Biochemistry--chapter 1

What is biochemistry?

Study of biological processes at molecular and cellular levels.

What is the core discipline of life sciences?

Biochemistry.

What is the interface of biology and chemistry?

Biochemistry.

What does biochemistry rely heavily on?

Quantitative analysis of data.

What does biochemistry often study?

In vitro systems (outside a living cell).

What is fermentation?

Conversion of rotting fruit or grain into alcohol solutions through yeast action.

What is the catalyst in fermentation?

Yeast.

What can be produced from yeast fermentation?

Wine and beer.

When did fermentation start?

Around 2000 BC.

Who demonstrated the production of CO2 and CH3CH2OH from sugar using yeast?

Buchner.

What did Buchner propose?

That enzymes help speed up fermentation.

What are catalysts?

Biomolecules that dramatically increase the rate of biochemical reactions.

Where are catalysts found?

In all living cells.

What are some reactions that catalysts are responsible for?

Aerobic respiration, fermentation, nitrogen metabolism, energy conversion, programmed cell death.

What are examples of catalysts?

Proteins or ribonucleic acid (RNA).

What does biochemistry use advanced experimental methods for?

Developing in vitro conditions for exploiting cellular processes and enzymatic reactions.

What is the foundation of the hierarchical perspective of the chemical basis of life?

1. Chemical elements and functional groups.
2. biochemicals
3. macromolecules
4. metabolism
5.cells
6. organisms
7.ecosystems

What are the chemical elements that make up the majority of dry weight in living organisms?

Carbon, nitrogen, oxygen, hydrogen.

What are the percentages of the chemical elements in terms of dry weight?

Carbon (62%), nitrogen (11%), oxygen (9%), hydrogen (6%).

What are some other chemical elements found in living organisms, although in smaller amounts?

Calcium, phosphorus, potassium, sulfur, chlorine, sodium, magnesium, manganese, iron, cobalt, copper, zinc, selenium, molybdenum, iodine, fluorine, chromium, tin.

What are the most common carbon bonds observed in biochemistry?

C-C, C\=C, C-H, C\=O, C-N, C-S, C-O.

How many unpaired electrons does a hydrogen atom have?

1.

How many unpaired electrons does an oxygen atom have?

2.

How many unpaired electrons does a nitrogen atom have?

3.

How many unpaired electrons does a carbon atom have?

4.

What is the molecular geometry of a carbon atom when it forms four single bonds?

Tetrahedron.

Why is rotation around a single bond in carbon-carbon molecules easy?

Due to the sigma bond between the carbon atoms.

What is a double bond?

Includes a pi bond and rotation is not possible without breaking this pi bond.

What are trace elements?

Elements used as cofactors in proteins and required in smaller amounts.

Name some trace elements.

Zinc, Iron, Manganese, Copper, Cobalt.

What are essential ions?

Ions that play a key role in cell signaling and neurophysiology.

Name some essential ions.

Calcium, Chloride, Magnesium, Potassium, Sodium.

What is the role of functional groups?

They play an important role in the structure and function of biomolecules.

What are the four major types of biomolecules?

Amino acids, Nucleotides, Simple sugars, Fatty acids.

What are the primary cellular functions of amino acids?

Building blocks of protein, protein function, neurotransmission, nitrogen metabolism, energy conversion.

What are the primary cellular functions of nucleotides?

Nucleic acid function, energy conversion, signal transduction, enzyme catalysis.

What are the primary cellular functions of simple sugars?

Energy conversion, cell wall structure, cell recognition.

What are the primary cellular functions of fatty acids?

Cell membranes, energy conversion, cell signaling.

What are amino acids?

Nitrogen-containing molecules that function primarily as the building blocks of protein.

How are amino acids linked together?

Covalently linked into a linear chain to form polypeptides.

How do amino acids differ from each other?

They differ by the side chain attached at the central carbon.

What are nucleotides?

They include the nucleic acids DNA and RNA.

What are the components of nucleotides?

Nitrogenous base, five-membered sugar, 1-3 phosphate groups.

Name some examples of nucleotides.

Cytosine, ATP, cAMP, NAD+.

What are simple sugars?

Carbohydrates containing C, H, and O atoms only.

What is the ratio of hydrogen atoms to oxygen atoms in carbohydrates?

2:1

What are the two types of carbohydrates?

Monosaccharides and disaccharides

What are fatty acids?

Amphipathic molecules that act as components of plasma membrane lipids and as a storage form of energy.

What is the structure of fatty acids?

A carboxyl group attached to a hydrocarbon chain.

What is the difference between saturated and polyunsaturated fatty acids?

Saturated fatty acids have no C\=C double bonds, while polyunsaturated fatty acids have multiple C\=C double bonds.

What are macromolecules?

Higher end structural forms of biomolecules, including proteins, nucleic acids, and polysaccharides.

What are the polymers in macromolecules?

Proteins, nucleic acids, and polysaccharides.

What are nucleic acids?

Covalently linked nucleotides, including DNA and RNA.

How are nucleotides linked together in nucleic acids?

By phosphodiester bonds.

What are proteins?

Covalently linked amino acids, also known as polypeptides.

What is the difference between proteins and polypeptides?

Proteins have different amino acid side chains (R groups).

What are polysaccharides?

Mixtures of simple sugars with repeating units of glucose, with covalent linkages between monosaccharide units.

What is the key to the identification and chemical properties of polysaccharides?

The glycosidic bond.

What are some examples of polysaccharides?

starch, glycogen, cellulose, chitin

What are metabolic pathways?

Processes that enable cells to coordinate and control complex biochemical processes in response to available energy.

Where do metabolic pathways function?

Within membrane-bound cells.

Examples of metabolic pathways

photosynthesis and cellular respiration

What are metabolites?

Small biomolecules that serve as both reactants and products in biochemical reactions within cells.

What is metabolic flux?

The rate at which reactants and products are interconverted in a metabolic pathway.

What is the urea cycle?

A metabolic pathway involved in the detoxification of ammonia in the body.

What is a genome?

All encoded genes and other DNA elements specifying genetic composition of cells.

What is the nucleolus?

The site of ribosome assembly.

What are ribosomes?

The location of protein synthesis.

What is glycolysis?

The metabolic pathway that converts glucose into pyruvate.

What is gluconeogenesis?

The metabolic pathway that synthesizes glucose from non-carbohydrate precursors.

What is the citrate cycle?

The metabolic pathway that converts acetyl-CoA into energy-rich molecules.

What is fatty acid oxidation?

The metabolic pathway that breaks down fatty acids for energy.

What is fatty acid biosynthesis?

The metabolic pathway that synthesizes fatty acids from acetyl-CoA.

What is the function of mitochondria?

Responsible for ATP production

What are the functions of peroxisomes and lysosomes?

Involved in macromolecule degradation and detoxification

What is the function of the endoplasmic reticulum?

Sequester ribosomes for protein synthesis

What is the function of the Golgi apparatus?

Involved in protein translocation and protein secretion in the plasma membrane

What is cell specialization?

A higher level of organizational complexity that allows multicellular organisms to exploit their environment through signal transduction

What is signal transduction?

The process by which cells communicate and respond to environmental changes

What are organisms?

A complex organization level that consists of specialized cells and allows multicellular organisms to respond to environmental changes

How do organisms adapt to change?

Through signal transduction mechanisms that facilitate cell-cell communication

What is the circulatory system?

The system responsible for transporting blood and nutrients throughout the body

What are ecosystems?

The highest level of hierarchical organization that includes co-habitation of different organisms in the same environmental niche and involves a shared use of resources and waste management

How do organisms interact with their environment and each other?

Through ecosystems

What is the significance of DNA in viral replication?

DNA was determined to be sufficient to promote viral replication in 1952

What did Rosalind Franklin contribute to the understanding of DNA?

She collected X-ray diffraction data to determine the structure of DNA

What did Watson and Crick discover about DNA?

They determined that DNA is a double helix in 1953

How does DNA pass on genetic material?

The discovery of the double helix structure explained how DNA is used to pass on genetic material

What did Watson and Crick receive the Nobel Prize in Physiology or Medicine for?

They were awarded the Nobel Prize in 1962 for their discovery of the double helix structure of DNA

What are deoxyribonucleotides?

Monomeric units of DNA without -OH on C-2' of ribose sugar.

What are ribonucleotides?

Structurally similar to deoxyribonucleotides, but contain -OH at C-2' position in ribose sugar.

What are the complimentary base pairs in DNA?

G-C and A-T.

What are the complimentary base pairs in RNA?

G-C and A-U.

What does the Central Dogma describe?

Transfer of information between DNA, RNA, and protein.

What is the relationship between DNA and protein?

DNA codes for RNA, which codes for protein.

What is the genome?

Collection of genes.

What is the transcriptome?

Collection of DNA transcripts generated by DNA transcription.

What is the proteome?

Collection of proteins produced by mRNA translation.

What determines the function of DNA?

Structure.

How do proteins acquire different molecular structures?

Through random mutations.