Biochemistry Chapter 1 Flashcards

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.

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.