Biochem Flashcards
the Rer pumps out generalized proteins, the … makes proteins specialized
golgi
smooth Er, … production in the adrenal cortex
steroid
mitochondria has … passed on by mother
double membrane layer
strongest bond?
covalent
examples of noncovalent bonds
electrostatic
hydrogen
van der waals
aspartate can be broken down into
oxaloacetate
what is tyrosine made from
phenylalanine
what can be made from tyrosine
dopa
epi
norepi
melanin
amino acids have a … group which lipids and carbs do not have
nitrogen
what is the precursor of serotonin?
tryptophan
decarboxylation of histidine leads to which vasodilator?
histamine
when the length of a polypeptide becomes very larger, > 100 AAs, the structure is termed a
protein
glutamate is a precursor of
GABA
… is a group of genetic disorders characterized by mutations in the enzyme tyrosinase which is necessary for the conversion of tyrosine to melanin
albinism
the primary structure level of aa’s is the order of aa’s and this determines it’s…
function
secondary structure level refers to local (non-covalent) interactions between neighboring amino acids, examples are ….
alpha helices
beta sheets
random coils
tertiary structure level refers to a polypeptide chain folding on itself creating a 3D shape that is often stabilized by … bonds. 2 examples of a tertiary structure are…
covalent disulfide
globular
fibrous
is a globular structure water soluble or insoluble?
soluble
whats an example of a globular structure protein?
albumin
is a fibrous structure protein water soluble or insoluble?
insoluble
fibrous structures are most often involved in protection and maintaining cell/tissue structure and include …, …, and …
collagen
keratin
elastin
collagen is …. +
glycine+x+y
w/in the globular shape of a protein, which aa’s will you find
leucine
valine
x-ray diffraction is the best way to analyze which structural level of a protein?
tertiary
… are proteins that serve as catalysts by lowering the activation energy needed to initiate a rxn
enzymes
…. bind to enzymes
substrates
IgM is ….
Made first. first antibody made in response to antigen
…. are highly specific y-shaped proteins produced by plasma cells in response to an antigen
antibodies
plasma cells are
mature B lymphocytes
…. is the most plentiful Ab in circulation, only one that can cross the placenta and is predominant Ab in gingivitis
IgG
… is the primary antibody in excretions such as mucous, saliva, tears, and breast milk. causes bacterial aggregation on mucosal surfaces
IgA
IgA causes bacterial …. but causes pathogens to not be able to ….
aggregation
adhere
IgE is the prominent antibody in what type of hypersensitivity rxn?
type 1
IgE binds to allergens and triggers … release from .. cells
histamine
mast
histamine is found in which 2 types of cells
mast cells
basophils
…. leads to histamine release
calcium depolarization
what are the symptoms of first exposure in a type 1 hypersensitivity rxn
no symptoms on first exposure but IgE antibodies are released and they bind to mast cells and basophils
is collagen water soluble or insoluble
water insoluble
… is the most abundant protein in the body
collagen
collagen consists of … polypeptide strands stabilized by … bonds that are eventually wound into a …
3
disulfide
triple helix
each polypeptide strand of collagen consists of ….
Glycine+x+y
Proline and lysine are commonly in the X and Y positions
what are the 3 cofactors that are important for hydroxylation of proline residues during collagen synthesis?
vitamin C
ferrous ions
a-ketoglutarate
vitamin C deficiency causes
scurvy
symptoms of scurvy
bleeding gums
weakened connective tissue
poor wound healing
… and … are autoimmune disorders that develop when the body attacks healthy collagen fibers
systemic lupus erythematous
rheumatoid arthritis
Lupus attacks …. and it occurs in …. and a distinct feature is…
DNA
young females
malar rash
the concentration of … may be used as an estimate of the amount of collagen present within a given tissue
hydroxyproline
… results from an AD genetic defect in production of type 1 collagen, causing weak bones and connective tissue. common signs include multiple fractures, poor wound healing, and blue sclera.
osteogenesis imperfecta
…. results from a mutation causing abnormal synthesis, structure and secretion of type 1 and type 3 collagen. signs include loose and hyperextended joints, hyperelastic skin, and aortic dissection.
Ehler’s Danlos syndrome
Elastin fibers are much more elastic than collagen because they do not contain …
hydroxyproline
on hemoglobin: what state must iron be in for binding to occur?
ferrous or reduced state (fe2+)
…. comprise 90% of enamel proteins and are involved in the organization of enamel rods during development
amelogenins
what 3 things could cause thin hypoplastic enamel ?
amelogensis imperfecta
def. of vit A
def. of vit D
when you have a competitive inhibitor, then binding affinity …. and Km….
and the michaelis-menten graph moves to the …
decreases
increases
right
when you have a noncompetitive inhibtor, vmax…and Km will be…
and the michaelis-menten graph is shifted…
decreases
unchanged
down
non competitive inhibtion will show an …. movement on the lineweaver-burke plot as … decreases
upward
vmax
on the lineweaver-burke plot, remember that competitive…
crosses
… ligands bind to an allosteric site away from the active site of the enzyme that binds to the substrate
allosteric
example of an allosteric ligand?
ATP
a reaction will proceed spontaneously if it is an ….. rxn that results in a high degree of …. resulting in a …
exothermic (-H)
randomness (large S)
-G
although G (in gibbs free energy eqn) provides info regarding the …. it does NOT provide info regarding the …
direction of reaction
rate of reaction
which thermodynamic measures is a measure of randomness?
S = entropy
when something is oxidized it …. electrons
loses
its an oxidized substance aka a reducing agent
when something is reduced it …. electrons
gains
it is a redued substance aka an oxidizing agent
NADH/FADH are electron …. so they act as … agents.
carriers
reducing
when NADH/FADH are oxidized, they become NAD+ and FAD+ and are important for producing … via the …
ATP
krebs cycle
NADPH is an… that is involved in the synthesis of biological molecules. it comes from the …
electron carrier
pentose phosphate shunt
what is the formal definition of pH
-log [H+}
pH + pOH =
so 10^-5 + ? = 14
14
that means pH is 5 so pOH is 9
what is the buffer when H+ ions are released in the cell?
dihydrogen phosphate
what is the buffer when H+ ions are released outside the cell (plasma/blood)
carbonic acid
proteins are capable of buffering solutions over a wide range of pH because …?
they contain many functional groups with different pKa values
according to the henderson-hasselbach equation, pH=pka when?
the acid is half neutralized
bacterial glycolysis is … and produces …. which is ….
anaerobic
lactic acid
cariogenic
… is the most common type of bacterial glycolysis that is used by anaerobic
embden-meyerhof pathway
transamination means
breakdown of proteins for ATP
nitrogen balance refers to the ratio between …. versus
nitrogen absorbed
nitrogen excreted by body
if nitrogen catabolism exceeds the amount of aa’a ingested in the diet, the body has a negative nitrogen balance, this happens in ….
if aa synthesis exceeds nitrogen excretion, the body hase a positive nitrogen balance, this happens in….
anorexia and other wasting diseases
growth spurts and pregnancy
hydrolysis of sucrose yields what?
fructose
disaccharides are 2 monosaccharides joined by a …
covalent O-glycosidic bond
what are the disaccharide forms
diehard MLS fan
maltose
lactose
sucrose
what is maltose made of
2 glucose
what is lactose made of
glucose + galactose
what is sucrose made of
glucose + fructose
monosaccharides are absorbed by…. in the small intestine
enterocytes
what are the 6 glycosaminoglycans (GAGs)?
chondroitin sulfate *main one hyaluronic acid heparin sulfate heparin keratan sulfate dermatan sulfate
GAGs are polysaccharides made up of repeating … they are … charged and strongly attracted to…
disaccharide units
negatively
H2O
GAGs exhibit high … and low… and are thus ideal for joint lubrication
viscosity
compressibility
why are proteoglycans able to attract water?
large number of alcohol groups
digestion is initiated in the saliva by … for … and …. for …
amylase
starch
lipase
lipids
main buffer in saliva?
bicarb
main antibody in saliva?
IgA
what gland produces 75% of salivary secretions?
submandibular gland
caries activity is determined by
pH lower than 5.5
and frequency of sugar contact
the first rxn of the krebs cycle involves the production of citric acid from…. and … via the enzyme…
aceyl coa
oxaloacetate
citrate synthase
the first step of glycolysis involves the conversion of glucose to … via the enzyme…
glucose-6-phosphate
glucokinase
in glycolysis, glucose is converted to …. and then into … if oxygen is present or …. if oxygen is not present
pyruvate
acetyl coa which then enters the krebs cycle
lactic acid which is transported to the liver
… is the rate limiting enzyme of the glycolytic pathway
phosphofructokinase
glycolysis results in a net gain of …. and … per glucose molecule
2 ATP
2 NADH
fluoride inhibits …., an important enzyme near the end of the glycolytic pathway in bacteria
enolase
the cell gains a net total of …. per gluccose molecule during anaerobic respiration
2 ATP
the conversion of pyruvate to acetyl coa occurs in the …. by the enzyme ….
this reaction generates … per pyruvate, for a total of …. per unit of glucose
cytoplasm
pyruvate dehydrogenase
1 NADH
2 NADH
where does the krebs cycle occur
mitochondrial matrix
low levels of citrate synthase may occur during …. or …. resulting in inability to produce … from… so instead … is converted to ….
starvation
diabetes
citric acid
acetyl coa
acetyl coa
ketone bodies
each TCA/krebs cycle produces … and …. per molecule of acetyl coa but because 2 moleculs of acetyl coa enter the krebs cycle per molecule of glucose, the net gain is …. and ….
3 NADH
1 FADH2
6 NADH
2 FADH2
for acetyl coa to transport into the mitochondria, it needs …
the pyruvate dehydrogenase complex
3 enzymes that make up the pyruvate dehydrogenase complex are
CoA
NAD
thiamine
pyruvate can be broken down into … which will then produce a fatty acid
malonyl coA
3 things that can be used in the liver for gluconeogenesis
Lactate
Aamino acids
Glycerol
can acetyl coa be used for gluconeogenesis?
NO
glycogenesis happens in the
liver
the brain can use … for energy if it doesnt have glucose
ketone bodies
what source does the body use for energy after 60 minutes of working out
lipids
what type of molecule is made from polyunsaturated fatty acids?
prostaglandins
are triglycerides part of the cell membrane?
no
… is the primary source of arachidonic acid
phosphatidyl inositol
phosphatidyl inositol is converted to arachiodonic acid through what enzyme?
and what drug can block that enzyme?
PLA2
steroids
arachiodonic acid can be converted to …. or ….. and ….
leukotrienes
prostaglandins
thromboxanes
… is a specific phospholipid that serves as an important structural component of nerve cell membranes and is the major component of the myelin sheath
sphingomyelins
arachiodonic acid is produced from …. and released from …. by the enzyme … and serves as a precursor for …. that are produced by these 2 pathways
linoleic acid
phospholipids
phospholipase A
eicosanoids
cyclooxygenase pathway
lipooxygenase pathway
the cyclooxygenase pathway produces… which protects the stomach and …. which promotes platelet aggregation
prostaglandins
thromboxane
the lipooxygenase pathway produces… which promote inflammation and play a role in allergic rxns (asthma)
leukotrienes
NSAIDS block … which can lead to ulcers
cyclooxygenase pathway
linoleic acid is a ….. fatty acid
polyunsaturate omega 6
a mixed micelle is made up of …
bile salts
free fatty acids
monosaccharides
… breaks down triglycerides into mixed micelles
pancreatic lipase
…. interactions help to maintain the structure of mixed micelles
hydrophobic
normal values for LDL, HDL, total cholesterol and triglycerides
LDL < 100
HDL>50
total cholesterol<200
triglycerides<150
1 cause of xanthelasma?
aging
…. are yellow sharply demarcated cholesterol deposits found under the periorbital skin
xanthelasma
once LDL reaches its target tissue, it is transported into the cell via…
receptor mediated endocytosis
why is HDL good?
takes excess cholesterol from the organs to the liver
beta oxidation is the breakdown of …. and it produces what 3 things?
fatty acids
acetyl coa
NADH
FADH2
ketone bodies are used as the main source of energy during periods of fasting, what are the 3 main ones?
acetoacetate
acetone
beta-hydroxybutyrate
fatty acids are produced in a four step process…. that is repeated 4x
condensation
reduction
dehydration
reduction
both reduction steps utilize NADPH as a reducing agent
acetyl coA is converted to malonyl coa (fatty acids) via the enzyme…
acetyl coa carboxylase
is omega 3 anti or pro inflammatory
anti-inflammatory
omega 3 include …, … and …
alpha-lenolenic acid
EPA
DHA
is omega 6 anti or pro inflammatory
pro inflammatory
omega 6 includes
alpha-lenoleic acid
arach. acid
how many calories/gram for carbs, proteins and lipids?
4
4
9 lipids
which vitamins are fat soluble
DEAK
most toxic fat soluble vitamin?
D
sunlight converts …. in the skin to vitamin D
cholesterol
vitamin D becomes active in the
kidneys
function of vitamin D?
increases intestinal absorption of calcium and phosphate
promotes hardening of bones and teeth
a deficiency of vit. D can cause … in children and … in adults
ricketts
osteomalacia
(body tries to maintain calcium levels by leaching it from the bone making them softer or brittle)
excess vitamin D can result in…
which is usually more common in?
sarcoidosis
middle aged african american females
which are the main vitamins that are antioxidants?
A C E + zinc
what is the precursor of vitamin A?
beta carotene
functions of vitamin A
epithelial tissue enamel rhodopsin antioxidant bone remodeling
deficiency of vit. A causes
night blindness
dryness of skin and eyes
enamel irregularities
… is a vitamin K antagonist
warfarin
vitamin K deficiency is most common in
newborns
deficiency of vitamin B1 (thiamine) may be associated with…
alcoholism (wernicke-korsakoff syndrome)
…. is an autoimmune disorder that destroys parietal cells of the stomach, causing a loss of production of intrinsic factor necessary for vitamin B12 absorption
pernicious anemia
what vitamin deficiency is most common worldwide
vitamin b12
you need …. which is produced by …. to absorb vitamin B12
intrinsic factor
parietal cells
is vitamin b12 deficiency associated with alcoholism?
yes
vitamin C is necessary for hydroxylation of …
proline and lysine residues
vitamin is a cofactor in … synthesis
collagen
deficiency of vitamin C leads to … which results in …
scurvy
delayed wound healing, rotting of teeth and gums, spontaneous hemorrhaging
….. aids in the synthesis of purines and pyrimidine nucleotides required for DNA synthesis
folic acid
most common vitamin deficiency in the US?
folate deficiency
folate deficiency can result in …
spina bifida
what disease results from too much copper
Wilson’s disease
hepatolenticular degeneration
fluoride inhibits …
bacterial enolase which is a key enzyme in glycolysis
fluoride converts … to … reducing enamel solubility and reversing or stopping caries formation
hydroxyapatite
fluoroapatite
… is critical for thyroid function as it serves as a component of thyroid hormones (T3 and T4). helps to regulate energy metabolism
iodine
what are T3, T4 and TSH levels in hyperthyroidism
T3 and T4 are high
TSH is low
iron deficiency results in … in children and .. in adults
cretinism
myxedema
iron is most commonly bound to … in blood plasma
transferrin
functions of zinc
- antioxidant
- required for DNA synthesis
- cofactor for carbonic anhydrase
zinc serves as a cofactor for carbonic anhydrase, the enzyme responsible for converting …. and …. to ….
CO2 and H2O
bicarb
…. are responsible for eliminating free radicals and thus help to protect cells from oxidative stress
antioxidants
vit. A,C,E zinc gluthathione peroxidase flavonoids/carotenoids are all
antioxidants
A and T are bonded by
2 hydrogen bonds
G and C are bonded by
3 hydrogen bonds
nucleotides are linked together by ….. bonds between the 5’ phosphate group and 3’ OH group of neighboring sugar molecules
covalent phosphodiesterase bonds
what increases melting temp, more G/C bonds or more A/T bonds
G/C bonds
what are the base pairs for RNA
A/U (instead of A/T in DNA)
G/C
DNA strands wrap around …. proteins to form nucleosomes.
…. proteins contain high concentrations of lysine and arginine, basic and positively charged amino acids that bind tightly to negatively charged phosphate groups within DNA
histones
histone proteins contain high concentrations of
lysine and arginine
what is the function of histones
stabilize DNA in compact form
… connects DNA fragments on the lagging strand
DNA ligase
…. unwinds the parent DNA in an ATP dependent manner
helicase
… synthesizes primers , which are short sequences of RNA on the parent DNA strand that will serve as an initiation site for DNA polymerase
Primases (RNA polymerase)
…. extends the new DNA strand from 5’ to 3’ and helps to proofread base pairs in the newly synthesized strand. …. CANNOT start de novo, must have a primer to initiate
DNA polymerase
purine ribonucleoside phosphates are all synthesized de novo from which common intermediate
inosine phosphate
what enzyme catalyzes the formation of uric acid from purines
xanthine oxidase
transcription is
translation is
DNA to RNA
RNA to proteins
… is coding RNA that serves as a blueprint for a specific amino acid sequence
mRNA
… is a cloverleaf shape RNA that matches the genetic information from an mRNA strand to specific amino acids
tRNA
…. assembles with proteins to form ribosomes necessary for protein synthesis
rRNA
RNA is copied into complimentary DNA by
reverse transcriptase
DNA that is complimentary to mRNA can be made by
reverse transcriptase
DNA damage by UV light is due to
induction of dimerization by way of covalent bonds between adjacent thymine groups
what is produced when a mutation occurs in an enzyme controlling a signal pathway involved in cell growth processes
oncogene
DNA replication, translation, or protein synthesis happen in all phases of the cell cycle except
M phase
when to use the different blot tests
Sunny Day- Southern DNA
No Rain- Northern RNA
Warm Picnic- Western protein
the isoelectric point is the pH at which a given molecule has …
no net charge and will not move
if pH is lower that the isoelectric point of a protein, which way will the protein migrate
toward negative pole
if pH is higher than the isoelectric point of a proteins, which way will the protein migrate
toward positive pole
