MCAT biochemistry

B12

Cyanocobalamin

D/L naming system

D- or L- •Assigned based on the molecule in question's relationship to the enantiomers of glyceraldehyde•All amino acids found in organisms are amino acids (almost)•All sugars found in organisms are sugars (almost)

Pentose is deoxyribose

DNA -OH of ribose replaced with -H

alpha anomer

OH group in the C1 is trans to the CH2OH *it will be axial and down*

isoelectric point

Point at which a compound is electrically neutral.

Respiratory Quotient (RQ)

RQ = CO2(produced)/O2(produced) Normal: 0.8 Range: 0.67-1.3

disulfide bonds

Strong chemical side bonds that can only be broken by chemical solutions

Tautomerization

The rearrangement of bonds within a compound, usually by moving a hydrogen and forming a double bond

B1

Thiamine

Chargaff's Rule

[A]=[T] and [G]=[C], they pair up across from one another forming two strands also called base pairing.

modified standard state

[H+] = 10^-7M and pH = 7 Under these conditions, deltaG° becomes deltaG°' meaning it is standardized to the neutral buffers used in biochemistry

lipid digestion

[digestion] when chyme is present, the duodenum secretes cck (cholecystokinin) hormone into the blood, which stimulates the secretion of pancreatic enzymes and bile and promotes satiety; bile made in the liver emulsifies fat in the small intestine but isn't an enzyme; lipase is an enzyme made in the pancreas that hydrolyzes lipids (also in the small intestine)

Flavin mononucleotide (FMN)

a coenzyme that functions in the transfer of electrons in the electron transport chain

replisome (replication complex)

a complex of DNA polymerase and other enzymes that catalyzes the synthesis of DNA

initiation complex

a complex of protein factors, mRNA, met-tRNA, and the small and large ribosomal subunit which is required to start translation

phosphate ester

a compound formed by reaction of an alcohol with phosphoric acid

lac operon

a gene system whose operator gene and three structural genes control lactose metabolism in E. coli

agarose gel

a jelly-like slab used to separate molecules on the basis of molecular weight

adenosine monophosphate (AMP)

a low-energy compound that results from the removal of two phosphate groups from ATP

Zwitterion

a molecule or ion having separate positively and negatively charged groups.

chiral

a molecule that is not superimposable on its mirror image

Exocytosis

a process by which the contents of a cell vacuole are released to the exterior through fusion of the vacuole membrane with the cell membrane.

Ketose

A carbohydrate whose carbonyl group is a ketone

Fermentation

A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid.

allosteric site

A specific receptor site on some part of an enzyme molecule remote from the active site.

alpha helix

A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.

noncompetitive inhibitor

A substance that reduces the activity of an enzyme by binding to a location remote from allosteric site, changing its conformation so that it no longer binds to the substrate. Km unchanged Vmax decrease

Complex I (NADH-CoQ oxidoreductase)

- transfers electrons from NADH to coenzyme Q - flavoprotein oxidizes NADH - coenzyme Q becomes CoQH2 - moves four protons to the intermembrane space

Benedict's reagent

-detects presence of reducing sugar -aldehyde group of an aldose is readily oxidized indicated by a red precipitate of Cu2O

Tollen's reagent

-detects presence of reducing sugar -uses Ag(NH3)2+ as oxidizing agent *in a + test, aldehydes reduce Ag+ to metallic silver

absolute configuration

-determined by the 3D arrangement of the groups attached to the chiral carbon

glycogen phosphorylase

-enzyme activated by glycogen that cleaves glucose from the non-reducing end of a glycogen branch by phosphorylation *permits rapid release of glucose from glycogen stores

alditol

-forms when the aldehyde group of an aldose is reduced to an alcohol

active muscle

-fuel source used depends on activity *short-lived (2-7 seconds) = creatine phosphate ADP to ATP. *moderate, high-intensity, continuous = oxidation of glucose and fatty acids *1-3 hours of continuous exercise = muscle glycogen stores depleted and intensity of exercise declines at a rate that can be supported by oxidation of fatty acids

triterpenes

-have 6 isoprene units -can be converted to cholesterol & various steroids

Denature DNA

-heat (near boiling) -salt solution (low ionic strength) -Chemical denaturants (urea/formamide)

Hormone Sensitive Lipase (HSL)

-hydrolyzes triacylglycerols, yielding fatty acids and glycerol -activated by a decrease in insulin levels and an increase in epinephrine and cortisol

number of stereoisomers

2^n where n is the number of chiral centers

Triose

3 carbon sugar

Peptides

Chains of amino acids that can function as neurotransmitters or hormones.

induced fit model

Change in the shape of an enzyme's active site that enhances the fit between the active site and its substrate(s)

Riboflavin (B2)

essential for carbohydrate fat and protein metabolism. Necessary for tissue maintenance. And healthy eyes

Oncogenes

genes that cause cancer by blocking the normal controls on cell reproduction

structural genes of operon

genes that code for proteins

1,3-BPG and PEP

high energy glycolysis intermediates generate ATP via substrate level phosphorylation

Outer Mitochondrial Membrane (OMM)

highly permeable due to large pores

connexons

hold tissues/membranes together; hollow cylinders composed of proteins that span the entire width of the abutting membranes

Ghrelin

hormone secreted by empty stomach; sends "I'm hungry" signals to the brain

Keratins

intermediate filament proteins found in epithelial cells; contribute to the mechanical integrity of the cell and also function as regulatory proteins; the primary protein that makes up hair and nails

Amino acid behavior

ionized groups protonate in low pH and high pH deprotonated greater than pKa = deprotonated less than pKa= protonated

heme

iron-based, pigment part of hemoglobin

isocitrate dehydrogenase

isocitrate to alpha-ketoglutarate inhibited by ATP and NADH activated by ADP and NAD+

Enantiomers

isomers that are identical and mirror images of each other

Diastereoisomers

isomers that are identical but not mirror images

Anomers

isomers that differ at a new asymmetric carbon atom formed on ring closure

Hybridization

joining of complementary base pair sequences can be DNA-DNA or DNA-RNA recognition

cDNA library (complementary DNA)

lack introns and only includes genes expressed in tissue from which mRNA was isolated

lipid absorption

leave chylomicrons then lacteals in small intestine absorb dietary lipids that are not absorbed by the blood capillaries, then re-enter blood steam via thoracic duct

fatty acid synthase (palmitate synthase)

major enzyme complex in fatty acid synthesis found in the cytosol becomes rapidly induced in the liver following a high meal in carbohydrates - because of the elevated insulin levels

steriod hormones

make secondary sex characteristic in pubery. Female (estrogen, Progesterone), Male (testosterone)

Backbone of DNA

made up of alternating sugar and phosphate, bases are attached to the deoxyribose or sugar reads from 5' to 3' complementary join by 3' to 5' phosphodiester bonds

Endocytosis

process by which a cell takes material into the cell by infolding of the cell membrane

enzyme activity and pH

pH effect the ionization of the active site changes in it can lead to denaturation optimal active at 7.4 exceptions stomach pepsin - ph = 2 pancreatic enzymes pH= 8.5

coupled reactions

pairs of chemical reactions in which some of the energy released from the breakdown of one compound is used to create a bond in the formation of another compound

B5

pantothenic acid

chimera

patches of cells, including germ cells, derived from two lineages

integral proteins

penetrate the hydrophobic interior of the lipid bilayer

Glycerophospholipids (phosphoglycerides)

phospholipids that contain a glycerol backbone bonded by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head group

vitamin K

phylloquinone (K1) and menaquinones (K2) bloodclotting

emulsification

physical process of breaking up large fat globules into smaller globules, thereby increasing the surface area that enzymes can use to digest the fat

Cellulose

polysaccharide consisting of glucose monomers that reinforces plant-cell walls

Polycrylamide Gel Electrophoresis

positive charge move toward anode

osmotic pressure

pressure that must be applied to prevent osmotic movement across a selectively permeable membrane

where is body protein catalyzed

primarily in muscles and liver

palmitic acid (palmitate)

primary end product of fatty acid synthesis (16:0)

protein level of structure

primary, secondary, tertiary, quaternary

pyruvate dehydrogenase complex regulation

regulated by pyruvate dehydrogenase kinase (respond to high ATP) and pyruvate dehydrogenase phosphatase (respond to high ADP)

aromatic rules

stable ring 1. is cyclic 2. is planar 3. is conjugated 4. has 4n+2, pi electrons

Prokaryote DNA replication

starts from a single point and proceeds in two directions until the entire chromosome is copied

malate formation

step 7: Fumarase = Fumarate → Malate

Oxaloacetate Formed Anew

step 8- catalyzed by malate dehydrogenase

Catecholamines (epinephrine and norepinephrine)

stimulates by sympathetic NS; increases heart rate, blood pressure, blood glucose levels and dilates lung passageways

N-terminus

the end of a polypeptide or protein that has a free amino group

C-terminus

the end of a polypeptide or protein that has a free carboxyl group

Saponification

the ester hydrolysis of triacylglycerols using a strong base

intermembrane space

the fluid filled space between the inner and outer mitochondrial membranes

micelle formation

the free fatty acids, 2 monoacyclglycerol, cholesterol with bile salts all form into micelles

Elute

to extract one material from another, usually by means of a solvent.

Why must pyruvate undergo fermentation for glycolysis to continue?

to replenish NAD+ and produce ATP

Siamese cats and tyrosinase

tyrosinase (enzyme responsible for pigmentation) is mutated - active at cooler temps and inactive at body temp pigmentation only in the cooler lower extremities

Amylopectin

a soluble polysaccharide and highly-branched polymer of glucose found in plants as one of the two components of starch (the other being amylose).

lye

a strong solution of sodium or potassium hydroxide

aldonic acid

a sugar produced by oxidation of an aldose aldehyde group to a carboxylic acid group

Glycogen phosphorylase regulation

activated bu glycogen by phosphorylation in skeletal muscles: activated by AMP/epinephrine and inhibited by ATP

positive control of transcription

activation of transcription; controlled by binding of activator protein when inducer is present

Lysases

add groups to or remove groups from double-bonded substrates

3' polyadenosyl tail (poly-A)

added 3' end of mRNA transcript and protect message against rapid degradation and export mature mRNA from nucleus

DNA methylase

adds a methyl group to cytosine and adenine nucleotides often linked to gene silencing

hexose monophosphate shunt (HMP)

aka PPP, occurs in cytoplasm of most cells, generates NADPH and sugars for biosynthesis (derived from ribulose 5-phosphate, irreversible)

glucogenic amino acids

all except leucine and lysine; can be converted into intermediates that feed into gluconeogenesis

Calorimeter

an insulated device used to measure the absorption or release of heat in chemical or physical processes

arachidonic acid

an omega-6 fatty acid derived from linoleic acid

Holoenzyme

apoenzyme + cofactor

ApoE

apolipoprotein permits uptake of chylomicron remnants and VLDL by the liver

embedded proteins

are associated with only the interior/cytoplasmic or exterior/extracellular surface of the cell

Bradford protein assay

assay to determine the concentration of protein in solution with Coomassie Brilliant Blue Dye protonated form = brown green color deprotonated form = blue

elongation factors

assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used

Hemidesmosomes

attach epithelial cells to the basement membrane

single strand DNA binding proteins

attach to the separated strands to prevent them from closing and degrading

protein catabolism

begins in stomach (pepsin) and continues with pancreactic proteases

cholesteryl ester transfer protein (CETP)

catalyzes the transition of IDL to LDL by transferring cholesteryl esters from HDL

ketogenic amino acids

converted to ketone bodies

Galactose-1-phosphate uridyltransferase

converts galactose 1-phosphate to glucose 1-phosphate

pyruvate dehydrogenase

converts pyruvate to acetyl-CoA. - stimulated by insulin - inhibited by acetyl-CoA

lactate dehydrogenase

converts pyruvate to lactate

pyruvate carboxylase

converts pyruvate to oxaloacetate by adding a carboxyl group to it activated acetyl CoA

Glycogenin

core protein found in the glycogen protein start of glycogenesis

Ketogenesis

creation of ketone bodies when in fasting state

excision endonuclease

cuts and patches helix-deforming lesions such as thymine dimers

Melting DNA

denaturing; added heat breaks H-bond between DNA strands; A-T separates more readily than G-C;

terpenoids/isoprenoids

derivatives of terpenes that have undergone oxygenation or rearrangement of the carbon skeleton

Process of Replication

dna unwinds- helicase breaks hydrogen bonds (unzips- replication forks), works in 5' to 3' direction only, polymerase brings complimentary nucleotide, ligase joins all DNA (OKAZAKI), polymerase proofreads and corrects mistakes

enzyme activity and temperature

double in velocity for ever 10 degrees Celsius until optimal temperature is reached human body optimal temp is 37C/98.6F/310K activity falls sharply after that because proteins start to become denatured

NADPH

electron donor synthesis of fatty acids and cholesterol assist cellular bleach production replenish glutathione

Fructose

fruit sugar

probe DNA

(DNA with known sequence) added to a mixture of target DNA sequences, when it binds to target DNA sequences, it may provide evidence of the presence of a gene of interest

gap junctions

(communicating junctions) provide cytoplasmic channels between adjacent cells

Pyrimidines

(cytosine, thymine, and uracil) have a single six-membered ring

Sesquiterpenes

* sesqui means ½ *contain 3 isoprene units

Watson-Crick Model

*DNA is a double helix w/ 2 linear polynucleotide chains wound together in spiral orientation along a common axis *Antiparallel strands (oriented in opposite directions) *Sugar-phosphate backbone is on the outside of the helix w/ nitrogenous bases on the inside *Adenine always pairs with thymine via 2 H bonds *Guanine always pairs with Cytosine via 3 H bonds *Hydrogen bonds and hydrophobic interactions b/w bases provide stability to the double helix *DNA is a right handed helix (B-DNA) *turns at every 10th base pair

Citric Acid Cycle (Krebs Cycle)

- 2 Pyruvates enter the mitochondrion - releases 2 ATP, 6NADH, and 2 FADH2 for each glucose

Fructokinase

- Traps fructose into the cell - catalyzes fructose into fructose 1-phosphate

alpha-ketoglutarate dehydrogenase complex

- acts similarly to PDH complex - metabolizes alpha-ketoglutarate to form succinyl-CoA - inhibited by ATP, NADH, and succinyl-CoA - activated by ADP and Ca2+

Succinyl CoA and CO2 Formation

- catalyzed by α-Ketoglutarate dehydrogenase complex produce CO2 then produce NADH

glycogen synthase

- creates alpha-1,4 glycosidic links between glucose molecules - activated by insulin in liver and muscle -inhibited by epinephrine and glucagen

glycerol 3-phosphate shuttle

- electrons are transferred from NADH to dihydroxyacetone phosphate (DHAP), forming glycerol 3-phosphate - these electrons can then be transferred to mitochondrial FAD, forming FADH2

malate-aspartate shuttle

- electrons are transferred from NADH to oxaloacetate, forming malate - malate can then cross the inner mitochondrial membrane and transfer electrons to the mitochondrial NAD+, forming NADH

GLUT 2 transporter

- facilitated glucose transport - Km= 15mM - located in liver, kidney, pancreas B cells

GLUT 4 transporter

- facilitated glucose transport, INSULIN dependent - Km=5mM, becomes saturated - located in skeletal/heart muscle, adipocytes

Globosides

- glycosphingolipids - have two or more sugars attached to sphingosine

branching enzyme

- hydrolyze a oligoglucose from one chain and adds it to the growing glycogen as a new branch using and alpha-1,6 glycosidic link

prolonged fasting (starvation)

- levels of glucagon & epinephrine are markedly elevated - increased levels of glucagon relative to insulin result in rapid degradation of glycogen stores in the liver

prostalglandins

- modified fatty acids - induce fever, pain sensation, inflammation

termination of translation

- occurs when the codon in A-site is a stop codon - release factor places a water molecule on the polypeptide chain and thus releases the protein

Dihydrolipoyl transacetylase (E2)

- oxidizes remaining two-carbon molecule using lipoic acid, and transfers the resulting acetyl group to CoA, forming acetyl CoA

Glyceraldehyde-3-phosphate dehydrogenase

- produces NADH which can feed into electron transport chain

Complex III (CoQH2-cytochrome c oxidoreductase)

- transfers electrons from coenzyme Q to cytochrome c - iron is reduced on heme groups from Fe 2+ to Fe 3+ - contribution to the proton motive force via Q cycle - in the Q cycle, 2 electrons are shuttled from CoQH2 to CoQ - moves four protons to the intermembrane space

Complex II (Succinate-CoQ oxidoreductase)

- transfers electrons to coenzyme Q - receives electrons from succinate - oxidizes to FADH2 - FADH2 reoxidized to FAD - coenzyme Q is reduced - no hydrogen pumping occurs

Hill's Coefficient (cooperativity)

- value indicated nature of binding by the molecule - if > 1, positively cooperative binding is occuring - if < 1, negatively cooperative binding is occuring - if = 1, enzyme does not exhbit cooperative binding

amino acid derivative hormones

-derived from 1 or 2 amino acids w/ additional modifications -Include epinephrine, norepinephrine, triiodothyronine, and thyroxine

nucleosides

-a 5 carbon sugar (pentose) linked to a nitrogenous base - formed by covalently linking the base to C-1' of the sugar

transgenic mice

-altered at their germ line by introducing a cloned gene into fertilized ova or into embryonic stem cells -Transgene is a cloned gene that is introduced -If transgene is a disease-producing allele, the transgenic mice are used to study the disease process from early embryonic development through adulthood

reducing sugar

-any monosaccharide w/ a hemiacetal ring (since they can be oxidized, they are considered reducing agents)

size exclusion chromatography

-beads contain tiny pores -small molecules enter the pores & get stuck so they elude later -large molecules don't fit in the pores so they move around taking a shorter path & elude faster

vitamin A

-carotene -unsaturated - important in vision, growth, development, & immune function

peptide bond hydrolysis

-catalyzed by hydrolytic enzymes such as trypsin and chymotrypsin, only cleave at specific points in the peptide chain •break by adding a H atom to the amide nitrogen and an OH group to the carbonyl carbon

Sphingomyelin

-class of sphingolipids and phospholipids (sphingophospholipids) -have either phosphatidylcholine or phosphatidylethanolamine as a head group (contain phosphodiester bond) -its head groups have no charge

genomic libraries

-contain large fragments of DNA - include both coding (exon) and non-coding (intron) regions of DNA

Propionyl-CoA carboxylase

-converts propionyl-CoA to methylmalonyl-CoA -requires biotin (vitamin B7)

regulation of cholesterol synthesis

-increased levels of cholesterol can inhibit further synthesis by a feedback inhibition mechanism -insulin promotes cholesterol synthesis -control over de novo cholesterol synthesis is dependent on regulation of HMG-CoA reductase gene expression in the cell

Terpenes

-metabolic precursors to steroids and other lipid signaling molecules built from isoprene -grouped by # of isoprene units present

Lipid Mobilization

-mobilized from adipocytes by hormone-sensitive lipase -mobilized from lipoproteins by lipoprotein lipase

Phosphofructokinase-2 (PFK-2)

-produces fructose 2,6-bisphosphate (F2,6-BP) that activates PFK-1 - activated by insulin - inhibited by glucagon

vesicle-coating proteins

-proteins that initiate and carry out the process of cell membrane invagination during endocytosis

translocation (elongation)

-ribosome translocated tRNA from A-->P sites and empty tRNA goes from P-->E to be released -requires GTP

Ceramide

-simplest sphingolipid - has a single hydrogen atom as its head group

ion exchange chromatography

-stationary phase is made of either negatively or positively charged beads (attract & bind compounds that have opposite charge) -salt is added to elute proteins stuck to column

3-hydroxy-3-methylglutaryl (HMG) CoA reductase

-the key enzyme in cholesterol biosynthesis -most active in the absence of cholesterol and when stimulated by insulin -cholesterol reduces the activity of HMG-CoA reductase, which is located in the smooth ER

Edman degradation

-used to analyze small proteins - selectively & sequentially removes the N terminal AA of the protein which is analyzed by mass spectroscopy -larger proteins, synthetic reagent can be used

Complex IV (cytochrome c oxidase)

-uses cytochromes and Cu2+ to transfer electrons in the form of hydrdie ions (H-) from cytochrom c to oxygen, forming water -two protons are translocated

affinity chromatography

-uses specific interactions to slow down select molecules -can make use of receptor-ligand, enzyme-substrate, and antigen-antibody interactions

elongation cycle

1. codon recognition 2. peptide bond formation 3. translocation

Reversible inhibition types

1. competitive 2. noncompetitive 3. mixed 4. uncompetitive

insulin increases

1. glucose and triglyceride uptake by fat cells 2. lipoprotein lipase activity - which clears the VLDL and chylomicrons from the liver 3. triglyceride synthesis (lipogenesis) in adipose tissue and the liver from acetyl coA

Steps and proteins involved in DNA replication

1. origin of replication 2. unwinding of DNA double helix (helicase) 3. stabilization of unwound template strand (single-stranded DNA-binding Protein) 4. synthesis of RNA primers (primase) 5. Synthesis of DNA (DNA polymerase) 6. removal of RNA primers 7. replacement RNA with DNA 8. Joining of Okazaki fragments (DNA ligase) 9. removal of positive supercoils ahead of advancing replication forks (DNA Topoisomerases/DNA Gyrase) 10. synthesis of telomeres

insulin decreases

1. triglyceride breakdown/lipolysis in adipose tissue 2. formation of ketone bodies in the liver

Four steps of beta-oxidation

1.oxidation of fatty acid to form a double bond (creates FADH2) 2. hydration of the double bond to form a hydroxyl group (req. H2O) 3. oxidation of the hydroxyl group to form a carbonyl; called a beta-ketoacid (generates NADH) 4. splitting of the beta-ketoacid into a shorter acyl-CoA and acetyl-CoA (req. CoA-SH) -process continues until chain has been shortened to two carbons (for even chained fatty acids)

Michaelis constant (Km)

1/2Vmax -indicates how highly concentrated the substrate must be to speed up the reaction high Km= low affinity low Km= high affinity

Lineweaver-Burk Plot

1/v = (Km/Vmax)(1/[S]) + 1/Vmax

how much down APT produce

30kJ/mol

tetrose

4 carbon sugar

oligopeptide

4-10 amino acids joined together

pentose

5 carbon sugar

Hexose

6 carbon sugar

Recombinant DNA

A DNA molecule made in vitro with segments from different sources.

Southern Blot

A DNA sample is electrophoresed on a gel and then transferred to a filter. The filter is then soaked in a denaturant and subsequently exposed to a labeled DNA probe that recognizes and anneals to its complementary strand. The resulting ds labeled piece of DNA is visualized when the filter is exposed to film.

replication fork

A Y-shaped region on a replicating DNA molecule where new strands are growing.

Sphingosine

A complex alcohol backbone sphingolipids lipids

glycosidic linkage

A covalent bond formed between two monosaccharides by a dehydration reaction.

lactone

A cyclic ester; named according to the number of carbon atoms other than the carbonyl carbon and for the straight-chain form of the compound.

Disaccharide

A double sugar, consisting of two monosaccharides joined by dehydration synthesis. sucrose, lactose, maltose

deoxyribonucleic acid (DNA)

A double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell's proteins.

saturated fatty acid

A fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that can attach to the carbon skeleton.

unsaturated fatty acid

A fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail. Such bonding reduces the number of hydrogen atoms attached to the carbon skeleton.

furanose

A five-membered ring sugar.

hemiacetal

A functional group that contains a carbon atom bonded to one -OR group, one -OH group, an alkyl chain, and a hydrogen atom.

hemiketal

A functional group that contains a carbon atom bonded to one -OR group, one -OH group, and two alkyl chains

Triacylglycerols (triglycerides)

A glycerol molecule esterified to three fatty acid molecules; the most common form of fat storage in the body Overall nonpolar and hydrophobic Can be seen in oily droplets

glycosidic bond

A glycosidic bond is a covalent bond in which a carbohydrate binds to another group, which could also be a carbohydrate. A glycosidic bond is found between the two glucose molecules in maltose.

operator site of operon

A nontranscribable region of DNA that is capable of binding a repressor protein

amphoteric species

A species capable of reacting as either an acid or base, depending on the nature of the reactants

Leptin

A hormone produced by adipose (fat) cells that acts as a satiety factor in regulating appetite.

spliceosome

A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

Heterotrimeric G proteins

A large group of proteins consisting of three subunits (α, β, and γ) that can be activated by exchanging bound GDP for GTP, resulting in the liberation of two signaling molecules‚ αGTP and the βγ dimer.

conformational coupling

A less-accepted mechanism of ATP synthase activity in which the protons cause a conformational change that releases ATP from ATP synthase

Body Mass Index (BMI)

A measure of body fat that is the ratio of the weight of the body in kilograms to the square of its height in meters. normal: 18.5-25 overweight: 25-30 obese: over 30

semipermeable membrane

A membrane that allows some molecules to pass through but does not allow other molecules to pass through.

antiport

A membrane transport process that carries one substance in one direction and another in the opposite direction.

symport

A membrane transport process that carries two substances in the same direction across the membrane.

Pentose Phosphate Pathway (PPP)

A metabolic process that produces NADPH and ribose 5-phosphate for nucleotide synthesis.

beta oxidation

A metabolic sequence that breaks fatty acids down to two-carbon fragments that enter the citric acid cycle as acetyl CoA.

Haworth projection

A method for depicting cyclic sugars as planar rings with -OH groups sticking up or down from the plane of the sugar

UV spectroscopy

A method of determining the concentration of protein in an isolate by comparison against a protein standard; relies on the presence of aromatic amino acids Can also be used with nucleic acids and other compounds

Fischer projection

A method of drawing organic molecules in which horizontal lines are coming out of the page (wedges) and vertical lines are going into the page (dashes)

respirometry

A method of measuring metabolism through the consumption of oxygen

Colloid

A mixture containing small, undissolved particles that do not settle out.

Phospholipids

A molecule that is a constituent of the inner bilayer of biological membranes, having a polar, hydrophilic head and a nonpolar, hydrophobic tail.

prosthetic group

A non-protein, but organic, molecule (such as vitamin) that is covalently bound to an enzyme as part of the active site.

Polypeptide

A polymer (chain) of many amino acids linked together by peptide bonds.

Heterosaccharide

A polysaccharide made up of more than one type of monosaccharide

negative feedback

A primary mechanism of homeostasis, whereby a change in a physiological variable that is being monitored triggers a response that counteracts the initial fluctuation.

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex.

promoter region

A regulatory region a short distance upstream from the 5' end of a transcription start site that acts as the binding site for RNA polymerase. A region of DNA to which RNA polymerase binds in order to initiate transcription.

nucleotide excision repair (G1 and G2 phase)

A repair system that removes and then correctly replaces a damaged segment of DNA using the undamaged strand as a guide.

electron transport chain

A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.

Glucose

A simple sugar that is an important source of energy.

ribosome binding sites

A site, P site, E site

pyranose

A six-membered ring sugar.

G-protein coupled receptors

A special class of membrane receptors with an associated GTP binding protein; activation of a G protein-coupled receptor involves dissociation and GTP hydrolysis

polymerase chain reaction (PCR)

A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides. reannealing is an important step!

Chromatography

A technique that is used to separate the components of a mixture based on the tendency of each component to travel or be drawn across the surface of another material.

enzyme-substrate complex

A temporary complex formed when an enzyme binds to its substrate molecule(s).

Messenger RNA (mRNA)

A type of RNA, synthesized from DNA and attached to ribosomes in the cytoplasm; it specifies the primary structure of a protein.

Phagocytosis

A type of endocytosis in which a cell engulfs large particles or whole cells

Pinocytosis

A type of endocytosis in which the cell ingests extracellular fluid and its dissolved solutes.

Cholesterol

A type of fat made by the body from saturated fat; a minor part of fat in foods. maintain fluidity of cell membranes and form steriods

operon

A unit of genetic function common in bacteria and phages, consisting of coordinately regulated clusters of genes with related functions.

ATP hydrolysis

ATP is converted to ADP & phosphate energized myosin heads (removal of phosphate) need energy

Acetyl CoA

Acetyl coenzyme A; the entry compound for the citric acid cycle in cellular respiration, formed from a fragment of pyruvate attached to a coenzyme.

ApoA-1

Activates *LCAT* and found on HDL

allosteric activator

Allosteric activators bind to an enzyme and induce its active form.

Transfer RNA (tRNA)

An RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA

flavin adenine dinucleotide (FAD)

An energy carrier that accepts electrons and feeds them into the electron transport chain

creatine phosphate

An energy storage molecule used by muscle tissue. The phosphate from creatine phosphate can be removed and attached to an ADP to generate ATP quickly.

peptidyl transferase

An enzyme in the ribosome responsible for peptide bond formation during translation. (GTP energy source)

Glucose-6-phosphate dehydrogenase (G6PD)

An enzyme that aids in the proper functioning of red blood cells; its deficiency, a genetic condition, leads to hemolytic anemia. induced by insulin activated by NAD+ and inhibited by NADPH

nuclease

An enzyme that cuts DNA or RNA, either removing one or a few bases or hydrolyzing the DNA or RNA completely into its component nucleotides.

Primase

An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.

Helicase

An enzyme that untwists the double helix of DNA at the replication forks.

zymogen

An inactive precursor of an enzyme, activated by various methods (acid hydrolysis, cleavage by another enzyme, etc.)

mevalonic acid

An intermediate in Steroid biosynthesis that converts to Acetone in metabolic crisis

Cytochromes

An iron-containing protein that is a component of electron transport chains in the mitochondria and chloroplasts of eukaryotic cells and the plasma membranes of prokaryotic cells

repressible system

An operon that requires a repressor to bind to a corepressor before binding to the operator site to stop transcription of the relevant gene; also called a negative control system

inducible system

An operon that requires an inducer to remove a repressor protein from the operator site to begin transcription of the relevant gene; also called a positive control system.

Desmosomes

Anchoring junctions that prevent cells from being pulled apart

cofactors and coenzymes

Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. can be permanently bound to the active site or may bind loosely with the substrate during catalysis

Purines

Bases with a double-ring structure. Adenine and Guanine

beta-oxidation in mitochondria

Beta-oxidation oxidizes and releases (rather than reducing and linking, as in fatty acid synthesis) acetyl-CoA

B7

Biotin

Monoterpenes

C10H6 two isoprene units abundant in essential oils and turpentine

carbonyl carbon

C=O

Polysaccharides

Carbohydrates that are made up of more than two monosaccharides cellulose, starch, glycogen

column chromatography

Chromatography in which the substances to be separated are introduced onto the top of a column packed with an adsorbent (as silica gel or alumina), pass through the column at different rates that depend on the affinity of each substance for the adsorbent and for the solvent or solvent mixture, and are usually collected in solution as they pass from the column at different times

ApoB-48

Chylomicron assembly and secretion by the intestine

Exons

Coding segments of eukaryotic DNA.

transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.

lipid rafts

Collections of similar lipids with or without associated proteins that serve as attachment points for other biomolecules assist in signaling

starches

Complex carbohydrates that are composed of many sugars linked together.

amino acids

Compounds with an amino group on one end and a carboxyl group on the other end.

negative control of transcription

Condition where binding of a repressor protein to a regulatory DNA sequence prevents transcription of a gene or a cluster of genes.

Thiophorase (Succinyl CoA: acetoacetate CoA Transferase)

Converts acetoacetate (ketone bodies) into acetoacetyl CoA, which then gets broken down into acetyl CoA. Only present in tissues outside of the liver.

2,4-dienoyl-CoA reductase

Converts two conjugated couble bonds to one double bond at the 3,4 position to undergo isomerization by enoyl-CoA isomerase, allowing for the oxidation of polyunsaturated fatty acids.

base excision repair

DNA repair that first excises modified bases and then replaces the entire nucleotide

Eukaryote DNA replication

DNA replication occurs at many places at the same time move

Enhacers

DNA sequence that acts as a regulatory element to increase the level of transcription when regulatory proteins, such as transcription activators, bind to it

glucogenic

Describes amino acids that can be converted into intermediates that feed into gluconeogenesis; all amino acids except leucine and lysine

ketogenic

Describes amino acids that can be converted into intermediates that feed into ketogenesis

epimer

Diastereomers that differ at only one chiral center.

Activation of Amino Acid for Protein Synthesis

Each type of amino acid is activated by different aminoacyl-tRNA syntheses that requires two high-energy bonds from AT, implying that the attachment of the amino acid is an energy rich bond.

Tetraterpenes

Eight isoprene units Contain carotenoids group (i.e. beta-carotene and lutein)

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

RNA polymerase

Enzyme similar to DNA polymerase that binds to DNA and separates the DNA strands during transcription does not undergo proofreading

enzyme specificity

Enzyme specificity is the concept that each enzyme catalyzes only one kind of reaction.

Kinases

Enzymes that catalyze the transfer of phosphate groups from ATP to acceptor molecules.

restriction enzymes (restriction endonucleases)

Enzymes that recognize specific double-stranded DNA sequences (palindromic sequences - the 5'-3' of one strand matches the 5'-3' strand of another in antiparallel fashion)

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.

fatty acyl CoA synthetase

Fatty Acids must be activated before transport into mitochondria by adding CoA

Acetyl-CoA carboxylase (ACC)

Fatty acid synthesis: rate determining enzyme acetyl-CoA -> malonyl-CoA

Collagen

Fibrous protein that gives the skin form and strength trihelical fiber

Intermediate Density Lipoprotein (IDL)

Formed from the degradation of very low density lipoproteins; enables fats and cholesterol to move within the bloodstream

gylcogen

Found in the pancreas; stores glucose (stored sugar for energy source) has many branches allowing more enzyme cleaving

Ketones

Fragments formed by the tissues during incomplete use of fat for energy, and released into the blood.

Glycine

Gly, G, nonpolar tends to not be optically active (achiral)

Substrates for gluconeogenesis

Glycerol, Amino acids, Lactic Acid

Gangliosides

Glycolipids with a head group composed of oligosaccharides with a terminal sialic acid (NANA) molecule.

Cerebrosides

Glycosphingolipids with one sugar

G proteins types

Gs=stimulates adenylate cyclase and increase cAMP Gi=inhibits adenylate cyclase and decrease cAMP Gq=activates phospholipase C

5 histone proteins

H1, H2A, H2B, H3, and H4. (H1 is the only one not in the histone core)

Hypotonic

Having a lower concentration of solute than another solution

insulin effects fat metabolism

Increases fatty acid synthesis in liver. Increases triglyceride synthesis in adipose tissue.

competitive inhibition

Inhibition of an enzyme's ability to catalyze a chemical reaction via a non-reactant molecule that competes with the substrate(s) for access to the active site. Km increases Vmax unchanged

transmembrane proteins

Integral proteins that span the membrane.

molten globule

Intermediate states in the folding of a protein

methylmalonyl CoA mutase

Involved in the oxidation of odd-numbered carbon fatty acids, producing succinyl-CoA for entry into the TCA; requires B12.

catalytic efficiency

Kcat/Km higher = more efficient

ATP synthase

Large protein that uses energy from H+ ions to bind ADP and a phosphate group together to produce ATP

de novo

Latin, meaning "anew." A trial de novo is a completely new trial. Appellate review de novo implies no deference to the trial judge's ruling.

membrane-associated proteins

May act as recognition molecules or enzymes. proteins which are bound through electrostatic interactions with the lipid bilayer, particularly at lipid rafts or to other membrane proteins

tight junctions

Membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid

facilitated diffusion (passive transport)

Movement of specific molecules across cell membranes through protein channels

high energy electron carriers

NADH, NADPH, FADH2, ubiquinone, cytochromes, glutathione

Retinol

Natural form of vitamin A; stimulates cell repair and helps to normalize skin cells by generating new cells.

sodium dodecyl sulfate (SDS)

Negatively-charged detergent used to denature and confer a negative charge to proteins before separation by electrophoresis

B3

Niacin

Introns

Noncoding segments of nucleic acid that lie between coding sequences.

start codon (AUG)

On mRNA, the specific three-nucleotide sequence (AUG) to which an initiator tRNA molecule binds, starting translation of genetic information.

beta sheet

One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.

Alpha-linolenic acid (ALA)

One type of omega-3 fatty acid, polysaturated

citrate synthase

Oxaloacetate + acetyl-CoA --> citrate. Inhibited by citrate, ATP, NADH, and succinyl-CoA (competes with acetyl-coA)

Phosphoenolpyruvate carboxykinase (PEPCK)

Oxaloacetate -> phosphoenolpyruvate Gluconeogenesis, irreversible enzyme In cytosol Requires GTP

pyruvate kinase

PEP to pyruvate activated by 1,6-biphosphate from PFK-1 rxn (feed-forward activation)

secondary structure and proline

Proline will introduce kink in petite chain when found in a-helix more found in a-helices across membrane proline is often found between turns of B-sheet and reside of a-helix

dipeptidase and aminopeptidase

Protein digestion is completed by the small intestinal brush-border enzymes

Apolipoproteins

Protein molecules responsible for the interaction of lipoproteins with cells and the transfer of lipid molecules between lipoproteins; also called apoproteins

catabolite activator protein (CAP)

Protein that functions in catabolite repression. When bound with cAMP, CAP binds to the promoter of certain operons and stimulates transcription.

Chaperones

Proteins that assist in protein folding during posttranslational processing

B6

Pyridoxine

Net Results and ATP Yield from Krebs

Pyruvate Dehydrogenase Complex: 1NADH Citric Acid Cycle: 3NADH, FADH2, GTP ATP Production: 10, 1.5, 1 = 25 Glycolysis Yields another seven molecules of ATP

Pentose is ribose

RNA

small nuclear RNA (snRNA)

RNA molecule of around 200 nucleotides that participates in RNA splicing

enoyl-CoA isomerase

Rearranges cis double bonds at the 3,4 position to trans double bonds at the 2,3 position once enough acetyl-CoA has been liberated to isolate the double bond within the first three carbons (permits beta-oxidation to proceed in monounsaturated fats)

B2

Riboflavin

B-DNA

Right-handed helical structure of DNA that exists when water is abundant; the secondary structure described by Watson and Crick and probably the most common DNA structure in cells.

Z-DNA

Secondary structure of DNA characterized by 12 bases per turn, a left-handed helix, and a sugar-phosphate backbone that zigzags back and forth.

origins of replication

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.

How does soap work?

Soap works by having a polar end and a nonpolar end which allows the water and oil to interact indirectly by forming colloid

initiator tRNA

Special tRNA that initiates the translation of an mRNA in a ribosome. It always carries the amino acid methionine (AUG).

Citrate formation

Step 1 of citric acid cycle Acetyl-CoA and oxaloacetate undergo a condenstaion reaction to form citryl-CoA

Citrate Isomerized to Isocitrate

Step 2 of Citric Acid Cycle Achiral citrate is isomerized to one of four possible isomers of Isocitrate

alpha-ketoglutarate and CO2 formation

Step 3 and rate limiting step of Citric Acid Cycle Produces first CO2 and first NADH molecule of the cycle Uses isocitrate dehydrogenase

Succinate Formation

Step 5; only time we directly produce ATP in the citric acid cycle (in the form of GTP)

Fumarate formation

Step 6: succinate becomes oxidized to form fumarate takes place in the mitochondrial inner membrane Only step of the cycle that does not occur in the matrix

optical isomers

Stereoisomers that are non-superimposable mirror images of each other

fluid mosaic model

Structural model of the plasma membrane where molecules are free to move sideways within a lipid bilayer.

Nuclear magnetic resonance spectroscopy

Technique used for determining the three-dimensional structure of a protein. It is performed in solution without requiring a protein crystal.

5' cap

The 5' end of a pre-mRNA molecule modified by the addition of a cap of guanine nucleotide.

DNA methylation

The addition of methyl groups (—CH3) to bases of DNA after DNA synthesis; may serve as a long-term control of gene expression. CONDENSE

allosteric effects

The binding of a ligand to one site on a protein molecule in such a way that the properties of another site on the same protein are affected

mismatch repair (G2 phase)

The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides.

peptide bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid

monocistronic

The coding pattern of eukaryotes in which one mRNA molecule codes for only one protein.

polycistronic

The coding pattern of prokaryotes, in which one mRNA may code for multiple proteins.

Jacob-Monod Model

The description of the structure and function of operons in prokaryotes, in which operons have structural genes, an operator site, a promoter site, and a regulator gene

Phosphofructokinase-1 (PFK-1)

The enzyme that catalyzes the phosphorylation of fructose-6-phosphate to form fructose-1-6-bisphosphate in the third step of glycolysis. inhibited by ATP and citrate activated by AMP

substrate-level phosphorylation

The enzyme-catalyzed formation of ATP by direct transfer of a phosphate group to ADP from an intermediate substrate in catabolism.

Hexokinase

The enzymes that catalyzes the phosphorylation of glucose to form glucose-6-phosphate in the first step of glycolysis. inhibited by glucose-6-P low Km

Gluconeogenesis

The formation of glucose from noncarbohydrate sources, such as amino acids.

gene therapy

The insertion of working copies of a gene into the cells of a person with a genetic disorder in an attempt to correct the disorder

Euchromatin

The less condensed form of eukaryotic chromatin that is available for transcription.

leading strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.

active site

The part of an enzyme or antibody where the chemical reaction occurs.

proton-motive force

The potential energy stored in the form of an electrochemical gradient, generated by the pumping of hydrogen ions across biological membranes during chemiosmosis.

Transamination

The process by which an amino group from one amino acid is transferred to a carbon compound to form a new amino acid.

oxidative phosphorylation

The production of ATP using energy derived from the redox reactions of an electron transport chain; the third major stage of cellular respiration.

Shine-Dalgarno sequence

The prokaryotic ribosome-binding site on mRNA, found 10 nucleotides 5' to the start codon.

connexins

The proteins that make up gap junctions

Mutarotation

The rapid interconversion between different anomers of a sugar

HMG-CoA synthase

The rate-limiting enzyme of ketogenesis.

Regulation of Oxidative Phosphorylation

The rates of the citric acid cycle and oxidative phosphorylation are very close, because the products of the citric acid cycle feed into the ETC, and therefore oxidative phosphorylation

Esterification

The reaction of an alcohol with a carboxylic acid to produce an ester and water. ester transferred by using ATP to form ADP

Enol

The resonance form of a carbonyl that has a carbon-carbon double bond (ene) and an alcohol (-ol)

gene amplification

The selective synthesis of DNA, which results in multiple copies of a single gene, thereby enhancing expression.

Q cycle

The shuttling of electrons between ubiquinol and ubiquinone in the inner mitochondrial membrane as a part of Complex III's function

lagging strand

The strand that is synthesized in fragments using individual sections called Okazaki fragments opposite direction as parent strand

cooperative binding

The tendency of the protein subunits of hemoglobin to affect each other's oxygen binding such that each bound oxygen molecule increases the likelihood of further oxygen binding.

lock and key theory

Theory of enzyme catalysis stating that the active site's structure is complementary to the structure of the substrate.

vitamin E

Tocopherol, serves as an antioxidant to the body

3-phosphoglycerate kinase

Transfers the high-energy phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate

Dipeptide

Two amino acids bonded together

quanternary structure

Two or more polypeptide chains bonded together in a single protein; hemoglobin is an example of a protein molecule with this structure. allows stability, reduce protein DNA needed to encode protein complex

Stop codons

UAA, UAG, UGA

chemiosmotic coupling

Utilization of the proton-motive force generated by the electron transport chain to drive ATP synthesis in oxidative phosphorylation.

Proofreading by DNA polymerase (s phase)

Verifies accuracy Can back up, excise nucleotide Incorporate correct nucleotide Very efficient but not flawless

apurinic/apyrimidinic (AP) site

abasic site, site on DNA lacking nucleotide

Selectins

allow cells to adhere to carbohydrates on the surfaces of other cells and are most commonly used in the immune system

enzyme cooperativity

allows for an enzyme to become increasingly receptive to additional substrate molecules after a substrate molecule has attached to an active site

peptide bond formation

amide bond formed by amino group attacking carboxyl group and eliminating the OH non-spontaneous process that needs enzymes!

residues

amino acids that are incorporated into a protein

retention time

amount of time a compound spends in stationary phase

acetaldehyde dehydrogenase (ALDH)

an alcohol-metabolizing enzyme found in the liver that converts acetaldehyde to acetate

ApoC-II

an apoprotein that activates lipoprotein lipase

ApoB-100

an apoprotein that permits uptake of LDL by the liver

Glucokinase

an enzyme induced by insulin, adds a phosphate group to a molecule of glucose sound in hepatocyte and beta islet cells high Km

hormone sensitive lipase

an enzyme inside adipose cells that responds to the body's need for fuel by hydrolyzing triglycerides so that their parts (glycerol and fatty acids) escape into the general circulation and thus become available to other cells for fuel. The signals to which this enzyme responds include epinephrine and glucagon, which oppose insulin.

DNA topoisomerase

an enzyme that alleviates DNA supercoiling during DNA replication

lipoprotein lipase

an enzyme that sits on the outside of cells and breaks apart triglycerides, so that their fatty acids can be removed and taken up by the cell

linoleic acid

an essential polyunsaturated fatty acid of the omega-6 family, polysaturated

xray crystallography

an important method used to determine a protein's three-dimensional structure

carrier proteins

bind to molecules and change shape to shuttle them across the membrane

RNA polymerase II

binds to TATA box and begins to transcribes mRNA

Lowry reagent assay

biochemical assay for determining the total level of protein in a solution. The total protein concentration is exhibited by a color change of the sample solution in proportion to protein concentration, which can then be measured using colorimetric techniques.

High-density lipoprotein (HDL)

blood fat that helps transport cholesterol out of the arteries, thereby protecting against heart disease

low-density lipoprotein (LDL)

blood fat that transports cholesterol to organs and tissues; excess amounts result in the accumulation of fatty deposits on artery walls

chemical denaturation

break disulfide bridges, hydrogen bonds, and reducing cystine to cysteine

amino acid catabolism

breakdown of amino acids for use as energy; includes 2 processes: transamination or deamination.

Glycogenolysis

breakdown of glycogen to glucose

HMG-CoA lyase

breaks down HMG CoA into acetoacetate this acetoacetate can be broken down into 3 hydroxybutarate

Reannealed DNA

brought back together when denaturing condition is slowly removed

expression libraries

cDNA library where it only includes genes that are expressed in the tissue from which the mRNA was taken from

Cadherins

calcium-dependent glycoproteins that hold similar cells together

glycoprotein coat

carbohydrates associated with membrane-bound proteins

Zwitterions at intermediate pH

carboxylic acids become deprotonated at neutral pH, forming zwitterions--two charges neutralize each other; molecule that has both positive and negative charge; pH is above pKa of carboxylic acid so it is deprotonated, but pH is below pKa of amine group so, protonated

regulation of body mass

carbs and proteins relatively stable water quickly adjusted by endocrine/kidneys lipids are primary factor in gradual change of body mass over time

occluded state

carrier is not open to either side of the phospholipid bilayer

Hydrolases

catalyze cleavage with the addition of water

Oxidoreductases

catalyze oxidation-reduction reactions that involve the transfer of electrons

Ligases

catalyze the formation of bonds with the input of ATP and the removal of water

Isomerase

catalyzes the rearrangement of bonds within a single molecule

Mutase

catalyzes the shifting of a chemical group from one position to another within a molecule

Nernst Equation

cell in equilibrium has an actual cell potential of 0 and a standard cell potential of not 0 *E = E0 - (RT/nF)lnQ* E0 = (RT/nF)lnK -as temp increases, Ecell decreases -as battery approaches equilibrium, Ecell approaches 0 -E0 is constant

Centromere

central part of chromosome, joining the two sister chromatids composed of heterochromatin and have high G-C content

Glycogen storage disease

characterized by the accumulation or lack of glycogen in one or more tissues due to isoforms of glycogen enzymes most common is Von Gierke's disease

beta amylase

cleaves amylose at the nonreducing end of the polymer the end with the acetal to yield maltose

Aldolase B

cleaves fructose-1-phosphate into glyceraldehyde and DHAP

alpha-amylase

cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, and glucose

isoforms

closely related proteins whose function is similar but whose affinity for ligands differs

Lipoproteins

clusters of lipids associated with proteins that serve as transport vehicles for lipids in the lymph and blood

regulatory gene of operon

codes for repressor protein

fibrous proteins

collagen, elastin, keratin

DNA libraries

collection of clones containing all the DNA fragments from one source (tissue type, cell type, or single individual)

resting muscle

conserves carbohydrates as glycogen and uses free fatty acids for fuel

-ogen suffix and enzymes

contain catalytic domain and regulatory domain

oxidation and reduction of carbohydrates

enables the body to use carbohydrates to yield energy

dihydrolipoyl dehydrogenase

enzyme in the PDH complex used FAD to re oxidize lipioc acid so it is ready to be reduced once more lip -SH-SH +FAD+ --> LipS-S + FADH2 NAD+ oxidizes FADH2 to FAD+ and NADH

Covalently Modified Enzymes

enzymes can be activated or deactivated by phosphorylation or dephosphorylation Can also be modified by covalent attachment of sugar groups (glycosylation)

Epimerase

enzymes that catalyze the conversion of one sugar epimer to another

Mannose

epimer of glucose

Adipocytes

fat cells that make up most of the subcutaneous layer

cardiac muscle

fatty acids fuel the muscle or ketones during prolonged fasting decline in heart muscle results glucose oxidation and beta oxidation falls

Stationary phase of chromatography

filter paper; allows elute

codon recognition

first stage of elongation; tRNAs recognize through their anticodon and bring appropriate amino acid to the A site

protein processing

folding, cleaving, adding sugar groups, targeting for transport

B9

folic acid

lariat of excised introns

form lasso shape then degrade

Glycogenesis

formation of glycogen from glucose 1. glucose-6-P to glucose-1-P (activated by UDP) 2. UDP converted to UTP to form UDP-glucose and pyrophosphate

Acetals

formed when hemiacetals react with alcohol the anomeric hydroxyl group is transformed into a alkoxy group - making alpha and beta acetals with water as the leaving group

diterpenes

four isoprene units ex. vitamin A --> makes retinal (pigment necessary for sight)

counterregulatory hormones

glucagon cortisol epinephrine norepinephrine growth hormone have the opposite effects of insulin

irreversible enzymes of glycolysis

glucokinase/hexokinase PFK1 pyruvate kinase

Glucose-6-phosphatase

glucose 6-phosphate to glucose only in ER if not found in skeletal muscle then glycogen can not be used

Monosaccharides

glucose, fructose, galactose

furanosides

glycosides derived from furanose rings

pyranosides

glycosides derived from pyranose rings

Anti-codon

group of three bases on a tRNA molecule that are complementary to an mRNA codon

antioncogenes

growth inhibiting cancer suppressor genes

allosteric enzymes

have both an active site for substrate binding and an allosteric site for binding of an allosteric effector (activator, inhibitor)

amphipathic

having both a hydrophilic region and a hydrophobic region

protonated

having received and containing an additional H+

Orexin

hunger-triggering hormone secreted by hypothalamus

termination factors

hydrolyzes the completed polypeptide chain from the final tRNA during translation allows tRNA release in P site and A/E subunits release

Glucagon second messenger

increase glycogenolysis, glucogeonesis, ketogenesis, lipolysis. decrease lipogenesis

max velocity of enzyme

increase max velocity by increase

heat denaturation

increases kinetic energy of protein and this affects hydrophobic and hydrophilic interactions cause protein to unfold

operon types

inducible and repressible

uncompetitive inhibition

inhibitor binds only to enzyme-substrate complex locks substrate in enzyme preventing its release (increasing affinity b/w enzyme and substrate so it lowers Km) Lower Km and vmax

mixed inhibition

inhibitor binds to allosteric site in either enzyme or enzyme-substrate complex vmax decreases If inhibitor binds to enzyme, it increases Km (lowers affinity) If inhibitor binds to enzyme-substrate complex, it lowers Km (increases affinity)

irreversable inhibition

inhibitor covalent bonds to side chains in the active site and permanently inactivates the enzyme

inner mitochondrial membrane

innermost membrane of the mitochondria. Oxidative phosphorylation and chemiosmosis take place at the inner mitochondrial membrane, which produces ATP via the flow of protons across the membrane.

postabsorptive (fasting) state

insulin secretion decreases while glucagon and catecholamine secretion increases

non-template synthesis

lipid and carbohydrate synthesis process that does not rely directly on the coding of nucleic acids (unlike protein and nucleic acids synthesis)

micelle

lipid molecules that arrange themselves in a spherical form in aqueous solutions

Steriods

lipids whose structures resemble chicken-wire fence. include cholesterol and sex hormones

nucleic acid prosthetic group

lipoproteins glycoproteins nucleoproteins

very low density lipoproteins (VLDL)

lipoproteins that transport triglycerides and other lipids from the liver to various tissues in the body

RNA polymerase I

located in the nucleolus and synthesizes rRNA

RNA polymerase III

located in the nucleus and synthesizes tRNA and some rRNA

Sphingolipids

long fatty acid chain polar head group backbone=amino alcohol (not glycerol)

Denaturation

loss of normal shape of a protein due to heat or other factor

Adenosine Diphosphate (ADP)

low-energy molecule that can be converted to ATP

urea cycle

mechanism that takes nitrogen across the rumen wall back to the salivary glands in order to preserve nitrogen in the system

Integrins

membrane proteins; they transmit signals between the ECM and cytoskeleton promote cell division, apoptosis, etc

Vitamin D (cholecalciferol)

metabolized to calcitrol in the kidneys and regulates calcium and phosphorus homeostasis in the intestines (increasing calcium and phosphate absorption), promotes bone formation

semiconservative

method of replication that implies that each new strand of DNA is half original and half new

Electrophoresis

method of separating serum proteins by electrical charge

knockout mice

mice in which a gene of interest has been silenced or deleted by genetic engineering

Galactose

milk sugar

Nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

debranching enzyme

moves a block of oligoglucose from one branch and connects it to the chain using an alpha-1,4 glycosidic link

tissues in which glucose uptake is not affected by insulin

nerve, kidney tubules, intestinal mucosa, red blood cells, beta cells.

outcomes of antibody-antigen binding

neutralizating antigen, opsonization, agglutinating antigen and antibody into large protein complexes

ungated channels

no gates, unregulated, ex. potassium channels

recombinant vector

nucleic acid (vector) with the DNA of interest ligated to it also needs to make sure that this plasmid has antibiotic resistance

alcohol dehydrogenase (ADH)

one of the alcohol-metabolizing enzymes, found in the stomach and the liver, that converts ethanol to acetaldehyde

anomeric carbon

only carbon attached to two oxygens -OH may point up or down

voltage gated channels

open and close in response to changes in membrane potential

ligand-gated channels

open in the presence of a specific binding substance, usually a hormone or neurotransmitter

pyruvate dehydrogenase complex

oxidative decarboxylation, pyruvate oxidized to acetyl-CoA (loses a carbon) uses up CoA, NAD+ reduced to NADH, releases CO2 acetyl-CoA inhibitor

biphosphoglycerate mutase

produces 2,3-biphosphoglycerate (2,3-BPG) from 1,2-BPG in glycolysis

colligative properties

properties that depend on the concentration of solute particles but not on their identity

elastin

protein base similar to collagen that forms elastic tissue

apoprotein

protein component of a lipoprotein

Histones

protein molecules around which DNA is tightly coiled forming chromatin

Apoenzyme

protein portion of an enzyme

secondary structure of protein

protein structure is formed by folding and twisting of amino acid chain

tertiary structure of protein

protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure contain hydrophobic interactions, acid-base/salt bridges, and disulfide bridges

Flippase

protein that facilitates the movement of membrane lipids from one leaflet to the other leaflet of a phospholipid bilayer use energy to flip

histone acetylases

proteins that are involved in chromatin remodeling can be recruited due to transcription factors they acetylate (CH3C=O) lysine residues found on the N terminal of the histone tail region it increases the space between the histones, allowing for better access to DNA for other transcription factors

histone deacetylases

proteins that function to remove the acetyl groups from histones make the chromatin in a more closed conformation overal decreases the gene expression levels of the cell

Nucleosome

proteins with nucleic acid prosthetic groups

Aromatic Heterocycles

purines and pyrimidines are biological __ __

Glucocorticoids

raises blood sugar levels

Carnitine acyltransferase I

rate limiting enzyme of fatty acid oxidation following beta oxidation

Fructose-1,6-bisphosphatase

rate limiting step of glycolysis fructose 1,6-bisphosphate to fructose 6-phosphate activated my ATP and inhibited by AMP/fructose-2,6-phosphate

respiratory control

rates of oxidation phosphorylation and citric acid cycle are very closely linked - the TCA cycle gives the reactants for the ETC O2 and ADP are key regulators O2 limited rate of oxidation phosphorylation decreases concentration of NADH and FADH2 increase - inhibiting the TCA cycle enough O2 - dependent of the availability of ADP ADP and ATP are reciprocally related a lot of ADP - not much ATP a lot of ATP - not much ADP a lot of ADP - need for ATP synthesis ADP activated isocitrate dehydrogenase - increasing the rate of the TCA cycle and thus increasing the production of NADH and FADH2

Substrate

reactant of an enzyme-catalyzed reaction

glycoside formation

reaction between an alcohol and a hemiacetal or hemiketal group on a sugar to yield an alkoxy group dehydration rxn and hydrolysis required to break glycoside bonds

Glutathione

reducing agent that can help reverse radical formation before damage is done to the cell

ketolysis

regenerates acetyl-CoA for use as an energy source in peripheral tissues

R state

relaxes state of an enzyme subunit high affinity state

AP endonuclease

removes the damaged sequence during base excision repair

Motif

repetitive organization of secondary structures

Telomere

repetitive unit (TTAGGG) at the end of a eukaryotic chromosome that prevents them from unraveling from high G-C content can be shortened or replaced by telomerase

Heterocycles

ring structures that contain at least two different elements in the ring

enzyme activity and salinity

salt concentration can change the enzyme activity in vitro increasing concentration can disrupt hydrogen and ionic bonds this can cause partial changes in the conformation of the enzyme also can lead to denaturation

fatty acid oxidation (beta oxidation) of saturated

saturated fatty acids- dehydrogenase to create double bond (produce FADH2), then produce NADH to create ketone, breaks off acetyl-CoA, repeat needs *2 ATP* to initially activate fatty acid need 1 FAD, 1 NAD+ for each 2 C removed produces *1 FADH2, 1 NADH*

peptide bond formation (elongation)

second stage of elongation; peptide bonds form between amino acids that are linked to tRNAs in the P and A sites

DNA cloning

set of procedures that uses living cells to make many identical copies of a DNA fragment

Dihydroxyacetone

simplest ketose

ribonucleic acid (RNA)

single-stranded nucleic acid that contains the sugar ribose

promoter site of operon

site of RNA polymerase binding (similar to promoters in eukaryotes)

liposome

small membrane bounded transport vesicles

initation of translation

small ribosomal subunit binds to a special initiator tRNA (methionine), then binds to mRNA, large ribosomal unit then attach to small ribosomal unit, in the end initiator tRNA is in P site of ribosome, and A and E sites are empty

alternatice splicing

splicing can occur more than one way to produce different products

Structure of glycogen

straight chain of alpha-glucose (1,4-glycosidic bond) with side branches (1,6-glycosidic bond)

paracellular route

substances pass through gaps between the cells

Homosaccharides

sugar composition is the same

deoxy sugars

sugars with a -H replacing an -OH group

Aldoses

sugars with aldehydes as their most oxidized group

isoelectric point for basic amino acids

tend to be high

isoelectric point for acidic amino acids

tend to be low

T state

tense state of a enzyme subunit low affinity state

proteinogenic amino acids

the 20 alpha amino acids encoded by the human genetic code

7-methylguanylate triphosphate cap

the 5' cap added to the end of the hnRNA molecule during RNA processing of eukaryotes during transcription and is recognized by the ribosome as the binding site, and protects the mRNA from degradation in the cytoplasm

beta anomer

the OH group of the C1 cis to the CH2OH group *it will be equatorial and up*

primary structure of protein

the amino acid sequence of the polypeptide chain

histone acetylation

the attachment of acetyl groups (-COCH3) to certain amino acids of histone proteins, the chromatin becomes less compact, and the DNA is accessible for transcription

Proteolysis

the breakdown of proteins or peptides into amino acids by the action of enzymes starts in stomach (pepsin)

Chylomicrons

the class of lipoproteins that transport lipids from the intestinal cells to the rest of the body

Proto-oncogenes

the corresponding normal cellular genes that are responsible for normal cell growth and division

solvation layer

the layer of solvent particles that interacts directly with the surface of a dissolved species

allosteric inhibition

the mechanism for inhibiting enzyme action in which a regulatory molecule binds to a second site (not the active site) and initiates a conformation change in the active site, preventing binding with the substrate

Goldman-Hodgkin-Katz equation

the membrane potential that results from the contribution of all ions that can cross the membrane

phosphoryl group transfers

the overall free energy of the reaction will be determined by taking the sum of the energies of the individual reactions - due to a transfer of phosphate groups from ATP free energy of hydrolysis (transfer of phosphate group to water) ATP + H2O --> ADP + Pi 𝛥G°'= -30kj/mol

heterogeneous nuclear RNA (hnRNA)

the precursor to processed mRNA; converted to mRNA by adding a poly-A tail and 5' cap, and splicing out introns

ketone bodies

the product of the incomplete breakdown of fat when glucose is not available in the cells acetoacetate and 3-hydroxybutyrate

post-translational processing

the protein needs modifications for proper folding chaperones - help in the folding process ex) phosphorylation carboxylation glycosylation prenylation

basal metabolic rate (BMR)

the rate at which the body burns energy when the organism is resting

van't Hoff factor

the ratio of moles of particles in solution to moles of solute dissolved

feedback regulation

the regulation of the activity of an enzyme by one of its products

Deamination

the removal of an amino group from an organism, particularly from an amino acid

Saturation

the state or process that occurs when no more of something can be absorbed, combined with, or added.

coding strand

the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine

Bioenergetics

the study of how energy flows through living organisms

ATP cleavage

the transfer of a high-energy phosphate group from ATP to another molecule

membrane potential

the voltage difference across a membrane -40 to -80 mV can rise to 35mV during depolarization

degenerate code

there are more codons (64) than there are amino acids to be coded, so most amino acids are coded by more than one code.

globular proteins

these are compact, generally rounded, and soluble in water.

small nuclear ribonucleoproteins (snRNPs)

these enzymes cut out introns and splice together exons in the pre-RNA to create a functional mRNA

pyruvate dehydrogenase complex cofactors and coenzymes

thiamine pyrophosphate, CoA, FAD, NAD+, lipoic acid

wobble position

third position of the codon two bases are usually the same - the third base in the codon is usually variable this is an evolutionary development used to protect against mutations in the coding regions of DNA mutations in this position tend to be *silent or degenerate*

tripeptide

three amino acids bonded together

Transferases

transfer functional groups from one substrate to another

Shuttle Mechanism

transfers the high-energy electrons of NADH to a carrier that can cross the inner mitochondrial membrane

cell adhesion molecules

transmembrane proteins that bind to each other and to extracellular materials cadherins, integrins, selectins

Galactokinase

traps galactose inside the cell by phosphorylating it galactose --> galactose 1 phosphate

pancreactic proteases

trypsin, chymotrypsin, and carboxypeptidases A and B secretes as zymogens when protein catabolism occurs

trp operon

tryptophan binds to the repressor protein and enables it to repress gene transcription.

Supercoiling

twisting in the opposite direction to the turns of the double helix during the first stage of mitosis.

Ribosomal RNA (rRNA)

type of RNA that combines with proteins to form ribosomes

dideoxynucleotide

type of nucleotide used during DNA sequencing to terminate synthesis

fatty acid oxidation (beta oxidation) of unsaturated

unsaturated fatty acids- isomerase to move double bond, then produce NADH to create ketone, break off acetyl-CoA, repeat in mitochondrial matrix needs *2 ATP* to initially activate fatty acid need 1 FAD, 1 NAD+ for each 2 C removed produces *1 FADH2, 1 NADH*

Bicinchoninic Acid (BCA) Assay

used for quantitation of total protein in a sample. The principle of this method is that proteins can reduce Cu+2 to Cu+1 in an alkaline solution (the biuret reaction) and result in a purple color formation by bicinchoninic acid

omega numbering system

used for unsaturated fatty acids omega described the position of the last double bond relative to the end of the chain identifies the major precursor fatty acid

dihydroxyacetone phosphate

used in hepatic and adipose tissue for triacylglycerol synthesis can be ismoerized to glycerol 3 phosphate to be converted to glycerol

Brain metabolism

uses glucose except in prolonged starvation, when it can use ketolysis

F1 portion of ATP synthase

uses the energy released by the gradient to phosphorylate ADP into ATP

Michaelis-Menten equation

v = (vmax [S])/(Km + [S]) when rxn rate= half of Vmax, Km =[S] substrate concentration increases, enzyme increase rxn rate until Vmax is reached

migration velocity

v = Ez/f -directly proportional to the electric field strength (E) and to the net charge on the molecule (z) -inversely proportional to a frictional coefficient (f)

Michaelis-Menten equation and Kcat

v= Kcat [E][S]/Km + [S]

Km >> [S] (low substrate concentration)

v=(Kcat/Km)[E][S]

Vmax and Kcat

vmax = kcat[E] -kcat = measures the # of substrate molecules converted to product per enzyme molecule per second

postprandial state

well fed/absorptive state --> insulin secretion is high and anabolic metabolism prevails

Hypertonic

when comparing two solutions, the solution with the greater concentration of solutes

ketolysis in the brain

when the body has been in ketosis for longer than a week - 2/3 of of the energy comes from ketone bodies when ketones are broken down into acetyl CoA, pyruvate dehydrogenase will be INHIBITED glycolysis and glucose uptake by the brain will be inhibited

isotonic

when the concentration of two solutions is the same

negatively charged under basic conditions

~ At basic pH carboxyl group = deprotonated (COO-) ~ Amino group = deprotonated

positively charged under acidic conditions

~ pH 1 (many protons) Amino group = fully protonated and + charged. Carboxyl group = fully protonated and neutral ~ Sums to + charge

Lecithin-cholesterol acyltransferase (LCAT)

• made in the liver • activated by apo-a1 • constituent of HDL • job is to esterify cholesterol and make it really hydrophobic

Glycosphingolipids

• sphingolipids w/ head groups composed of sugars bonded by glycosidic linkages -not phospholipids b/c they have no phosphodiester linkage - found on the outer surface of the plasma membrane