biochem basicis

Question 1

major groups of biomolecules + their monomers

Answer 1

carbs (monosaccharides), proteins (amino acids), lipids (fatty acid tails + glycerol), nucleic acids (nucleotides)

Question 2

main elements in molecules

Answer 2

nitrogen, oxygen, hydrogen, carbon
also bulk elemtns + trace elements

Question 3

what process can be used to study cellular composition?

Answer 3

subcellular fractionation

Question 4

Three major components of the animal cell cytoskeleton

Answer 4

Stress fibres and cortical networks (made of ACTIN)
Microtubules - arise from centrosome - also called MTOC - comprised of TUBULIN
Intermediate filaments (KERATIN + other proteins)

Question 5

Light microscopy
- Identify the diff structures acc to their colours

Answer 5

Red- actin
Green- microtubules
Blue - nuclei

Question 6

Light microscopy
- Identify the diff structures acc to their colours
- what is happening

Answer 6

A dividing (mitotic) animal cell where the intermediate filaments made up of
keratin(red) and
microtubules(green)
attached to chromosomes(blue)
can be seen

Question 7

Water structure

Answer 7

• Both H atoms share e- with O atom
• Polar - forms electrical dipole
• Forms hydrogen bonds

Question 8

hydrogen bonds - what are they?

Answer 8

• weak electrostatic interactions
• Between Oxygen of one water molecule and the hydrogen of another

Question 9

hydrogen bonds - properties

Answer 9

• Max 4 H bonds per H2O molecule
• Hydrogen bonds are transient, they are
  constantly broken and reformed at
  physiological temperatures (25 – 37C)
• Hydrogen bonds are relatively weak
  Bond dissociation energies;
  *Hydrogen bond: 23 kJ/mol
  *Covalent H-O bond: 470 kJ/mol
  *Covalent C-C bond: 348 kJ/mol

Question 10

hydrogen bonds - why important?

Answer 10

• Increases cohseiveness +surface tension
• Thus higher melting + boiling points than other solvents
• hydrogen bonds – non-covalent – no e- shared
• makes water an excellent solvent for biomolecules

Question 11

How water acts as a solvent

Answer 11

• good solvent for other charged or polar compounds – readily dissolves most biomolecules
• BUT nonpolar molecules are hydrophobic
  EXAMPLE: biologically important gases e.g. CO2, O2, and N2 are nonpolar, therefore they are poorly soluble in
  water – thus oxygen carried by haemoglobin
• Dipole of H2O – forms electrostatic attractions with CHARGED solutes

Question 12

How water acts as a solvent for crystalline salts (containing ions)

Answer 12

Do so by hydrating their component ions:
- NaCl kept together by electrostatic attractions btwn thm
- In water - water surrounds the individual ions
- negative dipoles of water are attracted to the positively charged ions and vice versa
- Pure water – poor electrical conductor
- water with ions – good conductor

Question 13

Ion product of water (Kw)

Answer 13

• Is a constant in aqueous solutions
• Kw= [H+]*[OH-]

= 1x10^-14 M^2

Question 14

Bonds in ATP

Answer 14

There are two Phosphanhydride bonds - btwn the phosphoryl groups
One phospoester bond - btwn phopshpryl gro and ribose

Question 15

Hydrolysis of ATP

Answer 15

ATP –> ADP + Pi(HPO4^2-) +energy

Question 16

Laws of thermodynamics

Answer 16

1st law: Energy cant be destroyed or created only transferred
2nd law: In a closed system the entropy remains constant or is increased

Question 17

Enthalpy, Entropy, Gibbs free energy

Answer 17

Enthalpy (H) = The internal energy in a system - heat content of a reacting system

Entropy (S) = The randomness/disorder in a system

Gibbs free energy (G) = amt of energy capable of doing work during a reaction at a constant temp and pressure

G = H - TS
G= 0 when H = TS
G>0 –> endergonic – non-spontaneous
G<0 –> exergonic – spontaneous

Question 18

Why cant cells use heat as a form of energy

Answer 18

Cells are isothermal – function at a constant temp

Question 19

Which one of the macromolecules isnt a polymer?

Answer 19

Lipids - arent polymer but still macromolecules
– due to high molecular weight

Question 20

Write a note on nucleic acids

Answer 20

• They are a macromolecule/polymer
• 2 major nucleic acids: DNA and RNA
• Monomer: nucleotides
• A nucleotide consists of a nitrogenous base, a phosphate group and a 5-carbon sugar (deoxy or ribose sugar)
• The nitrogenous bases are of two types:
  – Purines: Adenine and guanine – have a double ringed structure
  – Pyrimidines: Uracil, Thymine, Cytosine
• Nucleosides: nucleotides without the phosphate group ie. DNA base and 5-C sugar
  —-> DNA: deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine

PHOSPHODIESTER BONDS BETWEEN THE NUCLEOTIDES:
- The nucleotides are attached together by covalent phosphodiester bonds
- Formed between the 5’ phosphate group and 3’ OH group of the next nucleotide

BASE PAIRS:
A–T (2 H bonds)
C—G (3 H bonds)

DNA:
- Deoxyribose sugar – no Hydroxide on carbon 2
- double and right handed helix
- Antiparallel strands
- Bases on inside and phosphates and sugars outside forming the backbone
- Bases and strands held together by hydrogen bonds
- There’s a major and minor groove
- DNA is condensed into chromosomes within the nucleus
- Each chromosome has 2 chromatids and 2 DNA molecules
- 23 different chromosomes – 22 autosomes and 1 sex chromosome
- GENOME– all of the DNA in an organisms set of chromosomes

RNA:
- Ribose sugar
- Uracil base instead of thymine
- Single-stranded
- Can leave the nucleus
- Can form secondary structures if there are complementary base sequences on parts of the strand including:
— Stem loops, hairpins, bulges, internal loops
- Include rRNA, tRNA, mRNA, miRNA, lnRNA etc.
- Formed by RNA transcription:
— A DNA strand is used as a template
—- RNA pol adds new ribonucleotides to a free 3’ OH to make RNA thats complementary to the DNA strand
—- synthesis in 5’-3’ direction
— No primer needed
— No proofreading activity thus higher error rate than DNA replication
— Initiation, elongation and termination
— RNA pol binds to promoters

Question 21

Linkage btwn nucleotides?

Answer 21

PHOSPHODIESTER BONDS BETWEEN THE NUCLEOTIDES:
- The nucleotides are attached together by covalent phosphodiester bonds
- Formed between the 5’ phosphate group and 3’ OH group of the next nucleotide

Question 22

Human genome project

Answer 22

• Project with the aim of sequencing all the DNA in a human cell and identifying the location of all the genes.
  MAIN GOALS:
• Determining the sequences of all the 3 billion chemical base pair that make up human DNA
• Identifying the location of all the genes
• Storing this information in databases

Question 23

DNA structure

Answer 23

BASE PAIRS:
A–T (2 H bonds)
C—G (3 H bonds)

DNA:
- double and right handed helix
- Antiparallel strands
- Bases on inside and phosphates and sugars outside forming the backbone
- Bases and strands held together by hydrogen bonds
- There’s a major and minor groove
- DNA is condensed into chromosomes within the nucleus
- Each chromosome has 2 chromatids and 2 DNA molecules
- 23 different chromosomes – 22 autosomes and 1 sex chromosome
- GENOME– all of the DNA in an organisms set of chromosomes

Question 24

RNA structure

Answer 24

RNA:
- Ribose sugar
- Uracil base instead of thymine
- Single-stranded
- Can leave the nucleus
- Can form secondary structures if there are complementary base sequences on parts of the strand including:
— Stem loops, hairpins, bulges, internal loops
- Include rRNA, tRNA, mRNA, miRNA, lnRNA etc.
- Formed by RNA transcription:
— A DNA strand is used as a template
—- RNA pol adds new ribonucleotides to a free 3’ OH to make RNA thats complementary to the DNA strand
—- synthesis in 5’-3’ direction
— No primer needed
— No proofreading activity thus higher error rate than DNA replication
— Initiation, elongation and termination
— RNA pol binds to promoters

Question 25

Write a note on proteins

Answer 25

- Proteins also known as polypeptides - type of macromolecule - Most abundant macromolecule - They are made of amino acids (monomers) - 20 main amino acids (residues) ---> 11 can be synthesised by humans 9 cannot - called essential amino acids (PVT TIM HaLL) STRUCTURE OF AMINO ACIDS: - Has an amino group (NH2) -- In amino acids its prnated to form NH3+ - A carboxyl group (COOH) -- at physiological pH it dissociates into carboxylate ion (COO- ) - R group -- a side chain thats diff for each amino acid - The Carbon atom next to the carboxyl group is known as the ALPHA CARBON - There's also an H atom bound to the alpha carbon - All alpha carbons in in amino acids are chiral centres except in glycine. - Amino acids are linked to each other by PEPTIDE BONDS - Peptide bond formed by a condensation reaction between an alpha carboxyl of one amino acid and the alpha amino of another DIFFERENT FORMS OF AMINO ACIDS: - isomers, stereoisomers, enantiomers - All molecules with one chiral centre have 2 stereoisomers - Amino acids can exist as either L form or D form enantiomers - ALL of the amino acids in humans are in L form enantiomers - D form enantiomers found in peptides in bacterial cell walls and antibiotics AMINO ACIDS ARE CLASSIFIED BASED ON THEIR R GROUPS: - Non-polar, Alipathic R groups (PROLINE, valine, leucine, isoleucine) - Aromatic non-polar R grp (Tryptophan, Tyrosine, Phenylalanine) - Polar, uncharged grp (serine, threonine, asparagine, cysteine) - Positively charged grp (LAH - Lysine, Arginine, HISTIDINE) - Negatively charged grp (NAG- Aspartate, glutamate) UNCOMMON AMINO ACIDS: Creatine - amino acid not part of a protein present in skeletal muscle Phosphocreatine + ADP ---> Creatine + ATP TRANSLATION: - 3 nucleotides form a codon - each codon codes for a specific amino acid - Methionine (AUG) --> Start codon - 3 stop/nonsense codons (UAA, UAG, UGA)

Question 26

List some proteins and what they do

Answer 26

Haemoglobin and Myoglobin: -- Haem. - acts as an O2 transporter within the body and is present in RBCs -- Myo. - Acts as an O2 store within the musc. cells of the body - used when O2 levels drop in musc. Keratin: -- Present in all vertebrates -- Main structural component in the hair, scales, wool, feathers and nails Luciferase: -- Present in fireflies -- Catalyses the PRODUCTION of light from the protein luciferin and ATP Green fluorescent protein: -- from a jellyfish -- Fluoresces when excited with a light of a specific wavelength

Question 27

9 essential amino acids?

Answer 27

PVT TIM HaLL Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Lysine, Leucine

Question 28

What is a chiral centre - which amino acid doesnt have a chiral carbon?

Answer 28

- A chiral centre is where a carbon atom is bonded to four different groups - All amino acids except glycine have their alpha carbon as a chiral centre as they're bonded to an H atom, COOH, NH2 and an R group. - Glycine has an H atom as its R group thus the alpha carbon is not a chiral centre

Question 29

Isomers, stereoisomers, enantiomers -- define

Answer 29

Isomers: -- They are molecules that have the same chemical formula but different chemical structures Stereoisomers: -- They are isomers with the same chemical formula and bond structure but different geometrical positioning of atoms and functional groups in the space Enantiomers: -- They are stereoisomers which are mirror images of each other but cant be superimposed on each other A molecule with ONE chiral centre can have two stereoisomers

Question 30

What enantiomer form do all of the alpha amino acids exist as? which one is more common in humans? where can both of them be found?

Answer 30

- All alpha amino acids exist as either L or D enantiomers - L (levo) form amino acids are the only ones that make up all human proteins (NH3/NH2 group on left and carboxyl grp on right) - D (dextro) form amino acids are very rare and are only mainly found in peptides bacterial cell walls and some antibiotics (NH3/NH2 group on right and carboxyl grp on left)

Question 31

How are amino acids classified? what are the classifications?

Question 32

Give an example of an Uncommon amino acid that exists as a free molecule and no incorporated into a protein

Answer 32

Creatine in skeletal muscle cells Phosphocreatine + ADP ---- exertion----> Creatine +ATP

Question 33

Which proteins are relevant to the following and what type of r group do they have: - Imino acid - Can be phosphorylated at OH group - Can have an oligosaccharide added to their amide group/ O group - Present in collagen - Absorb UV light - can form disulphide bonds - relevance of Histidine? - Have negatively charged R grps - Most non-polar aa with aromatic R group

Answer 33

- Proline --- has a ring structure - makes proteins its present in more rigid - like in collagen (bones teeth) --- Non-polar, alipathic R group - doesnt have an R group with a linear carbon side chain - Serine and Threonine -- Polar, uncharged grps - Amide grp: Asparagine (N-glycosylation) Oxygen grp: Serine + threonine (O-glycosylation) - Proline -- Non-polar, alipathic - Tryptophan and tyrosine -- Aromatic R groups - Cysteine -- Polar uncharged group -- Contains sulfhydryl which forms disulphide bonds within and between proteins -- Strongly hydrophobic - Histidine has a positively charged R-group -- it's basic amino acids along with Lysine and Arginine -- It's the least basic of the two due to its imidazole ring - NAG -- Aspartate and Glutamate - Aromatic R groups: Tryptophan, Tyrosine, Phenylalanine These are relatively non-polar Tryptophan and Tyrosine are relatively more polar due to the presence of an N-indole ring and and OH grp respectively

Question 34

Reading frame def.?

Answer 34

- The sequence of codons that runs from a start to a stop codon known as a reading frame - mRNA can be read in 3 diff reading frames - The reading frame used depends on the polypeptide made - AUG determines the reading frame

Question 35

How many tRNAs in humans?

Answer 35

50

Question 36

Protein structure

Answer 36

Primary: -- The sequence of amino acids and a description of the covalent bonds linking the amino acids (peptide bonds) Secondary: -- Spatial arrangement of atoms in a protein is called its conformation -- Secondary structure describes the conformation of the polypeptide: -- Alpha helix and beta pleated sheets 2 main secondary conformations Tertiary: -- overall 3-D arrangement of 2 or more polypeptide subunits: 2 subunites: dimeric 3: trimeric 4: tetrameric Quaternary: