exam 2 -study guide 7

Question 1

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?

Answer 1

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

Question 2

What are the different levels of protein structure?

Answer 2

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

Question 3

What are the chemical determinants of protein structure

Answer 3

Hydrogen bonding, polar groups, non-polar groups, covalent bonds, and a linear sequence of amino acids.

Question 4

What is protein denaturation, and what chemical and/or physical conditions can cause protein denaturation?

Answer 4

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.

Question 5

What is a protein chaperone, and what does a protein chaperone do

Answer 5

A protein that helps other proteins fold properly.

Question 6

What is a prion? What is it composed of? What effects can it have on the structure of other proteins?

Answer 6

A prion is a misfolded protein that induces misfolding in normal variants of the same protein, leading to cellular death.

Question 7

What slow, degenerative diseases in humans and/or animals are caused by prions

Answer 7

Transmissible spongiform encephalopathy.

Question 8

glycoproteins

Answer 8

proteins with sugar molecules covalently bonded to their side chains

Question 9

lipoproteins

Answer 9

proteins with lipid molecules covalently bonded to their side chains

Question 10

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?

Answer 10

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.

Question 11

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?

Answer 11

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

Question 12

What are virulence factors? What are some protein molecules that can act as virulence factors?

Answer 12

Molecules or protein produced by pathogen that enhance their ability to cause disease, colonize hosts, evade the immune system, and obtain nutrients.

Question 13

What is an exotoxin? What is an exoenzyme (also called an extracellular enzyme)? What are some examples of exoenzymes that act as virulence factors?

Answer 13

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

Question 14

substate

Answer 14

the substance on which an enzyme acts; the surface on which an organism will grow

Question 15

active site

Answer 15

the site on an enzyme shaped to fit with the substrate

Question 16

allosteric site

Answer 16

A site that allows molecules to either activate or inhibit enzyme activity

Question 17

apoenzyme

Answer 17

protein portion of the enzyme

Question 18

cofactor

Answer 18

chemical species needed by some enzyme for enzymes to catalytic

Question 19

coenzyme

Answer 19

organic cofactors

Question 20

holoenzyme

Answer 20

apoenzymes + cofactor

Question 21

How do enzymes increase reaction rate?

Answer 21

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.

Question 22

how many classes of enzymes are known to exist

Answer 22

6 functional classes

Question 23

names of important coenzymes

Answer 23

Nicotinamide adenine dinucleotide (NAD), flavin adenine dinucleotide (FAD), Coenzyme A, thiamine pyrophosphate, pyridoxal phosphate, tetrahydrofolate

Question 24

enzyme activity affected by enzyme concentration

Answer 24

increased, reaction rate increases

Question 25

enzyme activity affected by substrate concentration

Answer 25

There is a maximum substrate level that will cap off the amount of enzymatic activity; the active site will be continually occupied

Question 26

enzyme activity affected by pH

Answer 26

affects the ionization of groups that help stabilize the tertiary structure

Question 27

enzyme activity affected by temperature

Answer 27

There is an optimal temp for most enzymatic activity for each activity. Ift temp is too high, change in conformation occurs

Question 28

enzyme activity affected by inhibitors

Answer 28

bind at allosteric site which changes the enzymes activity

Question 29

What are competitive enzyme inhibitors

Answer 29

Compete with normal substrate for active site. - Have similar size/shape/structure as substrate - Sulfonamide & PABA

Question 30

What are non-competitive enzyme inhibitors?

Answer 30

Binds to site other than active site. Often that is at allosteric site which alters structure of active site. Is reversible.

Question 31

What are enzyme poisons, and some examples of these?

Answer 31

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

Question 32

What is the difference between reversible and non-reversible non-competitive inhibitors?

Answer 32

Reversible – inactivates enzymes through noncovalent, reversible interactions, bind weakly and dissociate Non-reversible – form strong, covalent bonds that permanently inactivate the enzyme.

Question 33

selective toxicity

Answer 33

The ability of a drug to targets sites that are relative specific to the microorganism responsible for the infection

Question 34

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)?

Answer 34

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

Question 35

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)?

Answer 35

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

Question 36

What are extracellular enzymes (also called exoenzymes), and what do they do?

Answer 36

Moved outside of the cell and act to digest polymers into monomers which can be transported inside the cell.

Question 37

What are inducible enzymes (also called regulated enzymes) & what are constitutive enzymes? How are they alike, and how do they differ?

Answer 37

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.

Question 38

What is an allosteric site (also called a regulatory site)? What is allosteric regulation?

Answer 38

Distorts enzyme shape, prevents or enhances binding. Enzyme activity controlled by binding to allosteric site.

Question 39

What is the central dogma of molecular biology?

Answer 39

Enzymes are genetically controlled: DNA  mRNA  protein

Question 40

What is enzyme repression? How does it differ from feedback inhibition (also called end-product inhibition)?

Answer 40

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

Question 41

What is feedback inhibition (also called end-product inhibition), and how does it work?

Answer 41

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.

Question 42

What are some different ways in which metabolic pathways are arranged

Answer 42

linear, branched, cyclic

Question 43

clostridium botulinum domain, movement, effects of botulinum

Answer 43

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

Question 44

botulism, treatments, and prevention

Answer 44

* 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)