Biochemistry Chapter 1 Flashcards

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Questions and Answers

Describe the relationship between a living organism and its surroundings in terms of both matter and energy.

Living organisms are open systems and exchange both matter and energy with their surroundings.

How do cells accomplish the formation of a protein from individual amino acids despite it being an endergonic reaction?

The endergonic reaction is coupled to an exergonic reaction through a shared intermediate.

Explain how instant cold packs can get cold when the contents are mixed.

The dissolution reaction is spontaneous with a negative ΔG and absorbs heat, thus ΔH is positive.

What is meant by feedback inhibition and why is it important?

Feedback inhibition is the regulation of a biochemical pathway by a reaction product inhibiting an earlier step. Signup and view all the answers

How is genetic information encoded in DNA and synthesized?

Genetic information is encoded in the linear sequence of deoxyribonucleotides and synthesized by unwinding DNA strands. Signup and view all the answers

Explain the balance between stability and change in hereditary transmission of genetic information.

It involves accurate replication of DNA, resulting in stability, while mutations introduce changes essential for diversity. Signup and view all the answers

Discuss how a mutation in DNA could be harmful or beneficial to an organism.

Some mutations may lead to defective proteins and harm the organism, while others may enhance enzyme stability or function. Signup and view all the answers

Describe Stanley Miller's experiment (1953) and its relevance.

Miller subjected a gaseous mixture to electrical sparks, producing amino acids and demonstrating abiotic biomolecule production. Signup and view all the answers

What is the 'RNA world' hypothesis?

Initially, RNA molecules acted as both genes and catalysts, leading to the evolution of DNA for genetic storage. Signup and view all the answers

How did the rise of O2-producing bacteria influence aerobic organisms?

The rise increased O2 levels, giving aerobic organisms a selective advantage over anaerobic ones. Signup and view all the answers

What is meant by endosymbiotic association?

It refers to one organism enveloping another to form a mutually beneficial relationship. Signup and view all the answers

Which is a list of organelles?

Mitochondria, endoplasmic reticulum, peroxisomes Signup and view all the answers

The catalog of all proteins functioning in a cell is the:

Proteome Signup and view all the answers

Identify the correct statement: Carnivores are _ and herbivores are _.

Chemoheterotrophs, chemoheterotrophs Signup and view all the answers

When two genes in an organism share detectable sequence similarity, they are said to be:

A and C Signup and view all the answers

What is the difference between cytosol and cytoplasm?

Cytoplasm is the internal volume enclosed by the plasma membrane; cytosol is the aqueous portion of the cytoplasm. Signup and view all the answers

Explain why macromolecules diffuse slower in cytosol compared to dilute solutions.

The cytosol is crowded and gel-like, slowing diffusion due to collisions with other molecules. Signup and view all the answers

Describe the functions of proteins, nucleic acids, polysaccharides, and lipids.

Proteins serve as enzymes and structural elements; nucleic acids store genetic information; polysaccharides serve as fuel stores; lipids function as membrane components. Signup and view all the answers

Why is an asymmetric carbon atom called a chiral center?

It has four different substituents attached and cannot be superimposed on its mirror image. Signup and view all the answers

Differentiate between configuration and conformation.

Configuration refers to fixed spatial arrangement due to double bonds or chiral centers; conformation refers to freely assumes positions due to bond rotation. Signup and view all the answers

What is optical activity?

It is the capacity of a substance to rotate the plane of plane-polarized light. Signup and view all the answers

Why is it important for a chemist to separate enantiomers of a racemic mixture?

Each enantiomer may have different biological effects; one may be harmful while the other beneficial. Signup and view all the answers

Explain why living organisms can produce specific chiral forms of biomolecules compared to laboratory synthesis.

Living organisms use chiral enzymes, whereas laboratory syntheses usually involve achiral reagents, leading to racemic mixtures. Signup and view all the answers

Why don't protein molecules in a living cell lead to cell destruction?

The cell maintains a dynamic steady state, continuously synthesizing and degrading proteins. Signup and view all the answers

What is meant by feedback inhibition and why is it important in a living organism?

Feedback inhibition is the regulation of a biochemical pathway in which a reaction product inhibits an earlier step in the pathway. It ensures that energy is not wasted producing unneeded molecules. Signup and view all the answers

How is the genetic information encoded in DNA and how is a new copy of DNA synthesized?

The genetic information is encoded in the linear sequence of the four different deoxyribonucleotides. A new copy of DNA is synthesized when the two strands unwind and each serves as a template for new strands. Signup and view all the answers

Explain how hereditary transmission of genetic information reflects a balance between stability and change.

It occurs via replication of DNA with few changes, maintaining stability, while mutations introduce changes for genetic diversity. Signup and view all the answers

How could a mutation in DNA be harmful or beneficial to an organism?

Some mutations lead to inactive proteins, which are harmful, while others can produce beneficial traits by enhancing enzyme stability or function. Signup and view all the answers

Describe Stanley Miller's experiment (1953) and its relevance.

Miller subjected a gaseous mixture to electrical sparks, producing organic compounds, including amino acids. This demonstrated abiotic production of biomolecules. Signup and view all the answers

Describe the 'RNA world' hypothesis.

Initially, RNA acted as both genes and catalysts, leading to the development of proteins and eventually the evolution of DNA as the genetic storage. Signup and view all the answers

How might the rise of O2-producing bacteria have led to the predominance of aerobic organisms?

It increased atmospheric O2 levels, giving a selective advantage to aerobic organisms that used O2 while being harmful to anaerobic organisms. Signup and view all the answers

What is meant by endosymbiotic association?

It is when one organism envelops another, leading to a mutually beneficial relationship, contributing to the evolution of organelles in eukaryotic cells. Signup and view all the answers

In which reaction does water not participate as a reactant?

Production of gaseous carbon dioxide from bicarbonate Signup and view all the answers

When mixing sodium hydroxide with an acetate buffer at pH 4.76, what happens?

ratio of acetic acid to sodium acetate in the buffer falls Signup and view all the answers

What does the Henderson-Hasselbalch equation relate?

It relates the pH of a solution to the pKa and concentrations of acid and conjugate base Signup and view all the answers

Where is DNA located in a bacterial cell?

Nucleoid Signup and view all the answers

What was a major change occurring in the evolution of eukaryotes from prokaryotes?

The nucleus Signup and view all the answers

What encloses the nucleus in eukaryotes?

Nuclear envelope Signup and view all the answers

What is the range of lengths and diameters of living cells?

0.3 m to 100 m Signup and view all the answers

Which group of single-celled microorganisms has many members found growing in extreme environments?

Archaea Signup and view all the answers

The bacterium E. coli requires simple organic molecules for growth and energy. What is this characteristic?

Chemoheterotroph Signup and view all the answers

Which of the following has components arranged in order of increasing size?

Amino acid < protein < ribosome < mitochondrion Signup and view all the answers

Which of the following is not considered a noncovalent interaction?

Carbon-carbon bonds Signup and view all the answers

Which of the following is not among the four most abundant elements in living organisms?

Phosphorus Signup and view all the answers

What geometry do the four covalent bonds in methane (CH4) form?

Tetrahedral Signup and view all the answers

What functional groups are present on a specific molecule?

Hydroxyl and aldehyde Signup and view all the answers

The macromolecules that serve in the storage and transmission of genetic information are:

Nucleic acids Signup and view all the answers

Stereoisomers that are nonsuperimposable mirror images of each other are known as:

Enantiomers Signup and view all the answers

In a bacterial cell, the DNA is in the:

Nucleoid Signup and view all the answers

A major change occurring in the evolution of eukaryotes from prokaryotes was the development of:

The nucleus Signup and view all the answers

In eukaryotes, the nucleus is enclosed by a double membrane called the:

Nuclear envelope Signup and view all the answers

Except for highly elongated cells, living cells usually have lengths and diameters in the range of:

0.3 um to 100 um Signup and view all the answers

Which group of single-celled micro-organisms has many members found growing in extreme environments?

Archaea Signup and view all the answers

The bacterium E. coli requires simple organic molecules for growth and energy—it is therefore a:

Chemoheterotroph Signup and view all the answers

Which one of the following has the cellular components arranged in order of increasing size?

Amino acid < protein < ribosome < mitochondrion Signup and view all the answers

Which one of the following is not considered a noncovalent interaction?

Carbon-carbon bonds Signup and view all the answers

Which one of the following is not among the four most abundant elements in living organisms?

Phosphorus Signup and view all the answers

The four covalent bonds in methane (CH4) are arranged around carbon to give which one of the following geometries?

Tetrahedral Signup and view all the answers

What functional groups are present on this molecule?

Hydroxyl and aldehyde Signup and view all the answers

The macromolecules that serve in the storage and transmission of genetic information are:

Nucleic acids Signup and view all the answers

Stereoisomers that are nonsuperimposable mirror images of each other are known as:

Enantiomers Signup and view all the answers

The enzyme fumarase catalyzes the reversible hydration of fumaric acid to l-malate, but it will not catalyze the hydration of maleic acid. This is an example of:

Stereospecificity Signup and view all the answers

Humans maintain a nearly constant level of hemoglobin by continually synthesizing and degrading it. This is an example of a(n):

Dynamic steady state Signup and view all the answers

If heat energy is absorbed by the system during a chemical reaction, the reaction is said to be:

Endothermic Signup and view all the answers

If the free energy change ΔG for a reaction is -46.11 kJ/mol, the reaction is:

Exergonic Signup and view all the answers

The major carrier of chemical energy in all cells is:

Adenosine triphosphate Signup and view all the answers

Enzymes are biological catalysts that enhance the rate of a reaction by:

Decreasing the activation energy Signup and view all the answers

Energy-requiring metabolic pathways that yield complex molecules from simpler precursors are:

Anabolic Signup and view all the answers

Hereditary information (with the exception of some viruses) is preserved in:

Deoxyribonucleic acid Signup and view all the answers

When a region of DNA must be repaired by removing and replacing some of the nucleotides, what ensures that the new nucleotides are in the correct sequence?

The new nucleotides basepair accurately with those on the complementary strand Signup and view all the answers

The three-dimensional structure of a protein is determined primarily by:

The sequence of amino acids in the protein Signup and view all the answers

According to Oparin's theory for the origin of life, the prebiotic atmosphere:

Had an abundance of methane, ammonia, and water Signup and view all the answers

What six characteristics distinguish living organisms from inanimate objects?

<ol> <li>Chemically complex and highly organized, 2. Extract, transform, and use energy from their environment, 3. Capacity to self-replicate and self-assemble, 4. Exploit chemical interplay with their environment, 5. Possess programmatically defined functions, 6. Evolve to new forms over generations.</li> </ol> Signup and view all the answers

What is the function of the plasma membrane?

Acts as a barrier to the free passage of inorganic ions and most charged or polar compounds, while allowing specific transport and signal transduction. Signup and view all the answers

How is E. coli determined to be a gram-negative bacterial species?

Gram-negative bacteria have little affinity for the dye gentian violet, while gram-positive bacteria retain it. Signup and view all the answers

How do gram-negative bacteria differ structurally from gram-positive bacteria?

Gram-negative bacteria have an outer membrane and a thinner peptidoglycan layer, while gram-positive bacteria lack an outer membrane and have a thicker peptidoglycan layer. Signup and view all the answers

What is the function of the cell wall in higher plants?

Provides a rigid protective shell and resists swelling while allowing the passage of small molecules. Signup and view all the answers

List the types of noncovalent interactions important for macromolecule stability.

Hydrogen bonds, ionic interactions, van der Waals interactions, hydrophobic interactions. Signup and view all the answers

Why is it important that noncovalent interactions are weak?

Weak interactions can form, break, and re-form rapidly, allowing flexibility in macromolecules. Signup and view all the answers

What is the underlying biochemical principle that accounts for similarity in living organisms?

Living things are composed of macromolecules formed from a few types of simple compounds with diverse sequences. Signup and view all the answers

How are living organisms able to produce particular chiral forms of biomolecules?

Enzymes, which are inherently chiral, lead to the selective production of chiral products. Signup and view all the answers

Why doesn't the number of protein molecules become too great in a living cell?

Proteins are continuously being synthesized and degraded. Signup and view all the answers

Study Notes

Structure of Bacterial Cells

Bacterial DNA resides in the nucleoid.
Eukaryotes evolved from prokaryotes primarily through the development of the nucleus.

Eukaryotic Cell Structure

The nucleus is surrounded by a nuclear envelope, a double membrane.

Size and Dimensions of Cells

Living cells typically measure between 0.3 um to 100 um, influenced by biomolecule functions and diffusion rates.

Micro-organisms and Environments

Archaea thrive in extreme conditions, distinct from typical bacteria.

Nutritional Classification

E.coli is classified as a chemoheterotroph, relying on organic molecules for energy.

Cellular Component Sizes

The increasing size order of cellular components: Amino acid < protein < ribosome < mitochondrion.

Noncovalent Interactions

Key noncovalent interactions maintaining macromolecule structure include hydrogen bonds, ionic interactions, van der Waals interactions, and hydrophobic interactions.
Carbon-carbon bonds are not noncovalent.

Abundant Elements in Organisms

Four most abundant elements in living organisms: Carbon, Hydrogen, Nitrogen, and Oxygen.
Phosphorus is notable but less abundant.

Molecular Geometry

The geometry around carbon in methane (CH4) is tetrahedral.

Macromolecules

Nucleic acids store and transmit genetic information.
Proteins perform diverse functions including catalysis, structure, and signaling.

Optical Activity

Chiral centers refer to asymmetric carbon atoms that cannot be superimposed on their mirror images, leading to stereoisomers.

Enantiomers and Biological Activity

Stereoisomers can have different biological effects; thus, separating enantiomers is crucial for therapeutic efficacy.

Chiral Synthesis

Living organisms produce chiral biomolecules due to the nature of enzymes as chiral catalysts.

Dynamic Steady State

Cells maintain a dynamic steady state through ongoing synthesis and degradation of proteins.

Energy and Matter Exchange

Living organisms are open systems, continually exchanging matter and energy with their environment.

Coupling Reactions

Endergonic reactions can be driven by coupling to exergonic reactions via shared intermediates, yielding an overall exergonic process.

Spontaneous Dissolution and Energy

The formation of cold packs demonstrates a spontaneous reaction where heat is absorbed (endothermic) despite negative free-energy change, explained by significant entropy change during dissolution.

Enzymatic Reactions

Enzymes enhance reaction rates by lowering the activation energy, facilitating biological processes efficiently.

Biological Complexity

Living organisms show chemical complexity and organizational structure that distinguish them from non-living entities, enabling self-replication and evolution over generations.### Reaction Energetics
An exergonic reaction releases energy, characterized by a negative change in free energy (ΔG).
The presence of an enzyme can lower the activation energy, promoting a more efficient reaction pathway.

Feedback Inhibition

Feedback inhibition regulates biochemical pathways by using the end product to inhibit earlier steps.
This mechanism prevents unnecessary energy and resource expenditure in organisms.

Genetic Information and DNA Synthesis

Genetic information is stored in the linear order of four deoxyribonucleotides in DNA.
DNA replication involves unwinding the double helix, where each strand acts as a template for synthesizing a new strand.

Stability and Change in Hereditary Transmission

DNA replication is highly accurate, maintaining stability in genetic information crucial for species characteristics.
Mutations, though infrequent, generate genetic diversity, enabling species adaptation over generations.

Impact of DNA Mutations

Mutations can be detrimental, resulting in nonfunctional proteins or enzymes critical for survival.
Conversely, some mutations create advantageous traits, enhancing function or stability in specific environments.

Stanley Miller's Experiment

Miller's 1953 experiment simulated early Earth conditions, generating organic compounds, including amino acids.
Findings supported the hypothesis of abiotic synthesis of biomolecules in specific environments.

RNA World Hypothesis

RNA molecules likely functioned as both genetic material and catalysts in early life forms.
Over time, some RNA replicated and gave rise to DNA, which became the primary genetic storage.

Evolution of Aerobic Organisms

The emergence of O2-producing bacteria enhanced atmospheric oxygen levels, favoring aerobic organisms.
Aerobic organisms utilize oxygen as an electron acceptor, improving survival compared to anaerobic counterparts.

Endosymbiotic Association

Endosymbiosis describes the mutualistic relationships between primitive eukaryotic cells and engulfed bacteria.
This association led to the development of mitochondria and chloroplasts, enabling aerobic metabolism and photosynthesis in eukaryotic cells.

Organelles and Cell Functions

Common organelles include mitochondria, endoplasmic reticulum, and peroxisomes, essential for cellular processes.
The proteome encompasses all proteins within a cell, while a proteasome functions to degrade unneeded proteins.

Distinct Types of Organisms

Chemoheterotrophs (carnivores and herbivores) obtain energy from organic sources.
Non-covalent interactions such as hydrogen bonds and van der Waals interactions stabilize macromolecular structures.

Cytosol vs. Cytoplasm

Cytoplasm is the entire internal volume of a cell, while cytosol is the aqueous component.
Macromolecule diffusion in cytosol is slower due to crowded, gel-like conditions caused by macromolecular interactions.

Chiral Centers and Optical Activity

Asymmetric carbon atoms, or chiral centers, can lead to stereoisomers that are non-superimposable.
Optical activity is the ability of substances to rotate plane-polarized light, significant in the study of biomolecules.

Dynamic Steady State in Cells

Cells continuously synthesize and degrade proteins, maintaining a balance to prevent overaccumulation.
Living organisms maintain a dynamic interaction with their environment, exchanging energy and matter to sustain life.

Coupling of Reactions

Cells can drive endergonic processes by coupling them with exergonic reactions, creating an overall negative free-energy change.
This principle illustrates the efficiency of cellular energy management through shared intermediates.### Endosymbiotic Association
Endosymbiotic association involves the envelopment of one organism by another, creating a mutually beneficial relationship.
Primitive eukaryotic cells likely formed associations with photosynthetic and aerobic bacteria.
Aerobic bacteria evolved into mitochondria, while photosynthetic bacteria became chloroplasts in modern eukaryotic cells.

Biochemical Reactions

In the reaction to produce gaseous carbon dioxide from bicarbonate, water does not act as a reactant.
An acetate buffer at pH 4.76 maintains its pH when mixed with sodium hydroxide, but the ratio of acetic acid to sodium acetate decreases.
The Henderson-Hasselbalch equation connects pH to pKa and the concentrations of acid and conjugate base.

Cellular Components and Structures

Bacterial DNA is located in the nucleoid.
A key evolutionary advancement from prokaryotes to eukaryotes was the development of the nucleus.
The nucleus in eukaryotes is encased by a nuclear envelope, a double membrane structure.

Cell Dimensions and Microbial Groups

Living cells typically have dimensions ranging from 0.3 µm to 100 µm, determined by minimum biomolecules for function and diffusion rates.
Archaea, a group of single-celled microorganisms, thrive in extreme environments.

Energy and Growth Requirements

E. coli is classified as a chemoheterotroph, requiring simple organic molecules for energy and growth.

Cellular Organization

The hierarchy of cellular components in order of increasing size is amino acid < protein < ribosome < mitochondrion.
Carbon-carbon bonds are not considered noncovalent interactions; other interactions include hydrogen bonds, hydrophobic interactions, ionic interactions, and van der Waals interactions.

Abundant Elements and Molecular Geometries

The four most abundant elements in living organisms are carbon, hydrogen, nitrogen, and oxygen; phosphorus is not among them.
Methane (CH4) exhibits a tetrahedral geometry due to its four covalent bonds around carbon.

Functional Groups and Genetic Information

The molecule in the query contains hydroxyl and aldehyde functional groups.
Nucleic acids are the macromolecules responsible for the storage and transmission of genetic information.

Stereoisomers

Stereoisomers that are nonsuperimposable mirror images are categorized as enantiomers.

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Test your knowledge on the foundational concepts of biochemistry with these flashcards from Chapter 1. Explore key differences between prokaryotes and eukaryotes and other essential terms in the field. Perfect for students seeking to reinforce their understanding of biological molecules.

Biochemistry Chapter 1 Flashcards

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Questions and Answers

Describe the relationship between a living organism and its surroundings in terms of both matter and energy.

How do cells accomplish the formation of a protein from individual amino acids despite it being an endergonic reaction?

Explain how instant cold packs can get cold when the contents are mixed.

What is meant by feedback inhibition and why is it important?

How is genetic information encoded in DNA and synthesized?

Explain the balance between stability and change in hereditary transmission of genetic information.

Discuss how a mutation in DNA could be harmful or beneficial to an organism.

Describe Stanley Miller's experiment (1953) and its relevance.

What is the 'RNA world' hypothesis?

How did the rise of O2-producing bacteria influence aerobic organisms?

What is meant by endosymbiotic association?

Which is a list of organelles?

The catalog of all proteins functioning in a cell is the:

Identify the correct statement: Carnivores are ___ and herbivores are ___.

When two genes in an organism share detectable sequence similarity, they are said to be:

What is the difference between cytosol and cytoplasm?

Explain why macromolecules diffuse slower in cytosol compared to dilute solutions.

Describe the functions of proteins, nucleic acids, polysaccharides, and lipids.

Why is an asymmetric carbon atom called a chiral center?

Differentiate between configuration and conformation.

What is optical activity?

Why is it important for a chemist to separate enantiomers of a racemic mixture?

Explain why living organisms can produce specific chiral forms of biomolecules compared to laboratory synthesis.

Why don't protein molecules in a living cell lead to cell destruction?

What is meant by feedback inhibition and why is it important in a living organism?

How is the genetic information encoded in DNA and how is a new copy of DNA synthesized?

Explain how hereditary transmission of genetic information reflects a balance between stability and change.

How could a mutation in DNA be harmful or beneficial to an organism?

Describe Stanley Miller's experiment (1953) and its relevance.

Describe the 'RNA world' hypothesis.

How might the rise of O2-producing bacteria have led to the predominance of aerobic organisms?

What is meant by endosymbiotic association?

In which reaction does water not participate as a reactant?

When mixing sodium hydroxide with an acetate buffer at pH 4.76, what happens?

What does the Henderson-Hasselbalch equation relate?

Where is DNA located in a bacterial cell?

What was a major change occurring in the evolution of eukaryotes from prokaryotes?

What encloses the nucleus in eukaryotes?

What is the range of lengths and diameters of living cells?

Which group of single-celled microorganisms has many members found growing in extreme environments?

The bacterium E. coli requires simple organic molecules for growth and energy. What is this characteristic?

Which of the following has components arranged in order of increasing size?

Which of the following is not considered a noncovalent interaction?

Which of the following is not among the four most abundant elements in living organisms?

What geometry do the four covalent bonds in methane (CH4) form?

What functional groups are present on a specific molecule?

The macromolecules that serve in the storage and transmission of genetic information are:

Stereoisomers that are nonsuperimposable mirror images of each other are known as:

In a bacterial cell, the DNA is in the:

A major change occurring in the evolution of eukaryotes from prokaryotes was the development of:

In eukaryotes, the nucleus is enclosed by a double membrane called the:

Except for highly elongated cells, living cells usually have lengths and diameters in the range of:

Which group of single-celled micro-organisms has many members found growing in extreme environments?

The bacterium E. coli requires simple organic molecules for growth and energy—it is therefore a:

Which one of the following has the cellular components arranged in order of increasing size?

Which one of the following is not considered a noncovalent interaction?

Which one of the following is not among the four most abundant elements in living organisms?

The four covalent bonds in methane (CH4) are arranged around carbon to give which one of the following geometries?

What functional groups are present on this molecule?

The macromolecules that serve in the storage and transmission of genetic information are:

Stereoisomers that are nonsuperimposable mirror images of each other are known as:

The enzyme fumarase catalyzes the reversible hydration of fumaric acid to l-malate, but it will not catalyze the hydration of maleic acid. This is an example of:

Humans maintain a nearly constant level of hemoglobin by continually synthesizing and degrading it. This is an example of a(n):

If heat energy is absorbed by the system during a chemical reaction, the reaction is said to be:

If the free energy change ΔG for a reaction is -46.11 kJ/mol, the reaction is:

The major carrier of chemical energy in all cells is:

Enzymes are biological catalysts that enhance the rate of a reaction by:

Energy-requiring metabolic pathways that yield complex molecules from simpler precursors are:

Hereditary information (with the exception of some viruses) is preserved in:

When a region of DNA must be repaired by removing and replacing some of the nucleotides, what ensures that the new nucleotides are in the correct sequence?

The three-dimensional structure of a protein is determined primarily by:

According to Oparin's theory for the origin of life, the prebiotic atmosphere:

What six characteristics distinguish living organisms from inanimate objects?

What is the function of the plasma membrane?

How is E. coli determined to be a gram-negative bacterial species?

How do gram-negative bacteria differ structurally from gram-positive bacteria?

Identify the correct statement: Carnivores are _ and herbivores are _.