Exam 2 Flashcards
what is the monomer of a protein?
amino acid
what is the structure of an amino acid
amine group (NH2), carboxyl group (COOH), an R group, all bonded to a central (alpha) carbon
All proteins are built from _____ amino acids
20
how many neutral AA?
15
why are side chains so important?
they enable proteins to perform their functions
are nonpolar side chains hydrophobic or hydrophilic?
hydrophobic, gather into clusters (oil and water)
are polar, basic, and acidic side chains hydrophobic or hydrophilic?
hydrophilic, surface of folded proteins impart water solubility of proteins
how many AA are chiral?
19
which AA is achiral?
glycine
what is the only secondary amine?
proline
what is the importance of intermolecular forces of proteins?
important in determining interactions between amino acids
what are the 4 different intermolecular forces in order from strongest to weakest?
- ionic + covalent bonds
- hydrogen bonds
- dipole-dipole forces (disulfide bond)
- van der waals forces
explain a hydrogen bond b/w AAs
side chains can form hydrogen bonds, connecting different parts of a protein molecule
explain van der waals forces
the overall charge of the molecules brings them together (weak)
explain hydrophobic interactions of AA
hydrophobic (nonpolar) molecules come together and expel the water between them
explain a disulfide bond
creates a covalent bond b/w sulfurs
what is a peptide bond?
an amide bond that links 2 AA together, PLANAR, releases a water molecule
how do you name peptides?
citing AA residues in order
define zitterion
a neutral dipolar ion that has one pos charge and one neg charge
amino acid net charge
0, NH3 is + and COOH is - so cancels = 0
define isoelectric point (pi)
describes the ph at which a sample of an amino acid has an equal number of + and - charges
(AA each have their own pi due to the side chain)
how many essential AA are there?
9
what are essential AA?
amino acids that the human body cannot produce, must be consumed in the diet
define metabolism
chemical reactions maintaining living state
define catabolism
breakdown of molecules to form energy
define anabolism
synthesis of compounds needed by cells
define a primary structure
sequence of AA in a protein chain (order of the AA)
be able to label a primary structure (protein backbone, peptide bonds, and side chains
check notes
why is the primary structure important?
primary function is crucial to the function of the protein that the change of even one AA can drastically alter a proteins biological properties
define secondary protein structure
spatial arrangement of the polypeptide backbones determines the secondary protein structure
what does the alpha helix of the secondary protein structure look like?
coil, stabilized by h bonds along the backbone with r groups positioned on the Purdue of the helix, carbonyl group + amide
what does the beta sheet of the secondary protein structure look like?
flat sheet-like structure, adjacent protein chains held together by h bonds along the backbones
parallel beta sheet
peptide chains in same direction
anti parallel beta sheet
turned around/ladder
2 classes of proteins from the secondary structure
- fibrous (tough, insoluble)
- globular (globe shape, water soluble)
examples of fibrous proteins
wool, hair, fingernails
examples of globular proteins
alcohol dehydrogenase, serum albumin
what is collagen?
secondary structure protein, found in skin, cartilage, blood vessels, bone
–> left handed alpha helix
what disease is associated with collagen?
scurvy, lack of vitamin C causing alpha helix to destabilize
define tertiary protein structure
the way an entire protein chain is coiled and folded into its specific 3D shape (determined by primary structure)
define native protein
a protein with the shape in which it functions in living systems
define simple protein
composed of only AA residues
what are simple proteins?
they can function alone
what are conjugated proteins?
aided by a non-amino acid unit
define quaternary protein structure
the way in which two or more protein chains aggregate to form large, ordered structures
what is hemoglobin?
a protein in a quaternary structure composed of 4 polypeptide chains held together by hydrophobic interactions and 4 heme groups (function: carries O2 around the body and CO2 out of the body)
what is protein hydrolysis?
breaking down proteins, peptide bonds hydrolyzed to yield AA (proteases can do this)
what is chymotrypsin’s function?
hydrolyzes a peptide bond on the carboxyl-terminal side of aromatic AA
what is trypsin’s function?
hydrolyzes peptide bonds on the carboxyl side of lysine and arginine
what is the n-terminal of a peptide?
the AA on the end (left) with amine group on the end
what is the c-terminal of a peptide?
the AA on the end (right) with the carboxyl group on the end
define denaturation
loss of the secondary, tertiary, and quaternary protein structure
agents that cause denaturation
- heat
- mechanical agitation
- detergents
- organic compounds
- ph change
- inorganic salts
what is the connection between protein misfolding and neurodegeneration?
neurodegeneration is often attributed to proteins that are not folded the correct way
what are some causes of protein misfolding/neurodegeneration?
- head trauma
- genetic mutation
- age
what are amyloid fibrils?
stable protein aggregates that form under certain conditions, makes long, stiff fibers of proteins that cause damage to cells and leads to neurodegeneration
what causes Alzheimers?
brain tissue formed from the amyloid B peptides
how to prevent Alzheimers?
- diet/eating healthy
- exercise
- low doses of aspirin
define enzymes
a special class of proteins that act as a catalyst for a biological reaction
What is an enzymatic unit?
the time it takes for an enzyme to perform a task
(number of molecules changed from reactant to product per unit of time)
How are enzymes named?
most end with -ase
How are enzymes catalysts?
- lowers the energy barrier for a reaction
- gives direction to a biochemical reaction
Can enzymes be reused?
yes
explain specificity with enzymes
the limitation of the activity of an enzyme to a specific substrate or type of reaction
- structure of enzyme
- specific to chiral centers
- relates to rate
What is a turnover number?
- measures catabolic activity
- the max number of substate molecules acted upon
- (per enzyme unit time)
define active site
pocket with a specific shape and chemical makeup necessary to bind a substrate
define substrate
a reactant in an enzyme (catalyzed reaction)
How enzymes work, 4 steps written out?
E + S –> ES –> EP –> E +P
- E=enzyme
- S=substrate
- P=product
Why are cofactors needed?
the functional groups of proteins are limited to those of the AA side chains, so by combining with cofactors enzymes gain chemically reactive groups that are not available as side chains
What are cofactors?
METALS
- get from the diet
- bind to the enzyme
- ex: Cu2+, Fe2+, etc.
What are coenzymes?
organic molecules
- NOT BOUND
- ex: NAD
How are vitamins and coenzymes related?
vitamins help to build/synthesize coenzymes
4 major factors affecting enzyme activity
- substrate concentration
- enzyme concentration
- temperature
- ph
How does substrate concentration affect enzyme activity?
- more substrates = higher rate
- less substrates = lower rate
- there is a maximum
(exponential)
How does enzyme concentration affect enzyme activity?
more enzymes in a given volume, the quicker the rate will be
(linear)
How does temperature affect enzyme activity?
- max is when it reaches the optimal temperature
- too hot, will denature
(bell curve)
How does pH affect enzyme activity?
- enzymes vary on optimal ph
- (most enzymes max activity at about 5-)
- most enzymes will denature in extreme ph
(multiple bell curves dependent on enzyme)
6 main classes of enzymes
- oxidoreductases
- transferases
- hydrolyses
- isomerases
- lyases
- ligases
function of oxidoreductases
- oxidoses –> oxidation of O2 to substrate
- reductases –> reduction of a substrate
- require coenzymes
EXAMPLE: NAD –> NADH
function of transferases
- catalyze transfer of a group from one molecule to another
EXAMPLE: ATP –> ADP + PO3^2-
function of hydrolases
- breaking down (lipases, proteases, amylases, etc)
- important in digestion
EXAMPLE: polypeptide chain –> AA
function of isomerases
- rearrange the bond placement (change chirality)
EXAMPLE: A –> B
function of lyases
- addition of simple organic groups (H2O, CO2, NH3) yo a double bond
- no energy required
function of ligases
- addition (bonding 2 substrates)
- NEED ENERGY
- proteins and DNA formed
enzymes act as catalysts because of:
- proximity
- orientation
- catalytic effect
- energy effect
- rate of reaction
what are the 2 theories on how a substate fits into an active site?
- lock and key model
- induced fit model
what is the lock and key model?
- a substrate will only fit into an enzyme with the correct shape
- flaw = assumes enzymes are static
what is the induced fit model?
- enzyme changes shape as substrate fits into active site
is the lock and key model or induced fit model more accurate for how an enzyme fits into an active site?
induced fit model because it accounts for the enzyme moving
3 general enzyme regulators
- activation
- inhibition
- feedback and allosteric control
define an enzyme regulator: activation
any process that starts or increases the action of an enzyme
define an enzyme regulator: inhibition
any process the slows or stops the action of an enzyme
define an enzyme regulator: feedback control
regulation of an enzymes activity by the product of a reaction later in the pathway
- negative feedback = stops reaction
- positive feedback = continues reaction
what is negative feedback?
the product at the end of the pathway stops the reaction
what is positive feedback?
the product at the end of the pathway continues the reaction
define an enzyme regulator: allosteric control
product binds to enzyme in a place separate from the active site and changes shape of the enzyme/active site
- negative = substrate cannot bind
- positive = substrate can now bind
what is negative allosteric control?
the allosteric regulator is bound the the enzyme and the substrate cannot bind
what is positive allosteric control?
the allosteric regulator is bound the the enzyme and the substrate can now bind
what are the 2 types of inhibition?
- competitive
- noncompetitive
what is competitive inhibition?
the wrong substate will come in and keep out the actual substate
what is noncompetitive inhibition?
an inhibitor binds to a different place and changes the enzymes shape so the substate cannot bind to the active site
what is an irreversible inhibitor?
- inhibitor binds to enzyme (covalent) and NEVER COMES OFF
- the enzyme is useless and is destroyed
EXAMPLES: penicillin, aspirin, sarin
examples of poisons that are enzyme inhibitors
- venom
- heavy metals (irreversible)
- cyanide (irreversible)
examples of enzyme inhibitors that are drugs
- ace inhibitor
- HIV protease inhibitor
- proton pump inhibitor
- cox-2 inhibitors
explain the ace inhibitor
inhibitor of angiotensin I converting enzyme
- competitive inhibitor
- brings down blood pressure
explain the HIV protease inhibitor
ritonovir, binds to HIV protease active site
- inhibits HIV production
- competitive inhibitor
explain the proton pump inhibitor
inhibits the hydrogen potassium ATPase in parietal cells of stomach, inhibiting HCl secretion
- noncompetitive inhibitor
- helps with heart burn
explain the COX-2 inhibitor
bind to COX-2 enzyme responsible for inflammation and pain
- ibuprofen! (competitive) and Celebrex
define zymogen
enzyme is released as inactive and undergoes a chemical change to be activated
explain the genetic control of enzyme regulation
the synthesis of all proteins, including enzymes, are regulated by genes
(example: lactase is not typically synthesized in adults)
draw glycine
R chain = H
draw alanine
R chain = CH3
draw cysteine
R chain = CH2-SH
draw aspartate
R chain = CH2-COO-
draw lysine
R chain: CH2(x4)-NH2+
define vitamin
an organic molecule, essential in trace amounts, that must be obtained in the diet because it is NOT synthesized in the body
what are the 2 classifications of vitamins?
- fat soluble
- water soluble
what vitamins are fat soluble?
A, D, E, K
what vitamins are water soluble?
vitamin b complex and C
why can you eat a lot of water soluble vitamins?
because excess can be easily removed in urine
vitamin c deficiency and excess
deficiency: scurvy
excess: kidney stones
what is vitamin B3 (niacin)
- sources: grains, cheeses, nuts, chicken
- precursor to NAD+ (oxidoreductase coenzyme)
- deficiency: dermatitis, weakness, mental confusion
what is vitamin B7 (biotin)
- sources: shampoos, fruits, vegetables, nuts, grains
- benefits: energy support, healthy liver, skin, eyes, hair, nerves, nails, and glucose
what is vitamin C used for
need vitamin C to transfer of hydroxyl groups to proline to stabilize alpha helix structure
- left handed helix
what is vitamin E
- prevents breakdown of vitamins A and FA (antioxidants)
- source: meat, milk, vegetables
- deficiency: anemia, other
- excess: none
what is vitamin K
- essential for liver synthesis of prothrombin and other clotting factors
- source: vegetables, intestinal bacteria
- deficiency: bleeding disorders
- excess: liver disfunction, jaundice
define antioxidants
a substance that prevents oxidation by reacting with and oxidizing agent (diffuse free radicals)
define free radicals
reactive molecular fragments with unpaired electrons that gain stability by picking up electrons from nearby molecules
why are free radicals bad?
- they steal from healthy atoms
- uncontrolled, domino effect of damage, attracted to DNA
how do antioxidants diffuse free radicals?
give the electron to the free radical thereby diffusing it
What causes free radicals?
- UV damage
- inflammation
- air pollution
- smoking
- ionizing radiation
- metabolism
dietary antioxidants
- vitamin C
- vitamin E
- selenium (cofactor)
define mineral
an enzyme cofactor, metals in the diet
transition metals as minerals
- form positive charge ions
- different ionic states (+1 to +5)
- all combine to enzymes
what are macro minerals?
required daily amounts (greater than 100mg/d)
examples of macro minerals
Ca, P, Mg, K, Na, Cl, S
what are micro minerals?
need less of these (transition elements)
examples of micro minerals
transition elements
- chromium, copper, manganese, molybdenum, selenium, zinc
Calcium as a macro nutrient: use, source, deficiency, excess
- use: bone formation + muscle contraction
- source: dairy, eggs, beans
- deficient: osteoporosis, muscle cramps
- excess: kidney stones, heart arrhythmias
define carbohydrates
a large class of naturally occurring polyhydroxy aldehydes and ketones
carbohydrates general formula
CnH2nOn
how to name carbohydrates?
- family name ending in -ose
- simple sugars = common names
- number of carbons = prefix (try, treat, pent, hex, hept)
define monosaccharide
contain 3-7 carbon atoms and one aldehyde or ketone group
naming a monosaccharide
- identify ketone (ketose) or aldehyde (aldose)\
- count amount of carbons and determine the prefix
- combine with -ose
name this molecule: aldehyde, 6 carbons
aldohexose
what is special about carbohydrate functional groups?
they are involved in reactions with alcohols, lipids, or proteins to form biomolecules
are all carbohydrates chiral?
no, proline is achiral
D vs L carbohydrate?
chiral carbon atom furthest from the carbonyl group before the last carbon
- D = right
- L = left
what are more often seen in nature: D or L carbohydrates?
D
how many carbons is in an aldehyde ring?
6
how many carbons is in an pentose ring?
5
draw glucose
check notes
draw fructose
check notes
draw sorbitol
check notes
What is d-glucose used for in the human body?
dextrose or blood sugar
What is the most widely occurring monosaccharide and most important functionally?
glucose
what is the most important simple carbohydrate in human metabolism?
glucose
what 2 hormones regulate glucose?
insulin and glucagon
what is galactose used for?
d-galactose is distributed in plant gums, pectins, and a component in disaccharide lactose
what is galactosemia?
galactose deficiency, an inherited (recessive) deficiency of several enzymes needed to metabolize galactose
–> build up causing vomiting, liver failure, brain damage, and cataracts
what is fructose used for?
it is a fruit sugar (in honey and many fruits)
what is ribose and deoxyribose
both are 5 carbon aldehyde sugars, RNA and DNA
what happens when you oxidize a sugar?
it burns fast, very controlled in our body
glucose reduces to sorbitol
an addition of H2, aldehyde converted to a ketone
what is type 2 diabetes?
- increase of sorbitol buildup in intestines
- higher glucose
define glycosidic bond
bond that connects 2 monosaccharides
define hydrolysis
adding water to break the bonds
define disaccharide structure
- 2 monosaccharides connected by glycosidic bond (alpha or beta)
- create a 1,4 link
glucose + fructose
sucrose
galactose + glucose
lactose
glucose + glucose
maltose
explain maltose
- fermenting grains
- alpha 1,4 link
- food sweetener
- digested in the small intestine
explain lactose
- milk sugar
- beta 1,4 link
- lactose intolerance
explain sucrose
- 1,2 anomeric link
- table sugar (beets and cane)
- sucrase enzyme
what are the sweetest sugars?
synthetic sugars
how do we taste?
- molecules are “sensed” by taste cells
- cells release a signaling compound
- ion channel conformational channels trigger a neuron to the brain (sweet, salty, bitter, like, don’t like)
define polysaccharides
polymers of tens, hundreds, or even thousands of monosaccharides linked together through glycosidic bonds
examples of polysaccharides
- cellulose (fiber)
- amylose (starch)
- amylopectin (starch)
- glycogen
cellulose source
plant – fiber (structure)
cellulose subunit
glucose (1000s)
cellulose bond
beta 1,4
cellulose structure
compact, dense structure with NO BRANCHES
what are some examples of cellulose?
- plants
- wool/cotton
- wood/paper/cardboard
- thickener in food
starch examples
- amylose (~20%)
- amylopectin (~80%)
ex: beans, wheat, rice, potatoes
starch source
plant
starch subunit
glucose
what bond does amylose have?
only alpha 1,4, NO BRANCHING
what bond does amylopectin have?
alpha 1,4 and 1,6 BECAUSE BRANCHING
is cellulose digestible by humans?
NO
are starches digestible by humans?
YES
what enzyme breaks down starches?
amylase
glycogen source
animal (liver and skeletal muscle)
glycogen subunit
glucose
glycogen bonds
1,4 and 1,6 (branches)
what is glycogen storage disease?
- cannot break down glycogen
- continues to store
how is glycogen stored in athlete’s different than average?
- athletes can train their body to store more glycogen
- rate of consumption is regulated by effort
what are the blood types?
- A
- B
- AB
- O
what are the differences between blood types?
the differences are based on the presence of 3 different oligosaccharide units = A, B, O
why is O blood type the universal donor?
O has a similar composition to A and B so A, B, and AB will lack the antibodies to cell type O
why can AB receive all blood types?
has A and B molecules on red cells so it has no antibodies to A, B, or O
define energy
can be converted from one form to another but can be neither created or destroyed
animal cell respiration formula
food + O2 —> CO2 + H2O + energy
(oxidation reaction)
plant formula
CO2 + H2O —> C6H12O6 + O2
what are our bodies specific requirements for energy?
- must be released from food gradually
- stored in an accessible form
- release must be finely controlled
- just enough energy released for temp
- energy needs to be available to drive chemical reactions that are not favorable at body temp
explain Gibbs Free Energy
equation to explain whether a reaction is favorable or not depends on either release to absorption of energy as heat, together with the increase and decrease of disorder
Gibbs free energy equation
G= H - T(S)
G means (Gibbs free energy)
Gibbs free energy
H means (Gibbs free energy)
enthalpy
T means (Gibbs free energy)
temperature
S means (Gibbs free energy)
entropy
what does it mean is Gibbs free energy is negative
exergonic reaction (reaction will spontaneously occur)
what does it mean if Gibbs free energy is positive
endergonic reaction (reaction will NOT spontaneously occur)
exergonic definition
A spontaneous reaction or process that
releases free energy and has a negative G
endergonic definition
A nonspontaneous reaction or process
that absorbs free energy and has a positive G
what is a favorable reaction?
exergonic reaction, high reactant energy and low product energy
what is an unfavorable reaction?
endergonic reaction, low reactant energy and high product energy
does the number size matter in Gibbs free energy?
yes, larger the number the more energy they need
what are pathways?
a series of enzyme - catalyzed chemical reactions that are connected by their intermediates, product of first reaction is used in the next reaction and so on
define prokaryotic cell
single celled organism (bacteria, blue green algae)
define eukaryotic cell
found in single celled yeast and all plants and animals
what are the differences between prokaryotic cells and eukaryotic cells?
- eukaryotic are 1000 times larger
- prokaryotic have a cell wall and no membrane bound organelles
what are organelles?
small, functional units that perform specific tasks
what is a membrane bound nucleus?
stores DNA in eukaryotic cells
what is cytoplasm?
region between cells and nuclear membranes
what is cytosol?
fluid of cytoplasm (electrolytes, nutrients, enzymes)
what is the function of mitochondria?
small molecules are broken down to provide energy (ATP) for an organism
structure of the mitochondria
- matrix = citric acid cycle
- inner surface of cell membrane = ETC
- cristae = folds in the inner membrane
- double lipid bilayer
- contains own set of DNA (from the mother)
metabolism definition
the sum of all chemical reactions that take place in an organism
catabolism definition
breaking down, releasing energy
anabolism definition
building larger molecules
activation definition
any process that starts or increases the action of an enzyme
inhibition definition
Any process that slows or stops the action of an enzyme
feedback and allosteric control
two strategies for enzyme regulation
3 Types of Metabolic Pathways
- a linear sequence
- a cyclic sequence
- a spiral sequence
4 Stages of Metabolism
- digestion (catabolism)
- acetyl-coenzyme A production
- citric acid cycle
- ATP production
what is a derivative of B5?
acetyl-CoA
Stage 1: Digestion
enzymes break down molecules
Stage 2: Acetyl-Cozenzyme A Production
Acetyl groups are attached to coenzyme A by a bond
between sulfur of the thiol group on coenzyme A and
the carbonyl carbon of the acetyl
(thiol group=the AA cystine)
Stage 3: Citric Acid Cycle
break down acetyl CoA to produce energy (NADH and FADH2)
Stage 4: ATP Production
NADH and FADH2 are passed through the ETC to produce ATP
