Biology 302 Test 1 Flashcards
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Questions and Answers

What kind of bonds hold amino acids together?

Covalent bonds

What are peptide bonds?

Covalent bonds formed between the carboxyl group of one amino acid and the amino group of another

What are polypeptides?

Proteins

Each type of protein has its own unique amino acid sequence.

<p>True</p> Signup and view all the answers

What is the amino group made of?

<p>NH3</p> Signup and view all the answers

What's the carboxyl group made of?

<p>CO2</p> Signup and view all the answers

How are peptide bonds formed?

<p>O from one amino acid's carboxyl group breaks off and bonds with two H atoms from the amino group of another amino acid, allowing the C and N to bond.</p> Signup and view all the answers

Peptide bond formation is not a condensation reaction.

<p>False</p> Signup and view all the answers

What is the polypeptide backbone?

<p>Repeating sequence of N-C-C in all amino acids</p> Signup and view all the answers

Each end of the polypeptide chain is the same.

<p>False</p> Signup and view all the answers

What is the N-terminus?

<p>End of the polypeptide carrying the amino terminus (NH3)</p> Signup and view all the answers

What is the C-terminus?

<p>End of the polypeptide chain carrying the free carboxyl terminus</p> Signup and view all the answers

What are side chains?

<p>Project out from the backbone</p> Signup and view all the answers

Side chains aren't involved in peptide bonding.

<p>True</p> Signup and view all the answers

The C-terminus gives proteins their unique properties.

<p>False</p> Signup and view all the answers

What is aspartic acid abbreviated as?

<p>Asp (D)</p> Signup and view all the answers

What is glutamic acid abbreviated as?

<p>Glu (E)</p> Signup and view all the answers

What is arginine abbreviated as?

<p>Arg (R)</p> Signup and view all the answers

What is lysine abbreviated as?

<p>Lys (K)</p> Signup and view all the answers

What is histidine abbreviated as?

<p>His (H)</p> Signup and view all the answers

What is asparagine abbreviated as?

<p>Asn (N)</p> Signup and view all the answers

What is glutamine abbreviated as?

<p>Gln (Q)</p> Signup and view all the answers

What is serine abbreviated as?

<p>Ser (S)</p> Signup and view all the answers

What is threonine abbreviated as?

<p>Thr (T)</p> Signup and view all the answers

What is tyrosine abbreviated as?

<p>Tyr (Y)</p> Signup and view all the answers

What is alanine abbreviated as?

<p>Ala (A)</p> Signup and view all the answers

What is glycine abbreviated as?

<p>Gly (G)</p> Signup and view all the answers

What is valine abbreviated as?

<p>Val (V)</p> Signup and view all the answers

What is leucine abbreviated as?

<p>Leu (L)</p> Signup and view all the answers

What is isoleucine abbreviated as?

<p>Ile (I)</p> Signup and view all the answers

What is proline abbreviated as?

<p>Pro (P)</p> Signup and view all the answers

What is phenylalanine abbreviated as?

<p>Phe (F)</p> Signup and view all the answers

What is methionine abbreviated as?

<p>Met (M)</p> Signup and view all the answers

What is tryptophan abbreviated as?

<p>Trp (W)</p> Signup and view all the answers

What is cysteine abbreviated as?

<p>Cys (C)</p> Signup and view all the answers

Polar amino acids are hydrophilic.

<p>True</p> Signup and view all the answers

Nonpolar amino acids are hydrophobic.

<p>True</p> Signup and view all the answers

What allows proteins to be flexible and fold in numerous ways?

<p>Peptide bonds that link carbon atoms in the backbone</p> Signup and view all the answers

What are the restrictions of the shape of proteins?

<p>Noncovalent bonds in the atoms of the amino acid side chains and atoms in the polypeptide backbone</p> Signup and view all the answers

Covalent bonds help proteins fold up and hold their shape.

<p>False</p> Signup and view all the answers

What are the types of noncovalent bonds that exist in proteins?

<p>Hydrogen bonds, electrostatic attraction (ionic), van der Waals forces</p> Signup and view all the answers

More noncovalent bonds result in a more stable protein structure.

<p>True</p> Signup and view all the answers

What happens to hydrophobic molecules in the aqueous environment of the cell?

<p>They're forced together to minimize their disruptive effect on the hydrogen bond network of surrounding water.</p> Signup and view all the answers

How do proteins fold in terms of the polar and nonpolar amino acids?

<p>Nonpolar amino acids fold into the center and polar amino acids arrange themselves to the outside to form hydrogen bonds.</p> Signup and view all the answers

What are polar amino acids bonded to within a protein?

<p>Hydrogen bonded with each other or the polypeptide backbone</p> Signup and view all the answers

What is conformation in proteins?

<p>Final folded structure of the protein</p> Signup and view all the answers

What energetic considerations determine the folded structure of proteins?

<p>Folds into a shape that minimizes their free energy (G) and releases heat which increases the disorder of the universe (S)</p> Signup and view all the answers

What does it mean when a protein is denatured?

<p>When the protein is unfolded</p> Signup and view all the answers

What happens when a protein is denatured?

<p>Loses its shape</p> Signup and view all the answers

All information necessary to fold a protein is in its amino acid sequence.

<p>True</p> Signup and view all the answers

All proteins have one conformation that is unchanging.

<p>False</p> Signup and view all the answers

What are prions?

<p>Misfolded proteins</p> Signup and view all the answers

Misfolded proteins cause numerous neurodegenerative diseases.

<p>True</p> Signup and view all the answers

Prions cannot convert normal proteins.

<p>False</p> Signup and view all the answers

What are chaperone proteins?

<p>Help proteins fold along the most favorable energy pathway</p> Signup and view all the answers

What is the backbone model of proteins?

<p>Shows overall organization of the polypeptide chain and makes it easy to compare structures</p> Signup and view all the answers

What is the ribbon model of proteins?

<p>Emphasizes the backbone and makes it easy to see how it folds</p> Signup and view all the answers

What is the wire model of proteins?

<p>Shows positions of all amino acid side chains and makes it easy to predict which amino acids may be involved in the protein's activity</p> Signup and view all the answers

What is the space-filling model of proteins?

<p>Contour map of its surface that reveals which amino acids are exposed on the surface and how the protein looks to other molecules</p> Signup and view all the answers

What is the alpha helix?

<p>Pattern where the polypeptide chain twists around itself and looks like a spiral staircase</p> Signup and view all the answers

What are beta sheets?

<p>Pattern where neighboring regions of the polypeptide chain associate side by side with each other</p> Signup and view all the answers

Why are alpha helices and beta sheets common patterns?

<p>Because side chains aren't involved in hydrogen bonding</p> Signup and view all the answers

What are properties of alpha helices?

<p>C=O of one chain is hydrogen bonded to N-H of another; complete turn every 3.6 amino acids; transmembrane proteins are often shaped like this</p> Signup and view all the answers

How do alpha helix shaped proteins pass through membranes?

<p>Backbone is hydrogen bonded to itself (hydrophilic) with nonpolar side chains on the outside shielding from the hydrophobic environment of the phospholipid bilayer.</p> Signup and view all the answers

What is a coiled-coil?

<p>When two or more alpha helices wrap around each other</p> Signup and view all the answers

Most coiled-coils have the hydrophilic amino acids on the inside.

<p>False</p> Signup and view all the answers

What are the properties of beta sheets?

<p>Can run parallel or antiparallel; gives silk fibers tensile strength; hydrogen bonds hold them together</p> Signup and view all the answers

What are amyloid fibers?

<p>Insoluble protein aggregates associated with prions that are stabilized by beta sheets</p> Signup and view all the answers

What is the primary structure of proteins?

<p>Amino acid sequence</p> Signup and view all the answers

What is the secondary structure of proteins?

<p>Alpha helices and beta sheets that form within segments of the polypeptide chain (folds)</p> Signup and view all the answers

What is the tertiary structure of proteins?

<p>Full 3D conformation of an entire polypeptide chain and includes all the loops and folds between the N and C terminus</p> Signup and view all the answers

What is the quaternary structure of proteins?

<p>Complex of more than one polypeptide chain</p> Signup and view all the answers

What is a protein domain?

<p>Any segment of a protein that can fold independently</p> Signup and view all the answers

What are the properties of protein domains?

<p>Usually have a secondary structure; different domains have different functions; can be composed of just beta sheets or just alpha helices; linked by unstructured lengths of polypeptide chain</p> Signup and view all the answers

What is an intrinsically disordered sequence?

<p>Unstructured regions of the polypeptide chain</p> Signup and view all the answers

What are the properties of intrinsically disordered sequences?

<p>Continually bend and flex due to thermal buffering; wrap around target proteins with high specificity and low affinity; increases frequency of encounters between domains; ideal substrates for addition of chemical groups that control the way proteins behave; give rubber-like qualities to skin and tendons</p> Signup and view all the answers

Few of the many possible polypeptide chain combinations are useful.

<p>True</p> Signup and view all the answers

Slight changes don't affect most proteins.

<p>False</p> Signup and view all the answers

What are protein families?

<p>Groups of proteins with different functions whose conformations still resemble each other greatly</p> Signup and view all the answers

Noncovalent bonds hold proteins together.

<p>True</p> Signup and view all the answers

What are binding sites?

<p>Region on the protein's surface that interacts with other molecules</p> Signup and view all the answers

What is a subunit in proteins?

<p>In large proteins with multiple polypeptide chains, each individual polypeptide chain</p> Signup and view all the answers

What is a dimer?

<p>Two identical subunits combine</p> Signup and view all the answers

What are globular proteins?

<p>Polypeptide chains fold up into a compact ball with an irregular surface</p> Signup and view all the answers

What are fibrous proteins?

<p>Proteins with elongated rod-like shapes</p> Signup and view all the answers

What are the properties of fibrous proteins?

<p>Often extracellular; form a gel-like extracellular matrix that binds cells together to create tissue; secreted by cells to assemble into sheets or long fibrils</p> Signup and view all the answers

What are polypeptide chains often stabilized with to withstand being outside the cell?

<p>Covalent cross-links</p> Signup and view all the answers

What is a disulfide bond?

<p>Most common covalent cross-link that involves S-S bond</p> Signup and view all the answers

Disulfide bonds change the conformation of a protein.

<p>False</p> Signup and view all the answers

Proteins bind to only one or a few select things.

<p>True</p> Signup and view all the answers

What is a ligand?

<p>General name for a molecule that binds to a specific site on a protein</p> Signup and view all the answers

What allows a protein to bind with a ligand?

<p>Many simultaneous noncovalent bonds and hydrophobic forces</p> Signup and view all the answers

Molecules with poorly matching surfaces can persist for a long time.

<p>False</p> Signup and view all the answers

Study Notes

Amino Acids and Peptide Bonds

  • Amino acids are joined by covalent bonds known as peptide bonds.
  • Peptide bonds form between the carboxyl group of one amino acid and the amino group of another.
  • A polypeptide is a chain of amino acids that folds into a protein.

Protein Structure

  • Each protein has a unique amino acid sequence, critical to its function.
  • Amino groups consist of NH3, while carboxyl groups are composed of CO2.
  • The polypeptide backbone follows a repeating N-C-C pattern.

Polypeptide Chain Ends

  • Polypeptide chains have distinct ends:
    • N-terminus (NH3) indicates the start
    • C-terminus has a free carboxyl group.
  • The ends of the peptide chain differ, influencing protein behavior.

Side Chains

  • Side chains extend from the backbone and are not involved in peptide bonding.
  • The unique properties of proteins arise from their side chains, not the C-terminus.

Amino Acids

  • Key amino acids and their abbreviations:
    • Aspartic acid (Asp, D)
    • Glutamic acid (Glu, E)
    • Arginine (Arg, R)
    • Lysine (Lys, K)
    • Histidine (His, H)
    • Asparagine (Asn, N)
    • Glutamine (Gln, Q)
    • Serine (Ser, S)
    • Threonine (Thr, T)
    • Tyrosine (Tyr, Y)
    • Alanine (Ala, A)
    • Glycine (Gly, G)
    • Valine (Val, V)
    • Leucine (Leu, L)
    • Isoleucine (Ile, I)
    • Proline (Pro, P)
    • Phenylalanine (Phe, F)
    • Methionine (Met, M)
    • Tryptophan (Trp, W)
    • Cysteine (Cys, C)

Properties of Amino Acids

  • Polar amino acids are hydrophilic, and nonpolar amino acids are hydrophobic.
  • Peptide bonds allow for flexibility in protein structure, enabling various folding patterns.

Protein Folding and Stability

  • Proteins fold to minimize free energy and increase the universe's disorder.
  • Noncovalent bonds (hydrogen bonds, ionic interactions, and van der Waals forces) are crucial for maintaining protein structure.
  • More noncovalent bonds result in greater stability.

Protein Structures

  • Primary structure: amino acid sequence.
  • Secondary structure: local folding patterns, including alpha helices and beta sheets.
  • Tertiary structure: overall 3D conformation of a single polypeptide.
  • Quaternary structure: assembly of multiple polypeptide chains.

Functional Aspects of Proteins

  • Protein domains can fold independently and often have distinct functions.
  • Intrinsically disordered sequences enhance flexibility and interaction potential with other proteins.
  • Proteins evolve, and slight changes can significantly impact functionality.

Protein Types

  • Globular proteins: compact, ball-like structures.
  • Fibrous proteins: elongated and rod-like, contributing to structural functions in tissues.

Stabilization and Bonds

  • Fibrous proteins often have covalent cross-links to maintain stability outside cells.
  • Disulfide bonds reinforce protein conformation without changing it.

Protein Interactions

  • Proteins typically bind to specific molecules (ligands) using many simultaneous noncovalent bonds.
  • High specificity in binding ensures proteins interact with one or few selected targets.

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Prepare for your Biology 302 Test 1 with these flashcards. Each card focuses on key concepts such as amino acids, peptide bonds, and polypeptides. Test your knowledge and improve your understanding of proteins and their structures.

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