Biology Exam 1 and 2 Review

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Questions and Answers

Which component is essential for the identification of successfully transformed cells in plasmid construction?

An antibiotic resistance gene (correct)

A splice donor site

A promoter sequence

A replication origin

Which elements are the four most abundant in the human body?

H, O, P, S

C, N, O, H (correct)

C, H, Ca, K

N, O, C, I

What significant structures developed during the evolution of eukaryotic cells from prokaryotic cells?

Nuclear membranes (correct)

Plasma membranes

Chloroplasts

Cell walls

Which statement about the conservation of proteins in humans is inaccurate?

Most human proteins are unique to vertebrates. Signup and view all the answers

What is a necessary component for performing PCR?

DNA fragment, primers, dNTPs, and DNA polymerase Signup and view all the answers

For a reaction characterized by delta H = 23 kJ/mol and delta S = 22 J/kmol at 2 degrees Celsius, which statement is true?

The reaction is nonspontaneous. Signup and view all the answers

What process is involved in the formation of a dipeptide from two amino acids?

Loss of water occurs through condensation. Signup and view all the answers

Which noncovalent interaction is considered the strongest?

Ionic interactions Signup and view all the answers

In a pair of homologous proteins, which amino acid is likely to replace a Glu residue in a conservative substitution?

Asp Signup and view all the answers

In a urea molecule, how many atoms can act as hydrogen bond acceptors?

3 Signup and view all the answers

Which enzyme is primarily responsible for unwinding the DNA during replication?

DNA helicase Signup and view all the answers

Why does a prokaryotic replisome contain 2 molecules of DNA polymerase 3 but only one molecule of DNA polymerase 1?

DNA Pol 1 replaces RNA primers, which predominantly happens on the lagging strand. Signup and view all the answers

What type of mutation can result from the insertion or deletion of one or two nucleotides in a DNA sequence?

Frameshift mutations Signup and view all the answers

Which of the following correctly identifies the role of the sigma factor in prokaryotic transcription?

It recognizes the promoter to assist RNA polymerase binding. Signup and view all the answers

What is the function of aminoacyl-tRNA synthetase in protein synthesis?

It covalently attaches the correct amino acid to its corresponding tRNA. Signup and view all the answers

What is the role of proteoglycans in tissues such as cartilage?

They form hydrated gels that resist compression. Signup and view all the answers

Which structure is a primary component of bacterial cell walls?

Peptidoglycan Signup and view all the answers

N-linked glycosylation specifically involves the addition of which sugar to which amino acid?

N-acetylglucosamine to Asparagine Signup and view all the answers

What type of glycosylation occurs at serine or threonine residues?

O-linked glycosylation Signup and view all the answers

Which of the following statements is true about selectins?

They are specialized lectins on leukocytes that bind to endothelial cells. Signup and view all the answers

Which lipid type serves as the primary energy storage molecules in animals?

Triacylglycerols Signup and view all the answers

Which component is NOT typically found in phospholipids?

Amino acid side chains Signup and view all the answers

How does vancomycin affect bacterial cells?

It inhibits transpeptidation in cell wall synthesis. Signup and view all the answers

What is the primary role of glycosaminoglycans in connective tissues?

Providing structural support and shock absorption Signup and view all the answers

What distinguishes heparin from heparan sulfate?

Heparin is primarily found in mast cells while heparan sulfate is found in the brain. Signup and view all the answers

In which way does hyaluronate contribute to tissue viscosity?

It binds water and expands significantly in its dry state. Signup and view all the answers

What effect do tetanus and botulinum toxins have on SNARE proteins?

They cleave SNARE proteins, impairing neurotransmitter release. Signup and view all the answers

Which characteristic of glycosaminoglycans contributes to their high viscosity and elasticity?

They consist of repeating disaccharide units of uronic acid and hexosamine. Signup and view all the answers

What role do biofilms serve in bacterial environments?

They provide protection against threats like antibiotics. Signup and view all the answers

What are the stages involved in virus-mediated membrane fusion?

Host cell recognition, activation of the viral membrane, and fusion. Signup and view all the answers

What type of bond links the disaccharide units in hyaluronate?

Beta 1-4 bonds. Signup and view all the answers

Which function does heparin primarily serve in the human body?

Acting as an anticoagulant. Signup and view all the answers

What feature of amino acids allows them to be classified as L?

They are optically active and correlate with L-glyceraldehyde configuration. Signup and view all the answers

Which type of amino acids primarily contributes to absorbance at 280 nm?

Aromatic amino acids Signup and view all the answers

Which characteristic is typically irrelevant in standard protein separation methods?

Stereochemistry Signup and view all the answers

What type of bond links the two peptides shown in a given diagram?

Disulfide bond Signup and view all the answers

What is the primary basis for the separation of proteins in SDS-PAGE?

Mass Signup and view all the answers

Which linkage describes the bond between an amino acid and its cognate tRNA?

Carboxyl group of AA linked to 3’OH of tRNA Signup and view all the answers

Which statement is true regarding alpha helices?

The presence of proline can disrupt alpha helices. Signup and view all the answers

What stabilizes the structure of proteins through non-covalent interactions?

Hydrogen bonds Signup and view all the answers

What environmental changes can lead to protein denaturation?

Changes in pH, temperature, and ionic strength Signup and view all the answers

Which protein structure determination technique is most effective for studying protein dynamics?

Nuclear magnetic resonance (NMR) Signup and view all the answers

Study Notes

Exam 1

Four most abundant elements in human body: Carbon, Nitrogen, Oxygen, Hydrogen
Nuclear membranes developed during evolution of eukaryotic cells from prokaryotic cells
Reaction with ΔH = 23 kJ/mol and ΔS = 22 J/kmol at 2°C is nonspontaneous (ΔG is positive)
Strongest noncovalent interactions: Ionic interactions (between oppositely charged particles)
Urea molecule has 3 atoms that can act as hydrogen bond acceptors
Hydrophobic effect is an entropic effect, water molecules increase entropy by excluding hydrophobic groups
Buffer capacity depends on pKa, pH, total concentration of weak acid and its conjugate base
Nucleic acids are composed of nucleotides linked by phosphodiester bonds (creating sugar-phosphate backbone of DNA and RNA)
DNA separated during replication is stabilized by single-stranded DNA binding proteins (SSB)
Termination of replication fork in E.Coli involves Tus protein binding to Ter sites

Exam 2

RNA primer acts as a starting point for DNA synthesis by DNA polymerase
Transfer RNA molecules deliver amino acids to ribosomes during translation
Percentage of cytosine residues in a double-stranded DNA fragment with 12% adenine is 38%
RNA can store genetic information, as seen in retroviruses
Genetic material must not only mutate and replicate, but also direct protein synthesis
Major groove of B-DNA allows protein binding for regulation of transcription and replication
DNA polymerase 1 (Pol 1) has 3′ to 5′ exonuclease activity to proofread and remove mismatched nucleotides
DNA polymerase 3 (Pol 3) has a higher turnover rate than Pol 1 and is the primary replicase in E.Coli
Replication fidelity is maintained by mechanisms to tolerate or repair minor mutations
DNA polymerase with high processivity, low fidelity and replacement of RNA and DNA likely has 5' to 3' exonuclease activity

Exam 3

Insertions or deletions of one or two nucleotides cause frameshift mutations, altering the entire downstream protein sequence
Sigma factor facilitates RNA polymerase binding and initiates RNA synthesis
Aminoacyl-tRNA synthetase attaches correct amino acid to tRNA
Start codon in E.Coli base pairs with the 16S rRNA at the shine-dalgarno sequence
Ribosome A site binds new aminoacyl-tRNA during elongation
Polypeptide synthesis proceeds from N-terminus to C-terminus
Stop codon triggers release of growing peptide from the P-site tRNA
Ribosome's 30s subunit binds mRNA

Exam 4

All tRNAs adopt an L shape that is important for proper ribosome positioning
DNA template strand during transcription is called the antisense or noncoding strand
AluI restriction enzyme produces blunt end fragments
Transformed organisms are identified using an antibiotic resistance gene in a plasmid
Human proteins are often conserved across species and not unique to vertebrates
Reagents needed for PCR: DNA fragment, primers, dNTPs, and DNA polymerase
Formation of dipeptide involves loss of water from condensation between two amino acids
Tyr-Ala-Ser describes the oligopeptide

Exam 5

Ribosomes use L-amino acids to synthesize proteins due to the configuration of groups around the C-alpha
Amino acids absorbance at 280 nm (UV region) is due to aromatic amino acids
Protein separation methods do not use stereochemistry
Peptides are linked through disulfide bonds
SDS-PAGE separates proteins based on their mass differences
Covalent bond between an amino acid and its cognate tRNA is carboxyl group of AA linked to 3'OH of tRNA
First steps of folding disordered polypeptides into functional proteins involve 2nd degree structure
Protein denaturation can occur due to changes

Exam 6

Changes in pH, temperature, or ionic strength can disrupt protein structure
Molecular chaperones facilitate native protein folding to prevent damage from heat
NMR is useful to study protein conformational changes over time
B cells produce antibodies as part of humoral immunity
Glycine every third residue enables tight packing in collagen
Enzymes require a group to be deprotonated to be active at higher pH
Rate-determining step in a multi-step reaction has the highest ΔG
DIPF irreversibly inactivates acetylcholinesterase by covalent binding
Oxyanion hole stabilizes the transition state in serine proteases

Exam 7

Cofactors (metals or organic molecules) aid enzyme function
Proton transfer from an acid lowers free energy of a reaction transition state, is a characteristic of general acid catalysis
Leucine lacks side chain for acid-base catalysis at physiological pH
Methyl groups are poor nucleophiles
Transition state analogs bind tightly to enzymes
Enzyme catalyzed reaction with a group requiring a low pK to be deprotonated and a group with a high pK to be protonated will have a peak in the middle region of the pH VS rate curve.

Chapter 8: Glycosaminoglycans

Linear polysaccharides with disaccharide repeating units (uronic acid + hexosamine)
Located in extracellular matrices (e.g., cartilage, tendons, skin)
Provide structural support, lubrication, and shock absorption
Hyaluronate (Hyaluronic acid): long chains, high viscosity, important for binding water and cations.
Sulfated glycosaminoglycans (e.g., heparin): Highly charged polymers, anticoagulant properties, found in mast cells in arteries
Plant polysaccharide pectin: major component of plant cell walls.

Chapter 9: Lipids

Insoluble in water, but soluble in organic solvents
Types include fatty acids, triacylglycerols, phospholipids, glycolipids, and steroids
Fatty acids: Saturated (straight chains, higher melting points) or Unsaturated (cis double bonds, lower melting points)
Triacylglycerols: primary energy storage in animals
Phospholipids: major components of cell membranes
Glycolipids: important for cell recognition and adhesion
Steroids: derived from a four-ring structure (e.g., cholesterol, precursor for steroid hormones)
Membrane lipids: Amphipathic (hydrophobic tails and hydrophilic heads)
Phospholipid bilayer with integral proteins.

Chapter 10: Polysaccharides, Glycoproteins, and Peptidoglycan

Polysaccharides (glycans): chains of monosaccharides linked by glycosidic bonds
Homopolysaccharides: composed of one type of monosaccharide unit
Heteropolysaccharides: composed of more than one type of monosaccharide unit
Important structural and functional components for cells (e.g., cartilage)
Glycoproteins: Proteins with covalently attached carbohydrates. Crucial for cell communication, recognition and adhesion
Proteoglycans: Proteins covalently linked to glycosaminoglycans.
Peptidoglycan: Bacterial cell wall structure consisting of alternating monosaccharides and peptides.
Polysaccharides in biological systems typically have a bottlebrush architecture with glycosaminoglycans extending from a central protein core.
Glycogens are storage polysaccharides for animals
Cellulose is a main component of plant cell walls

Chapter 18: Membrane Fusion

Membrane fusion a critical process for viral infection, cell signaling, and exocytosis.
Influenza A virus, is a crucial example of virus mediated membrane fusion.
Viruses trigger host cell protein recognition to initiate cell membrane fusion to establish infection.

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