the normal substrate? Are sulfa drugs bactericidal, or bacteriostatic? What type of enzyme inhibition does sulfanilamide cause (competitive or non-competitive)?
It inhibits bacterial growth rather than killing the bacteria.
Competitive inhibitor.
High selective toxicity because they target a process that is crucial for bacterial growth but is absent in human cells.
Sulfanilamide closely resembles p-aminobenzoic acid (PABA).
Sulfa drugs are bacteriostatic.
Competitive inhibition
imatinib (gleevec or glivec) What normal substrate does Gleevec resemble in having almost the same shape and size as the normal substrate? What type of enzyme inhibition does Gleevec cause (competitive or non-competitive)?
It has the same size & shape as ATP and is a tyrosine-kinase inhibitor.
Semi-competitive because it binds close to the ATP binding site
What are extracellular enzymes (also called exoenzymes), and what do they do?
Moved outside of the cell and act to digest polymers into monomers which can be transported inside the cell.
What are inducible enzymes (also called regulated enzymes) & what are constitutive enzymes? How are they alike, and how do they differ?
Inducible enzymes are only produced when needed, presence of substrate induces cell to produce inducible enzyme. Prevents cell from wasting energy and raw materials.
Constitutive enzymes are always produced & needed for routine metabolism.
Alike: enzyme catalysts, require transcription/translation, and both are controlled by gene expression.
Differ: Inducible are made when needed and are involved in specialized metabolic pathways while constitutive enzymes are constantly produced and perform basic, ongoing cellular functions.
What is an allosteric site (also called a regulatory site)? What is allosteric regulation?
Distorts enzyme shape, prevents or enhances binding.
Enzyme activity controlled by binding to allosteric site.
What is the central dogma of molecular biology?
Enzymes are genetically controlled: DNA mRNA protein
What is enzyme repression? How does it differ from feedback inhibition (also called end-product inhibition)?
Prevent enzyme synthesis by preventing gene expression (transcription).
Differ: regulation mechanism – repression – gene expression while feedback regulates enzyme activity. Repression reduces the synthesis of the enzyme while feedback decreases the activity of the enzyme
What is feedback inhibition (also called end-product inhibition), and how does it work?
Prevents activity of pre-existing enzyme. Next product of pathways binds to allosteric site of enzyme close to start of pathway, changing active site’s shapes and shutting down reaction pathway.
What are some different ways in which metabolic pathways are arranged
linear, branched, cyclic
clostridium botulinum domain, movement, effects of botulinum
Endospore-former, obligate anaerobe
* Domain: bacteria, gram positive rods
* Move by peritrichous flagella
* Some strains produce botulinum
o Affected muscles are weakened or paralyzed
o Inhibits NT release.
Toxin is taken up across gut epithelium via active transport via receptor-mediated endocytosis
Enter blood flow
Toxin has Zn-dependent protease that cleaves one or more proteins used by neuronal vesicles to replace AcH into the NT junction
botulism, treatments, and prevention
- Botulism is most potent toxin known (1.0ug lethal) and may cause illness
- Can cause
o Wound botulism
o Infant/intestinal botulism
o Foodborne botulism – ingesting toxin that had already been formed
Double vision/blurred vision
Drooping eyelids
Nausea
Vomiting
Abdominal cramps
Slurred speech
Difficulty breathing and swallowing
Muscle weakness
Diarrhea
Constipation - Treat with antitoxin within 24 hours and supportive therapy (ventilator) until nerves regenerate
- Prevent by not ingesting suspect food especially from swollen cans and alkaline pH foods (sausages, processed meats)
