Biochemistry Flashcards by Brett Gillespie

What is the term for an aminoacid with a net neurtral charge?

Zwitterion

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What is term where the pH is at a range where the AA is a net charge of 0?

pI (isoelectric point)

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What is the precursor for catecholamines?

Tyrosine (more-polar aromatic AA)

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What is the precursor for serotonin?

Tryptophan (more-polar, aromatic)

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What amino acid serves as a methyl-group donor in methylation reactions?

Methionine (sulfur-containing)

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What two amino acids are responsible for disulfide bonds?

Met and Cys

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What group of amino acids are hydrophilic, participate in hydrogen bond formations, and can be modified via phosphorylation and glycosylation?

Polar, uncharged amino acids

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What are the polar, uncharged amino acids?

Asparagine, Glutamine, Serine, and Threonine

asn, gln, ser, thr

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What are the aromatic amino acids?

Phenylalanine, Tyrosine, and Tryptophan

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What are the acidic amino acids?

Glutamate and Aspartate

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What are the basic amino acids?

Arganine, Lysine, and Histidine

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What are the nonpolar, aliphatic amino acids?

Glycine, Alanine, Proline, Valine, Leucine, and Isoleucine

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What are the basic amino acids?

Arganine, Lysine, and Histidine

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What are the essential amino acids?

His, Met, Threonine, Val, ILE, Phenylalanine, Tryptophan, Leucine, Lysine

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What are the non-essential amino acids?

Alanine, Argasnine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Proline, Serine, Tyrosine

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What are the conditional essential amino acids and Why?

Glutamine and Arganine (trauma and child growth)

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What are the main function of proteins?

Catalytic, Structure, Transport, Mobility, Immunity, and Communication

(STIM CC)

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What is the name of the bond that links the N terminal and C terminal of amino acids?

Peptide bond

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What is the primary protein structure?

The sequence of amino acids in a straight line

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What is the secondary protein structure?

Alpha helices and beta sheet

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How can a parallel and antiparallel B- pleated sheet be differentiated?

Parallel has both “sides” beginning and ending in N and C terminals respectively;

Antiparallel has N terminal (top) and C terminal (bottom) on the same side

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What are the regular secondary protein structure patterns?

A-helix and B- pleated sheet

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What are irregular secondary protein structure patterns?

Bends, loop,s and turns

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What is the tertiary protein structure?

Multiple secondary units forming a 3D structure

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What are structural domains?

Physically independent regions in the tert structure of a protein

What is the quaternary structure?

The associated of individual polypeptide chain subunits in a geometrically and stoichiometrically specific manner

What are the nonenzymatic denaturation of proteins?

Glycolysation, oxydation, nitrosylation, etc

What can denature a protein?

Very low/high pH and high temperatures

What class of enzymes catalyzes via redox reactions?

Oxidoreductases

What enzyme class catalyzes the transfer of C-, N-, or P- groups

Transferases

What enzymes catalyze the cleavage of bonds by addn of water

Hydrolases

What enzymes catalyze cleavage of C-C, C-S, and certain C-N groups?

Lyases

What enzymes catalyze rearrangement of optical or geometrical isomes?

Isomerases

What enzymes catalyze formation of bonds between C, O, S, and N coupled to hydrolysis of high energy phosphates?

Ligases

What are inorganic substances that are required for/increase the rate of catalysts?

Cofactors (Zinc, magnesium, iron II, iron III)

What are organic molecules that are required to carry out catalysis?

Coenzymes (NAD, FAD, NADP, CoQ, CoA, etc)

What term is used to quantify the measure of energy transfer between chemical reactions?

Gibbs Free Energy (G)

What is the energy diff between reactants & a highly reactive intermediate that occurs during the formation of a product?

Energy barrier

Difference between the G of the reactants and the high energy intermediates.

Ea (activation energy)

Human enzyme optimal temperature?

37 C

What temp do human enzymes begin to denature?

~40-42 C

What determines the optimal human enzyme pH?

Location

What kinetic theory do enzymes typically follow?

Michaelis-Menten kinetics

What assumptions are made with Michaelis-Menten kinectics?

- [S] is far greater than [E] - [ES] does not change with time - No substantial back reaction from product to substrate

What is Km in M-M kinetics?

the [S] needed to equal 1/2 Vmax

What is the inhibition where an I is bound to the E via covalent bonds that cant be broken?

Irreversible Inhibition

What is the type of reversible inhib where I binds to an allosteric site on E?

Noncompetitive

What is the reversable Inhib where I competes with S to bind to the active site of E?

Competitive inhibition

What is a primary property of lipids?

Soluble in organic solvents and hydrophobic

What are the classification of lipids?

Glycerol and non-glycerol based

What are some glycerol based lipids?

Simple: fats and oils Complex: Phospholipids and Glycolipids

What are some non-glycerol based lipids?

Steroids, Sphingolipids, and waxes

What are the two ends called in a fatty acid?

Carboxylic end and Omega End

What are the essential fatty acids?

Lineolic acid, alpha-lineolic acid | Human cells cant make cis-double bonds beyond 9 carbons

Glycerol + Fatty Acid -3 H2O=

Triacylglycerol

What are the functions of (glycero)phospholipids?

Strtuctural components of cell membrane, lipoproteins, pulmonary surfactant, bile, etc Precursors for: PIP3 and 4, Diacylglycerol (DAG)

What is the function of sphyngolipids?

Structural components of cell membranes and lipoproteins; Signaling precursors for secondary messengers

What is the general composition of steroids?

Four fused rings arranged in a specific configuration (AKA ABCD ring system)

What defines a sterol?

-OH group at position 3 of the A ring (cholesterol is an example)

What are the functions of cholesterol?

1: Structural component of cell membranes (30%) and lipoproteins 2: precursor for synth of: Bile, bile acids, steroid hormones, Vit D

What is mediator of the gene expression?

RNA

What are the basic building blocks of nucleic acids?

Ribose sugar (5 carbon sugar), nitrogenous base, triphosphate good

What are the five nitrogenous bases?

Adenine, Cytosine, Guanine, Thymine, Uracil

Removing an OH group from a ribose sugar makes it more or less stable (deoxyribose)?

MORE stable

What are the purines?

A,G (two rings, short name is bigger structure)

Pyrimidines?

T, U, C (one ring)

what is a nucleoside?

Ribose and nitrogenous base

What is a nucleotide’s structure?

Ribose, base, triphosphate

What bonds link nucleotides?

3’-5’ phosphodiester bonds (OH of C-3 of one sugar and OH of C-5 on the next one)

How many NT pairs per DNA turn?

~10 pairs per 360 degree turn

What direction do opposing DNA strands run?

Antiparallel

What bonds connect opposing DNA strands?

Hydrogen bonds

What are the three DNA forms? Right handed? Left handed?

B,A,Z DNA; B and A are right handed

How many H-bonds are between A-T and C-G

2 and 3 respectively

(A+G)=(C+T)

A%+T% and vice versa

What can denature DNA?

Alkaline solutions and heat (break H bonds)

What is the melting temperature of DNA (Tm) defined as?

When 50% of DNA is separated

What relative conc of DNA nucleotides would “melt” first? A-T prominent (>60%) or G-C prominent?

DNA with more A-T bonds will “melt” faster since energy requirements to denature due to only two bonds is less

What is a nucleosome?

~150 bp DNA wrapped around histone core proteins (8) and H1 linker histone Contain Arganine and Lysine (basic charged that can bind to phosphate negative group backbone)

What is the transcriptionally active segment of chromatin? Inactive?

Euchromatin; heterochromatin

When is a chromosome visible?

Metaphase of mitosis/meiosis

How do euchromatin and heterochromatin availability affect protein expression?

All cells have the same DNA, but different segments of that DNA is packed into heterochromatin depending on cell specialization (ie liver, kidney, etc)

Is there a difference between stop codons of mitochondrial DNA and nuclear DNA?

Yes

What is the structure of Mitochondrial DNA

Circular, double helix with 17 bp per turn

What are RNA hairpins?

Self-bound double-stranded regions of RNA that form a loop

What is the function of mRNA, tRNA, rRNA, miRNA?

m: carries genetic info from DNA to ribosomes t: presents amino acids for synthesis on ribosomes r: forms ribosomal subunits with ribosome mi: not much known, various function

What are the most diverse RNA types?

mRNA

What is unusual about tRNA?

Has a high % of unusual bases (hydroxy-U, dihydro-U, etc)

What is 80% of all RNA?

rRNA

Where are haploid and diploid sets found?

Mature gametes and somatic cells respectively

How many chromosomes in diploid? Haploid?

46 (2 pairs of 23) and 23 (no pairs)

Where do single chromosomes in each pair come from?

Maternal and paternal DNA (via recombination)

What are the protein coding sequences, introns or exons?

Exons, introns are excised

How many genes are coded in DNA?

20-25,000 genes

What two types of single copy genes exist?

Tissue-specific genes and housekeeping genes

What are the DNA replication proteins?

DNA pol 3, DNA pol 1, Primase, DNA helicase, DNA ligase, Topoisomerase (prokaryotes)

Which direction can DNA Pol add nucleotides?

5’-3’ direction (these are added nucleotides)

What does topoisomerase do?

Removes supercoils in the helix by cleaving one or both DNA strands

What is the DNA replication protein that some new anti-cancer drugs target?

Topoisomerase

What does DNA polymerase do to prevent and correct mistakes in genetic code?

Proofreading and removal of incorrect nt (3’-5’ exonuclease activity)

What is telomerase and how does it work?

Enzyme that has a short RNA molecule that acts as a reverse transcriptase that extends the short 3’ end formed via cell replication on the telomeres

What cells are telomerase active in?

Stem cells and germ lines, not active in somatic cells

How does telomerase activation in somatic cells present usually?

Cancer activates this, prevents rapid cell expansion aging

Where are most reverse transcriptase enzymes found?

Retroviruses