Protein Structure and Function

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Questions and Answers

What is one of the primary functions of telomeres?

Prevents degradation of DNA (correct)

Facilitates protein synthesis

Codifies genetic information

Replicates DNA strands

In which direction is new DNA strand synthesis carried out during replication?

3' to 5'

5' to 5'

3' to 3'

5' to 3' (correct)

Which process helps ensure accurate DNA replication?

Recombination

Mutagenesis

Proofreading (correct)

Telomere elongation

What type of mutation occurs without a known cause?

Spontaneous mutations Signup and view all the answers

How do mutations contribute to evolution?

They generate genetic variation Signup and view all the answers

Which of the following is NOT a component of DNA replication?

Mitigation Signup and view all the answers

What is the role of pyrophosphate hydrolysis in DNA synthesis?

Gives energy to create phosphodiester bonds Signup and view all the answers

What defines the semiconservative mode of DNA replication?

Parent strands serve as templates for new daughter strands Signup and view all the answers

What kind of interactions primarily stabilize the α-helix structure in proteins?

Hydrogen bonds Signup and view all the answers

Which amino acid type would not be found in the polar region of a protein's structure?

Alanine Signup and view all the answers

What type of bond is primarily involved in substrate binding during enzyme activity?

Noncovalent bonds Signup and view all the answers

Which of the following amino acids has a negatively charged side chain?

Glutamic Acid Signup and view all the answers

What structural characteristic defines a β-pleated sheet in proteins?

Extended polypeptide chains with hydrogen bonding between different chains Signup and view all the answers

Which factor influences the energy favorability in the formation of right-handed α-helices?

Steric hindrance between R groups Signup and view all the answers

Which of the following is NOT a type of noncovalent interaction that contributes to protein structure?

Covalent bonds Signup and view all the answers

If an enzyme alters covalent bonds in a substrate, which of the following activities is it primarily involved in?

Covalent catalysis Signup and view all the answers

Which of the following properties is characteristic of only L-amino acids?

Presence in nature Signup and view all the answers

How many amino acids are typically found per turn of an α-helix?

3.6 Signup and view all the answers

What role do nonpolar side chains play in the structure of folded polypeptides in an aqueous environment?

They create a hydrophobic core region. Signup and view all the answers

Which level of protein structure is characterized by the specific sequence of amino acids?

Primary Structure Signup and view all the answers

How do enzymes typically increase the rate of biological reactions?

By providing a complementary active site for substrates. Signup and view all the answers

What is a key characteristic of the enzyme active site?

It is relatively small compared to the enzyme's overall size. Signup and view all the answers

What type of bond is primarily responsible for stabilizing protein structure among non-covalent interactions?

Hydrogen bonds Signup and view all the answers

What is the primary function of allosteric regulation in enzymes?

To increase or decrease enzyme activity via modulator binding. Signup and view all the answers

In the context of enzyme kinetics, what is the effect of activating a positive modulator on enzyme activity?

It enhances the enzyme's activity. Signup and view all the answers

What is a defining feature of the enzyme-substrate complex?

It occurs at the active site of the enzyme. Signup and view all the answers

What happens when an enzyme reaches its saturation point?

The reaction velocity remains constant despite substrate increases. Signup and view all the answers

What is one of the main advantages of having a hydrophobic cleft in an enzyme's active site?

It stabilizes nonpolar substrates more effectively. Signup and view all the answers

Which of the following best describes the process of enzyme catalysis?

It decreases the activation energy required for the reaction. Signup and view all the answers

What is the significance of covalent modification in regulating enzyme function?

It can modify the activity of the enzyme temporarily. Signup and view all the answers

In terms of enzyme-substrate interactions, what is meant by 'transition state stabilization'?

It lowers the energy barrier needed for the substrate to reach the product state. Signup and view all the answers

What type of interaction primarily determines the specificity of binding between enzymes and substrates?

Non-covalent interactions Signup and view all the answers

Study Notes

Nonpolar Amino Acids in Folded Polypeptide in an Aqueous Environment

Nonpolar side chains create a hydrophobic core region in the folded conformation of a polypeptide
Polar side chains line the outside of the molecule and can form hydrogen bonds with water

Four Levels of Protein Structure

Folding is a process that minimizes the total free energy
Primary Structure: sequence of amino acids
Secondary Structure:

-helices
-pleated sheets
Tertiary Structure: three-dimensional shape of a single polypeptide chain
Quaternary Structure: structure formed by the assembly of multiple polypeptide subunits

Folded proteins form functional structures called domains

Protein Assemblies

Exact structure depends on the orientation of binding sites on each subunit
Assemblies are also known as polymers
- Some polymeric structures exhibit polarity, but not necessarily in the electrical sense
Rigid Structures:
- Collagen
  - Very tightly packed in a triple helix
Elastic Structures:
- Elastin
  - Elastin molecules cross link to one another and are able to stretch and relax due to those cross links
Covalent Bonds:
- Disulfide bonds help stabilize protein structure
  - Can occur interchain or intrachain
Formation of Sheets or Tubes:
- Some proteins can form sheets or tubes through multiple points of contact with other subunits
  - Viral Capsids
Interactions between two proteins or another kind of molecule and a protein involve specific non-covalent interactions that determine the specificity of binding
Amino acids involved in binding are often far apart from one another in the unfolded protein but are close to one another in the folded conformation

How do Antibodies Generate Diversity of Binding to Thousands of Different Antigens Without Losing Basic Structure or Function?

Noncovalent bonds mediate specificity of binding between molecules
The function of proteins is regulated by covalent modification

Kinetic Properties of Enzymes

Enzymes increase the rate of biological reactions without altering reaction equilibriums
- All chemical reactions can be described in terms of equilibrium
  - The degree to which a reaction will proceed forward to yield a product or backwards to the starting point
Decrease the activation energy of a reaction
Accelerate reactions through stabilization of transition states
The enzyme active site

Reaction Equilibrium

Reaction equilibrium is linked to the standard free energy change (ΔG)
- Energy states of reactants and products remain unchanged in both the enzyme-catalyzed and uncatalyzed reactions
Reaction rates are linked to the activation energy (E A)
- Enzymes increase the reaction rate by lowering the E A
As K’ increases, ΔG decreases eq

Enzyme Active Site

Enzyme is complementary to the transition state
The catalytic site is relatively small compared to the rest of the enzyme
The catalytic site is three-dimensional
Substrates are bound to enzymes by multiple weak noncovalent interactions:
- Electrostatic bonds
- Hydrogen bonds
- Van der Waals interactions
- Hydrophobic interactions

Catalytic Site Forms Clefts or Crevices

Substrate molecules bound within the cleft
Water is normally excluded unless involved in catalysis
Overall nonpolar character of the cleft can enhance binding of substrate
Cleft may also contain polar residues which may take on catalytic properties within this nonpolar microenvironment

Enzyme-Substrate Complex

First step in catalysis
Enzymes derive much of their catalytic power by bringing in a substrate molecule at a favorable orientation
- This is how enzymes reduce free energy
Enzymes have a saturation point where the velocity of the reaction cannot increase any more

Posttranslational Regulation of Enzyme Activity

Allosteric Regulation:
- Positive modulator increases activity of the enzyme
- Feedback inhibition
- A way of regulating levels of synthesized endproduct

Regulation of Enzyme Activity

Covalent Modification:
- Attachment of another molecule to a substrate can modify enzyme activity
Proteolytic Modification:
- Protease cleaves one or more bonds in a target protein to modify its activity

Proof that Genetic Information is Stored in DNA

Evidence:
- Most DNA is located in chromosomes
  - RNA and Proteins are distributed throughout the cell
- Precise correlation between amount of DNA and number of chromosomes
- Diploid organisms have somatic cells with 2x the DNA as germ cells
- Molecular composition of DNA is unchanged throughout cells of organisms, which composition of RNA and proteins are variable in different cell types
- DNA is more stable than proteins or RNA

Bacterial Transformation

Type R:
- Lack polysaccharide capsule
  - Avirulent strain
Type S:
- Large, round colonies are encapsulated
  - Protected from attack by white blood cells
  - Virulent

Structure of DNA

Packaged into chromosomes
Form begets function
Nuclein: Nitrogen and Phosphorus containing acidic material generated by treating pus cells with pepsin
Nucleotides:
- Monomer Subunits
- Pyrimidines:
  - Cytosine
  - Thymine
- Purines:
  - Adenine
  - Guanine
Nomenclature:
- Nucleoside:
  - No phosphate group
- Nucleotide:
  - Phosphate group
- dNMP vs dNDP vs dNTP:
  - (Deoxyribonucleotide mono/di/triphosphate)
- dNTP vs NTP:
  - Deoxyribonucleotide triphosphate vs ribonucleotide triphosphate

Phosphodiester Linkage

Formation of polynucleotide chain is formed by phosphodiester bonds
Occurs between the 5’ and 3’ ends of deoxyribose

RNA Structure

Differences between DNA and RNA:
- RNA has a 2’ OH group
- In RNA, Uracil replaces Thymine
- Structure:
  - RNA is single stranded
  - RNA folds back on itself
    - Functions in expression of genetic information

Chargaff

[Thymine] = [Adenine]
[Cytosine] = [Guanine]
[T] + [C] = [A] + [G]

DNA Replication Occurs in a Semiconservative Manner

DNA Organization

Organismal DNA divided into units called chromosomes

Eukaryotic Chromosome Structure

Humans have 23 different chromosomes

Multineme vs Unineme

Multineme:
- Multiple double helices running through chromosome
Unineme:
- Single strand of DNA running through chromosome

Unineme, so how does DNA condense?

Levels of Chromatin Packaging:
1. DNA double helix
2. DNA + Histones
3. Solenoid or Zigzag
4. 30nm fiber organized into loops via chromatin scaffold
5. Condensed chromosome

Telomere

At the end of chromosomes
Three Functions:
- Prevents degradation
- Prevents fusion of ends with other DNA molecules
- Facilitates faithful replication of linear end of DNA
Single stranded overhang of the 3’ strand
G rich

Semiconservative Mode of Replication

Each parental strand of DNA serves as a template for new daughter strands
New strand synthesis is in the 5’ to 3’ direction

DNA Polymerases Catalyze the Synthesis of DNA

Pyrophosphate hydrolysis gives energy to create the phosphodiester bonds in DNA

DNA Replication

Beginning:
- Initiation
Middle:
- Elongation
End:
- Termination
Initiation at Origin
- Prokaryotes:
  - Single point of origin
- Eukaryotes:
  - Multiple points of origin
Elongation
- DNA polymerase III
- Leading strand synthesis
- Lagging strand synthesis
  - Okazaki fragments
  - DNA polymerase I
  - DNA ligase
- Topoisomerase
- Helicase

Mutation, DNA Repair, and Recombination

Proofreading helps to ensure accurate replication of DNA between generations
Mutation: Heritable change in genetic material
- Refers to the process in which the change occurs
- Mutant: An organism that exhibits a novel phenotype resulting from a mutation

Mutations

Spontaneous Mutations:
- Occur without a known cause/Rare
  - Inherent errors in replication
  - Unknown agents in the environment
- Rate in Prokaryotes is lower than in Eukaryotes
Induced Mutations:
- Mutations that result from a known cause
  - Exposure to physical or chemical mutagens
  - Ionizing radiation, Ultraviolet light and a variety of chemicals
- Frequency of mutations depends on the agent
  - Rate can increase dramatically if the mutagen is potent
  - Up to 1% of genes in an organism can be mutated

What Role Does Mutation Play in Evolution?

Mutation is the raw material of evolution
Mutation leads to genetic variation
- Changes in genotype that can lead to changes in phenotype
- Ability to respond to environmental changes
Can mutation level be too high??

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Description

This quiz explores the intricate details of protein structures, including nonpolar and polar amino acids in polypeptides, and the four levels of protein structure. It covers concepts such as primary, secondary, tertiary, and quaternary structures, as well as the formation of protein assemblies and domains.