Proteins

Question 1

4 categories of bio molecules

Answer 1

1. Proteins
2. Carbohydrates
3. Lipids
4. Nucleic acids

Question 2

Protein functions

Answer 2

structural support, storage, transport, cellular communications, movement and defense against foreign substances.

Question 3

Amino acids

Answer 3

General structure:have an amino group,have a carboxyl group

Question 4

Bioactive Amino Acids

Answer 4

• Tryptophan is a precursor of the serotonin neurotransmitter.
• Tyrosine is a precursor of the dopamine neurotransmitter.
• Aspartate, glutamine, glycine are precursors of nucleotides.
• Arginine is a precursor of nitric oxide.

Question 5

Precursor meaning

Answer 5

A substance from which another is formed

Question 6

Peptide bonds

Answer 6

Binding occurs between the amino group of one amino acid and the carboxyl group from another amino acid.
= Condensation reaction or dehydration synthesis

Question 7

Cysteine

Answer 7

Sulfhydryl (SH) group of cysteine is highly reactive Reversible oxidation that forms a disulfide bond

Question 8

Types of peptides

Answer 8

Dipeptide 2 Aa
Tripeptide = 3 aa and so on.
Oligopeptides = <25 aa residues
Polypeptides = >25 aa residues
Proteins are oligomers containing 50 or more aa residues.

Question 9

Role of peptides

Answer 9

Insulin (two polypeptides, 21 and 10 aa)

Glucagon (29 aa)

Oxytocin (9 aa)

Question 10

Primary structure of proteins

Answer 10

the number and sequence of amino acids in a protein
Primary structure is determined by inherited genetic information

Question 11

Secondary structure of Proteins

Answer 11

The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of
the polypeptide backbone.
Typical secondary structures are:
1) a coil called an  helix.
2) a folded structure called a  pleated sheet.

Question 12

3) Tertiary structure

Answer 12

Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents

Hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals, covalent bonds (disulphide bridges)

Question 13

4) Quaternary structure

Answer 13

Quaternary structure results when two or more
polypeptide chains form one macromolecule.
- Collagen is a fibrous protein consisting of three polypeptides coiled like a rope.
- Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains.

Question 14

Results of change in primary structure

Answer 14

▪ A slight change in primary structure can affect protein structure and ability to function
▪ Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin

Question 15

What determines protein structure

Answer 15

▪ In addition to primary structure, physical and chemical conditions can affect structure.
▪ Environmental factors: pH, salt concentration, temperature can cause proteins to unravel (denaturation).
▪ A denatured protein is biologically inactive

Question 16

How is protein structure determined

Answer 16

▪ X-ray crystallography.
▪ Nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization.
▪ Bioinformatics is another approach to prediction of protein structure from amino acid sequences

Question 17

The Roles of Nucleic Acids

Answer 17

▪ There are two types of nucleic acids ▪ Deoxyribonucleic acid (DNA)
▪ Ribonucleic acid (RNA)
▪ DNA provides directions for its own replication (Dr Zubko).
▪ DNA (genes) directs synthesis of messenger RNA (mRNA) which controls protein synthesis.
▪ This process is called gene expression: transcription and translation.

Question 18

What are the 3 stages of transcription

Answer 18

Initiation
Elongation
Termination

Question 19

Steps in trasncription

Answer 19

Hydrogen bonds (between DNA bases) break;

(Only) one DNA strand acts as a template; (Only) one DNA strand acts as a template;

(Free) RNA nucleotides align by complementary base pairing;

(In RNA) Uracil base pairs with adenine (on DNA) OR (In RNA) Uracil is used in place of thymine;

RNA polymerase joins (adjacent RNA) nucleotides;

(By) phosphodiester bonds (between adjacent nucleotides);

Pre-mRNA is spliced (to form mRNA) OR Introns are removed (to form mRNA);

Question 20

Molecular components of initiation

Answer 20

• Promoter: DNA sequence where RNA polymerase attaches. TATA box in Eukaryotes.
• Transcription factors: mediate binding of RNA polymerase II.
+
• RNA polymerase II: pries the DNA strands apart and links together the RNAnucleotides.
• Transcription initiation complex (RNA polymerase II + transcription factors).

Question 21

Molecular components of Elongation

Answer 21

▪ RNA polymerase unwinds the DNA double helix, 10
to 20 bases at a time. Links RNA nucleotides.
▪ mRNA is complementary to the DNA template strand.
▪ Nucleotides are added to the 3′ end of the growing RNA molecule
▪ Transcription rate of 40 nucleotides / s in Eukaryotes.
▪ RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine

Question 22

Termination of transcription

Answer 22

▪ Bacteria: polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification.
▪ Eukaryotes: RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10–35 nucleotides after this poly-A sequence / tail.

Question 23

RNA processing in eukaryotes

Answer 23

1) Both ends of the primary transcript are altered.
2) Interior sections of the molecule can be excised and
the remaining parts spliced together
3) Enzymes in the eukaryotic nucleus modify pre-
mRNA.
ALL OCCUR IN THE NUCLEUS OF THE CELL

Question 24

Alteration of mRNA ends

Answer 24

-5′ end receives a modified nucleotide 5′ (prime) cap
-3′ end has a poly-A tail
-modified guanine nucleotide added to the5 end
-50-250 adenine nucleotides added to the 3 end

Why?

• Facilitate the export of mRNA to the cytoplasm.
• Protect mRNA from hydrolytic enzymes.
• Assist ribosomal attachment to the 5′ end

Question 25

RNA splicing

Answer 25

Only exon are expressed and translated to amino acids

Splicing remove introns and joins exons creating an mar molecule with a continuous coding sequence

Question 26

Spliceosome

Answer 26

Large rna protein complex that catalyses the remove of introns

Question 27

Function of introns

Answer 27

▪ Some contain sequences that may regulate gene expression.
▪ Some genes encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing.
▪ This is called alternative RNA splicing Which means…
Number of different proteins an organism can produce is much greater than its number of genes

Question 28

Codons: Triplets of Nucleotides

Answer 28

▪ Gene to protein is based on a triplet code: a series
of nonoverlapping, three-nucleotide words.
▪ The words of a gene are transcribed into three- nucleotide words of mRNA.
▪ These words are then translated into a chain of amino acids, forming a polypeptide.

Question 29

tRNA

Answer 29

▪ tRNAs transfer amino acids to the growing polypeptide in a ribosome.
▪ RNA molecules, 80 nucleotides long.
▪ Flattened into one plane to reveal its base pairing.

Question 30

Structure of tRNA

Answer 30

Clover shape
Amino acid attachment at the top
Anticodon at the bottom
Some hydrogen bonding

Question 31

Steps of translation

Answer 31

(1) a correct match between a tRNA and an amino acid, performed by the enzyme aminoacyl-tRNA synthetase.
(2) a correct match between the tRNA anticodon and an mRNA codon.

Question 32

Translation step by step

Answer 32

Amino acid and tRNA enter active site
Using atp synthethase catalyses convalescent bonding
Aminoacyl tRNA released

Question 33

Structure and function of ribosomes

Answer 33

▪ Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis.
▪ The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA).
▪ Bacterial and eukaryotic ribosomes differ.

The have 2 ribaosomal subunits and 3 binding sites

Question 34

3 stages of translation

Answer 34

1) Initiation
2) Elongation
3) Termination

Question 35

Molecular Components of Translation

Answer 35

▪ mRNA
▪ tRNAs (with amino acid added)
▪ Ribosome (large and small subunits): made of protein and rRNA molecules.
▪ Translation factors
▪ Start codon (AUG)
▪ Stop codons

Question 36

What happens at each stage of translation

Answer 36

1 initiation
>codon recognition
2 elongation
>peptide bond formation
>translocation
3 termination
>ribosome reaches a stop codon
>release factor promotes hydrolysis
>ribosomal subunits and other components dissociate

Question 37

What happens to polypeptide chais after translation

Answer 37

Polypeptide chains are modified after translation (post-translational modification), maybe required for correct folding (tertiary structure etc). Glycosylation, acetylation, methylation etc.
Protein targeting to specific sites in the cell (use of signal peptide) such as the ER.