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biochem basicis Flashcards

1
Q

major groups of biomolecules + their monomers

A

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

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2
Q

main elements in molecules

A

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

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3
Q

what process can be used to study cellular composition?

A

subcellular fractionation

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4
Q

Three major components of the animal cell cytoskeleton

A

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

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5
Q

Light microscopy
- Identify the diff structures acc to their colours

A

Red- actin
Green- microtubules
Blue - nuclei

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6
Q

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

A

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

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7
Q

Water structure

A
  • Both H atoms share e- with O atom
  • Polar - forms electrical dipole
  • Forms hydrogen bonds
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8
Q

hydrogen bonds - what are they?

A
  • weak electrostatic interactions
  • Between Oxygen of one water molecule and the hydrogen of another
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9
Q

hydrogen bonds - properties

A
  • 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
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10
Q

hydrogen bonds - why important?

A
  • 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
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11
Q

How water acts as a solvent

A
  • 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
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12
Q

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

A

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

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13
Q

Ion product of water (Kw)

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

= 1x10^-14 M^2

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14
Q

Bonds in ATP

A

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

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15
Q

Hydrolysis of ATP

A

ATP –> ADP + Pi(HPO4^2-) +energy

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16
Q

Laws of thermodynamics

A

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

17
Q

Enthalpy, Entropy, Gibbs free energy

A

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

18
Q

Why cant cells use heat as a form of energy

A

Cells are isothermal – function at a constant temp

19
Q

Which one of the macromolecules isnt a polymer?

A

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

20
Q

Write a note on nucleic acids

A
  • 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

21
Q

Linkage btwn nucleotides?

A

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

22
Q

Human genome project

A
  • 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
23
Q

DNA structure

A

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

24
Q

RNA structure

A

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

25
Q

Write a note on proteins

A
  • 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)

26
Q

List some proteins and what they do

A

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

27
Q

9 essential amino acids?

A

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

28
Q

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

A
  • 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
29
Q

Isomers, stereoisomers, enantiomers – define

A

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

30
Q

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?

A
  • 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)
31
Q

How are amino acids classified? what are the classifications?

A
32
Q

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

A

Creatine in skeletal muscle cells

Phosphocreatine + ADP —- exertion—-> Creatine +ATP

33
Q

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

A
  • 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
34
Q

Reading frame def.?

A
  • 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
35
Q

How many tRNAs in humans?

A

50

36
Q

Protein structure

A

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:

biochem (10 decks)

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