Chapter 1: Principles of Biochemistry

The birth of modern biochemistry can be traced to the

end of the 19th century

The study of biochemistry attempts to explain

biological processes at the molecular and cellular level.

Enzymes function as reaction catalysts in cells. If the enzymes were removed from a cell, the

rate of biochemical reactions would

decrease

The essential ions calcium, magnesium, potassium, and sodium are all

cations

Given that methane (CH4) has a bond angle of 109.5° and ethylene (C2H2) has a bond angle of

120°, what is the correct bond angle for acetylene (C2H2)?

180°

Amino acids are the building blocks for which biomolecule(s)?

proteins

The __________ differentiates amino acids from one another.

side chains attached to the central carbon

A nucleotide consists of

nitrogenous base, five-membered sugar and phosphate groups

Simple sugars are made of

carbon, oxygen, and hydrogen

If energy in the form of ATP is required to make a polymeric macromolecule, what will happen if there is no ATP available?

The polymer is broken down to release ATP.

Why are fewer polypeptide sequences encountered biologically than are theoretically possible?

Not all have useful structural and functional properties.

Humans do not have the enzyme cellulase. Is it likely that a human could survive on a

plant-only diet?

No, not enough ATP would be produced to generate energy.

Which two functional groups are involved in producing a peptide bond?

amino and carboxyl

Even though amylose and cellulose contain the same repeating unit of glucose, they are very different in terms of function. Why?

The orientations of the glycosidic bond are different

The correct definition of a pathway intermediate is a molecule that

is both a product and a reactant in a pathway.

Plasmids are small, circular DNA molecules that are used in which of the following?

a. gene cloning

b. production of chromatin

c. cell movement

d. replication of nucleus

gene cloning

What is the function of the chloroplast in a plant cell?

conversion of light energy to chemical energy

If a plasma membrane is hydrophobic, what kinds of amino acids are MOST likely to be found in the membrane?

hydrophobic amino acids

When a ligand binds to a receptor, it causes the receptor to

activate

How does the molecule adenosine monophosphate fit into the seven hierarchical levels that define the chemical basis of life?

biomolecule

The main difference between deoxyribonucleotides and ribonucleotides is that they have

a different

functional group on the 2′ carbon.

A hydrogen bond can best be described as a

weak noncovalent interaction.

Why can a guanine not be paired with adenine?

Guanine can form three hydrogen bonds and adenine can form two.

What structural feature of DNA is attributed to the fact that the two DNA strands are

antiparallel?

DNA is a right-handed helix.

The "central dogma of molecular biology" can best be described as the transfer of information

between

nucleic acids and proteins.

A segment of DNA containing 20 base pairs includes 8 adenine residues. How many uracil

residues are present?

0

A genome is a set of

genes

Given a DNA sequence of 3′-CAT-5′, what is the complementary sequence in mRNA?

5′-GUA-3′

Who received the Nobel Prize in 1962 for elucidating the molecular structure of DNA?

Maurice Wilkins, James Watson, and Francis Crick

A single nucleotide base substitution in a wild-type DNA is an example of

random mutation

An inherited disease comes from the mutation of DNA in a __________ cell.

germ-line

The RNA world model is based on the hypothesis that __________ is stable.

DNA

Bioinformatics shows that 98% of human DNA is identical to that of chimpanzees. If human

DNA contains 3.2 billion nucleotides, how many nucleotides are different between the two

species?

64 million

Highly conserved gene sequences that encode proteins with the same function in different

organisms are called __________ genes.

orthologous

If a mutation was made to the gene for glucose-6-phosphate dehydrogenase that prevented it

from functioning, a possible outcome would be the production of

less NADPH

The appearance of new gene speciation is an example of

gene singulation

The amino acid sequence of a protein determines its structure. Which of the following

statements is true?

a. Two proteins with similar amino acid sequence should have similar structures.

b. Two proteins with different amino acid sequences will have identical structures.

c. Two proteins with similar amino acid sequences will always have the same function in

a cell.

d. It is impossible to determine how proteins will fold based on the amino acid sequence

alone.

Two proteins with similar amino acid sequence should have similar structures

Which of the following is NOT a common functional group?

a. COOH

b. CH3

c. SH

d. CHO

CHO

By convention, nucleic acid chains are written starting at the __________ end.

5'

The proposal that DNA is a double helix was based on what experimental evidence?

x-ray crystallography

mRNA is used for what process in the cell?

as a template for protein synthesis

In DNA the phosphate groups are on the outside of the helix. Why does this stabilize the

structure?

ionic interactions with the solvent

What is the cause of the overall negative charge of a molecule of DNA?

the phosphate backbone

Mutations to proteins typically occur starting

with DNA

Hydrogen bonds form between hydrogen and

oxygen

The DNA double helix is stabilized by the interactions between nucleotides because of

__________ between nucleotides.

pi-pi stacking

In structures of tRNA, base pairs form between

the same strand

Ribose is a

five-carbon sugar

The process of fermentation uses sugar to produce which molecules?

alcohol and carbon dioxide

An example of experimental biochemistry is trying an experiment and

optimizing experimental design

What side products of pyruvate are being converted into alcohol and carbon dioxide by yeast?

CO2 and NAD+

Pyruvate decarboxylase converts pyruvate into

carbon dioxide and acetaldehyde

Which of the following is an example of a metabolic pathway?

glycolysis

Which of the following is an example of an ecosystem?

forest

A requirement for a covalent bond to form between two atoms is that

there are unpaired electrons on each atom.

What is the maximum number of covalent bonds a carbon atom can make?

4

The correct name for the VSEPR arrangement around a carbon in methane is

tetrahedral

Cell signaling and cell membranes are examples of functions performed by which biomolecule?

fatty acid

ATP is an abbreviation for which energy currency molecule?

adenosine triphosphate

Which of the following is the correct formula for glucose?

C6H12O6

What is another way to describe the amphipathic nature of a fatty acid?

polar head and nonpolar tail

Triacylglycerols are neutral molecules made of

three fatty acid esters covalently linked to glycerol

Proteins are a polymer of __________, whereas nucleic acids are polymers of __________.

amino acids; nucleotides

Vitamin B2 is a metabolite. Lack of vitamin B2 can lead to blurred vision and a swollen tongue.

Vitamin B2 has such a strong effect on health because metabolites

are the catalysts that drive biochemical reactions necessary for life-sustaining

processes.

Cyclic pathways contain several metabolites that regenerate during each turn of the cycle.

Another way to describe a metabolite is that it functions as a

reactant or product.

Enzymes and chromosome are found where in the bacterial cell?

cytoplasm

What does chromatin in eukaryotic nucleus contain?

DNA packaged with proteins.

The function of chloroplasts in plant cells is to convert

light energy to chemical energy.

What process replicates DNA to make more DNA?

DNA replication

What process converts DNA to RNA?

DNA transcription

What process describes using mRNA templates to produce proteins?

mRNA translation

What are the three biochemical principles that together provide a framework for

understanding life at the molecular level? How are they interrelated?

answer found in introduction

Hierarchical organization of biochemical processes within cells, organisms, and ecosystems

underlies the chemical basis of life on Earth. DNA is the chemical basis for heredity and

encodes the structural information for RNA and protein molecules, which mediate biochemical

processes in cells. The function of a biomolecule is determined by its molecular structure,

which is fine-tuned by evolution through random DNA mutations and natural selection. These

processes cannot function without each other.

List three examples of how biochemistry has made advancements in the lives of many

humans.

A list can be found in Section 1.1 of the book

Examples include developing new

pharmaceutical drugs, diagnostic tests, improved detergents, and faster ripening of fruit and

vegetables.

Which six elements make up 97% of the weight of most organisms?

Section 1.2

Hydrogen, oxygen, carbon, nitrogen, phosphorus, and sulfur

What functions can polysaccharides perform?

Section 1.2

They provide structural support to cells and energy storage.

What is an advantage of using polypeptides for storage and information transmission?

Section 1.2

The complexity of monomeric units forms a stable arrangement that is perfect for

information storage and transmission.

Explain how a linear pathway is different from a forked pathway

Section 1.2

In a linear pathway, a reaction generates only one product that is then used in the next

reaction. In a forked pathway, two products are produced that each enter a different metabolic

pathway.

Compare and contrast at least three different characteristics of prokaryotic and eukaryotic cells.

Section 1.2

Prokaryotes are often 1 μm in diameter, their cytoplasm contains all the enzymes and

chromosomes, and they have flagella and pili. Eukaryotic cells are 10 to 100 μm in diameter,

chromatin is contained in the nucleus, and they have a cytoskeleton.

Name four organelles found in a eukaryotic cell.

Section 1.2

Many answers are correct including the following: lysosome, smooth endoplasmic reticulum,

rough endoplasmic reticulum, ribosomes, peroxisome, mitochondria, nucleus, Golgi apparatus,

and cytoskeleton.

Name the three components of a nucleotide

Section 1.3

Nucleotide base, five-carbon ribose, and one or more phosphate groups

Compare and contrast the bases found in DNA and RNA.

Section 1.3

DNA is composed of the deoxyribonucleotides (lacking an hydroxyl group on the 2′ position

of ribose) guanine, cytosine, adenine, and thymine. RNA is composed of ribonucleotides

(containing an hydroxyl group on the 2′ position of ribose) guanine, cytosine, adenine,

and uracil.

Define the central dogma of molecular biology.

Section 1.3

The central dogma of molecular biology describes how genetic information stored in DNA is

used to direct the biological processes in cells.

Compare and contrast a transcriptome and a proteome.

Section 1.3

Although both transcriptomes and proteomes are collections of genetic material, a collection

of DNA transcripts (RNA products) generated by DNA transcription is called a transcriptome,

whereas a proteome is the collection of proteins produced by mRNA translation.

Differentiate between germ-line cell mutations and somatic cell mutations.

Section 1.4

Although both are mutations in DNA, if the mutation is passed from the parent to the

offspring, then the mutation is contained within the DNA of a germ-line cell. If the DNA

mutation occurs during the lifetime of the organism in a somatic cell, then this disease is

limited to that individual organism.

Differentiate between orthologous genes and paralogous genes.

Section 1.4

Orthologous genes are highly conserved gene sequences that encode proteins with the same

function in different organisms and are believed to have arisen from a common ancestral gene.

Paralogous genes are related genes within a species. Paralogous genes have orthologous genes

in other species.

Evaluate the following statement: Two amino acid sequences with high sequence conservation

must have the same function in an organism.

Section 1.4

Although two amino acid sequences with high sequence conservation may have the same

structure, it does not mean that those two proteins will perform the same function in a body.

As is shown in Figure 1.30, similar structures may have different function.

Describe the difference between a deoxyribonucleotide and a ribonucleotide

Section 1.2

Deoxyribonucleotides are monomeric units of DNA and lack a hydroxyl group on the carbon

on the 2′ position, whereas a ribonucleotide does have a hydroxyl group on the carbon on the

on the 2′ position.

Give an example of each of the following: element, biomolecule, macromolecule, metabolism,

cell, organism, and ecosystem

Section 1.2

Any element from the periodic table is acceptable;

Biomolecules: amino acids, nucleotides, simple sugars, fatty acids;

Macromolecules: DNA/RNA, proteins, carbohydrates;

Metabolism: glycolysis, citrate cycle, urea cycle;

Cells: cell wall, plasma membrane, organelles;

Organisms: trees, mammals, fish, bird, insects;

Ecosystems: rivers, islands, forest, desert.

Amino acids are the building blocks of proteins. There are 20 amino acids; how do these amino

acids differ from one another?

Section 1.2

Amino acids differ from one another in the side chain attached to the central carbon.

Describe the differences between the structures of pyrimidine and a purine.

Section 1.3

A pyrimidine is an aromatic molecule with nitrogen at positions 1 and 3 on the ring, along

with a carbonyl at position 4. Examples of pyrimidines are cytosine, thymine, and uracil. A

purine is a heterocyclic aromatic molecule with nitrogen at positions 1, 3, 7, and 9. Examples

of purines are guanine and adenine.

What is the function of mRNA in the cell?

Section 1.3

mRNA is used as templates for protein synthesis in a process referred to as mRNA translation.

If you were a biochemist who just discovered a new protein, how would you gain insight into

the function of the protein?

Section 1.4

One way to gain insight into the function of a protein is to compare its amino acid sequence to

those of other proteins to see if conserved regions appear that might suggest an important

function. This is done using the genetic code to convert the DNA sequence in the coding stand

of a gene into the inferred amino acid sequence of the encoded protein.