Biochemistry Exam 4 Flashcards

Components of a nucleotide

Phosphate group, Pentose sugar (ribose or deoxyribose), Nitrogenous base

Difference between ribose and deoxyribose

Ribose has an -OH group on the 2' carbon; deoxyribose has an -H.

Purines

Adenine (A) and Guanine (G)

Pyrimidines

Cytosine (C), Thymine (T), and Uracil (U)

Base found only in DNA

Thymine (T)

Base found only in RNA

Uracil (U)

Bonds in a nucleotide

Phosphoester bond, N-glycoside bond, Phosphoanhydride bond

Structure of DNA

Double-stranded, antiparallel helix stabilized by hydrogen bonds and base stacking.

Structure of RNA

Single-stranded, found in nucleus and cytoplasm.

Types of RNA

mRNA, tRNA, rRNA

Central Dogma

DNA -> RNA -> Protein (Replication, Transcription, Translation)

Stabilization of separated DNA strands during replication

Single-strand binding proteins

Codon

Three-nucleotide sequence on mRNA that codes for an amino acid.

Anticodon

Complementary sequence on tRNA to a codon on mRNA.

Recombinant DNA

DNA formed by combining DNA from two different sources.

Types of metabolic pathways

Linear, Spiral, Circular

Catabolism

Breaking down molecules to release energy.

Anabolism

Building up molecules using energy.

Fats digestion location

Small intestine

Carbohydrates digestion location

Mouth and small intestine

Proteins digestion location

Stomach and small intestine

Glycolysis location

Cytoplasm

Important regulatory steps of glycolysis

Steps 1, 3, and 10

End products of glycolysis

2 pyruvate, 2 ATP (net), 2 NADH

Pyruvate under aerobic conditions

Converted to Acetyl-CoA and enters the Citric Acid Cycle.

Pyruvate under anaerobic conditions

Converted into lactic acid (humans) or alcohol (yeast).

Gluconeogenesis

Synthesis of glucose from non-carbohydrate sources.

Citric Acid Cycle location

Mitochondrial matrix

Main products of the Citric Acid Cycle

3 NADH, 1 FADH2, 1 GTP (per Acetyl-CoA)

Electron transport chain location

Inner mitochondrial membrane

Final electron acceptor in the electron transport chain

Oxygen

ATP synthesis driver in oxidative phosphorylation

Proton gradient

Activation of β-oxidation

Attachment of CoA to fatty acids.

Products of one β-oxidation cycle

1 Acetyl-CoA, 1 NADH, 1 FADH2

Production of ketone bodies

To provide an alternative energy source during low carbohydrate availability.

Risks of high ketone body levels

Ketoacidosis

Reactions involved in amino acid catabolism

Transamination and Oxidative deamination

Glucogenic amino acids

Amino acids that can be converted into glucose.

Ketogenic amino acids

Amino acids that can be converted into ketone bodies.

What are oxidation-reduction (redox) reactions?

Chemical reactions where electrons move from a donor to an acceptor; fuels are stripped of electrons during oxidation.

What are ATP and ADP known for in metabolism?

They act as energy exchange tokens; energy is stored in the phosphate bonds.

What are electron carriers in metabolism?

NADH and FADH₂ are electron carriers that shuttle electrons during redox reactions.

What happens to large molecules during digestion?

They are broken down into building blocks: triglycerides → fatty acids, carbohydrates → monosaccharides, proteins → amino acids.

Where does fatty acid oxidation occur?

mitochondrial matrix

What is the primary purpose of fermentation?

To replenish the pool of NAD⁺ so glycolysis can continue under anaerobic conditions.

In glycolysis, what happens during steps 1-5?

Energy-requiring phase where 1 glucose is broken into 2 glyceraldehyde-3-phosphate molecules, using 2 ATP.

In glycolysis, what happens during steps 6-10?

Energy-releasing phase producing 2 pyruvates, 4 ATP, and 2 NADH.

What happens to pyruvate under aerobic conditions?

It crosses the mitochondrial membrane and is converted into Acetyl-CoA.

What happens to pyruvate under anaerobic conditions?

It is converted into lactate, which can later be recycled into glucose by the liver.

What is the net energy yield from fermentation of two pyruvates?

2 ATP

What type of organism can switch between fermentation and aerobic respiration?

Facultative anaerobes.

Why is gluconeogenesis not simply the reverse of glycolysis?

It uses different enzymes at the irreversible steps (1, 3, and 10 of glycolysis).

What are the main precursors for gluconeogenesis?

Amino acids, glycerol, and lactate.

Where does gluconeogenesis mainly occur?

In the liver.

What controls entry into the Citric Acid Cycle?

Conversion of pyruvate into Acetyl-CoA.

What is the role of the electron transport chain?

To transfer electrons from NADH/FADH₂ to oxygen, pumping protons and creating a gradient for ATP synthesis

What enzyme produces ATP during oxidative phosphorylation?

ATP synthase.

How much ATP is produced per glucose molecule under ideal conditions?

About 36-38 ATP.

How are fatty acids transported into the mitochondria for oxidation?

They are attached to coenzyme A and moved into mitochondria via carnitine.

What are the 4 steps of the β-oxidation spiral?

Repeated removal of 2-carbon units as Acetyl-CoA with generation of NADH and FADH₂.

How many ATP are produced from one full oxidation of a fatty acid (e.g., palmitic acid)?

Approximately 131 ATP.

What are examples of ketone bodies?

Acetoacetate, 3-hydroxybutyrate, and acetone.

What are signs of ketosis?

Odor of acetone on the breath and presence of ketone bodies in urine and blood.

What condition can result from high levels of ketone bodies?

Ketoacidosis (drop in blood pH).

What is the ATP production hierarchy for macronutrients?

Fats > Sugars > Proteins.

How much of human DNA codes for proteins?

About 5%

What is the purpose of telomeres?

They protect the chromosome ends from deterioration during replication.

What is semiconservative replication?

Each original DNA strand serves as a template for a new strand.

What enzyme glues DNA fragments together during replication?

DNA Ligase.

What is the role of single-strand binding proteins (SSBs)?

They stabilize and protect single DNA strands during replication.

What are the three types of RNA and their functions?

mRNA (carries code), tRNA (brings amino acids), rRNA (forms ribosomes)

What establishes the reading frame during translation?

The start codon AUG.

What is translocation during translation?

Ribosome shifts 3 nucleotides toward the 3' end after peptide bond formation.

What happens during post-translation modification?

Polypeptides are trimmed, cut, and folded into active proteins.

What is an operon?

A group of genes under control of one promoter site (example: lac operon).

What are the genes of the lac operon and what do they code for?

lacZ (β-galactosidase), lacY (lactose permease), lacA (transacetylase).

What is a mutation?

A permanent change in the DNA sequence

What is recombinant DNA?

DNA created by combining sequences from two or more sources.

What is the purpose of PCR (polymerase chain reaction)?

To amplify small DNA samples for analysis.

What enzyme allows PCR to work at high temperatures?

Heat-resistant DNA polymerase.