General Biochemistry Flashcards
What powers ATP synthase?
charge difference between inner membrane (high concentration of +) and mitochondrial matrix
think of it like a battery
What type of reactions does the ETC use?
redox reactions
move electrons across the chain
What are FAD and NAD?
coenzymes that interact with the ETC enzymes
also they are oxidizing/reducing agents depending
NADH
reduced form of NAD+
FADH2
reduced form of FAD
If you add double bonds to a hydrocarbon, does this make the hydrocarbon more or less oxidized?
this makes the hydrocarbon more oxidized
some of its electrons are pulled away from the carbons through double bonds
What is more oxidized a carboxylic acid or an alcohol?
carboxylic acid
has more oxygen pulling electrons away from the carbon
Where will H-bonding occur?
-OH -FH and -SH bonds
Amphipathic molecules
polar and nonpolar regions
ex: cholesterol and phospholipids
Is CO2 polar or nonpolar?
nonpolar by symmetry
Where does the polarity of amino acids make a big impact?
the active site of enzymes
transmembrane proteins
protein folding
What does plasma membrane keep out?
hydrophillic / polar molecules
Peptide hormones
composed of amino acids
large and polar
must use extracellular receptors
they quickly trigger a signal pathway to make short-term changes
Steroid hormones
derivatives of cholesterol
small and nonpolar
cross the plasma membrane and interact with nuclear receptors
trigger long-term changes more slowly
How do histones work generally?
histones are positively charged so they can attract negatively charged DNA
What do modifications like acetylation, phosphorylation and methylation do to histones?
normally replace the positively charged lysine with either neutral or negatively charged groups
this weakens the interaction between DNA and histones and the DNA loosens
when the DNA loosens, more gene expression can happen
What are the stereochemical configurations of most of our amino acids?
L and S configurations
Exceptions to configurations of amino acids
cysteine is R and glycine is not chiral
How can proline affect a protein?
can introduce kinks and make the protein more rigid
How can glycine affect a protein?
can decrease steric hindrance and make the protein more fluid
Which amino acid can form disulfide bridges?
cysteine
Which two amino acids have sulfur?
cysteine and met
Which amino acids are negatively charged / acidic?
D (aspartate)
E (glutamate)
both have carboxylic acids on their ends
Which amino acids are positively charged / basic?
lysine, arginine, and histidine
histidine is neutral in physiological conditions
Why are positively charged amino acids basic?
because they already ACCEPTED a proton
Why are negatively charged amino acids acidic?
because they already DONATED a proton
What are two ways to artificially synthesis amino acids?
Strecker and Gabriel synthesis
Proteases
catalyze breaking down proteins / peptides
Is formation or hydroylsis of peptide bonds energetically favorable?
hydrolysis
but it is so slow that it doesn’t occur
What increases the stability of peptide bonds?
resonance between the carbonyl carbon and amide nitrogen
creates a rigid planar configuration
How are peptide bonds formed?
dehydration / condensation through the nitrogen’s nucleophilic attack on the carbonyl carbon
Key points of Strecker synthesis
Start with: aldehyde
End with: amino acid
Process: use nitrogen reagents to form an intermediate, then go through multiple protonation and deprotonation steps to form an amino acid
Key points of Gabriel synthesis
Start with: highly protected nitrogen, phtalimide
End with: amino acid
Process: use MALONIC ESTER to attach amide to carboxylic acid. then, add R-group and remove unwanted groups
Pepsin
a protease that breaks down peptide bonds in the stomach
Around how much does 1 Amino acid weight?
100 Da
What levels of protein folding would changes in temperature or pH influence?
mostly 3º and 4º
also affects 2º
1º is very strong due to covalent peptide bond
What terminus is a new amino acid added to?
C-terminus
What stabilizes the 2º structure of amino acids?
H-bonds on the backbone!
Where are alpha helices commonly found?
transmembrane proteins and DNA binding proteins
Where do R-groups face in alpha helices?
outwards
What can cause amyloid diseases?
misfolded B-pleated sheets
If there is a large amount of proline, what secondary protein structure would we expect?
B-pleated sheets because it introduces a kink
What creates the 3º and 4º structure of proteins?
interactions between side chains, mostly noncovalent
ex: h-bonding, salt bridges, disulfide bonds, hydrophobic interactions
Salt bridges
seen in protein folding
ionic interaction between oppositely charged side chains
ex: K and D
Disulfide bonds
formed by oxidation of two cysteine side chains
covalent
How to break disulfide bonds?
introduce a reducing agent
reduce the sulfur-sulfur bond back to two sulfur-H bonds
Is protein folding spontaneous?
yes, due to decrease in entropy and thermodynamics
How do misfolded proteins aggregate together?
exposed nonpolar regions attach to each other
Where is activation energy on a graph?
difference between the maximum energy (transition state) and reactants’ energy
What do the two subunits of the active site do?
binding site is where intermolecular interactions occur
catalytic site is where catalysis happens
Orthosteric regulation
regulation of enzymes at the active site
What supports the induced fit model?
stabilization of the transition state
lyases
cleave bonds through mechanisms other than hydrolysis
ligases
join molecules together with covalent bonds
kinases versus phosphatases
kinases add phosphate groups
phosphatases remove phosphate groups
What are the respective pKas of the carbonyl and amino groups in an amino acid?
2.2 and 9
amphipathic versus amphoteric
amphoteric: molecule can act as acid or base
amphipathic: molecule has nonpolar and polar regions
example of negative feedback in glycolysis
rate limiting step is fructose 6-phosphate to fructose 1,6-bisphophate
catalyzed by PFK (phosphofructokinase)
ATP (end product of glycolysis) limits PFK’s activity
feed forward regulation
intermediates upstream make downstream enzymes better
What type of feedback is insulin an example of?
insulin is an example of negative feedback
when blood glucose levels are high, insulin is produced and tells body to uptake glucose
glucose levels go from high to low
What type of curve do we see for cooperativity?
sigmodial (S) curve
stronger cooperativity = more of an S shape
What is the Hill Coefficient? What do its values mean?
Hill Coefficient is measure of cooperativity
> 1 is positive cooperativity (like hemoglobin)
=1 is no cooperativity
<1 is negative cooperativity (rare)
how does a substrate bind to an enzyme?
through noncovalent, temporary interactions
where does phosphorylation of an enzyme happen?
at serine, threonine, and tyrosine residues
places where there is an -OH group
What type of enzyme dephosphorylates?
phosphatases
how can cleavage modify enzymes?
can make an inactive zymogen active
example of cleavage of enzymes to activate
trypsinogen being cut to trypsin in the stomach
zymogens
inactive, non-cleaved form of enzymes
How do allosteric enzyme regulators work?
interact at site outside of active site
noncovalent
change the 3º structure of an enzyme
Cofactors versus coenzymes
coenzymes are an organic form of a cofactor
all coenzymes are cofactors, but not all cofactors are coenzymes
prosthetic groups
coenzymes tightly/covalently bound to their enzymes
example of a prosthetic group
Heme group with the covalently bound Fe
Holoenzyme versus apoenzyme
holoenzyme: WHOLE set of coenzymes/cofactors needed are present
apoenzyme: missing certain needed coenzymes/cofactors
What are FAD and NAD+ examples of?
coenzymes needed for redox reactions
Do enzyme inhibitors normally bind covalently or noncovalently?
noncovalently
Vmax
maximum rate of enzyme catalyzed reaction
relianet on enzyme concentration
Km
concentration of substrate needed to reach 1/2Vmax
What does Km tell us?
the affinity of an enzyme for a particular substrate
high Km = low affinity
low Km = high affinity
What are the x and y intercepts in a Lineweaver-Burke plot?
x-intercept: -1/Km
y-intercept: 1/Vmax
If x-intercept of Lineweaver Burke plot moves to the left was does this indicate?
more negative x-intercept
means that -1/Km is greater, so Km is smaller
Km is lower means that affinity is higher
If If x-intercept of Lineweaver Burke plot moves closer to the origin what does this indicate?
less negative x-intercept
means that -1/Km is smaller, so Km is higher
Km is higher means that affinity is lower
would see this with competitive inhibition
competitive inhibitors effect on kinetic parameters
Vmax stays the same (can flood system with substrate to overcome inhibit)
Km increase (less affinity, need more substrate to reach 1/2Vmax)
noncompetitive inhibitors effect on kinetic parameters
Vmax decreases (can’t overcome inhibitor by flooding system)
Km stays the same
noncompetitive versus uncompetitive inhibitors
noncompetitive inhibitors bind to the empty enzyme
uncompetitive inhibitors bind to the ES complex
uncompetitive inhibitors effect of kinetic parameters
Vmax decreases (can’t overcome inhibitor by flooding the system)
Km decreases (in uncompetitive inhibition, the ES complex doesn’t release product. there is a higher affinity for the substrate)
Mixed inhibitors
always decrease Vmax
can increase or decrease Km depending on when and where the inhibitor binds
In general, how can we reduce a molecule?
make more constituents bound to hydrogen
pI
isoelectric point
where net charge is equal to 0
When a protein is denatured what levels of folding are affected?
2º, 3º and 4º
Does water flow to higher or lower osmotic pressure?
higher osmotic pressure
osmotic pressure = solute concentration
Does cholesterol always increase fluidity?
no
at temperatures greater than the physiological temp (37ºC), cholesterol makes membrane more rigid
What is the physiological temperature?
37ºC
How are phospholipids formed?
attach fatty acids to glycerol through esterfication
amphipathic
polar and nonpolar regions on same molecule
glycolypids
a carbohydrate group is attached to two fatty acids through either glycerol or sphingosine
sphingomyelin
a type of glycolipid, amphipathic
clusters with cholesterol to form lipid rafts
signaling and adhesion
integral proteins
also called transmembrane proteins
nonpolar amino acids inside and polar outside
examples of integral proteins
proton pumps, ion channels, G-protein receptors
example of a lipid anchored protein
G-protein complexes attached to intracellular side of membrane through a lipid
peripheral protein
temporarily attached to the membrane in the cytoplasmic side
ex: enzymes
surfactants
can reduce surface tension of a solution
amphipathic molecules like phospholipids and glycerolipids
flippase
move phospholipids from outer to inner surface
floppase
move phospholipids from inner to outer surface
scramblases
move phospholipids in both directions
what happens at lower temperatures?
decreased membrane fluidity
at higher temperatures, do we want more or less unsaturated phospholipids?
less
want to reduce fluidity and have the membrane be more tightly packed
What molecules can always freely diffuse across the cell membrane?
gases
O2 and CO2
(water normally can)
hypotonic
extracellular solution is low in solutes and water moves into cell
hypertonic
extracellular solution is high in solutes and water moves out of cell
osmotic pressure
minimum amount of pressure that prevents further osmosis
equation for osmotic pressure
pi = iMRT
i= number of molecules a solute can dissociate into M= total concentration of solutes
relationship between osmotic pressure and solutes
higher osmotic pressure = higher solutes
something to be careful of when doing calculations with osmotic pressure
need to consider the number of molecules a solute can dissolve into
osmolarity
molarity of all solute particles
Why is diffusion thermodynamically favorable?
increase in entropy
sodium potassium pump
moves 3 Na+ out and 2 K+ in
creates net negative charge
think of salty bannana
example of primary active transport
Voltage gated ion channels and ligand gated ion channels are examples of?
facilitated diffusion
What type of channels do neurotransmitters act on?
ligand gated ion channels
Is facilitated diffusion active or passive?
passive
diffuse down concentration gradient
primary active transport
couples ATP/energy source hydrolysis to directly move solutes
secondary active transport
active transport generates concentration gradient where passive transport then occurs
antiporter
type of secondary active transport
moves two solutes in opposite directions
symporter
type of secondary active transport
moves two solutes in the same direction
endocytosis
engulfment of particles by the cell membrane
receptor-mediated endocytosis
takes up very specific molecules into the cell through endocytosis
do you need ATP for primary active transport?
no. can use light or other sources of energy
endosomes
organelles that sort products of endocytosis
what organelle is responsible for digesting and repurposing materials ingested during endocytosis?
lysosome
what type of endosomes are used for pinocytosis?
early and late endosomes
what type of endosomes are used for phagocytosis?
phagosomes
how can exocytosis be regulated?
through Ca2+
ex: in neurons, more Ca2+ triggers the release of neurotransmitters through exocytosis
How is ATP used for energy?
add water (hydrolysis) to cleave the gamma phosphate
gamma phosphate becomes an inorganic phosphate group (Pi)
What are two types of ATP hydrolysis?
substrate level phosphorylation
oxidative phosphorylation
substrate level phosphorylation
transfer a phosphate group directly to ADP
use an enzyme to catalyze this transfer
ex: glycolysis
oxidative phosphorylation
use the ETC to generate ATP
requires oxygen
why does the ETC require oxygen?
diatomic oxygen serves as the last electron acceptor in the ETC due to it’s high reduction potential
What happens to FADH2 and NADH in the ETC? Why?
they are oxidized as the enzymes in the chain have higher reduction potentials
Reduction potential
ºE
measures how energetically favorable reduction (gain) is
What does a more positive ºE indicate?
more favorable to reduce
What happens when electrons move to higher ºE?
energy is released as it is more favorable to go to a higher ºE
Glycogen
hydrolyzed to glucose which releases energy
What is the first step the body makes regarding how to use glucose?
determines what type of glucose membrane receptor to display
GLUT1
glucose transporter found on nearly all tissues to serve as baseline glucose uptake
What happens to receptors when glucose levels are low?
more GLUT1 is expressed to uptake more glucose for energy
GLUT2
glucose transporter found on kidney, liver and pancreas cells as it allows for 2 way transport of glucose
GLUT3
glucose transporter found on neurons and placenta
has a high affinity for glucose so these cells have glucose even when food is scarce
GLUT4
glucose transporter found on muscles + adipose tissues
takes up glucose for energy and storage
Which glucose receptor does insulin work on?
GLUT4
Ka
the association constant
greater Ka = greater affinity
units M-1
Kd
the dissociation constant
lower Kd = greater affinity
unit M
the inverse of the association constant, Ka
Km
halfway substrate concentration to Vmax
Kt
equivalent to Km
is affinity for transport and is independent of solute concentrations
What denaturants can break disulfide bonds?
strong reducing agent or strong bases
How can you denature hydrophobic interactions?
with a detergent
Majority of fibrous proteins
are hydrophobic and used for structure
Majority of globular proteins
are hydrophilic and often perform enzymatic roles
How does SDS work?
it breaks up hydrophobic interactions
SDS is an amphipathic molecule
How can you disrupt salt bridges?
change the pH of the solution
pH will make different amino acids charged and ionic interactions are what constitute salt bridges
Triglycerides
three fatty acids connected through ester bonds to a glyceride backbone
Saponification
use a strong base to break triglycerides into soap and glycerol
Phosphatidyl
prefix that indicates a phospholipid
Sphingolipids
fatty acids connected to a sphingosine head that has a nitrogen atom
Sphingomyelin
type of sphingolipid that clusters in lipid rafts in the plasma membrane
plays a role in biosignalling
What are two types of eicosanoids?
thromboxanes and prostaglandins
prostaglandins
lipid that mediates pain and inflammation
type of eicosanoid
thromboxanes
found in platelets and mediate clotting
type of eicosanoid
terpenes
derived from isoprenes
make up cholesterol
vitamin D
cholesterol derivative
Which vitamins are water soluble?
B and C
What type of lipid makes up steroid hormones?
cholesterol NOT fatty acids
omega notation for fatty acids
starts counting carbons on the non-carbonyl end
omega - (double bond location)
lipid numbering notation
only gives the total number of carbons and the number of double bond
ex: 16:1
delta notation
starts counting at the carbonyl end
ex: ∆9
Which type of unsaturated fatty acid is typically more solid at room temperature?
trans - fatty acids because they can pack together more tightly
Why are trans-fats considered more unhealthy than cis-fats?
trans-fats can increase the number of LDL to HDL
lipoproteins
made of proteins and lipids
transport fats into the bloostream
chylomicrons
can transport lipids through aqueous bloodstream
chylomicrons are similar to VLDL
Order how a newly synthesized chylomicron would move through the body
intestinal epithelium lacteals lymphatic vessels adipose tissue liver
Where are lipoproteins made?
the liver
Do more or less lipids make a lipoprotein less dense?
more lipids = less dense
LDL
low-density lipoprotein (has lots of lipids)
delivers cholesterol to cells
HDL
high-density lipoproteinn (doesn’t have many lipids)
can pick up cholesterol and take it back to the liver
What do higher LDL levels indicate?
higher risk of cardiovascular disease and atherosclerosis
What triggers the release of fatty acids from adipose cells?
epinephrine and glucagon
Lipase
breaks down triglycerides to free fatty acids
catabolism
refers to breaking molecules down
lipolysis
fatty acid molecules are mobilized from storage and made available to cells that need energy
occurs in adipose cytosol
Beta oxidation
fatty acids are oxidized to produce intermediates that can be used to make energy
How can lipids enter the mitochondria for beta-oxidation?
tagged with a CoA tail
Where does beta-oxidation primarily occur?
the mitochondria
carnitine shuttle
acts as a control point for regulating fat metabolism
allows larger CoA tagged lipids to enter mitochondria
What does each round of B-oxidation include?
1) oxidation
2) hydration
3) oxidation
4) thiolysis cleavage
What do odd-numbered unsaturated fatty acids need to do before beta-oxidation?
use an isomerase to move the double bond between the alpha and beta carbons
What do even-numbered saturated fatty acids need to do before beta-oxidation?
2 double bonds will occur
so, first need to reduce one double bond and then, isomerase the other to between the alpha and beta carbons
Calculation for how many ATP molecules produced per lipid
a little less than 7 * the number of carbons
Calculation for how many round of Beta-oxidation needed?
number of carbons/2 minus 1
Ketone bodies
made from acetyl-CoA in the liver in times of low glucose
What can ketone bodies be used for?
can be used to transport acetyl-CoA to heart and brain tissues for energy production during times of low glucose
Where are ketone bodies made?
the liver
hepatocytes
liver cells
3 common ketone bodies
acetoacetate
acetone
D-B-hydroxybutyrate
when does ketoacidosis occur?
occurs when insulin does not work so glucose is not being used for energy and this leads to a reliance on ketogenesis for energy
Why are lipids used for energy storage?
they are more reduced than carbs/proteins
they carry less water than carbs/proteins so they are lighter
Where does fatty acid synthesis occur?
cytoplasm of adipocytes
What lipid can the body naturally produce?
palmitic acid
Where is cholesterol synthesized?
in the smooth ER of heptacytes (liver cells)
What transports cholesterol from the liver to the tissues?
LDL
G-actin
the monomer form of actin
F-actin
the polymer form of actin
How is F-actin created?
actin hydrolyzes ATP to catalyze its own reaction
What are microfilaments made of?
actin
Treadmilling
when actin is being added to + end while being simultaneously removed from - end
can also happen with microtubules
Keratin
an example of an intermediate filament
What is needed for microtubule creation?
GTP and tubulin dimers
Kinesin
a motor protein that walks from the center of the cell to the periphery down microtubules
transports cargo
require ATP to walk
Dyneins
walk from periphery to center of cell down microtubules
transports cargo
requires ATP to walk
Myosins
attach to actin filaments during muscle contraction
requires ATP
Selectins
a type of cell adhesion molecule that mediate the inflammatory response
selectins help slow down leukocytes when they come to an infected area
Cadherins
a type of cell adhesion molecule involved in growth and development
Ca2+ dependent adhesion
Formation of cell to cell connections
Integrins
a type of cell adhesion molecule that helps cells adhere to the extracellular matrix and also act as signaling molecules
Anchoring junctions
stabilize cells and tissues
Gap junctions
bring 2 cytoplasms into contact with each other
seen in tissues that conduct chemical and electrical signals to coordinate function
Tight junctions
found in epithelial cells
link cells together without allowing transport
ex: BBB
Antibody abbreviation
Ig for immunoglobulin
Class switching
changes the type of antibody by modifying the constant domain of the heavy chain
keeps hypervariable region
IgG
the most abundant class of antibody
does most work during the humoral immune response
only antibodies that can get passed to fetus
