Biochem Study guide 1 Flashcards
1
Q
Name the types of bonds, describe how they are formed and what characteristic of the atoms involved determines the type.
A
- Polar Covalent Bond: electrons are pulled more to one atoms nucleus making the electrons shared unequally, has partial charges. Electronegativity difference > 0.4</=2
- Nonpolar Covalent Bond: has no charges, electrons are shared equally
Covalent bonds are usually between non-metals. Electronegativity difference </=0.4 - Ionic Bond: Has full charges, electrons are transferred. Electronegativity > 2
Ionic bonds are usually between metal and non-metal.
2
Q
Be able to distinguish between and name types of bonds when given molecular formulas.
A
Slide 7 1a lecture notes
3
Q
Name and define types of molecules.
A
- Polar Molecules: have a partial positive pole (side) and a partial negative pole (side)
- Non-polar Molecules: lack a partial positive pole (side) AND a partial negative pole (side).
4
Q
Be able to distinguish between and name molecule type when given a molecular formula.
A
Slide 11 1a lecture notes
5
Q
Name and define the major types of intermolecular forces. Include the types of molecules involved in each type and the relative strength of each.
A
- Covalent Bond:strongest
-Ionic Interaction: second strongest
- Electrostatic (Ion-Ion, Dipole-Dipole, Ion-Dipole, interactions): between permanent + and - (full/partial charges). Includes H-bonding (dipole-dipole interaction) (H bonds w/ F, O, N): 3rd strongest
- Dispersion forces (van der waals): Between Temporary partial + and - charges. Weakest
- Hydrophobic Effects: Between non-polar molecules when surrounded by polar molecules (water), reduces lost of H-bonding, maintains more disorder
Strongest-weakest
covalent bond, electrostatic interaction, van der walls force
6
Q
Given molecules be able to predict the intermolecular forces that may exist between them.
A
Slide 19 and do of lecture 1a notes
7
Q
List the four major categories of biological macromolecules.
A
- Lipids
- Nucleic Acid
- Proteins
- Carbohydrates (Sugars-polysaccharides)
8
Q
Define polymer and monomer. Name and explain the chemical reactions that convert between them.
A
- Polymers: chains of repeated small molecules
- Monomers: small individual molecules that make up polymers. The same monomers are used everywhere. All monomers are broken & put together using the same processes
- Polymers are made by linking many linked monomers (subunits)
- Monomers are linked via dehydration reactions (condensation)
- Polymers are broken apart by hydrolysis
9
Q
Be able to give the monomer and polymer for each of the major biological macromolecule types.
A
Carbohydrates:
- Monomer: Monosaccharides
- Polymer: Polysaccharide
Nucleic Acid:
- Monomer: Nucleotide
-Polymer: Nucleic Acid
Proteins:
- Monomer: Amino Acid
-Polymer: Protein (AKA polypeptides)
10
Q
Explain what is meant by “monomer types are conserved”.
A
The same monomers are used everywhere. They are used in both prokaryotic and eukaryotic cells. They are also used in different types of specialized cells. This is very handy b/c we can get monomers anywhere.
Ex: to replace ourselves/cells we need to make new proteins. We can eat anything to get amino acids, break them down and put them together in a new way
11
Q
Explain how large variety is generated from universally limited monomer types.
A
There is a smaller number of monomer types but many different combinations they can be formed into
12
Q
For carbohydrates give the general characteristic, molecular formula and names on different levels of polymerization.
A
- General Characteristic: hydrophilic organic molecule
- molecular formula: (CH2O)n C6H12O6
- Different polymerization
- Monosaccharides- monomers, simplest surgars (glucose, galactose, fructose)
- Disaccharides- sugar molecule composed of 2 monosaccharides (Sucrose, Lactose, maltose)
- Polysaccharides- long chains of glucose, 3 polysaccharides of interest in cells (glycogen, starch, cellulose)
13
Q
Give the functions of carbohydrates in general and be able to give the functions of glycogen, starch and cellulose specifically.
A
- Carbohydrates: quickly mobilized source of energy, all digested carbohydrates converted to glucose, oxidized to make ATP
- Glycogen: energy storage polysaccharide in animal cells, large, chained, and highly branched (animals have to access energy faster than plants thats why their energy storage molecule is branched, and why plants is not
- Starch: Energy storage polysaccharide in plant cells
-Cellulose: Structural molecule of plant cell walls (have cell walls for structure instead of skeletons)
14
Q
Define conjugated carbohydrate and give an example of where it can be found in cells and its function there.
A
Carbohydrate covalently bound to lipid (glycolipid) or protein (glycoproteins)- this allows for them to act as markers. This is how our body distinguishes between different cells such as liver cells and red blood cells. This is also how it distinguishes from self and non-self cells. When doing transplants you want to find cells w/ as similar markers to the ones of the person retrieving the transplant as possible
This can be found on the external surface of cell membrane as markers
15
Q
Describe the composition and characteristics (including functions) of lipids.
A
Lipids are non-polar hydrophobic organic molecules, composed of carbon, hydrogen, and oxygen. Has a high ration of hydrogen to oxygen, 2x more H.
Lipids are more energy (calories/gram) than carbs.
Lipids make up membranes that make up all of the organelles
Fatty acids: chain of 4-24 C atoms: carboxyl (acid grou at one end, methyl group on the other end, and hydrocarbon chain in between.
16
Q
Name and define the primary types of lipids
A
- Triglycerides: 3 fatty acids covalently bonded to 3 C alcohol, glycerol molecule. (Oil, and fat) primary function is energy storage
-Phospholipids: glycerol and 2 fatty acids and phosphate group. similar to triglyceride except one fatty acid is replaced by phosphate group. Structural foundation of cell membrane: amphiphilic- fatty acid tail is hydrophobic, and phosphate head is hydrophilic
-Steroid: a lipid w/ 17 of its carbon atoms in 4 rings. Signaling molecule that changes protein production (regulated at transcription level). Released by 1 cell, travel through body and send signal to another cell made from cholesterol.
- Cholesterol: the parent steroid from which the other steroids are synthesized. Cortisol, progesterone, estrogens testosterone, and bile acids, synthesized only by animals, important component of cell membranes
17
Q
Define saturated, unsaturated and polyunsaturated.
A
-Saturated carbon atoms are saturated with hydrogen
-unsaturated contains a carbon carbon double bond w/out H
-Polyunsaturated contains many carbon carbon double bonds
18
Q
Name the chemical components of and be able to recognize the structure of triglycerides.
A
3 fatty acids covalently bonded to 3 carbon alcohol (glycerol molecule)
19
Q
Name the chemical components of and be able to recognize the structure of phospholipids.
A
glycerol (three carbon alcohol), 2 fatty acids, and a phosphate group
20
Q
Define amphiphilic and describe how the term applies to phospholipids
A
Amphiphilic: when a molecule has a hydrophobic (non polar) region and a hydrophilic (polar) region
fatty acid “tails” are hydrophobic, and phosphate “head is hydrophilic
21
Q
Describe the chemical components of and be able to recognize the structure of steroids, including cholesterol.
A
Steroid: lipid w/ 17 of its carbon atoms in four rings. signaling molecule that changes protein production
Cholesterol: the parent steroid form which others are synthesized
22
Q
Give the major function of triglycerides, phospholipids, steroids and cholesterol.
A
Triglycerides: energy storage
Phospholipids: structural foundation of cell membrane, plasma membrane and organelle membranes
Steroids: signaling molecules that changes protein production (regulate at transcription level). released by one cell, travel through body, and send signal to another cell. Made from cholesterol
Cholesterol: Synthesize steroids, important component of cell membranes
23
Q
List the names and biological functions of the four major types of nucleotides.
Adenosine triphosphate (ATP)
Guanosine triphosphate (GTP)
Cyclic adenosine monophosphate (cAMP)
Nucleic Acids (DNA and RNA)
A
- ATP: Cells most important energy transfer molecule. Briefly stores energy gained from exergonic reactions (doesnt last long). Releases energy w/in seconds for physiological work. Creates bonds to hold energy, breaks bonds to release energy. hydrolysis adding water, water breaks the bonds, energy is released
- GTP: involved in energy transfer, similar reactions to ATP. Can donate phosphate group to other molecules. energy source in protein synthesis
- cAMP: Acts as “second messenger”
- Polymer (nucleic acids):
-DNA: deoxyribonucleic acid. made up of deoxyribonucleotides. makes up cells genetic inherited information- RNA Ribonucleic acid. made up of ribonucleotides. Intermediate between DNA and protein. May fold to form complex 3D structures. Ribosomes- rRNA gives structure, can be catalytic. Ribozymes have catalytic activity, catalytic RNA.
24
Q
Name and describe the chemical reactions by which ATP stores and releases energy.
A
- holds energy in covalent bonds between phosphates.
- Hydrolysis: adding H2O, H2O breaks bond, and energy is released. Adenosine Triphosphatases hydrolyze the 3rd high energy phosphate bond, this enzyme is used to help break energy bond. Separates into ADP + Pi + energy
- Phosphorylation of ADP: addition of free phosphate group to another molecule. Carried out by enzymes called kinases (phosphokinases). Works on ADP to generate more ATP
25
Name and describe the chemical reactions by which GTP stores and releases energy.
-Hydrolysis: - adding H2O, H2O breaks bond, and energy is released. Adenosine Triphosphatases hydrolyze the 3rd high energy phosphate bond, this enzyme is used to help break energy bond. Separates into GDP + Pi + energy
- Phosphorylation of ADP: addition of free phosphate group to another molecule. Carried out by enzymes called kinases. Works on GDP to generate more GTP
26
Give the full names of DNA and RNA.
DNA: Deoxyribonucleic Acid
RNA: Ribonucleic acid
27
Describe the roles and chemical structures of DNA and RNA. Be able to recognize each when given structures.
DNA: makes up cells genetic inherited information
1. 5 carbon sugar Deoxyribose
2. a phosphate group
3. a nitrogenous base
RNA: Fold to form complex 3D structures.
1. 5 carbon sugar ribose
2. phosphate group
3. nitrogenous base
SLIDE 30 & 31 for given structures on 1b lecture notes
28
Be able to list what is always the same between DNA and RNA and what is always different.
Same:
1. phosphate group
2. nitrogenous base
3. uses bases: adenine, cytosine, and guanine
Difference:
1. Sugar Ribose and deoxyribose
2. DNA uses the base thymine, and RNA uses the base Uracil
3. DNA is a 2 polynucleotide strands while RNA is a single polynucleotide strand
29
Given a structure be able to differentiate between a purine and a pyramidine.
Purines: 2 N, C rings
Pyrimidines: 1 N, C ring
SLIDE 32 on 1b lecture notes
30
Define polynucleotide and be able to name the chemical components of the monomer (the nucleotide) that connect and the component that is not directly involved in linking to make a polymer (polynucleotide).
Polynucleic acid polymer of nucleotides
Repeating sugar phosphate backbone which are directly linked to form the polymer w/ protruding nitrogenous bases that are not directly involved in linking the nucleotides together
31
Be able to name the type of polynucleotide that often exists as two associated polynucleotide strands. Describe how the two polynucleotide strands associate/are held together.
DNA Double Helix: two polynucleotide strands wrap around each other. Produced by base pairing (hydrogen bonding (dipole-dipole)) of bases of two strands
A pairs w T
C & G
producing base pairs
32
Name the chemical components of and be able to recognize the structure of an amino acid.
- Monomers
- Central (alpha) carbon with 3 attached groups.
- amino group (NH2)
- Carboxyl group (COOH)
- Radical (R) group
about 20 types
- identical except for R group
- polar charged, polar uncharged, nonplar (determined by R group)
- properties of amino acid determined by -R group
33
Be able to list what is always the same between amino acids and what is always different.
Same:
-has a central alpha carbon
- has an amino group (NH2)
-has a carboxyl group (COOH)
Different:
- Different R groups
- Some are polar charged, polar uncharged, and non polar
34
Given the amino acid structures at physiological (~ neutral) pH, be able to identify those that are polar charged, polar uncharged, nonpolar and the unique properties of Gly, Cis and Pro.
Slide 39 and 40
Glycine: side chain consists of only H atom and can fit into either a hydrophilic or hydrophobic environment. Resides at sites where 2 polypeptides come into close contact
Cysteine: side chain is polar uncharged, but it has a unique property a covalent bond w/ another cysteine to form a disulfide link, this is the only AA that can covalently bond using its R group
Proline: side chain has hydrophobic character, but it has the unique property of creating kinks in polypeptide chains and disrupting ordered secondary structure
35
Define peptide and peptide bond.
Peptide: two or more amino acids joined by peptide bonds
Peptide Bond: covalent, joints the amino group of one amino acid to the carboxyl group of the next. Covalent bond formed by dehydration synthesis
36
Give the chemical reaction that creates peptides from amino acids (include the name of the reaction, what portions of the amino acids react and the bond and products formed).
Dehydration synthesis (condesation) forms a covalent bond between the amino group of one AA to the carboxyl group of the next.
37
Be able to state why a given protein (i.e. a given amino acid sequence) forms a specific structure.
Protein function depends on protein structure. structure made is lowest energy option
Communication: some hormones and other cell to cell signals. receptors to which signal molecules bind
Membrane Transport: Channels in cell membranes that governs what passes through. Carrier proteins transports solute particles to other side of membrane
catalysis: enzymes
Recognition and protection: immune recognition, antibodies, clotting proteins
Movement: motor proteins molecules with the ability to change shape repeatedly
Cell adhesion: proteins bind cells together, immune cells to bind to cancer cells, keeps tissues from falling apart
38
Name and describe the names of the levels of protein structure.
-Primary structure: AA sequence
- Secondary structure: alpha helix, beta sheet
- Tertiary Structure: secondary structure of 1 strand interacting w/ each other. polypeptide (single subunit of transthyretin)
- protein structure will be primary, secondary, or tertiary if 1 strand (subunit)
- Quaternary Structure: subunits/strands interactions. Transthyretin, w/ four identical polypeptide subunits
39
Define the central dogma and the processes that it is composed of.
The central dogma is how information flows in the body. Information is held in the sequence of deoxynucleotides, ribonucleotides, and amino acids
DNA is synthesized by replication, and then RNA is synthesized by Transcription, finally proteins are created by translation
-Replication duplicates DNA. Nucleotides are added in the correct order by base pairing with parental strands. Hydrogen bonds are formed between bases of nucleotides from different strands.
-Transcription give rise to RNA. ribonucleotides are added in the correct order by base pairing w/ deoxyribonucleotides from a DNA strand. same process makes all kinds of RNA (mRNA, tRNA, and rRNA). RNA polymerase is the transcription enzyme makes RNA polymers. DNA enters RNA polymerase, nascent RNA pull strands apart and a RNA-DNA hybrid helix forms making RNA.
-Translation gives rise to proteins. RNA enters ribosomes (translation enzymes) that takes the information in RNA and translates it into a specific polypeptide chain that will become a protein
40
Be able to give the ionization reaction and equilibrium constant equation (Keq) of water.
Keq= [H+] [OH-] = 1X10^-14
Ionization reaction on SLIDE 19 in 1c NOTES
41
Be able to write the equilibrium constant equation for an acid (Ka).
Ka= [H+][A-]/[HA]
42
Be able to convert between the Ka and the pKa.
pKa= -logKa = log (1/Ka)
Low pKa = high Ka
43
Define buffer and describe its importance in biological systems.
Buffers: solutions that resist pH change
- have acid components to neutralize base
- have base component to neutralize acid
Help maintain the optimal pH required for cellular function and processes, thus contributing to overall homeostasis within an organism
44
List common buffers in biological systems.
Carbonates, proteins, and phosphates
45
Be able to write the equation relating between pH and pKa. Be able to use the equation to determine ion concentration ratios at given pHs and how to make a buffer (ex. #18 on page 32 of book).
ph = pKa + log([A-]/[HA)
SLIDE 25 IN 1C LECTURE NOTES
46
Name the chemical components of an amino acid.
Alpha carbon
Amino group
Carboxyl
R-group- a side chain tha tis distinctive for each amino acid
47
Be able to list what is always the same between types of amino acids and what is always different.
Same:
- Alpha carbon
- Amino group
- Carboxyl group
Different:
-R group
48
Be able to describe and differentiate between types of chirality in amino acids. Know which chiral isomer is more prevalent in cells.
L isomer clockwise CAR (carboxyl, amino, and then the r- group) is L
L amino acids are much more prevalent in cells
D isomer CRA isomer
Carboxyl, R-group, and then amino group
49
Define zwitterion and describe how the term applies to amino acids.
Zwitterion = 1 compound w/ + and - but net charge = 0
Amino acids are zwitterionic at neutral pH, they have a + charge and a - charge, with a net charge = 0. the amino group is protonated, and the carboxyl group is deprotonated
50
Explain the relationship between pH, pKa and ionization.
If the pH is < pKa of a group by at least 1 unit then the group is mostly protonated
if the pH is > pKa by at least 1 unit then the group is mostly deprotonated.
51
Be able to explain the unique properties of Gly, Cis and Pro.
-Glycine (Gly): side chain consists only of hydrogen atom and can fit into either a hydrophilic or hydrophobic environment. Glycine often resides at sites where two polypeptides come into close contact
-Cysteine (cys): though side chain has polar, uncharged character, it has the unique property of forming a covalent bond w/ another cysteine to form a disulfide link
- Proline (pro): though side chain has hydrophobic character, it has the unique property of creating kinks in polypeptide chains and disrupting ordered secondary structure
52
Given amino acid structures (at neutral pH) be able to determine which are polar uncharged, polar charged, non-polar, hydrophobic and hydrophilic.
- Polar Charged: hydrophilic side chains act as acids/bases which tend to be fully charged (+ or -) under physiologic conditions. Side chains form ionic bonds and are often involved in chemical reactions
- Polar uncharged: hydrophilic side chains tend to have partial + or - charge allowing them to participate in chemical reactions, form H-bonds, and associate w/ water
- Non-polar: Hydrophobic side chain consists almost entirely of C and H atoms. these amino acids tend to form the inner core of soluble proteins, buried away from the aqueous medium. they play an important role in membranes by associating with the lipid bilayer
Hydrophobic:
Hydrophilic:
53
Name and describe the names of the levels of protein structure. For each level, include the types where applicable, and the interactions or bonds that determine/stabilize each.
- Primary structure: AA sequence. Determined by DNA sequence. held by covalent peptide bonds. peptide bond is planar due to resonance, limiting structure
- Secondary Structure: alpha helix(coil) and beta sheet (fold). Repeating 3D structures. results from coiling or folding of the polypeptide. From hydrogen bonding between polypeptide backbones (amino and carboxy groups) No R-group interactions
- Tertiary Structure: secondary structure of 1 strand interacting w/ each other. polypeptide (single subunit of transthyretin). 3D shape of a protein (one AA strand). interactions between the R-groups of amino acids that are often far apart in sequence. Hydrophobic interactions, disulfide bridges covalent bond between cys-cys, van der waals forces, and electrostatic attractions (including H-bonding), dispersion forces. Globular proteins: compact, generally hydrophilic outside and hydrophobic inside. Fibrous proteins: slender filaments, insoluble. Metamorphic proteins: multiple structures are equally favored at equilibrium
- Quaternary Structure: subunits/strands interactions. Transthyretin, w/ four identical polypeptide subunits. Two or more polypeptide chains associate. can be any type of interactions between R-groups. contain additional groups (carbs or lipid) to make glycoprotein/lipoprotein. same interaction types as tertiary but between >1polypeptide chain. >2 ends >1 polypeptide and a quaternary structure
54
Give the chemical reaction that creates peptides from amino acids (include the name of the reaction, what portions of the amino acids react and the bond and products formed). Also be sure to know that the reaction requires energy.
Peptide bond (covalent): joins the amino group of on amino acid to the carboxyl group of the next. Covalent bond is formed by dehydration synthesis. water is released, and a peptide is formed
55
Be able to explain the limitations on rotation in a polypeptide chain. (i.e. Which bonds in a polypeptide chain can rotate, which can’t and why.)
peptide bond is planar (due to resonance), which limits structure. single bonds can rotate anything >1 cannot 1.5 bonds (C double bonded to O, C-N)
56
State the length (#aa) of most proteins.
most active proteins have 100s of AA
57
17. Be able to define the following terms: dipeptide, tripeptide, oligopeptide and polypeptide.
- Dipeptide: 2 AA joined together by a peptide bond
- Tripeptide: 3 AA joined together by peptide bonds
- Oligopeptide: Few AA joined together by peptide bonds
- Polypeptide: Multiple AA joined together by peptide bonds
58
Be able to list the polypeptides components that can participate in non-covalent interactions and what they can interact with.
Tertiary R- groups: hydrophobic interactions, disulfide bridges, van der waals forces, electrostatic attractions (including H-bonding)
Quaternary r-groups: same as above
Secondary structure: H-bonding between polypeptide backbones (amino and carboxy groups)
charged amino acids
polar AA
hydrophobic AA
59
Define and differentiate between protein conformation and denaturation.
Conformation: unique 3D shape of protein crucial to function. Some can reversibly change
EX: hinge, enzyme function, muscle contraction, opening and closing of cell membrane pores
Denaturation; extreme conformational change (disruption of intermolecular forces) that destroys function
60
Explain what prions and prion disease.
Extremely small proteinacious infectious particles. Misfolded protein triggers misfolding in correctly folded prions and misfolded prions accumulate in cell membrane of brain cells and kill the cells
Ex: Mad cow disease, Scrapie, Kuru
61
Differentiate between kinetics and thermodynamics.
Thermodynamics determines IF the reaction will happen, Kinetics determines HOW FAST (rate) it will happen.
Thermodynamics is the free energy. endergonic or exergonic
Kinetics: average rate of average velocity. the amount of reactant disappearance in a given time. the amount of product formed in a given time.
62
Define free energy and change in free energy as it relates to a chemical reaction.
Free energy change: energy available to do the work
Gproducts - Greactants
determines spontaneity of reaction ( if it will happen w/out intervention) and if it is endergonic or exergonic
63
Define endergonic, exergonic and spontaneity as it relates to chemical reactions.
Endergonic: must add energy (non-spontanious)
Exergonic: energy is released (spontaneous)
Spontaneity: if the reaction will happen without intervention
64
Know what G and G’ stand for.
delta G = free energy change: energy available to do the work
Gproducts - Greactants
Delta G standard: specific to reaction in the specific conditions/environment it is in
65
Be able to state if enzymes affect free energy of a reaction and why.
No enzymes do not affect free energy, they do not change whether or not IF a reaction will occur. Enzymes are catalyst that speed up chemical reactions, affecting the rate or the reaction not the free energy (thermodynamics) of it.
66
Define standard free energy.
specific to reaction in the specific conditions/environment it is in. Known for chemical reactions under standard conditions. Not representative of cellular conditions
67
Differentiate between free energy and standard free energy. Be able to state where/in what situations each is useful.
delta G = free energy change: energy available to do the work
Gproducts - Greactants
Delta G standard: Still refers to the energy available to do the work. But is specific to reaction in the specific conditions/environment it is in. Known for chemical reactions under standard condition
68
Relate standard free energy to equilibrium.
All chemical reactions are theoretically reversible (not in living things). All chemical reactions spontaneously proceed toward equilibruim. at equilibrium delta G standard = 0, this means that same G in prod as react
69
Explain how reactions with positive standard delta Gs can still occur in cells.
in cells concentrations of reactants and or products can cause delta G to be negative (sponataneous), even when delta G standard is positive (indicates non spontaneous)
70
Define enzyme and describe how it works (be sure to include what it does in both a general sense and also the step-wise cycle, the type of macromolecule it most often is and where on the enzyme specificity is conferred).
Enzymes: catalysts that speed up chemical reactions (rate of reaction).
71
Define the following: substrate, active site, transition state, activation energy, apoenzyme, cofactor, coenzyme, holoenzyme.
- substrate: reactant binding to active sight of an ezyme
- Active site: the portion of the enzyme to which the substrate binds. specific for a substrate
-transition state: state that is mid-way between reactants and products
- activation energy: the minimum amount of energy needed for a reaction
- apoenzyme: inactive enzyme that requires cofactor for activation
72
Explain what determines if an enzyme-substrate complex will form.
when the enzyme binds with the substrate. The enzyme is specific to the substrate, so the shape and chemical properties of the enzyme have to match the active site of the enzyme
73
Explain what is meant by “sterically possible” and “energetically favorable”.
Sterically possible means that the substrate must fit and align correctly with the active site of the enzyme
Energetically favorable: the binding of the substrate to the enzyme should be spontaneous
74
Describe four mechanisms of enzyme catalysis.
- Acid-base Catalysis: AA of enzyme active site donate (acid) or accept (base) H+ from substrate, triggering substrate change to transition state
- Covalent Catalysis: enzyme active site contains strong nucleophile, which creates a temporary covalent bond w/ electrophilic region of substrate
- Metal Ion Catalysis: metal can stabilize ionic intermediates (transition state)
-Orientation Catalysis: Enzymes hold substrates in the optimal position of the reaction. Brings substrates closer together to speed up attachment. 1 enzyme w/ more than 1 substrate in active site
75
For each of the following types of enzymes be able to describe the type of reaction that is catalyzed: oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase.
Oxidoreductase: oxidation/reduction. transfer of electrons (often oxygen and hydrogen are gained or lost)
transferase: transfer of functional groups, such as amino group, acetyl group, or phosphate group
hydrolase: addition of water. hydrolysis
lyase: removal of groups of atoms w/out hydrolysis
isomerase: rearrangement of atoms w/in a molecule
ligase: joining of two molecules (using energy usually derived from the breakdown of ATP)
76
Be able to write and use the equations for calculating average rate (or average velocity) of a reaction.
Velocity (V) = -d[A]/dt = d[P]/dt
[A]=reactants
dt = time
[P] = product
d = delta/change
77
Describe the effects changing reactant concentration can have on the rate of the reaction. Include the terms collision theory, zero order, first order and second order.
Collision theory: generally more concentrated reactants have a faster reaction
Zero order: the reaction rate is not affected by the concentration of the reactant
First order: occurs when there is only 1 reactant. rate of reaction is directly proportional to the concentration of only one reactant. pseudo first order reaction: reaction has two reactants (so really second order) but the reaction is first order with respect to only 1 of the reactants
Second order: Usually occurs when there are two molecules of reactant. the rate of the reaction is directly proportional to the concentration of two reactants
78
Define Vmax and Km.
Vmax: max turnover (max velocity). When enzyme is saturated
Km: the substrate concentration at one-half of Vmax. Michaelis constant. combination of ks of enzymatic reaction
79
Define kcat .
the number of substrate molecules that an enzyme can convert into product per unit time when the enzyme is fully saturated with substrate.
higher Kcat = more efficient
Kcat # of substrate yeilding product per second
80
Define allosteric enzyme (include it’s roles).
Enzyme changes shape. Have separate binding sites; allosteric site for effector (inhibitor or activator) binding, active site for substrate binding. Can be quarternary structures (multiple subunits) of near identical peptides. Display cooperativity (change shape of 1 subunit changes the shape of its neighbor. substrate binding of one subunit changes affinity of other subunits for substrate. Catalyze the first commited step. have feed-back regulation (- feedback = feedback inhibition). negative and positive regulation by non-covalent binding of modulators (effectors) (activators and or repressors)
81
Explain feedback inhibition.
when too much of a product is formed then their is a negative feedback inhibition that inhibits (stops) the reaction. Once the product is broken down or used the inhibition is removed and the production of the product resumes
82
Explain negative and positive enzyme regulation.
Negative and positive regulation by non-covalent binding of modulators/effectors (activators and/or repressors). Activators stabilize active form. Inhibitors stabilize inactive form. Activators work to activate the enzyme to produce more product, while inhibitors act on the enzyme to prevent binding and stop production of product
83
Describe cooperativity in relation to enzymes.
Substrate binding of one subunit changes affinity to other subunits for substrate. Change shape of 1 subunit it changes the shape of its neighbor
84
Explain how allosteric enzymes can be regulated by activators and inhibitors.
Allosteric enzymes subject to repression are active in the absence of signal molecules, while allosteric enzymes that rely on activation are not active in the absence of signal molecules.
When signal molecules bind allosteric enzymes, they change the shape of the active site. repressors disrupt the active site while activators restore it\
Allosteric enzymes subject to repression are not active in the presence of signal molecules, while allosteric enzymes that rely on activation require signal molecules to be active
85
Describe where in a chemical pathway allosteric enzymes are found.
Allosteric enzymes catalyze the first committed step
86
Define the following types of enzyme inhibitors (include how each affects the Km and/or Vmax): competitive inhibitor, noncompetitive inhibitor, noncompetitive inhibitor.
-Competitive inhibitors: compete w/ the enzyme for active sites. can be overcome w/ high substrate/inhibitor ratios. Same Vmax different Km
-noncompetitive inhibitor: bind somewhere other than active site and change the shape of the enzyme so that the substrate will no longer fit the active site. Cannot be overcome w/ high substrate/inhibitor ratios. different Vmax and same Km
-uncompetitive inhibitor: bind only ES complexes and prevent product release. Cannot be overcome w/ high substrate/inhibitor ratios. Different Vmax and Km
