Biochemistry 1 Flashcards
How do retroviruses violate the central dogma? Ex?
They reverse transcribe their RNA genome to cDNA which is then integrated into host genome and replicated along with it. Ex: HIV.
How do ncRNA (noncoding RNA) violate the central dogma? Ex?
They skip translation into protein and they function in cell as RNA molecule. Ex: tRNA, rRNA.
How can we have same DNA in muscle cells and skin cells?
Due to Epigenetics which allows same DNA sequence but results in different phenotypes. Ex: DNA methylation, histone modification.
Why are Glycine and Cysteine similarly special?
Both don’t have S configuration. Glycine because achiral. Cysteine because R configuration.
What is released when forming a peptide bond?
Water (dehydration reaction).
Acid hydrolysis vs. proteolysis.
Acid hydrolysis when combined with heat does nonspecific cleavage of peptide bond. Proteolysis uses protease to do specific cleavage of peptide bond.
Where on a protein is Histidine useful and why?
At the active site where it can stabilize or destabilize a substrate because side chain has pKa 6.5 around physiological pH. So can be in protonated or deprotonated forms.
Why are Proline and Glycine similarly special?
Both are alpha helix breakers. Proline because secondary alpha amino group. Glycine because very flexible.
Cysteine vs. Cystine
Cysteine- intracellular, reducing environment due to antioxidants
Cystine- extracellular, oxidizing environment, disulfide bridge
What is isoelectric point for amino acids?
Isoelectric point is the pH where amino acid goes from positive to negative overall charge. Or where it exists as a zwitterion with neutral overall charge.
What is an indole ring and where is it found?
It is a double fused aromatic ring that contains nitrogen and is found in tryptophan.
How to calculate pI of acidic amino acid?
Average the pKa of C-terminus and pKa of side chain.
How to calculate pI of basic amino acid?
Average the pKa of N-terminus and pKa of side chain.
How to calculate pI of neutral amino acid?
Average the pKa of C-terminus and pKa of N-terminus.
What are the ketogenic and glucogenic amino acids?
ITFWY. Isoleucine, Threonine, Phenylalanine, Tryptophan, Tyrosine.
What amino acid pKas to memorize? These are all ionizable.
7: DEHCYKR. Aspartic acid: 3.9 Glutamic acid: 4.1 Histidine: 6.0 Cysteine: 8.4 Tyrosine: 10.5 Lysine: 10.5 Arginine: 12.5
Hydrophobic amino acids?
9: GAPWVILMF. Glycine, Alanine, Proline, Tryptophan, Valine, Isoleucine, Leucine, Methionine, Phenylalanine.
Hydrophilic amino acids?
6: STYNQC. Serine, Threonine, Tyrosine, Asparagine,
Glutamine, Cysteine.
Positively Charged Basic amino acids?
3: KRH. Lysine, Arginine, Histidine.
Negatively Charged Acidic amino acids?
2: DE. Aspartic acid, Glutamic acid.
Why does peptide bond formation need ATP?
Reaction is endergonic and thermodynamically unfavorable. Reactants having less energy than products.
If peptide formation is thermodynamically unfavorable then why doesn’t reverse reaction occur spontaneously?
Activation energy is too high for it to occur in normal conditions. Reverse reaction is kinetically unfavorable while peptide formation is kinetically favorable.
What are the links in primary structure of proteins?
Peptide bonds that make linear structure.
What are the links in secondary structure of proteins?
Hydrogen bonds that make alpha helices and beta sheets (both parallel and antiparallel).
What are the links in tertiary structure of proteins?
Hydrogen bonds, Van der Waals, hydrophobic effect, disulfide bridges, ionic bonds that make polypeptides.
What does quaternary structure consist of?
Multiple polypeptides and each one is called a subunit.
How to name quaternary structure?
Dimer, trimer, tetramer, anything above 4 called multimer.
Peptide bond forms between what 2 atoms?
Carboxyl group’s carbon and amino group’s nitrogen.
If a polypeptide has n amino acids, then how many peptide bonds does it have?
n-1 peptide bonds.
What does the double bond character of the peptide bond make?
Peptide plane.
Phi angle is between what 2 atoms?
Nitrogen and alpha carbon.
Psi angle is between what 2 atoms?
Alpha carbon and Carbonyl carbon.
What are 4 different secondary structure patterns?
Alpha helix, Beta pleated sheet, Beta turn, Omega loop.
What type of alpha helix predominates?
Right handed helix.
Each N-H reacts with C=O how far away?
4 units ahead or (13 atoms total).
What are the 2 types of quaternary structure? Ex?
Fibrous protein (Ex: keratin, collagen) and globular protein (Ex: hemoglobin, insulin, DNA polymerase).
Hemoglobin vs. Myoglobin
Both carry oxygen. Hemoglobin carries oxygen in blood. Myoglobin carries oxygen in muscles. Hemoglobin has quaternary structure because made of 4 polypeptides. Myoglobin has only tertiary structure because made of only 1 polypeptide.
Increased heat destroys which protein structures?
Secondary, Tertiary, Quaternary. Not Primary though.
Changing pH destroys which protein structures? What does it break?
Tertiary, Quaternary. Breaks ionic bonds.
Chemicals destroy which protein structures? What does it break?
Secondary, Tertiary, Quaternary. Breaks hydrogen bonds.
What can break protein primary structure?
Enzymes.
In Anfinsen’s experiment, urea broke down what?
Ionic interactions and hydrogen bonds.
In Anfinsen’s experiment, Beta mercaptoethanol broke down what?
Disulfide bonds.
Infectious aggregates formed from misfolded proteins and cause mad cow disease, scrapie in sheep, and Creutzfeldt-Jakob disease in humans. These cannot be denatured by typical methods.
Prions.
In Anfinsen’s experiment, what enzyme was he studying?
Ribonuclease.
What are two main methods for synthesizing amino acids?
Gabriel synthesis and Strecker synthesis.
Describe the differences in translation between (+)ssRNA viruses (like the Coronavirus) and (-)ssRNA viruses (like the influenza virus).
(+)ssRNA viruses have their genome stored as RNA that can readily be translated to form the proteins that they need.
(-)ssRNA Viruses, however, need to transcribe the (+) version of the RNA so it can be readily translated by the host cell’s machinery. These viruses need an extra step of processing!
What is the primary function of transfer RNA (tRNA) vs. ribosomal RNA (rRNA)?
Transfer RNA (tRNA) carries amino acids to the ribosome and acts as a “bridge” by matching a codon in mRNA with its corresponding amino acid.
Ribosomal RNA (rRNA) is responsible for the structure and function of the ribosome.
If there are only enough peptide bonds in a molecule so that you could count them all on your fingers, then what type of peptide would this be?
(A) Peptides
(B) Oligopeptides
(C) Proteins
(D) Polypeptides
(B) Oligopeptides
Oligopeptides have up to 20 amino acids in them.
Which of the following amino acids’ R groups could NOT be Phosphorylated by a Kinase?
(A) S
(B) T
(C) W
(D) Y
(C) W
W (Tryptophan) is the only one of the choices that does not include a hydroxy (-OH) group. A kinase adds on a phosphate group to a molecule by removing a hydrogen and creating a bond between the oxygen of the hydroxy group and the phosphate of the phosphate group (O-P).
True or False? Secondary structure is determined by interactions between the polypeptide’s backbone, while tertiary structure is determined by interactions between polypeptide R-groups.
True.
Which of the following levels of protein structure must be disrupted during Denaturation?
(A) Primary
(B) Secondary
(C) Tertiary
(D) Quaternary
(C) Tertiary
The Tertiary Structure of proteins must be disrupted in Denaturation.
Secondary or Quaternary Structure may be disrupted as well.
Compare and contrast the two following alpha amino acid synthesis reactions: Gabriel Synthesis and Strecker Synthesis.
The gabriel synthesis starts with N-pthalamidomalonic ester “Thad”, which protects both the amine group and carboxylic acid. The alpha-carbon will be alkylated, hydrolyzed, and then heated for a decarboxylation.
The strecker synthesis is much more simple and efficient. It starts with ammonia, HCN, and an aldehyde/ketone. The aldehyde/ketone and ammonia will react to form an imine, which in acid with HCN will form a nitrile, and hydrolysis in acid will yield the alpha-amino-acid.
Which of the following general statements about Amino Acids are true?
I. Bacteria can use D-amino acids in proteins, but humans typically do not.
II. Not all amino acids in the human body are in the genetic code and/or are incorporated into proteins.
III. All of the amino acids that are in the genetic code have their carboxyl and amine groups bound to the same carbon.
(A) III only
(B) I and II only
(C) I and III only
(D) I, II and III
(D) I, II and III.
Enzyme in human blood and saliva that makes carbonic acid turn into carbon dioxide quicker.
Carbonic anhydrase.
Why is DNA a negatively charged polymer?
Because of all the negatively charged phosphate. groups.
What are the 4 catalytic strategies?
Proton carrier in acid base catalysis, electron carrier in covalent catalysis, charge stabilizer in electrostatic catalysis, and increase frequency of successful collisions in proximity/orientation effects.
What does carbonic anhydrase help nonpolar CO2 dissociate into?
Bicarbonate which is polar and can dissolve into blood.
What is an apoenzyme bound to its cofactor called?
Holoenzyme.
What are tightly bound coenzymes called?
Prosthetic groups.
T or F. All enzymes are proteins.
F. Most are proteins but some RNA molecules are also enzymes.
Is ATP synthesis endergonic or exergonic?
Endergonic.
T or F. Enzymes affect Gibb’s free energy.
F. They only speed up rate by lowering activation energy.
What is it called when all enzyme active sites are filled with appropriate substrate?
Maximum enzyme velocity.
When is substrate most tightly bound to enzyme?
In transition state.
Where do regulators (activator or inhibitors) bind on an enzyme?
On allosteric site. It is different from active site.
What enzyme moves functional group from one molecule to another?
Transferase.
What enzyme joins two molecules together to form a complex?
Ligase.
What enzyme transfers electrons from one molecule to another?
Oxidoreductase.
What enzyme helps convert a molecule into one of its isomers?
Isomerase.
What enzyme help cleave covalent bonds using water?
Hydrolase.
What enzyme generates double bond or ring structure to break bonds?
Lyase.
What do coenzymes act as? Ex?
Carrier molecules. Ex: NADH, CoA.
What do cofactors do? Ex?
Directly assist with catalysis. Ex: Mg2+ ion with DNA polymerase.
What are organic cofactors and coenzymes called?
Vitamins.
What are inorganic cofactors called?
Minerals.
What 2 things must be precise for enzymes to function properly?
pH and temperature.
What are non enzymatic proteins?
TRAM. Transport, Receptor/Ion channels, Antibodies, Motor proteins.
What is co-translational protein modification? Ex?
Modification during translation of the protein. Ex: acetylation.
What is post-translational protein modification? Ex?
Modification after translation of the protein. GLUMP Ex: glycosylation (adds carb), lipidation (adds lipid), phosphorylation (adds phosphate to organic molecule), methylation (adding methyl groups to turn on/off genes), proteolysis (breaks protein), ubiquitination (marks for degradation).
What is inactive form of an enzyme?
Zymogen.
What inhibitors permanently bind?
Suicide inhibitors.
Why is phosphorylation an effective means of regulation?
Net negative charge, hydrogen bond properties, kinetics is adjustable, abundance of ATP, amplification effects, releases a lot of free energy, reversible.
What is Michaelis Menten equation?
V= (Vmax * S)/(Km + S).
What is Km (Michaelis constant)?
The substrate concentration needed to achieve the rate of Vmax/2. Also when half the active sites are occupied.
What does it mean if Km is large or small?
If Km is large then enzyme binds weakly to substrate and there is high probability of dissociation. If Km is small then enzyme binds strongly to substrate.
What is turnover number (k2 or Kcat)?
Maximum number of substrate molecules turned into product by a single active site in a given period of time.
What is Lineweaver burke plot equation?
1/V= Km/Vmax * 1/S + 1/Vmax. Remember y=mx+b.
What does competitive inhibitor make and do?
Makes EI. Km increases. Slope increases but y-intercept stays same (LWB plot). More substrate needed to reach Vmax.
What does uncompetitive inhibitor make and do?
Makes ESI. Both Km and Vmax decreases. Slope stays same but line goes left (LWB plot). Less substrate needed to reach Vmax.
What does noncompetitive inhibitor make and do?
Makes EI and ESI. Vmax decreases. Kcat decreases. Slope increases but x-intercept stays same (LWB plot).
What are irreversible inhibitors? Ex?
Inhibitors that bind tightly covalently or noncovalently. Ex: nerve gas, penicillin, aspirin.
What is it called when there are multiple enzyme binding sites and they affect or don’t affect each other?
Cooperativity (positive, negative or non).
What is it called when substrate and regulator same? different?
Homotropic, heterotropic.
What are 5 major mechanisms of enzyme regulation?
Allosteric control, reversible covalent modification, proteolytic cleavage, enzyme concentration, isoenzymes.
What are the rungs of DNA made of?
Nonpolar nitrogenous bases linked by hydrogen bonds.
What is the backbone of DNA made of?
Negatively charged phosphate and sugar linked with phosphodiester bonds.
What does a deoxyribose have missing?
An O in the 2’ position.
What pair of nitrogenous bases are harder to break?
Cytosine and guanine because 3 hydrogen bonds between them form.
Difference between nucleotide and nucleoside.
Nucleoside doesn’t have phosphate.
What are the 4 RNA nucleosides called?
Adenosine, guanosine, cytidine, uridine.
What are the 4 DNA nucleosides called?
Deoxyadenosine, deoxyguanosine, deoxycytidine, thymidine.
What are short sequences of DNA nucleotides synthesized discontinuously called?
Okazaki fragments.
Without telomerase what would happen?
Apoptosis (programmed cell death).
On what kind of DNA are most important genetic info found?
Single copy DNA.
Where are repetitive DNA found?
Near centromeres.
Telomeres are an example of what kind of DNA?
Highly repetitive DNA. It has no genes.
Which direction is DNA synthesized?
5’ to 3’.
What enzyme prevents the DNA double helix ahead of the replication fork from getting too tightly wound as the DNA is opened up?
Topoisomerase.
What did Meselson-Stahl experiment prove?
Semi-conservative model of DNA was correct. After one round of replication, every new DNA double helix would be a hybrid that consisted of one strand of old DNA bound to one strand of newly synthesized DNA.
What were the 3 possible models of DNA replication called?
Conservative, dispersive, semi-conservative.
What do spliceosomes remove from pre-mRNA?
Introns (noncoding segments of DNA).
What is function of microRNA (miRNA)?
Gene silencing.
mRNA vs. tRNA vs. rRNA
mRNA carries genetic information from the nucleus to ribosomes for the synthesis of proteins; while tRNA carries specific amino acids to the ribosomes to assist the protein biosynthesis, and on the other hand, rRNA provides the structural framework for the formation of ribosomes.
What is function of small nuclear RNA (snRNA)?
Splice together exons to form mature mRNA.
At what level of central dogma is gene expression usually regulated?
Transcription.
What is a unit of genomic DNA containing a cluster of genes that are under control of a single regulatory signal (promoter)?
Operon. They are usually found in bacteria.
What enzyme does lac Z code for and what does it do?
Beta-galactosidase (aka lactase) which breaks down lactose into glucose and galactose.
What enzyme does lac Y code for and what does it do?
Lactose permease which allows lactose into cell.
What detaches from operator site of lac operon when glucose concentration is low?
Repressor.
What is at the promoter site of lac operon?
RNA polymerase.
What is densely packed, transcriptionally inactive DNA?
Heterochromatin.
What is less densely packed, transcriptionally active DNA?
Euchromatin.
Does acetylation increase or decrease gene expression?
Increase.
What is template strand also known as?
Antisense strand.
What complex consists of the TATA binding protein?
Transcription factor II D.
What protein helps the TBP protein interact with RNA polymerase II?
Transcription factor II B.
What are enhancers?
DNA segments located upstream or downstream that bind special transcription factors.
TATA box is a common example of what?
Core promoter.
What do you call genes that code for proteins that normally direct cell growth and has potential to cause cancer?
Oncogenes.
What are the 5 categories of cancers?
Carcinoma (in epithelial cells lining internal organs), sarcoma (in soft tissue and bones), leukemia (in lymphoblastic or myeloid cells of blood-forming tissue), lymphoma (in lymphocytes (T or B cells)), brain and spinal cord tumors.
T vs. B cells
T cells are involved in cell-mediated immunity, whereas B cells are primarily responsible for humoral immunity (relating to antibodies).
What are nucleosomes?
Nucleosomes are the repeating unit in chromatin which is composed of DNA helix wrapped around a core of 8 histone proteins.
What are 3 mechanisms that alter proto-oncogenes into oncogenes?
Deletion or point mutation, gene amplification, chromosomal rearrangement.
In gel electrophoresis, what is positive and negative end?
Wells are negative (cathode). End is positive (anode).
Gel electrophoresis separates based on what?
Size. Smallest out first.
In the PCR method, a pair of these is used to hybridize with the sample DNA and define the region of the DNA that will be amplified.
Primers.
T or F. Prokaryotic cells have introns.
F.
Enzymes that can be used to cut out genes in DNA.
Restriction enzymes.
What are sticky ends?
They are single stranded DNA portions that form when digestive enzymes cut DNA in an asymmetric manner.
Northern vs. Southern blot
While both techniques are used to identify nucleic acid sequences, Northern blotting is performed to detect RNA sequences, while Southern blotting is done to detect DNA sequences.
How does adding ddNTP prevent further elongation of DNA strand?
ddNTP has no 3’ hydroxyl group so no condensation can occur to add another nucleotide.
What are all types of mutations?
Point mutation (swaps), frameshift mutation (insertion or deletion)
Nonsense mutation (puts stop codon), missense mutation (Silent mutation, conservative mutation (same type AA)), non-conservative mutation(different type AA))
What are the start and stop codons?
Start codon: AUG (methionine)
Stop codons: UAA, UAG, UGA
Frameshift vs. Non-frameshift mutation
Frameshift are insertion or deletion that aren’t a multiple of 3. Non-frameshift are insertion or deletion that are multiples of 3.
Transition vs. Transversion vs. Mispairing
Point mutations
Transition: Purine to purine, pyrimidine to pyrimidine.
Transversion: Purine to pyrimidine or vice versa.
Mispairing: Wrong pair forms.
What is the Hardy Weinberg equation?
p² + 2pq + q² = 1. Result of p + q = 1 whole squared.
What was the conclusion of Friedrich Miescher’s experiment?
Miescher’s experiment helped isolate the nucleus and identified the two main components of the nucleus: protein and nucleic acids.
What was the conclusion of Hershey-Chase experiment?
Hershey-Chase experiment dealt with bacteriophages and running multiple trails once with radio labeling protein coats and other trails radio labeling DNA. Their experiment concluded and confirmed that DNA is the genetic material.
Why is hemophilia and colorblindness more common in men?
Because the x-linked recessive traits and men only have one x chromosome.
If the incidence of colorblindness is 1/7 in men what is it in women?
1/49.
What is synapsis?
Process of chromosomes pairing up.
What is chiasma?
Point where chromosomes cross over.
If there is higher percent recombination what does that say about the distance between the genes on the chromosome?
More map units between the genes.
How do chloroplast and mitochondria not follow Mendelian genetics?
Both are maternally inherited and hence not from both parents like in Mendelian genetics.
Catabolism vs. Anabolism
Break down vs. build up
What helps fats be transported in the blood when they are so hydrophobic?
Lipoproteins.
What is bad and good cholesterol?
LDL (low-density lipoprotein), sometimes called “bad” cholesterol, makes up most of your body’s cholesterol. High levels of LDL cholesterol raise your risk for heart disease and stroke.
HDL (high-density lipoprotein), or “good” cholesterol, absorbs cholesterol and carries it back to the liver. The liver then flushes it from the body. High levels of HDL cholesterol can lower your risk for heart disease and stroke.
Is phosphorylation endothermic or exothermic?
Endothermic. It is like the opposite of ATP breakdown.
Aldoses and Ketoses mnemonics?
GETRAXLAAGMGIGT and DERXPFST.
Describe lactose.
Disaccharide made of galactose and glucose joined by beta-1,4-glycosidic bond. Reducing.
Describe maltose.
Disaccharide made of glucose and glucose joined by alpha-1,4-glycosidic bond. Reducing.
Describe sucrose.
Disaccharide made of glucose and fructose joined by alpha-1, beta-2-glycosidic bond. Nonreducing.
Cellulose vs. Starch.
Both are repeating units of glucose but cellulose has beta-1,4 linkages. Humans can break down starch which has alpha-1,4 linkages.
