Biology Chapter on Membrane Proteins

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Questions and Answers

Which type of proteins are primarily responsible for transporting solutes against their concentration gradient?

Receptor proteins

Structural proteins

Channel proteins

Carrier proteins (correct)

In facilitated diffusion, what kind of substances need assistance to cross the membrane?

Gases like oxygen

Small non-polar substances

Hydrophilic substances (correct)

Lipophilic substances

What two forms of energy can power active transport?

Mechanical energy and diffusion gradients

ATP hydrolysis and coupling of gradients (correct)

Passive diffusion and ATP synthesis

Light energy and chemical gradients

What characterizes the structure of proteins that span membranes with alpha helices?

They contain predominantly hydrophobic side chains. Signup and view all the answers

What distinguishes simple diffusion from facilitated diffusion?

Facilitated diffusion uses protein channels. Signup and view all the answers

How do the K+ and Na+ channels differ in their ion transport?

K+ channels allow ion flow in one direction only. Signup and view all the answers

What is the primary role of carrier proteins?

To transport molecules against a concentration gradient. Signup and view all the answers

In active transport, what is true about the net flow of ions through an ion channel?

It depends on the concentrations on both sides. Signup and view all the answers

In which diseases are mitochondrial DNA mutations believed to play a significant role?

Parkinson’s Disease Signup and view all the answers

What is the primary consequence of shunting pyruvate to lactate during oxidative phosphorylation?

Increased cellular acidosis Signup and view all the answers

Which component is NOT part of a nucleotide in DNA?

Amino acid Signup and view all the answers

What are the two subunits that make up a ribosome?

A large and a small subunit Signup and view all the answers

What type of bonds link nucleotides in a polynucleotide chain?

Covalent phosphodiester bonds Signup and view all the answers

Which of the following best describes the mitochondrial DNA (mtDNA)?

Involved in protein synthesis for respiration Signup and view all the answers

What is the function of tRNA during protein synthesis?

To carry specific amino acids to the ribosome Signup and view all the answers

Which binding sites are present on the ribosome for tRNA?

A site and P site Signup and view all the answers

What is a significant characteristic of nuclear DNA compared to mitochondrial DNA?

Nuclear DNA contains introns Signup and view all the answers

What initiates protein synthesis on the mRNA?

The binding of the start codon AUG with its corresponding tRNA Signup and view all the answers

Which of the following processes is NOT involved in the formation of functional proteins from DNA?

Replication Signup and view all the answers

Which tissues may exhibit cellular acidosis due to anaerobic ATP production?

CNS, heart, and skeletal muscle Signup and view all the answers

What is the role of the enzyme peptidyl transferase in protein synthesis?

To catalyze the formation of peptide bonds between amino acids Signup and view all the answers

What stops the addition of amino acids during protein synthesis?

The presence of a stop codon on the mRNA Signup and view all the answers

Which structure in the tRNA carries the specific amino acid?

Amino acid binding site Signup and view all the answers

How are amino acids added to the growing polypeptide chain during translation?

Through the formation of peptide bonds Signup and view all the answers

What is the function of DNA ligase during DNA replication?

It joins Okazaki fragments by forming phosphodiester bonds. Signup and view all the answers

What is the form of DNA that is suitable for distribution into daughter cells during mitosis?

Chromosomes Signup and view all the answers

Which processes are involved in gene-regulated protein synthesis?

Transcription and Translation Signup and view all the answers

What role do general transcription factors play in transcription?

They bind to the promoter region to initiate transcription. Signup and view all the answers

What is the approximate length of mitochondrial DNA (mtDNA)?

16,569 base pairs Signup and view all the answers

How many genes are encoded by the mitochondrial DNA?

37 genes Signup and view all the answers

What is the primary function of genes within DNA?

To direct the synthesis of specific proteins. Signup and view all the answers

What is the primary method of mitochondrial DNA inheritance?

Maternal inheritance Signup and view all the answers

Which type of RNA is involved in carrying the genetic message from DNA to the ribosome?

Messenger RNA (mRNA) Signup and view all the answers

What distinguishes mitochondrial DNA transcription from nuclear DNA transcription?

Termination codons are created post-transcriptionally Signup and view all the answers

What replaces thymine in messenger RNA?

Uracil Signup and view all the answers

What is the function of Twinkle helicase in mitochondrial DNA?

To unwind DNA Signup and view all the answers

What is the consequence of improper regulation of transcription factors?

Increased synthesis of non-specific proteins. Signup and view all the answers

What factor is increasingly recognized as a major contributor to ageing and degenerative diseases?

Mitochondrial dysfunction Signup and view all the answers

What percentage of mitochondrial DNA is considered junk DNA?

2% Signup and view all the answers

What happens once mitochondrial DNA copies reach a certain threshold of damage?

Cellular dysfunction occurs Signup and view all the answers

What type of bond forms between the 5ʹ phosphate of one nucleotide and the 3ʹ carbon of another nucleotide?

3ʹ-5ʹ phosphodiester bond Signup and view all the answers

What structural feature characterizes the strands of DNA?

They are antiparallel in direction. Signup and view all the answers

Which statement best describes histones?

They are proteins that compact DNA. Signup and view all the answers

What is the primary function of telomeres?

To protect chromosomes from degradation. Signup and view all the answers

What do nucleosomes consist of?

DNA wrapped around histones. Signup and view all the answers

In the context of the cell cycle, what role does DNA replication play?

It occurs before cellular division. Signup and view all the answers

What is a gene?

A segment of DNA that encodes a polypeptide. Signup and view all the answers

How do the oxygen atoms of the deoxyribose chains affect DNA structure?

They contribute to the double helix shape. Signup and view all the answers

Study Notes

Nutritional Biochemistry

Course details: DIET413/BHCS1019
Lecturer: Dr Nathaniel Clark FHEA RNutr MRSB
Email: [email protected]

Questions

Question 1: Proteins spanning the membrane with alpha helices contain amino acid side chains central to their complex structure.
Question 2: Transport proteins moving solutes against a concentration gradient are carrier proteins, not channel proteins. This is because carrier proteins change shape to move solutes, while channel proteins have a fixed pore through which solutes passively flow.
Question 3: Simple diffusion involves movement of a substance from high to low concentration across a membrane, while facilitated diffusion utilizes proteins to aid the movement, also from high to low concentration.
Question 4: Active transport uses two forms of energy: ATP and electrochemical gradients.
Question 5: Na+ and K+ channels, despite similar structures and arrangement, allow sodium and potassium to flow in opposite directions. This is because the channels have different 'gates' within their structures controlled by changes in voltage, leading to differences in ion passage.

Learning Outcomes

Outcome 1: Describe the structure of DNA and its organization in the nucleus.
Outcome 2: Describe the process of DNA replication.
Outcome 3: Outline the transcription and translation of a gene into a protein.
Outcome 4: Briefly outline the structure, control and role of mtDNA and linked diseases.

Genes and Genetics

Humans have 100 trillion cells in their body, with 46 chromosomes in each cell nucleus (except red blood cells).
Chromosomes are arranged in 23 pairs.
Each chromosome pair derives one chromosome from each parent.
Genes are sections of DNA that contain the codes for making proteins

The Genome

Every cell contains the same genetic information.
The genome controls biochemical activity within cells.
Genes are inherited between generations, passed on from parent to offspring.
The human genome was sequenced in 2003.
Approximately 20,000-21,000 genes are present.
Only 0.1% of human genes make up differences between individuals.

The Structure of DNA

The genome is made up of DNA.
DNA is a polymer of nucleotides (monomers).
DNA's structure is a double helix, resembling a twisted ladder.
The helix's width is 2 nanometers, with 10.5 steps per 3.4 nanometers.
The double helix structure's 'rungs' are formed by base pairs, specifically Adenine with Thymine, and Cytosine with Guanine.

DNA Methylation

DNA methylation is a process where methyl groups attach to cytosine bases in DNA.
This process can affect gene expression.
DNA demethylation removes methyl groups.

Nucleosides

Nucleosides consist of a sugar molecule and a nitrogenous ring.
These molecules are attached through a bond connecting the anomeric carbon of the sugar to a nitrogen atom in the ring.
Examples of nitrogenous rings are purines (adenine and guanine) and pyrimidines (thymine and cytosine).

Nucleotide Structure

Nucleotides are composed of a phosphate group, a sugar molecule (deoxyribose in DNA; ribose in RNA), and a nitrogenous base.
Nucleotides are linked through phosphodiester bonds, to form the backbone of DNA and RNA.
The sugar is a 5-carbon pentose.
The 2'-deoxyribose in DNA.
The 2' carbon in RNA is ribose with a hydroxyl (-OH) group

Hydrogen Bonding Between Bases

Adenine only bonds to Thymine (A-T)
Guanine only bonds to Cytosine (G-C)
In DNA hydrogen bonds connect the bases in complementary pairs in an anti-parallel configuration

Polynucleotides

Nucleotides link to form polynucleotides—structural units of DNA
The 5' phosphate of one nucleotide forms a bond with the 3' carbon of the next nucleotide.
Removing the OH from the 3' carbon forms the phosphodiester bond
The bond formed is a phosphodiester bond
The formation of the phosphodiester bond creates a phosphate-sugar backbone for the polynucleotides chain.

The DNA Double Helix

The deoxyriboses and their binding to bases give DNA its characteristic double helix shape
The DNA strands run in opposite directions (3' and 5') - antiparallel, and the oxygen of the ribose is above the carbon on one strand and below on the other.
The characteristic DNA structure (i.e., its directionality) is required for the processes of replication and transcription.

Histones, Chromatin and Chromosomes

DNA is compacted for storage in proteins.
DNA is first wrapped around specific histone proteins, forming nucleosomes.
Histones are chemically modified by enzymes to regulate gene transcription.
Nucleosomes condense into a chromatin fibre.
Chromatin, in turn, condenses to form chromosomes.

Structure of Genes

Genes are discrete segments of DNA.
Genes encode the amino acid sequence for a polypeptide.
The basic unit of inheritance responsible for physical characteristics.
Genes are located on chromosomes in bands.
Chromosome ends (telomeres) cap the ends of chromosomes.
Telomeres consist of repetitive elements, protecting chromosomes from degradation and fusion.

The Cell Cycle

DNA replication is part of the cell cycle.
The cycle encompasses the time a cell takes to divide into two daughter cells.
The G1 phase involves an increase in the cell's cytoplasm and organelles.
DNA is precisely duplicated in the S phase of the cell cycle
Further growth of the cell and organelles occurs during G2 Phase
Mitosis and cell division occur in the M phase.

Cell Cycle Checkpoints

Three checkpoints control the cell cycle:
- Cell Growth Checkpoint (G1)
- DNA Synthesis Checkpoint (S)
- Mitosis Checkpoint (M)

DNA Replication

DNA replication is the process of creating identical copies of a DNA molecule.
Each chromosome replicates DNA.
The double helix is unwound before synthesis of complimentary daughter strands on each parent strand.

DNA Replication - Unzipping

DNA separation is achieved by a helicase enzyme.
DNA replication occurs at defined origins where A-T base pairs are more prevalent.
DNA polymerase requires a short double stranded region to start synthesis—a primer—synthesised by RNA primase.

DNA Replication - Replication Fork

The location of the DNA unwinding is called the replication fork.
DNA polymerase only synthesizes DNA in the 5'->3' direction.
The two strands of DNA run in opposite directions (5'→3' and 3'→5').
This requires slightly different mechanisms.

DNA Replication - Leading/Lagging Strands

The leading strand is copied in the same direction as the unwinding.
The lagging strand is synthesized discontinuously opposite to the growing fork.
This lagging strand consists of fragments called Okazaki fragments.

DNA Replication - Lagging Strand

Synthesis ends when a new RNA primer is encountered.
RNA polymerase (different than the replicating one) removes the RNA primer and incorporates DNA instead.
Okazaki fragments need to be joined together by DNA ligase.
The daughter DNA strands are complementary to the original template DNA.

DNA Replication - Storage

Following replication, DNA is organized into chromosomes.
Chromosomes are the structures that organize the DNA for cell division.
DNA needs to be in a structure that facilitates separation into two cells.

From Genes to Proteins

Each DNA molecule is made up of several genes.
Each gene is a segment of the DNA molecule.
Genes direct the synthesis of very specific proteins.
Synthesis of proteins involves processes: transcription and translation

Transcription

Genes are segments of DNA containing genetic code to build proteins.
In transcription, genetic code in DNA is copied into mRNA (a messenger molecule), based on complementary base pairing.
This mRNA carries genetic information to ribosomes.
Uracil is present instead of thymine in RNA.

Initiation of Transcription - TFs

Transcription starts with specific proteins associated with DNA- general transcription factors (GTFs).
Associated with DNA sequences called promoters— where transcription begins.
The proteins control how often a gene is transcribed.
Transcription factors include binding sites for hormones and messengers which initiate transcription

Initiation of Transcription - Other Regions

Transcription is influenced by enhancers which can be distant from the starting point—general transcription factors
The TATA box is a short DNA sequence within a promoter.

Chain Initiation

The enzyme RNA polymerase is responsible for assembling the bases into an RNA molecule.
RNA synthesis initiation begins at the transcription start site and continues by adding nucleotides.
The nucleotides added are based on the template strand, using complementary base pairs

Chain Elongation

DNA acts as a template for RNA synthesis.
RNA polymerase aligns nucleotides in the 5' to 3' direction.
RNA polymerase moves along the 3' end of the DNA template.

Chain Termination

RNA transcription is terminated at a specific sequence—terminator sequence.
The RNA polymerase detaches from DNA.
Newly synthesized RNA transcript is released

Post-transcriptional Modification

Initial RNA transcripts contain introns and exons.
Introns need to be removed (mRNA splicing) to produce mature mRNA.
Exons are protein-coding sequences.

Translation

mRNA contains the genetic code for producing a protein.
Translation is carried out in ribosomes.
Ribosomes bind to mRNA, and transfer RNA (tRNA) delivers amino acids, according to the codons in mRNA.
Amino acids join together in sequence, based on mRNA codons.

Ribosomes

Ribosomes are the sites of protein synthesis.
mRNA passes through the ribosome to incorporate amino acids based on a triplet code (codon).

Transfer RNA (tRNA)

tRNA molecules carry specific amino acids.
They bind to the mRNA codons with their anticodon sequence.
tRNA has a 'clover leaf structure' with an amino-acid binding site and an anticodon.

The Triplet Code

mRNA codons are in a three base format
Each codon codes for a specific amino acid.
The triplet code consists of 64 possible codons (4 x 4 x 4)
Many codons code for the same amino acid (redundancy).

Elongation Peptide Chain

mRNA codons specify amino acids to be added to a growing polypeptide chain.
Following the start codon binding, tRNA binds to the adjacent codon on mRNA.
Enzyme (peptidyl transferase) facilitates the joining of amino acids, and the tRNA leaves to collect another amino acid.

Termination

The addition of amino acids continues until a stop codon appears on the mRNA.
Completed polypeptide is released.
Ribosome detaches from the mRNA.

Mitochondrial DNA (mtDNA)

mtDNA is the DNA located within mitochondria, not the nucleus.
mtDNA is responsible for energy production (ATP).
mtDNA contains 37 genes, including parts involved in oxidative phosphorylation.
mtDNA is a circular double-stranded DNA molecule.
mtDNA exists as multiple copies in the mitochondria

mtDNA Replication

mtDNA replication is similar to nuclear DNA replication but is controversial regarding the timing of lagging strand production.
Two replication theories: strand-asymmetric and strand-coupled.

mtDNA Transcription and Replication

The basal mechanism for mtDNA transcription is similar to that of nuclear DNA though it uses 3 specific proteins
- Mitochondrial RNA polymerase
- A helicase (called twinkle) that unwinds DNA
- A mitochondrial single-stranded DNA binding protein

mtDNA Replication Differences

There are no introns, few non-coding bases between genes
No termination codons
Polyaadenylation

Mitochondrial Disease

Mitochondrial dysfunction is increasingly recognized as a major factor in ageing and age-related diseases.
mtDNA can be damaged by free radicals (reactive oxygen species).
Cells may shunt pyruvate to lactate to increase cellular ATP levels, but this can lead to acidosis in cells with high metabolic demands
Diseases result when damaged mtDNA reaches critical numbers, affecting cellular function.

Energy Failure Through Damage

Cells with enough ATP through oxidative phosphorylation can shunt pyruvate to lactate.
This occurs when cells cannot aerobically produce enough ATP via oxidative phosphorylation.
Shunting leads to cellular acidosis.

Mitochondrial DNA Mutations

One example in which mtDNA mutations are associated is Parkinson's disease
There is some evidence that mtDNA mutations may be implicated in some cancers, but there is debate about levels of importance.

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Description

This quiz explores key concepts related to membrane proteins, transport mechanisms, and the role of nucleotides in DNA. Test your knowledge on active and facilitated diffusion, as well as the intricacies of protein synthesis and mitochondrial genetics. Great for students studying cellular biology and biochemistry.