Chapter 1: Biological Molecules Flashcards

Question

# 1.2 lipids Explain the difference between cis and trans double bonds in fatty acids.

Answer 1

Cis double bonds have both hydrogens on the same side of the hydrocarbon chain, causing a kink, while trans double bonds have hydrogens on opposite sides, resulting in a straighter chain.

Answer 2

Hydrogenation converts unsaturated fats into trans fats, which have similar physical properties to saturated fats due to their straighter chain structure.

Answer 3

Cis fats are the typical form of unsaturated fat found in nature. Cis fats have a different shape, so the physical properties are different.

Answer 4

Lipids act as insulators in structures like the myelin sheath, speeding up impulse transmission, and in subcutaneous layers to reduce heat loss in mammals.

Answer 5

Lipids have a low density, which causes them to float on water, aiding in buoyancy.

Answer 6

Lipids also have a hydrophobic nature, therefore are very good as acting as waterproof layers (especially in cell membranes).

Answer 7

Hydrophilic substances are attracted to water and will dissolve in it, while hydrophobic substances are not attracted to water and will not dissolve.

Answer 8

phospholipids

Answer 9

The phospholipids are arranged in a phospholipid bilayer

Answer 10

amphipathic

Answer 11

When surrounded by water the phospholipid will form a liposome-enclosed structure so none of the lipid tails are in contact with water.

Answer 12

* The fluid mosaic model explains the structure of cell membranes, highlighting that they are composed of a phospholipid bilayer with proteins interspersed throughout. * The phospholipids are not rigidly fixed; they can move laterally, providing fluidity. The proteins serve various functions, including transport, signaling, and structural support. * This model emphasizes the dynamic nature of membranes, where components can shift and rearrange, contributing to the membrane's functionality and adaptability.

Answer 13

An amino acid consists of a central carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom, and a variable R group (side chain) that determines the specific properties of the amino acid.

Answer 14

Linked by peptide bonds in a condensation reaction.

Answer 15

primary, secondary, tertiary and quarternary

Answer 16

R groups determine the properties of amino acids, influencing the folding and final tertiary structure of proteins.

Answer 17

The chain/sequence of amino acids

Answer 18

The secondary structure of proteins includes alpha helices OR beta pleated sheets, stabilized by hydrogen bonds.

Answer 19

The folding of a polypeptide chain into a compact, globular shape, involving various bond formations.

Answer 20

Quaternary structure involves the assembly of multiple polypeptide chains and may include the binding of prosthetic groups.

Answer 21

Ionic bonds form between positively and negatively charged R groups of amino acids, contributing to the stability and overall shape of the protein.

Answer 22

Hydrogen bonds form between polar R groups and are crucial in stabilizing secondary structures like alpha helices and beta pleated sheets in proteins.

Answer 23

Disulfide bonds form between the sulfur atoms of cysteine residues, providing additional stability and rigidity to the protein's tertiary and quaternary structures.

Answer 24

* Fibrous proteins are long coiled structures * Globular proteins are highly soluble in water and are more spherical in shape * Fibrous- structural/support * Globular-functional

Answer 25

Collagen has a fibrous structure providing strength and support in connective tissues, while hemoglobin has a globular structure allowing it to efficiently transport oxygen in the blood.

Answer 26

DNA is composed of nucleotides, which include a phosphate group, a sugar (deoxyribose), and nitrogenous bases (adenine, thymine, cytosine, guanine). It has two sugar-phosphate backbones and base pairs held together by hydrogen bonds.

Answer 27

DNA replication is semi-conservative, involving the unwinding of the double helix by DNA helicase, followed by the synthesis of new strands by DNA polymerase, and the joining of Okazaki fragments by DNA ligase.

Answer 28

Pyrimidine (6+5 membered ring)- Adenine and Guanine Purine (6 membered ring)- Cytosine, Uracil, Thymine

Answer 29

A gene is a sequence of bases on a DNA molecule that codes for a specific sequence of amino acids in a polypeptide chain.

Answer 30

All your genetic information

Answer 31

The genes found in a nucleus (23 pairs/46 chromosomes)

Answer 32

Deoxyribonucleic acid, protein that makes up genes

Answer 33

Genotype is the alleles/bases that you have in your genome. While phenotype is the characteristic you have/how you look.

Answer 34

Nitrogenous bases MUST be on the inside of the helix as they are relatively hydrophobic and will face inwards.

Answer 35

One strand must run antiparallel (upside down compared to the other) and purines will always pair with pyrimidine bases in order to obtain the tight packaging required for DNA to be a COMPACT molecule.

Answer 36

* The double helix is untwisted/uncoiled * Hydrogen bonds between the bases are broken apart to ‘unzip’ the DNA and expose the bases this is done by DNA helicase * Free DNA nucleotides are hydrogen bonded onto the exposed bases according to the base pairing rules (A-T and C-G) by DNA polymerase. * Covalent bonds are formed between the phosphate of one nucleotide and the sugar of the next to seal the backbone. * Because DNA runs antiparallel synthesis occurs in 2 directions. The Leading strand is made TOWARDS the fork as it opens. The lagging strand is made running AWAY from the fork. * Replications occurs as (okazaki) fragments on the lagging strand as it waits for more bases to be exposed at the fork.

Answer 37

When the replicaiton process occurs and the two new DNA molecules are formed. Each is an exact replica of the original DNA molecule because of the base pairing rules. This process is known as semi-conservative replication. Each new DNA molecule consists of one conserved strand plus one newly built strand DNA replication occurs in the direction of 5 to 3. this is because DNA polymerase can only add nucleotides to the 3’ end of a primer.

Answer 38

5 to 3 direction

Answer 39

Coding – contains the genes to form proteins Non coding – complimentary Sense strand – same as the non coding strand Antisense strand – same as the coding strand

Answer 40

mRNA is synthesised in the direction of 5 to 3 ON THE mRNA molecule. Which means the DNA antisense/template/coding strand must be synthesised in the direction 3 to 5.

Answer 41

t contains the base URACIL instead of THYMINE It contains a RIBOSE sugar instead of a DEOXYRIBOSE sugar. It is usually single stranded. It has three different forms (tRNA, mRNA and rRNA)

Answer 42

* A ALWAYS bonds to U (ONLY in RNA) * G ALWAYS bonds to C (in both RNA and DNA) * These base pairs are COMPLIMENTARY * Therefore a purine is always opposite a pyrimidine. * Between A and U there are 2 Hydrogen bonds. * Between G and C there are 3 Hydrogen bonds.

Answer 43

* DNA helicase unzips DNA at the beginning of the gene by breaking H bonds. * Leaving the bases exposed. * RNA polymerase binds to DNA at a specific sequence of nucleotides called the promoter (start). * Only one of the unwound DNA strands (template strand) acts as a template for the RNA synthesis. * RNA polymerase adds free nucleotides from the cytoplasm to the exposed DNA template strand bases. * RNA polymerase can only add nucleotides to the 3' end of the strand so like DNA, RNA must be synthesized in the 5' to 3' direction. * RNA polymerase moves along the DNA joining bases to form an mRNA strand. ON THE RNA T’S ARE REPLACED BY U’S * RNA polymerase continues this until it reaches the terminator, a specific sequence of nucleotides that signals the end of transcription. * Transcription stops and mRNA polymerase and the new mRNA transcript are released from DNA. * mRNA leaves the nucleus * The DNA double helix zips back up (DNA ligase)

Answer 44

* tRNA – carries AA’s to the ribosomes where they are bonded together to form polypeptides eg: enzymes/proteins etc. * rRNA – found in the ribosomes, reads mRNA * mRNA – is made as a complimentary strand to the DNA, therefore acts as a coding strand as a copy of the original DNA molecule.

Answer 45

Ribosomes have three binding sites for tRNA molecules, but only two can bind. The binding sites are the E (exit site), P (peptidyl site) and A (aminoacyl site). Also a binding site for mRNA

Answer 46

The genetic code consists of triplets of nucleotides (codons) that specify amino acids, including start and stop codons, and is characterized by its degenerate and non-overlapping nature. Triplet Code: The genetic code is made up of triplets of nucleotides called codons.Each codon specifies a particular amino acid. Start and Stop Codons: There are specific codons that signal the start (AUG) and stop (UAA, UAG, UGA) of protein synthesis. Degeneracy: The genetic code is degenerate, meaning that multiple codons can code for the same amino acid. Non-overlapping: Codons are read in a sequential manner without overlapping.

Answer 47

Each tRNA is recognized by a tRNA activating enzyme, which attaches using ATP Each tRNA has a slightly different base sequence and causes some variability in structure. Active sites are specific to both amino acid and correct tRNA. Once the amino acid and tRNA are bound to the enzyme the enzyme is activated by a bond forming between the enzyme and an AMP molecule (ATP minus a phosphate). Then the AA is covalently bonded to tRNA, energy from this bond is later used to form peptide bonds between amino acids in the polypeptide chain.

Answer 48

The process of elongation continues (in the direction of 5 to 3) until a stop codon is reached. This releases the polypeptide when it moves to the golgi apparatus.

Answer 49

Addition, deletion, duplication and inversion

Answer 50

After an insertion or deletion the following DNA will move (either towards or away from the mutations), this movement/shift is called a frame shift.

Answer 51

SCA is an autosomal recessive disease caused by a point mutation in the hemoglobin beta gene (HBB). This is a substitution mutation.

Answer 52

The tRNA is clover shaped, determined by hydrogen bonding

Answer 53

* Globular proteins * Water soluble * Act as biological catalysts (speed up reactions without being used up themselves) * Highly specific * Have an ‘active site’ * Activitiy is usually affected by pH and temperature

Answer 54

Their primary structure is the initial chain of AA’s.

Answer 55

The secondary structure is the initial folding.

Answer 56

Tertiary structure is its functional shape with hydrophobic groups in the middle and hydrophilic groups surrounding them on the outside.

Answer 57

The enzymes specifically shaped active site will only allow one kind of substrate to fit in. The substrate has to have a complimentary shape to the active site therefore can fit in.

Answer 58

Once in the active site the substrate is broken down, this process is aided by the ‘induced-fit hypothesis’. This suggests that the enzyme active site is malleable to fit the shape of the substrate. The enzyme will change shape slightly to hold the substrate in place, this change puts stress on the substrate further speeding up the process

Answer 59

A hydrogen (H+) ion carries a positive charge so is attracted to negative charges. And likewise repelled by positive charges. Hydrogen and ionic bonds are responsible for maintaining the tertiary structure and repulsion or attraction may alter tertiary structure. Some ‘R’ groups are slightly charged and therefore will be attracted/repelled by the presence of H+ ions.

Answer 60

...the highest.Maximum number of active sites available when compared to number of substrates.

Answer 61

**The inhibitor competes with the substrate for the active site of the enzyme. ** Inhibitor is structurally similar to the substrate, binding to the active site. When the inhibitor binds, substrate cant bind, decreasing RoR The presence of a competitive inhibitor can be overcome by increasing the concentration of the substrate. As more substrate molecules are available, they are more likely to outcompete the inhibitor

Answer 62

**In non-competitive inhibition, the inhibitor binds to a different site on the enzyme, not the active site. This other site is called the allosteric site. ** Inhibitor binds to the allosteric site, causing a conformational change in the enzyme. This change can either reduce the enzyme's ability to bind to the substrate or lower the catalytic activity - this MAY permenantly alter the enzymes shape making it inactive Cant be overcome by increasing concentration of substrates

Answer 63

In uncompetitive inhibition, the inhibitor binds to a site on the enzyme that is only available after the enzyme has bound to the substrate, forming the enzyme-substrate complex. This site is different from the active site and does not exist in the free enzyme alone. This is also called ‘end product inhibition’. **Effect on Enzyme-Substrate Complex:** - Inhibitor binds to enzyme-substrate complex, preventing product release. - "Locks" substrate in enzyme, reducing reaction rate. **Effect on Enzyme Activity:** - Decreases both Vmax (maximum reaction rate) and Km (apparent affinity). - Lower enzyme-substrate complex concentration reduces product formation. - Vmax and Km decrease proportionally, keeping the Km/Vmax ratio constant. **Kinetics of Uncompetitive Inhibition:** - **Decrease in Vmax:** Fewer active enzyme-substrate complexes available, lowering reaction rate. **Decrease in Km:** Lower effective enzyme-substrate complex concentration increases substrate affinity.

Answer 64

Makes DNA and amino acids Nitrification results in stores of nitrates in the soil that plants can absorb via their roots and assimilate into useful products (DNA and amino acids). If plants are unable to obtain sufficient amounts of nitrogen then they will develop deficiency symptoms. Cannot absorb nitrogen directly as it is inert

Answer 65

To form calcium pectate in the middle lamella Bind with pectins to form a rigid structure. They also play a role in regulating enzyme activity, signaling pathways, and membrane permeability.

Answer 66

Magnesium ions are essential for plants as they are the central atom in chlorophyll, crucial for photosynthesis.

Answer 67

Phosphate ions are vital for plants as they are key components of ATP, the molecule that stores and transfers energy for cellular processes. They are also crucial for nucleic acid synthesis, forming part of DNA and RNA, and play a role in cell membrane structure, signaling, and root development.

Answer 68

2 hydrogens 1 oxygen with 2 lone pairs on oxygen giving it a positive charge.

Answer 69

dotted line from hydrogen with sigma+ to oxygen sigma -

Answer 70

Because water is dipolar it allows chemicals to dissolve readily and easily, this makes it an ideal transport medium.

Answer 71

At 4°C, water’s dipole properties allow hydrogen bonds to form a more efficient arrangement, maximizing molecular packing. Below this temperature, water molecules form an open hexagonal structure due to hydrogen bonding, reducing density. Thus, water reaches its maximum density at 4°C before expanding upon freezing.

Answer 72

Water's dipole nature leads to strong hydrogen bonding between molecules at the surface, creating a cohesive "film" that resists external forces. This cohesive force, due to the alignment of water molecules, results in surface tension, allowing small objects to float and insects to walk on water.

Answer 73

Water's dipole nature creates strong hydrogen bonds between molecules, requiring significant energy to break. This extensive hydrogen bonding means that water can absorb a lot of heat energy before its temperature rises, resulting in a high specific heat capacity. This property stabilizes temperatures in living organisms and environments.

Answer 74

Incompressibility means that water does not significantly change in volume when a force is applied to it. This property is crucial for: Structural support: Water in cells and tissues provides structural support and shape to organisms. Buoyancy: The incompressibility of water allows aquatic organisms to float and move more easily.